EUROPEAN COMMISSION

SMEs in Health Research

Synopses of projects funded through
the SME call for “Life sciences,
genomics and biotechnology for health”
(FP6-2005-LIFESCIHEALTH-7)

2008 Directorate-General for Research EUR 23457 EN

Health
Acknowledgements

This catalogue has been produced thanks to the essential input from all project coordinators. Special thanks go
to Séverine Romain for her highly professional and dynamic assistance, pivotal for the catalogue completion.
I am very grateful to Rachida Ghalouchi, Christel Jaubert, Charles Kelly, Kristina Kyriakopoulou, and to all the officers
in Health Directorate responsible for the projects included in this synopses, for their efficient co-operation.
Finally, my warmest thanks to Stéphane Hogan, Head of Unit F1, Horizontal aspects and coordination in
the Health Directorate, for the commitment and lead provided.

Ludovica Serafini
Editor

Contact details for FP7 activities

Information on FP7 Health Theme

(including calls, available supports and information on SMEs and innovation):
http://cordis.europa.eu/fp7/cooperation/health_en.html

The SME Contact Officer in the Health Directorate is Ludovica Serafini, e-mail: ludovica.serafini@ec.europa.eu

Europe Direct is a service to help you find answers

to your questions about the European Union

Freephone number (*):

00 800 6 7 8 9 10 11

(*) Certain mobile telephone operators do not allow access to

00 800 numbers or these calls may be billed

LEGAL NOTICE

Neither the European Commission nor any person acting on behalf of the Commission
is responsible for the use which might be made of the following information.

The views expressed in this publication are the sole responsibility of the author and do
not necessarily reflect the views of the European Commission.

A great deal of additional information on the European Union is available on the Internet.
It can be accessed through the Europa server (http://europa.eu) and CORDIS
(http://cordis.europa.eu/en/home.html)

Cataloguing data can be found at the end of this publication.

Luxembourg: Office for Official Publications of the European Communities, 2008

ISBN 978-92-79-08803-2
DOI 10.2777/13756

© European Communities, 2008

Reproduction is authorised provided the source is acknowledged.
Printed in Luxembourg
Printed on white chlorine-free paper
SME CALL

Table of
content
• Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 • CILMALVAC . . . . . . . . . . . . . . . . . . . . . . . . . 30
The Tetrahymena system as an
• Introduction . . . . . . . . . . . . . . . . . . . . . . . . . 9 innovative approach to malaria
antigene expression
• AGLAEA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Development of novel animal models • cNEUPRO . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
of glutamatergic central nervous Clinical Neuroproteomics
system disorders using in vivo of Neurodegenerative Diseases
siRNA and transgenic approaches
• COBRED . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
• ANGIOSTOP . . . . . . . . . . . . . . . . . . . . . . . . 12 Colon and breast cancer diagnostics
Novel Anti-angiogenic treatment
for Cancer, Arthritis and Ocular • COMICS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Neovascularization based on Comet assay and cell array for fast
Inhibition of Placental Growth and efficient genotoxicity testing
Factor (PlGF)
• CVDIMMUNE . . . . . . . . . . . . . . . . . . . . . . . 38
• ARTEMIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 Immunomodulation and
In Vitro neural tissue system autoimmunity in cardiovascular
for replacement of transgenic disease and atherosclerosis
animals with memory/learning
deficiencies • DEPPICT . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Designing Therapeutic Protein:Protein
• AUTOSCREEN . . . . . . . . . . . . . . . . . . . . . . 16 Inhibitors for Brain Cancer Treatments
AUTOSCREEN for Cell Based
High-throughput and High-content • DeZnIT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Gene Function Analysis and Design of zinc metalloenzyme
Drug Discovery Screens targeted drugs using an Integrated
Technology approach
• BacAbs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Assessment of Structural • Diagnosis . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Requirements in Complement- Development of new and cost
Mediated Bactericidal Events: effective methods for non-invasive
Towards a Global Approach diagnosis of human pathogens
to the Selection of New Vaccine
Candidates • DIALOK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Development of Innovative Assays
• BioBridge. . . . . . . . . . . . . . . . . . . . . . . . . . . 20 and Locally acting therapies aiming
Integrative Genomics and Chronic at critical Kinases in hepatic and
Disease Phenotypes: modelling renal fibrosis
and simulation tools for clinicians
• DiaNa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
• CancerGrid . . . . . . . . . . . . . . . . . . . . . . . . . 22 Predictive diagnostics for diabetic
Grid-aided computer system nephropathy – Novel nanotechnology
for rapid anti-cancer drug design based test platforms

• CAPPELLA . . . . . . . . . . . . . . . . . . . . . . . . . . 26 • Drop-Top . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Combating cancer through novel Integration of DNA, RNA and protein
approaches to protein: protein markers in a tool for the prognosis
interaction inhibitor libraries and diagnosis of human disease

• ChILL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 • EACCAD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Chromatin Immuno-linked European approach to combat
ligation: A novel generation of outbreaks of clostridium difficile
biotechnological tools for research associated diarrhoea by development
and diagnosis of new diagnostic tests

3
• ENLIGHT . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 • IBDchip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 • MAMMI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
New molecular methods and image Usefulness of a new DNA array Mammography with molecular
analysis tools for analysis of cancer (IBDchip) to predict clinical course, imaging
biomarkers in situ development of complications and
response to therapy in patients with • MANASP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
• EPIVAC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 inflammatory bowel disease (IBD) Development of novel management
Development of a multi-step strategies for invasive aspergillosis
Improved Epidermis Specific Vaccine • IMMUNATH . . . . . . . . . . . . . . . . . . . . . . . . 82
Candidate against HIV/AIDS Translating innate immune • MEGATOOLS . . . . . . . . . . . . . . . . . . . . . . . . 104
receptor function into diagnostic New tools for Functional Genomics
• EURO-PHARMACO-GENE . . . . . . . . . 60 and therapeutic applications for based on homologous recombination
Design of targeted Gene atherosclerosis induced by double-strand break and
Pharmaceutics using self-assembling specific meganucleases
functional entities • Immuno-PDT . . . . . . . . . . . . . . . . . . . . . . . 84
Immunophotodynamic therapy • MEMORIES . . . . . . . . . . . . . . . . . . . . . . . . . . 106
• EXERA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 of cancer: concepts and applications Development, characterisation and
Development of 3D in vitro models validation of new and original models
of estrogen-reporter mouse tissues • INDABIP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 for Alzheimer’s Disease
for the pharmaco-toxicological Innovative diagnostic approaches
analysis of Estrogen Receptors- for biomarkers in Parkinson disease • Mimovax . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Interacting Compounds (ER-ICs) Alzheimer’s disease-treatment targeting
• INNOVAC . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 truncated Aβ 40/42 by active
• FASTEST-TB . . . . . . . . . . . . . . . . . . . . . . . . 66 Highly innovative strategies for immunisation
Development and Clinical Evaluation vaccination to poverty related
of Fast Tests for Tuberculosis Diagnosis diseases • MODEST . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Modular Devices for Ultrahigh-
• FGENTCARD . . . . . . . . . . . . . . . . . . . . . . . . 68 • INTELLIMAZE . . . . . . . . . . . . . . . . . . . . . . 90 throughput and Small-volume
Functional GENomic diagnostic High-throughput, fully automated Transfection
Tools for Coronary Artery Disease and cost-effective behavioural
phenotyping of normal, clinical • MUNANOVAC . . . . . . . . . . . . . . . . . . . . . . . . 112
• GLYFDIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 and genetic mouse models Mucosal Nano Vaccine Candidate
Glycans in Body Fluids- Potential for HIV
for Disease Diagnostics • InVitroHeart . . . . . . . . . . . . . . . . . . . . . . . . 92
Reducing Animal Experimentation in • MYASTAID . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
• HI-CAM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 Drug Testing by Human Cardiomyocyte Development of models to improve
Development of a high-resolution In Vitro Models Derived from management of Myasthenia Gravis: From
Anger camera for diagnosis and Embryonic Stem Cells basic knowledge to clinical application
staging of cancer diseases based on
state of the art detector technology • LIGHTS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 • MYOAMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Small ligands to interfere with Amplification of human myogenic
• HighReX . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 Thymidylate synthase dimer formation stem cells in clinical conditions
High Resolution X-Ray Imaging for as new tools for development of
Improved Detection and Diagnosis anticancer agents against • NanoSense . . . . . . . . . . . . . . . . . . . . . . . . . . 118
of Breast Cancer ovarian carcinoma Moving sensitive immunoassays
from slow and expensive to fast and
• HIVResInh . . . . . . . . . . . . . . . . . . . . . . . . . . 76 • liintop. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96 affordable nanoparticle-based methods
Preparation and Identification of Optimisation of liver and intestine
New HIV Reverse Transcriptase in vitro models for pharmacokinetics • NEOBRAIN. . . . . . . . . . . . . . . . . . . . . . . . . . . 120
Inhibitors Targeted Against HIV Strains and pharmacodynamics studies Neonatal estimation of brain
Resistant to anti-HIV/AIDS drugs damage risk and identification
• MagRSA . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 of neuroprotectants
• HIVSTOP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78 Fully automated and integrated
Development of an Effective RNA Microfluidic Platform for Real-time • Net2Drug . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Interference-Based Anti-HIV-1 Therapy Molecular Diagnosis of Methicillin- From gene regulatory networks
Using an SV40-Derived Vector resistant Staphylococcus Aureus to drug prediction

4
• NPARI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124 • RATstream™ . . . . . . . . . . . . . . . . . . . . . 146 • TargetHerpes . . . . . . . . . . . . . . . . . . . . . . . 166
Tailoring of Novel Peptide coatings European project on the Molecular intervention strategies targeting
and therapeutics derived from characterisation of transgenic rat latent and lytic herpesvirus infections
a newly identified component of models for neurodegenerative and
the human innate immunity Against psychiatric diseases: Automated • TargetScreen2 . . . . . . . . . . . . . . . . . . . . . . 168
Resistant Infections home cage analyses, live imaging Novel post-genomic cell-based screens
and treatment for drug targeting in membrane protein
• OMVac . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 disorders
Novel prevention and treatment • RespViruses . . . . . . . . . . . . . . . . . . . . . . 148
possibilities for Otitis Media through Immune response to viral respiratory • TB-DRUG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
the comprehensive identification of infections and vaccination in the A SME-STREP for Tuberculosis Drug
antigenic proteins elderly Development

• OptiCryst . . . . . . . . . . . . . . . . . . . . . . . . . . 128 • SAGE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150 • TB-trDNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172

Optimisation of protein crystallisation SME-led Antibody Glyco-Engineering Evaluation of transrenal-DNA
for european structural genomics detection to diagnose tuberculosis
• SERO-TB . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
• PHECOMP . . . . . . . . . . . . . . . . . . . . . . . . . 130 Development of a Specific • TEMPO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
Phenotypical characterisation of Serological Kit for the Diagnosis Temporal Genomics for Tailored
animal models for neuropsychiatric of TB Chronotherapeutics
disorders related to compulsive
behaviour • SMARTER. . . . . . . . . . . . . . . . . . . . . . . . . . 154 • USDEP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Development of small modulators Capture and enrichment of emerging
• PHOTOLYSIS . . . . . . . . . . . . . . . . . . . . . . 132 of gene activation and repression pathogens for multiple and ultra-
Development of flash photolysis by targeting epigenetic regulators sensitive diagnostic
for deep uncaging in vivo and
high-throughput characterisation • STEMDIAGNOSTICS. . . . . . . . . . . . . . 156 • VALAPODYN . . . . . . . . . . . . . . . . . . . . . . . . . 178
of neurotransmitter gated The development of new diagnostic Validated Predictive Dynamic Model
ion channels in drug discovery tests, new tools and non-invasive of Complex Intracellular PaCell Death
methods for the prevention, and Survival
• PlasmodiumdUTPase . . . . . . . . . . . . 134 early diagnosis and monitoring
Deoxyuridine triphosphate for haematopoietic stem cell • VASOPLUS . . . . . . . . . . . . . . . . . . . . . . . . . . 180
nucleotidohydrolase transplantation (HSCT) Placental Growth Factor (PlGF): new
as a drug target against Malaria diagnostic and therapeutic applications
• STREPTOMICS . . . . . . . . . . . . . . . . . . . . 158 in cardiovascular disease
• POC4life . . . . . . . . . . . . . . . . . . . . . . . . . . . 136 Systems biology strategies and
Multiparametric quantum dot metabolome engineering for the • VITAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
bioassay for point of care diagnosis enhanced production of recombinant Development of optimized recombinant
proteins in Streptomyces idiotypic vaccines for subset-specific
• PRIBOMAL . . . . . . . . . . . . . . . . . . . . . . . . 138 immunotherapy of B cell lymphomas
Preclinical studies towards an • SYSCO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
affordable, safe and efficacious two- Systematic Functional analysis of • ZF-TOOLS . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
component paediatric Malaria vaccine Intracellular Parasitism as a model High-throughput Tools for Biomedical
of genomes conflict Screens in Zebrafish
• PRISM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Phospholipid and glycolipid • SysProt . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162 Late submission:
recognition, interactions and System-wide analysis and • PREGENESYS . . . . . . . . . . . . . . . . . . . . . . . 186
structures by magnetic resonance modelling of protein modification Development of Early Non-Invasive
Biomarkers and Means for the Diagnosis
• PROLIGEN . . . . . . . . . . . . . . . . . . . . . . . . . 142 • TAMAHUD . . . . . . . . . . . . . . . . . . . . . . . . . 164 and Progression Monitoring of
Hypoxic renal proliferation Identification of early disease Preeclampsia and Tailoring
markers, novel pharmacologically Putative Therapies
• QuAGSIC . . . . . . . . . . . . . . . . . . . . . . . . . . 144 tractable targets and small molecule
Quantitative analysis of genes in phenotypic modulators in • Index by project number . . . . . . . . . . 188
single cells Huntington’s Disease
• Index by coordinator . . . . . . . . . . . . . . . 190

5
SME CALL

Foreword

he aim of health research under Framework Programmes is to help Europe

T exploit the unprecedented opportunities for generating new knowledge
and translating it into applications that enhance human health and boost the
competitiveness of health-related industries and businesses in support of the
Lisbon Growth and Jobs strategy.

Research intensive SMEs play a key role in the European Union’s economy, in
terms of competitiveness, innovation, growth and employment. Many of Europe’s
top pharmaceutical companies had modest beginnings. Indeed, yesterday’s suc-
cessful SMEs are often today’s global giants, employing large workforces and
generating enormous value.

Hundreds of SMEs are active in health-related R&D and, in recognition of their

innovative potential, scientific strength and strategic importance, a special
effort to mobilise research-intensive health and biotech SMEs was made during
the Sixth Framework Programme (FP6).

In particular, at the end of the Framework Programme, the Thematic Priority enti-
tled “Life sciences, genomics and biotechnology for health” published a very
successful “SME call” with a budget of € 200 million. This call for proposals was
particularly aimed at funding projects with high numbers of research intensive
SMEs. The call succeeded in mobilising high-tech companies to participate in
Framework Programmes: the 86 projects funded involved 270 SMEs, which were
allocated more than 40 % of the budget.

Through this call, research-intensive SMEs in the health and biotech sector
acceded to a leading role as key players and driving forces in the research
activities of EU-funded projects.

The momentum achieved through this special call for proposals is expected to
generate an even bigger impact in the Seventh Framework Programme (FP7)
projects, with increased participation of SMEs with a key role in research.

This publication presents those 86 projects and aims to illustrate the EU’s com-
mitment to health research, bringing together transnational and multidisciplinary
expertise from both industry and academia.

Manuel Hallen
Acting Director
Health Research

7
 SME CALL
Introduction
T hrough its Framework Programmes, the
European Union has provided support to med-
ical research for more than a quarter of a century,
striving to prevent and cure diseases, and helping
to improve patients’ chances of survival and their
quality of life. At the same time, the EU has aided
the efforts of the European healthcare industry
in maintaining a leading role in the world.
Between 2002 and 2006, the Sixth Framework
Programme (FP6) dedicated € 2.4 billion to the
Thematic Priority “Life sciences, genomics and
biotechnology for health” to support European
Research efforts, developing frontier technologies,
encouraging excellence in fundamental and clini-
cal research, bringing academics, clinicians and
industry together at every stage of the process
– from the laboratory bench to the hospital and
to the market.
The “Life sciences, genomics and biotechnology
for health” Thematic Priority emphasised the
importance of innovation and the integration of
industry, small and medium sized enterprises (1),
by ensuring that new knowledge is disseminated
and translated into new therapies, diagnostics
and clinical practice. Overall, of the € 2.4 billion of
the budget available for ‘health’, some € 335 million
was awarded to SMEs participating in EU-funded
projects, in particular through a special “Call for
proposals for STREPs dedicated to SMEs”, in the
last year of FP6. These “SME-STREPs” have been
specifically designed to support SME efforts
towards research and innovation. Such projects
were centred on the reinforcement of SME’s
scientific and technological knowledge and on
the validation of innovative solutions. Research-
intensive SMEs played leading roles – although
not necessarily coordinating the projects – and
participated alongside universities, research cen-
tres, other industries and industrial associations.
The expected project results had to be of clear
9
interest and potential benefit to one or more
SMEs. The share of the EU contribution going to
the participating SMEs was expected to be
(1) The official EU definition of an SME is an
autonomous company with less than 250 employees,
between 30 and 50 %. an annual turnover of not more than € 50 million
and/or an annual balance sheet total of not more
Through this Call, 86 projects, which are the the than € 43 million. For more details see:
focus of this publicationhave been funded for http://ec.europa.eu/enterprise/enterprise_policy/
a total contribution of € 200 million, from which sme_definition/index_en.htm
around 40 % goes to around 270 SMEs. The sci-
entific involvement included a wide range of
activities, such as identification of biomarkers,
elucidation of candidate genes and their role,
providing microRNA discovery and validation
platforms or bioinformatics and transcriptomic
analysis, developing photonic and electro-optics,
designing microchip or magnetic phase platforms,
etc. Specialised SMEs with expertise in intellectual
property management, technology transfer, project
management or training activities also participated
actively in some of these projects.
SMEs are the main economic drivers of health-
care, biotechnology and medical technologies.
Through EU-funded collaborative research, SMEs
can maximise the value of their expertise, network
internationally, learn from other key players and
reduce risk by collaborating with other SMEs and
larger industrial partners and academics from all
over Europe and beyond.
At the same time, the often pivotal technological
input from SMEs, as well as their business orienta-
tion and dynamism, will benefit other project partic-
ipants. In this way, the output and the exploitation
of the results can be optimised, and the spirit of
entrepreneurship in research supported.
The momentum achieved by this Call to mobilise
research intensive SMEs is expected to generate
an even bigger impact in the Seventh Framework
Programme (FP7) projects on the participation of
SMEs with a key role in research activity.
ACRONYM Contract number: LSHM-CT-2006-037554 | EC contribution: € 1 198 900 | Duration: 36 months
Starting date: 1 January 2007

AGLAEA

SUMMARY
Glutamate is the most abundant excita-
Development of novel animal models of
tory transmitter in the brain. However, glutamatergic central nervous system disorders
very few models exist to explore the
potential of drugs that modulate gluta-
using in vivo siRNA and transgenic approaches
mate transmission. Because altered
glutamate transmission is involved in
numerous psychiatric diseases, there is
a strong need for such models to charac-
terise the effects of hypo- and hyper-glu-
Background Expected results
tamatergic states on the onset and
development of such diseases. AGLAEA
Modulation of glutamate signalling levels is Access to improved animal models of specific psy-
will develop and characterise models of
associated with many psychiatric disorders. chiatric disorders will enhance the development of
selective, partial knockdown of specific
Creation of reliable and practical models of improved treatments, in particular for disorders
components of the brain glutamatergic
altered brain glutamate function has been diffi- such as schizophrenia where existing models
system in mice. This will provide a better
cult. Glutamate is the most abundant excitatory are often based on limited pharmacological and
understanding of the implication of glu-
transmitter in the brain and interacts with numer- neurobiological information about the disorder.
tamate signalling in diseases such as
ous receptors and transporters responsible for Targeting the glutamatergic system should lead to
schizophrenia, anxiety and cognitive dis-
both fast synaptic transmission and modulatory models that more closely resemble the human sit-
orders. AGLAEA will lead to breakthrough
functions. However, development of knockout uation with regard to the symptoms that are at
research on the neurobiological and neu-
(KO) rodents is expensive and time consuming, present not treated by existing drugs (e.g. cogni-
rochemical bases of psychiatric disorders
and gene KO is often associated with develop- tion in schizophrenia) or when existing drugs have
and will enable the further testing of new
mental alterations. Inducible and conditional side effect and/or dependence issues anxiety). The
drugs for treatment. In order to selectively
knockout technologies have helped to alleviate creation of these models will also increase fun-
turn off specific components of the gluta-
this problem. However, the gene is nearly com- damental research into the basic mechanisms of
matergic pathways, an siRNA approach
pletely suppressed when the induction occurs. glutamate function. In addition, the techniques
will be used. The effect of modulation of
Because glutamate is a ubiquitous excitatory used will expand the use of siRNA in vivo for the
glutamate signalling will be characterised
transmitter, full knockout of a specific glutamate creation of new models in CNS disease, provid-
using functional MRI (fMRI) and micro-
receptor or transporter often yields a phenotype ing new solutions for the exploration of such
dialysis/microsensor analysis. Specific
incompatible with behavioural testing. pathologies.
behavioural tests will be carried out
on live animals for the assessment of
glutamate-related psychiatric disorders.
Aim Potential applications
Furthermore, the data collected from
AGLAEA is aimed at developing models of selec- A certain number of CNS disorders, including
siRNA experiments will be applied to the
tive, partial knockdown of specific components schizophrenia, anxiety and cognitive disorders
generation of transgenic mice, in which
of the brain glutamatergic system that will result can be linked to glutamatergic dysfunction. The
modulation of glutamate signalling will be
in hypo- and hyper-glutamatergic states yield- existing treatments for patients suffering from
induced at different stages of develop-
ing animals amenable to behavioural investiga- these diseases have serious side effects and are
ment. Therefore, AGLAEA will provide
tion. The results will then drive the creation of not always efficient. For example, existing drugs
both the pharmaceutical and the aca-
specific transgenic lines with targeted knock- are unable to treat the social, emotional and
demic world with potent models. These
down of components of the brain glutamate sys- cognitive symptoms of schizophrenia and there
models will be used to test novel com-
tem yielding mice that can be studied over long are few marketed treatments for the cognitive
pounds and assess their therapeutic
periods of time. deficits of Alzheimer’s disease. By developing
value and will benefit researchers investi-
and characterising animal models with hypo-
gating the neurobiological and neuro-
and hyper-glutamatergic states, AGLAEA will
chemical bases of those diseases.
provide valuable data on the impact of gluta-
matergic signalling on such disorders, therefore
The consortium set up to reach the objec-
opening the way for better treatment and care of
tives of AGLAEA gathers 3 high tech SMEs,
patients.
2 academic groups and one large group for
the management of the project (ALMA),
altogether representing 4 European
countries (FR, HU, UK, NL).

10
Key words: animal models, glutamate, siRNA, transgenic mice

ROLE OF SMEs Scientific coordinator

Bernard Ludwig
ADDEX Pharmaceuticals France SAS
Three SMEs, representing 60 % of the budget, are key contributors to the project. Addex Behaviour Department
Pharmaceuticals, France, will coordinate the project and will study the effects of interfer- Immeuble Alliance – bat. A&C
FR-74160 Archamps
ence RNA and genetic manipulation of brain glutamate systems on behaviour in mice. Addex Bernard.Ludwig@addexpharma.com
has extensive expertise in the discovery and development of novel medications for central www.addexpharma.com
nervous system diseases and will also examine the effects of experimental and reference
drugs to further validate the mouse models produced in the project. BioTalentum Ltd., based Partners
in Hungary, has in-depth expertise in animal embryology, micromanipulation, embryonic Andras Dinnyes
stem cell transgenesis and cryopreservation, which will be applied to the production of BioTalentum Ltd.
transgenic mice for the project. BioTalentum will use innovative techniques developed in- Gödöllo, Hungary
www.biotalentum.hu
house to generate knockdown mice in mouse strains most useful for neurobiological and
behavioural analyses. BioTalentum will also employ the latest techniques in rapid deriva- Charles Marsden
tion of transgenic mouse lines to provide stable animal models as quickly as possible. Institute of Neuroscience
Brains On-Line, based in The Netherlands, has broad expertise in the application of micro- University of Nottingham
Nottingham, United Kingdom
dialysis to in vivo neuropharmacology and pharmacokinetic analysis of drugs in the brain.
Brains On-Line will study the neuropharmacological consequences of interference RNA and Ben Westerink
genetic knockdown of glutamate system genes in brain regions associated with diseases of Department of Biomonitoring & Sensoring
University of Groningen,
interest, including schizophrenia, anxiety and cognitive disorders. Brains On-Line will also Brains-On-Line, The Netherlands
perform detailed immunohistochemical analyses of brain tissue to determine the anatomi-
cal distribution and extent of genetic knockdown resulting from the interference RNA and Benjamin Questier
transgenic manipulations. The three SMEs, along with their academic and corporate partners, ALMA Consulting Group
Lyon, France
each bring unique expertise critical to the success of this project.

| A 2.3 Tesla magnetic resonance imaging (MRI) machine

used to investigate the effects of drugs on neuronal
activity in regions of the mouse brain. The method will
be used in the present project to identify the effects of
altering glutamate activity on brain region function.

11
ACRONYM Contract number: LSHB-CT-2006-037386 | EC contribution: € 1 993 208 | Duration: 24 months
Starting date: 1 June 2006

ANGIOSTOP

SUMMARY
ANGIOSTOP proposes an approach to
Novel Anti-angiogenic treatment for Cancer,
develop a new, safer and more effective Arthritis and Ocular Neovascularization based
anti-angiogenic medicine that reduces
the pathological blood vessel formation
on Inhibition of Placental Growth Factor (PlGF)
associated with solid tumor growth, ocu-
lar neovascularization (diabetic retinopathy
and macular degeneration) and rheuma-
toid arthritis. The proposed drug target is
Placental Growth Factor (PlGF) and the
Background Aim
candidate drug is a humanised neutral-
ising monoclonal antibody. This drug tar-
Most anti-angiogenic strategies are focused on ANGIOSTOP aims to elaborate a comprehensive
get selection is based on recent basic
blocking the interaction between VEGF and its approach to the accelerated development of new
research on the role of PlGF in patho-
receptor VEGFR-2. Despite the success of Avastin, efficacious and safer anti-angiogenic medicines
logical angiogenesis and ‘translational
it is unlikely that VEGF-inhibitors alone will be suf- that reduce the pathological blood vessel growth
research’ that established proof of con-
ficient to halt tumour angiogenesis. First, an and can be used for the treatment of major progres-
cept in experimental animal models.
increasing number of studies document that block- sive disorders such as cancer, ocular neovasculari-
Using a lead candidate anti-PlGF anti-
ing the VEGF pathway leads to the induction of sation (as observed in diabetic retinopathy and
body, it has been demonstrated that inhi-
alternative angiogenic signals. Secondly, it has age-related macular degeneration) and arthritis.
bition of PlGF reduces solid tumour
been reported that treatment of cancer patients The overall objective of ANGIOSTOP is to develop
growth, inhibits ocular neovascularisa-
with Avastin significantly upregulates the levels of an anti-PlGF monoclonal antibody. The roadmap
tion and alleviates arthritis symptoms.
PlGF. Finally, the currently available angiogenesis comprises ‘translational research’ to validate previ-
ANGIOSTOP will assure the development
inhibitors have serious side effects, thus mandat- ous proof of concept studies in new therapeutically
of an anti-PlGF antibody that may consti-
ing the development of additional angiogenesis relevant small animal models, both in terms of
tute a new, safer and efficacious medicine
inhibitors. Due to the potential application of safety and efficacy, to evaluate PlGF expression and
for the treatment of diseases that depend
angiogenesis inhibitors in disorders other than its possible upregulation in cancer patients, and to
on PlGF driven angiogenesis such as cancer,
cancer, where the treatment is expected to start at develop an industrial production process at the
ocular disease and arthritis.
earlier times after the disease onset and continue GMP level for critical path development.
for longer periods, safer anti-angiogenic drugs
without the risk of serious side effects are needed. The project aims to perform extensive validation
Through gene targeting studies in mice, it has been studies of its drug candidate to reduce the risk of
shown that loss of PlGF does not cause any vascu- failure as the drug advances into clinical trials and
lar defect during development, reproduction or to manufacture this product for clinical trials. The
normal adult life, while it severely impairs angio- ultimate goal of ANGIOSTOP is to develop an anti-
genesis and arteriogenesis during pathological PlGF monoclonal antibody for the safe and effec-
conditions including ischemia, inflammation and tive treatment of cancer, ocular disease and
cancer therefore indicating that the ANGIOSTOP arthritis. The research will focus on a selected drug
anti-angiogenic strategy targeting PlGF could candidate but the new models and strategies will
represent a safer and more effective approach. be of more general utility for the development of
new medicines aimed at increasing or reducing
blood vessel formation, as well as for the advance-
ment of the project’s understanding of pathologic
angiogenesis.

12
Key words: angiogenesis, cancer, ocular disease, arthritis, PlGF

ROLE OF SMEs Scientific coordinator

Titti Martinsson-Niskanen
BioInvent International AB
BioInvent is the project coordinator. Lund, Sweden
The purpose of the present consortium is to align a partnership strictly confined to partic- titti.martinsson.niskanen@bioinvent.com
www.bioinvent.com
ipants with unique essential assets (uniquely qualified academic research groups, SMEs
owning intellectual property as well as essential know-how, and experienced clinical trial Partners
experts) to allow a rapid focused development of new safe and efficacious medicines for
major diseases (i.e. solid tumours, AMD and diabetic retinopathy, and arthritis). The com- Jean Marie Stassen
ThromboGenics
plementarities and synergy between the academic groups and SMEs will allow a focused Leuven, Belgium
streamlined development strategy, avoiding levels of bureaucratic decision making that is
an unavoidable handicap of large networks and Big Pharma. Peter Carmeliet
Flanders Interuniversity Institute
for Biotechnology VZW
Leuven, Belgium

Expected results Christian Fischer

Charité Universitaetsmedizin Berlin
Berlin, Germany
• A lead humanised anti-PlGF antibody will be val-
idated in appropriate animal models. Eric Van Cutsem
Katholieke Universiteit Leuven
• Toxicology studies will identify a safe clinical Leuven, Belgium
dose and document the cross-reactivity profile
and any toxic effects of the lead candidate anti- Wen Jiang
body. Cardiff University
Cardiff, United Kingdom
• Process development and industrial GMP manu-
facturing of the lead candidate antibody for criti-
cal path development will be carried out.
• The protein expression of PlGF will be examined
in patient tumour samples. If PlGF levels corre-
late with certain tumour types and associate
with grade and prognosis, such information may
be beneficial for identification of appropriate
patients groups.
• Development of a fully human back-up antibody
with a similar or better pharmacological profile
as compared to the lead candidate antibody will
be performed for contingency purposes.

Potential applications

ANGIOSTOP has both strategic and specific deliver-

ables and milestones. The new animal models and
acquired knowledge on pathologic and therapeutic
angiogenesis will transcend the specific aims of the
drug development programs and be of strategic
significance for angiogenesis research in general.
The translational and critical path research pro-
gram has a clearly defined ultimate deliverable:
a new medicine based on PlGF-neutralizing anti-
body for anti-angiogenic treatment of certain solid
tumours, ocular diseases and arthritis.
| ANGIOSTOP is exploring the therapeutic potential and
pleiotropic mechanism of anti-PlGF, antibodies against
placental growth factor (PlGF), a VEGF homologue, which
regulates the angiogenic switch in disease but not in health.
Anti-PlGF antibodies inhibit tumour growth by blocking
angiogenesis. Distinct from VEGF inhibitors, however, targeting
PlGF has been found to prevent infiltration of angiogenic
macrophages, and thus do not switch on the angiogenic
rescue program responsible for resistance to VEGF inhibitors.
This mechanism is illustrated with anti-PlGF (depicted in blue)
preventing PlGF (green) binding to its receptor VEGFR-1+ (red)
expressed on macrophages (orange).

13
ACRONYM Contract number: LSHM-CT-2007-037862 | EC contribution: € 1 984 900 | Duration: 36 months
Starting date: 1 March 2007

ARTEMIS

SUMMARY
The ARTEMIS project aims to design,
In vitro neural tissue system for replacement
develop and optimise an in vitro system to of transgenic animals with memory/learning
replace the use of animals in transgenics
and toxicology experiments, and in studies
deficiencies
related to the effects of genes, chemicals,
and neural tissue structure and function,
such as memory and learning. From a sci-
entific perspective, the ARTEMIS partners
target the development of a three-dimen-
Background The objective is to use in vitro developed neural
sional neural tissue-like construct, which is
tissues instead of transgenic animals having
formed by the synaptic connections devel-
In vitro systems composed of synaptically inter- memory and learning deficiencies. For this rea-
oped among neurons produced from
connected neurons have already been developed son, the tissue will be developed in vitro from
mouse embryonic stem cells.
and used for pharmacological and toxicological embryonic cell lines that have the genes involved
studies, based on the extracellular recording of in memory/learning ‘switched-off’, (transgenic
For its operational goal, the consortium
cell electrical activity. The neurons used in these tissue). The ability of the transgenic tissue to
seeks to replace transgenic animals with
systems are usually taken from animal tissues, memorise electrical stimuli will be checked and
memory and learning deficiencies with
because a readily renewable cell source such as compared with this of normal tissue. In this way,
the in vitro developed neural tissues.
the tumour-derived neuronal cells, is of limited the role of genes in memory/learning can be
ARTEMIS will develop the tissue in vitro
applicability due to their altered physiology. checked in vitro, providing preliminary informa-
from embryonic cell lines with the genes
Consequently such approaches do not replace tion at the tissue level to orient the design of
involved in memory and learning ‘switched
the use of animals, since the cells they use must transgenic animals towards optimal ones that
off’. The consortium will assess and com-
be taken from animals each time a test or a num- have a high probability of having an altered phe-
pare the ability of transgenic tissue to
ber of tests is performed. In addition to this limi- notype, therefore decreasing the number of
memorise electrical stimuli with that of
tation, the existing in vitro neuronal systems transgenic animals currently generated by trial-
normal tissue.
cannot currently be considered as alternatives, and-error methods.
but rather as complementary to in vivo proce-
Assessing the role of genes in memory and
dures. This is because they provide only partial Due to the controlled complexity and the ease of
learning in vitro provides preliminary infor-
answers to more complex problems, where inter- biochemical analyses in the in vitro system com-
mation at tissue level, so as to determine
cellular synaptic network level processes are crit- pared to in vivo experiments, the system will be
the design of the transgenic animals
ical – rather than intracellular ones – in assessing used in tests aimed at providing information on
towards the optimal ones with a higher
human hazards, for example the chemical effect the biochemical mechanisms of memory defects
probability of having altered phenotypes.
on sensory or cognitive functions. in neural tissue generated from trangsenic cell
This would effectively reduce the number
lines, for which such defects in vivo experiments
of transgenic animals that are currently
produced by trial-and-error methods.
Aim failed to clarify the mechanisms. If this task is
successfully undertaken, the in vitro system
The proposed in vitro system can effec-
The development of an in vitro system of bioarti- could replace the use of transgenic animals in
tively integrate biochemical damage with
ficial neural tissue made from mouse embryonic some cases of memory/learning deficiencies.
behavioural damage.
stem cells with memory/learning capabilities.
In addition, the system will be used in neurotoxi-
The in vitro system consists of a three-dimensional city tests because it has the advantage of meas-
neural tissue-like construct. It is formed by the uring toxicity end-points at various levels of the
synaptic connections developed among neurons organisation of neural tissue such as sub-cellu-
generated from mouse embryonic stem cells. The lar, cellular and synaptic network levels, as well
neurons are inside a porous biomaterial which con- as behavioural-like in memory/learning, which
tains molecules that guide the development of the are currently measured in separate in vitro sys-
synaptic network. The tissue is interfaced on two tems (batteries), with the behavioural ones
opposite sides, with multi-electrode arrays for measured only in animal experiments. Specific
electrical stimulation and response recording. tests with neurotoxic compounds will be per-
During the development of the synaptic connec- formed in the system, to find what set of end-
tions, an electrical stimulation is applied so that the point biochemical measurements are necessary
final synaptic connectivity pattern will be stimulus- and sufficient for the prediction of memory dam-
specific and will generate a stimulus-specific elec- age, checking in this way the completeness of
trical response. Based on the signal features of the the complementarity of in vitro system-batteries
response, it can be evaluated when the tissue has currently in use. The developed in vitro system
‘memorised’ the electrical signal. is proposed as a system which can integrate

14
Key words: bioartificial neural tissue, embryonic stem cells, multielectrode arrays, in vitro neuronal development,
memory acquisition-learning, neurotoxicity, developmental toxicity

ROLE OF SMEs Scientific coordinator

Petros Lenas
Complutense University of Madrid
• Electronic Technology Team, (eTT) Department of Biochemistry and Molecular
eTT is responsible for the signal analysis of the response of the synaptic network, so that Biology IV, Veterinary Faculty
Parque Científico de Madrid
criteria to detect the memory/learning ability will be formulated. Santiago Grisolía, 2
28760 Tres Cantos, Madrid, Spain
• Bio Talentum Ltd., (BIO) petros.lenas@opt.ucm.es
www.ucm.es
BIO develops transgenic cell lines that have deficiencies in neural development and
memory, so that an assessment of the in vitro system will be made as a pre-screening Partners
system to switch-off genes before the generation of transgenic animals.
Janusz Marian Rosiak
Institute of Applied Radiation Chemistry
• Histopathology Ltd., (HISTO) Division of Applied Radiation Chemistry
HISTO performs all the histochemical analyses of the project for the detection of cells Politechnika Lodzka
inside the hydrogels and their state of differentiation. Lodz, Poland
www.p.lodz.pl
• BSL Bioservice Scientific Laboratories GmbH, (BSL) Daniel Horak
BSL participates in the design of the tests and performs the tests and various biochemical Department of Bioanalogous and Special
measurements and off-line analyses needed for the correlation of the end points. Polymers Group of Polymer Particles,
Institute of Macromolecular Chemistry,
Academy of Sciences of the Czech Republic
• Quattromed, (QM) Prague, Czech Republic
QM develops transgenic cell lines and memory function tests in the in vitro system, in order imc.cas.cz
to test the ability of the system to be used as transgenic tissue instead of transgenic animals. Antonio Novellino
Electronic Technology Team
Rome, Italy
www.ettsolutions.com

Andras Janos Dinnyes

biochemical damages with behavioural ones.
Based on the results of this project, a proposal
for formal pre-validation studies will be prepared,
so that in the near future the system will be vali-
dated and used instead of animals, in order to
predict behavioural damages.
Expected results
An in vitro neural tissue consisting of a three-
dimensional network of synaptically intercon-
nected neurons that exhibit higher-level, brain
tissue-like functionalities in memory acquisition
and learning. This tissue could replace the use of
memory/learning deficient transgenic animals
(in vitro transgenics), and the use of animals in
neurotoxicity test related to behavioural-like
(memory/learning) end points.
Potential applications
• Assessment of toxic or pharmacological effects
on the neuronal functions in direct relation with
the in vivo situation, i.e. the impairment of
memory or learning instead of end-point bio-
chemical markers when it is not known to what
extent they influence higher-level functions.
15
Bio Talentum Ltd.
Gödöllo, Hungary
www.biotalentum.hu
• Development of in vitro transgenic neural tis-
sue as memory/learning disease model sys- George Szekeres
tems, using genetically modified instead of Laboratory of Histopathology
Histopathology Ltd.
normal embryonic stem cells. Pecs, Hungary
www.histopat.hu
• Neurotoxicity studies related to the develop-
ment with application of neurotoxic substances Thomas Hartung
European Centre for the Validation
at different developmental stages. of Alternative Methods (ECVAM)
Institute for Health and Consumer Protection
• Drug tests directed at deciphering the effect at Ispra, Italy
www.jrc.cec.eu.int
the network level; for example, the anticonvul-
sant drugs for epilepsy, which is caused by a Thomas Becker
malfunction of a network of neurons instead of BSL Bioservice Scientific Laboratories GmbH
Planegg, Germany
defects in particular neurons, or the effects of
www.bioservice.com
agents used in anaesthesia due to the inhibi-
tion of the oscillations of the synaptic network Ernest Arenas
instead of electrical activities of single neurons. Department of Medical Biochemistry and
Biophysics Division of Molecular Neurobiology
Karolinska Institute
• Development of intelligent biosensors for the Stockholm, Sweden
detection of biohazards training the network to ki.se
neurotoxic compounds as stimuli, instead of Eero Vasar
electrical signals. Tiit Talpsep
Quattromed A. S.
• Development of neuroprostheses of the central Tartu, Estonia
www.quattromed.com
nervous system, intended to replace brain func-
tions that have been lost due to disease or José Mendes
trauma. Department of Physics, University of Aveiro
Campus Universitario de Santiago
Aveiro, Portugal
www.ua.pt
ACRONYM Contract number: LSHG-CT-2006-037897
Starting date: 1 January 2007
AUTOSCREEN
SUMMARY
The overall objective of the AUTOSCREEN
project is the establishment of an innova-
tive and automated screening instrument
for high-throughput and high-content
screens. This instrument will allow stan-
dardised, robust, automated and ultra-
sensitive high-resolution analysis of RNAs
and proteins at cellular and subcellular
resolution. The AUTOSCREEN consortium
is composed of six academic partners
(Research Institutes and Universities) and
four SMEs.
| EC contribution: € 3 217 280
AUTOSCREEN for Cell Based High-throughput
and High-content Gene Function Analysis and
Drug Discovery Screens
Background
As more and more genomes are being sequenced,
efficient methods to elucidate the functions of the
many unknown genes need to be developed. Such
methods will be crucial in future attempts to align
genes of unknown functions in biochemical path-
ways and networks that carry out the essential
processes in all living organisms. These methods
will also be an essential prerequisite for turning
biology from a qualitative, mostly descriptive sci-
ence, into a quantitative, ultimately predictive,
science.
Although quantitative tools such as DNA microar-
rays for transcriptome analysis of biological sys-
tems have been available for some years, they have
not yet been used to their full potential due to the
overwhelming complexity and indeterminate com-
position of biological systems. Such intricacy has
often prevented the integration of this information
into comprehensive and cohesive models.
Cells are built from thousands of different pro-
teins that are expressed, both temporally and
spatially, over an extremely wide dynamic range.
Proteins and other cellular components are regu-
lated through variations of their location, their
activity and their state of modification. Although
DNA microarrays have proved to be important
tools for gene discovery on the tissue level, and,
moreover, hold great promise for diagnostic
applications, they have major shortcomings in
their lack of cellular resolution. In order to obtain
qualitative and quantitative data on cellular path-
ways, equipment that allows recording of tran-
scripts and proteins at the high precision and at
high-throughput needs to be developed.
Aim
The main goal of the project is to develop an inno-
vative screening platform suitable for high-
throughput and high-content cell-based assays
and to demonstrate its suitability for high-resolu-
tion in situ techniques. This instrument, called
AUTOSCREEN, will not only provide the basis for
16
| Duration: 60 months
intelligent and efficient high-content screens, but
will also be designed for low cost genetic, medical,
chemical and pharmaceutical screens. The integra-
tion of novel technologies into a common platform
concept, the development of efficient cell-based
screens, and the demonstration of the feasibility of
this approach will constitute a significant competi-
tive advantage for the European pharmaceutical
and agrobiotechnological industry.
Expected results
The main expected result of the project is the gen-
eration of an innovative screening instrument,
called AUTOSCREEN. This instrument, which will
consist of the modular iMIC imaging microscopy
platform as a future microscopy standard, will inte-
grate ultra-sensitive CCD-technology and novel
software concepts that allow an adaptive, i.e.
results-based, shaping of the ongoing experiment.
This will facilitate the reduction of an otherwise
uninterpretable datastream. An ultra-sensitive flu-
orescence-based scanning device for single-mole-
cule measurements and a fully automated plate
feeder station for automated sample handling and
tracking will increase the flexibility and wide utility
of AUTOSCREEN. This system will be tested in
a large number of applications for performance and
excellence.
The project is expected to permit the qualitative
and quantitative monitoring of cellular con-
stituents (RNA, proteins, and metabolites) in liv-
ing cells at the highest possible cellular and
subcellular resolution and with maximal sensi-
tivity and specificity. This will allow quantifying
protein expression and monitoring its subcellu-
lar localisation, its state of modification and its
association with other proteins and ligands.
Furthermore, it will allow measuring of the change
of these processes over time. Characterisation
of the toponome will overcome major limitations
of contempory functional genomic and proteome
technologies, which do not provide cellular or
subcellular resolution, and will permit high-
content screens for pharmacological substances
with fewer side reactions.
Key words: high throughput analysis, imaging, screening, genomics, proteomics, drug screening

ROLE OF SMEs Scientific coordinator

Klaus Palme
University of Freiburg
Within the AUTOSCREEN project, the partner SME companies will establish a widely Center for Applied Biosciences
applicable robot-automated screening tool by conceptualising and assembling a first Institute for Biology II
Faculty of Biology
AUTOSCREEN prototype. The SMEs will develop a full automation of the prototype, Schanzlestr. 1
improve the innovative iMIC microscope platform in iterative improvement steps, and 79104 Freiburg, Germany
develop a variety of optimisations, assays and applications. The following partners are klaus.palme@biologie.uni-freiburg.de
www.uni-freiburg.de
involved in AUTOSCREEN as SMEs: TILL, MANZ, ANDOR and ARO.

The contribution of TILL will be the development of novel concepts for overcoming the current Partners
limitations of high throughput imaging, and to contribute to the development of new adap-
Stefanie Klemm
tive soft- and firm-ware concepts for automated imaging. Later, TILL will integrate new devel- TILL ID GmbH
opments both from within and outside the consortium, evaluating the overall performance of Munich, Germany
all evolutionary stages of the process and specifying future activities. TILL is also involved in www.till-photonics.com
the exploitation and dissemination of results and in the management of the project.
Andras Filep
Manz Kft
MANZ will concentrate on defining substrates, handling objects and system specifications Debrecen, Hungary
and on automated handling of substrates. manzautomation-c.cegbongeszo.hu/
nyito-en.htm
ANDOR will be responsible for further enhancing the new price/performance, single photon Jan Hesse
sensitive Luca EMCCD camera and will cooperate with TILL in developing novel readout patterns. Upper Austrian Research GmbH
Linz, Austria
www.uar.at
ARO will be involved in several WPs to assess the quality of AUTOSCREEN under a broad vari-
ety of experimental conditions, specifically with respect to proteome visualisation capabilities. Colin Coates
Andor Technology Plc
Belfast, United Kingdom
www.andor.com

Potential applications
AUTOSCREEN will have a strategic impact on func-
tional genomic, biotechnological and biomedical
research by permitting qualitative and quantita-
tive monitoring of cellular constituents in cells at
the highest possible cellular and subcellular reso-
lution and with maximal sensitivity and speci-
ficity. This will allow, for example, quantifying
protein expression, monitoring of its subcellular
localisation and state of modification, and charac-
terisation of the toponome.
The demonstration of the wide applicability of
AUTOSCREEN to the quantitative monitoring of
biological processes, within living cells, at highest
currently possible resolution and with sensitivity
to the limit set by the laws of physics, will have
a significant impact on biomedical research in
general. By combining interdisciplinary activities
from academic and industrial sources and by
interfacing biological research with nanotechnol-
ogy, computing and engineering, the team expect
to create an important tool for biomedical
research. Moreover, AUTOSCREEN-based assays
will allow the monitoring of cellular networks and
incorporate in vivo protein interaction assays and
Carmen Plasencia
Aromics S.L.
features like protein concentration and kinetic Barcelona, Spain
parameters. Thus, available information on gene www.aromics.es/eng/index.htm
expression networks will not only be useful for
identifying points of the network affected by the Martin Oheim
Institut National de la Santé et
drugs and for simulations of cellular processes, de la Recherche Médicale (INSERM)
but will also allow the assessment of drug side Neurophysiology and
reactions at an early stage and facilitate the New Microscopy Laboratory
Paris, France
design of novel, less toxic compounds. www.biomedicale.univ-paris5.fr/
neurophysiologie/labo/oheim.php
The project will reveal new, faster and better ways
to determine gene functions and regulatory net- Hartmann Harz
Ludwig-Maximilians-Universität
works in a much shorter period of time. The imple- BioImaging Zentrum
mentation of these technologies will lead to a Munich, Germany
higher competitiveness of European biomedical www.biz.uni-muenchen.de
SMEs, in the sense that the instrumentation to be Benedetto Ruperti
developed and assembled in this project will University of Padova
enable many European SMEs to efficiently per- Padova, Italy
www.unipd.it
form their screens. The estimated low cost of this
instrument is expected to be of great benefit for Ladislav Nedbal
SMEs as it will promote their market success. The Institute for Systems Biology
project will also provide the opportunity for estab- Nove Hrady, Czech Republic
www.greentech.cz
lishing a new industry standard for automated
microscopy and thus provide opportunities not
only on an individual basis, but also for larger
manufacturers who will benefit from the innova-
tive approach for which currently there is no equal
on the world market.

17
ACRONYM Contract number: LSHB-CT-2006-037325 | EC contribution: € 2 269 999 | Duration: 36 months
Starting date: 1 January 2007

BacAbs
www.bacabs.org

SUMMARY
High throughput cloning and expression
Assessment of Structural Requirements in
of large sets of genomic ORFs has Complement-Mediated Bactericidal Events:
become a preferred industrial strategy
for genome-wide searches of new vac-
Towards a Global Approach to the Selection
cine candidates. For invasive infections of New Vaccine Candidates
in particular, the aim is to find proteins
eliciting antibodies capable of binding to
the bacterial cell surface and, through
interaction with the complement system,
Background are also able to predict which antigens can lead to
effectively kill the bacteria. However,
the production of bactericidal antibodies.
current data accumulating from reverse
The development of antibiotic resistance in patho-
vaccinology studies (targeting of possi-
genic bacteria is potentially one of the most serious In principle, the capacity of a protein antigen
ble vaccine candidates starting from
threats in modern medicine (1). One approach to to raise bactericidal antibodies may depend on
genomic information) show that only
minimize the use of antibiotics is to vaccinate (a combination of):
a small fraction of surface-exposed pro-
against pathogenic strains of bacteria. A clear can- • size, shape, structural complexity, abundance,
teins appears to elicit antibodies with
didate to this approach is Neisseria meningitidis, solubility, and propensity to oligomerization; and
bactericidal activity. By using informa-
a major cause of bacterial septicemia and meningi- • sequence, structure, dynamics and location of
tion generated by reverse vaccinology
tis. N. meningitidis is a Gram-negative bacterium, specific protein regions (epitopes).
projects within the Consortium, the
capsulated in its invasive form, classified into five
BacAbs project will apply a novel multi-
major pathogenic serogroups on the basis of chem- These factors may in turn modulate the properties
disciplinary approach to single out the
ical composition of distinctive capsular polysac- of the Ag-Ab complex and its susceptibility to be
structural requirements for viable bacte-
charides (2,3). Although a promising candidate is recognised by the C1q component. The BacAbs
ricidal vaccine candidates and will
on clinical trials (4), there is not yet an effective vac- project aims at deciphering possible correlations
develop bioinformatics tools to predict
cine against serogroup-B N. meningitidis (MenB), between these factors and bactericidity.
compliance with such structural require-
responsible for over 50% of all meningococcal dis-
ments. To this end, a systematic analysis
of sequence, structure, dynamics and
ease in Europe(5). The capsular polysaccharide of Aim
MenB is identical to a widely distributed human car-
interactions of selected protein targets
bohydrate, making its use as the basis of a vaccine Following the framework outlined above, the
will be undertaken using model systems
for prevention of MenB diseases problematic(6). As BacAbs project is concerned with the identifica-
of medical interest such as serogroup-B
a consequence, most efforts have turned to devel- tion of (surface-exposed or exported) protein
Neisseria meningitidis, a pathogen
opment of vaccines based on surface-exposed or antigens that may elicit complement-mediated
causing septicemia and meningitis for
exported proteins(7). bactericidity in vitro. This includes early discrimi-
which no effective vaccine exists. The
nation of antigens that may induce production of
Consortium comprises an industrial
A bactericidal response, i.e. one which leads to bac- non-bactericidal antibodies. To achieve this goal,
partner with extensive experience on
terial-cell death, can be triggered through a variety the Consortium will investigate the requirements
vaccine development, three SMEs with
of mechanisms. For meningococcal infections, in for productive Ag-Ab-C1q complex formation and
strong expertises on several of the key
vitro bactericidity assays with immune sera corre- proposes to find relevant answers by studying
technological aspects of the project, and
late with protection in humans(8). Although in vivo with a multidisciplinary and comparative approach
five academic partners with internation-
protection against MenB may not be solely achieved the structure of a number of these complexes,
ally recognised tracks on experimental
by complement-dependent bacteriolysis (10,11), an taking the MenB vaccine-development project of
and theoretical studies of protein struc-
antigen that elicits (murine) antibodies capable of Novartis Vaccines & Diagnostics as a model and
ture and interactions.
triggering bacterial-cell death in vitro in a comple- source of useful data and reagent molecules. To
ment-dependent manner is normally considered a single out possible structural determinants,
candidate for human vaccine development (11,12). focus will be put on groups of antigens with simi-
lar size, abundance, solubility, etc. (eliciting and
In this context, one major obstacle to vaccine devel- not eliciting bactericidal antibodies).
opment, besides sequence and antigenic variabil-
ity(13), is the difficulty to identify antigens that will Although initially centred around group-B
generate a bactericidal response. Typically, only N. meningitidis, the specific target of the project
a very small fraction of the antibodies raised in is the development of tools that can be effectively
large-scale antigen-screening studies are bacterici- applied to genome-wide identification of vac-
dal(14). Thus, while potential antigens can be readily cine candidates against any bacterial pathogen
identified this information is of little use unless we susceptible of complement-mediated lysis.

18
Key words: vaccines, structural biology, computational biology, antigen, monoclonal antibody, complement system, bactericidity, protein
crystallogenesis, X-ray crystallography, NMR, mass spectrometry, molecular modelling, molecular-dynamics simulation, molecular docking

ROLE OF SMEs Scientific coordinator

Xavier Daura
Universitat Autònoma de Barcelona
The three SMEs involved in the BacAbs project have a principal technological role. The IT Campus UAB s/n
company INFOCIENCIA S.L. will be implementing the management and dissemination web 08193 Bellaterra (Cerdanyola del Vallès)
Spain
servers of the Consortium, performing bioinformatics analysis of antigen and epitope Xavier.Daura@uab.es
sequences, implementing algorithms, protocols and data emerging from the Consortium’s www.uab.es
work into computational tools and databases within a web-based technological platform,
and evaluating the commercial interest of this platform via demonstration. Two biotechs will Partners
be working on sample preparation and protein-structure determination. ASLA Biotech Ltd.
will be performing protein expression and labelling, screening and optimisation of sample Guido Grandi
conditions for NMR analysis, monoclonal antibody generation, and sequential backbone Novartis Vaccines and Diagnostics
Siena, Italy
assignment and structure determination via NMR. Bio-Xtal S.A. will be performing protein www.novartisvaccines.com
expression and purification, especially in connection to derivatives (seleno-methionine
labelled) for X-ray analysis, expression and solubilization screens on highly hydrophobic or Anatoly Sharipo
poorly soluble targets, exploration of protein crystallogenesis using nanodrop scale robotics ASLA BIOTECH, Ltd.
Riga, Latvia
techniques based on commercially available and proprietary screening approaches, devel- www.asla-biotech.com
opment and optimization of robotic processes for crystallization plate storage and drop visu-
alization, refinement of crystal growth conditions for selected hits to yield diffraction quality Etienne L’hermite
Bio-Xtal S.A.
crystals, and X-ray data collection and structure solution. Mundolsheim, France
www.bioxtal.com

Expected results
The BacAbs project shall provide:
• Structural information on a set of proteins that
are components of the cell surface (the bacterial
organ for interaction with eukaryotic host cells)
of a major human pathogen.
• Improved experimental protocols and tech-
niques, bioinformatics tools and databases to
assist the development of vaccines against
human bacterial pathogens in general, and
group-B Neisseria meningitidis in particular.
• A framework in which experimental and in silico
methods for determining protein structure and
studying macromolecular recognition, immuno-
logical response mechanisms, and sequence-
structure-function relationships can be further
developed.
Giorgio Colombo
Consiglio Nazionale delle Ricerche
• A web-based technological platform integrating Istituto di Chimica
this knowledge, with a potential to improving the del Riconoscimento Molecolare
effectiveness and reducing the costs of vaccine- Milano, Italy
www.icrm.cnr.it
candidate searches.
Martin Zacharias
Potential applications Jacobs University Bremen GmbH
School of Engineering and Science
Bremen, Germany
The results of the BacAbs project have potential www.jacobs-university.de
application in the selection of new vaccine candi-
dates against group-B Neisseria meningitidis and Martino Bolognesi
Università degli Studi di Milano
other bacterial pathogens. Dipartimento di Scienze Biomolecolari
e Biotecnologie
References Milano, Italy
www.unimi.it
(1) Borchardt, Drug. News Perspect. 2004, 17, 219; (2) Gotschlich
et al., J. Exp. Med. 1969, 129, 1349; (3) Gotschlich et al., J. Exp. Med. Alexandre Bonvin
1969, 129, 1367; (4) Giuliani et al., Proc. Natl. Acad. Sci. USA 2006, Universiteit Utrecht
103, 10834; (5) Cartwright et al., Vaccine 2001, 19, 4347; Department of Chemistry
(6) Hayrinen et al., J. Infect. Dis. 1995, 171, 1481; (7) Jodar et al., Utrecht, The Netherlands
www.uu.nl
Lancet 2002, 359, 1499; (8) Goldschneider et al., J. Exp. Med.
1969, 129, 1307; (9) Welsch et al., J. Infect. Dis. 2003, 188, 1730;
Jose Manuel Mas
(10) Vermont & Dobbelsteen, FEMS Immunol. Med. Microbiol. INFOCIENCIA S.L.
2002, 34, 89; (11) Pizza et al., Science 2000, 287, 1816; (12) Welsch Barcelona, Spain
et al., J. Immunol. 2004, 172, 5606; (13) Poolman, Infect. Agents www.infociencia.com
Dis. 1995, 4, 13; (14) Rappuoli, Science 2003, 302, 602.

| Solution structure of the antigenic domain of GNA1870,

a 28-kDa surface-exposed lipoprotein of Neisseria
meningitidis. This is one of the most potent antigens
of Meningococcus discovered by reverse vaccinology
(Protein-Data-Bank entry 1YS5).

19
ACRONYM Contract number: LSHG-CT-2006-037939
Starting date: 1 December 2006
BioBridge
SUMMARY
BioBridge will focus on the application of
simulation techniques on top of multi-
level data, in order to create models for
understanding how molecular mecha-
nisms are dynamically related to complex
diseases at the systemic level. The proj-
ect will explore and identify gaps in infor-
mation, and develop and apply standards
for the transfer and filtering of data from
existing molecular biology databases
and new high-throughput experiments
(microarray, in vivo metabolic profiling
and proteomics data) into metabolic
models of complex diseases. SMEs are
involved in BioBridge from its inception,
so that newly developed protocols will be
commercially exploitable. The project will
therefore drive the standardisation of
analysis of relevant aspects of disease.
| EC contribution: € 1 800 000
Integrative Genomics and Chronic Disease
Phenotypes: modelling and simulation tools
for clinicians
Background
Chronic diseases are usually the result of interac-
tions between individual susceptibility and differ-
ent environmental and/or lifestyle factors, and are
often modulated by multiple genes. The interplay
between these factors determines disease pheno-
type and hence, the prognostic and therapeutic
implications of the disease. This interplay between
genetically predetermined susceptibility and dis-
ease phenotype can, in turn, be revealed by com-
puter analysis integrating clinical and biomedical
data. Computer analysis related to clinical prob-
lems is currently in a phase of accelerated growth.
Some examples of the application of computer
analysis to clinical practice are the classification
and prognosis of ovarian cancer (1), the analysis of
myocardial perfusion images and cardiograms (2)
and the development of a screening device for the
diagnosis of heart murmurs (3). In addition, several
projects in the European Union are implementing
information technology-based services for dia-
betes management (4).
However, all the approaches currently implemented
in clinical practice use very limited datasets, despite
the availability of vast amounts of data from various
life science disciplines since the ‘-omics’ revolution.
Only by integrating genomic, proteomic and
metabolomic data, can knowledge that is useful for
the understanding and treatment of complex
human pathologies begin to be obtained. This is the
goal of the BioBridge project.
Aim
The BioBridge objectives are twofold. First, a bioin-
formatic aspect will involve the development of
software for integrated genomic, proteomic,
metabolomic and kinetic data analysis, in order to
build a bridge between basic science and clinical
practice. Secondly, a biomedical aspect will focus
on understanding the distortion of cellular metab-
olism that is associated with certain target dis-
eases. The diseases in question are congestive
heart failure (CHF), chronic obstructive pulmonary
20
| Duration: 30 months
disease (COPD) and type II diabetes. The available
facts strongly indicate that these diseases com-
prise a cluster of chronic conditions, all of which
are associated with nitroso-redox imbalance. The
integration of data into a dynamic framework will
enable the development of the first kinetic model
of the metabolism shared by COPD, CHF and type
II diabetes, thereby revealing the common and
individual traits of these three complex diseases.
Expected results
After 30 months, BioBridge will have achieved
the following goals:
• creation of a structured database for the collec-
tion of clinical information relating to COPD, CHF
and type II diabetes;
• identification of the metabolic pathways impli-
cated in the target diseases;
• recording of genomic, proteomic, metabolomic
and kinetic information onto the relevant struc-
tured databases;
• development of a software product designed for
specific disease-related data searching;
• development of standards for the different levels
of data, which will be useful for their integration
from genomic and metabolomic databases, and
from specific proteomics and metabolomics pro-
filing experiments, including microarray analysis
and stable isotope tracer data. These will be
mainly Bayesian networks and multivariate
analysis tools;
• development of protocols for transferring data
from the structured databases into dynamic
models;
• using a differential equation approach, the
design and development of an innovative simula-
tion environment that will accommodate the
dynamic behaviour of complex networks, and in
particular the metabolic pathways that are
altered by the target diseases;
• development of generic tools that will be clinically
useful beyond the target diseases addressed
during the lifetime of the project. BioBridge will
also focus on interfacing with end-users, in par-
ticular clinical researchers and clinicians.
Key words: diabetes, chronic obstructive pulmonary diseases, chronic heart failure, systemic effects, genomics,
proteomics, metabolomics, modelling, bioinformatic

ROLE OF SMEs Scientific coordinator

Josep Roca
Department of Pneumology
The Biobridge consortium brings together 3 selected SMEs with complementary skills in Institut d’Investigacions
the domains of semantic interoperability, heterogeneous data integration and simulation Biomèdiques August Pi i Sunyer
Barcelona, Spain
technologies. jroca@clinic.ub.es

MathCore Engineering AB develops integrated tools in modelling, simulation, control, and Partners
visualization of complex systems. This expertise is fundamental in the project tasks related
Peter Aronsson
to the creation of Mathmodelica Metabolic Pathway simulator. This tool will position MathCore Engineering AB
MathCore very solidly in the biological simulations field. Linköping, Sweden
www.mathcore.com
Biomax Informatics AG provides state-of-the-art software for the biopharmaceutical indus- John Brozek
try with a focus on data integration, data retrieval, knowledge aggregation and generation. Genfit Laboratories
The Biobridge project uses its BioXMTM Knowledge Management Environment to integrate Genfit S.A.
and organize heterogeneous data types. Additionally, its software BioRSTM allows ubiquitous Loos, France
www.genfit.com
retrieval of data for project participants.
Andrea Ramge
Genfit is a leading European drug discovery company in the field of cardiovascular, meta- Dieter Maier
Biomax Informatics AG
bolic, inflammatory and CNS disorders. Genfit brings its LSGraph® technology to the proj- Martinsried, Germany
ect that facilitates the handling of information individual graph nodes and integration of www.biomax.com/company/company.php
information from NCBI Gene, PubChem, Uniprot, GO, KEGG etc. This technology also fea-
tures: data mining capabilities, tracking of relations and evidence and an associated search Jordi Villà i Freixa
Computational Biochemistry
engine to elucidate the regulatory mechanism(s) behind the observed effects. and Biophysics Laboratory,
Universitat Pompeu Fabra
Barcelona, Spain

Pranav Sinha
Potential applications variable selection, also using a genetic algorithm Institut für Medizinische und
search strategy. BioBridge will build on and Chemische Labordiagnostik,
Landeskrankenhaus Klagenfurt
The main outcome of the project will be a protocol improve these and other computational models. Klagenfurt, Austria
for organising multilevel data related to the target
diseases into a convenient form for use in the con- References Francesco Falciani
struction and refinement of kinetic models of (1) Wu et al, 2003; (2) Fletcher et al, 1978); (3) (Bhatikar et al, School of Biosciences
2005); (4) (Bellazzi et al, 2004).
University of Birmingham
intracellular metabolic pathways. The software Birmingham, United Kingdom
developed will be applicable to more general
cases of multilevel data integration.

In helping to provide insights into the key molec-

ular mechanisms that determine poor prognosis
in the CHF/COPD/type II diabetes disease cluster, | The increasing size and complexity of
BioBridge will generate novel strategies for per- biological database and the capacity of
new experimental designs to determine
sonalised prevention and enhanced delivery of
high throughput data for specific
patient care. emphasises the significance of the three
levels in the figure: a) the need for
Existing computational models have already structured databases related with the
proved powerful in this context. For example, one problem, b) the need for formats, like
SBML, able to translate the structured
of the BioBridge partners has recently developed data into dynamical models, and c) the
a statistical framework for analysis of multivariate development of powerful modeling
models from large-scale datasets. This software techniques ultimately able to make use of
environment (GALGO) uses a genetic algorithm and to interpret clinical data. Note that
the connecting SBML spans both the
search procedure, coupled with statistical model-
structure of the database and the
ling methods, for supervised classification and modeling environment, gluing together
regression. GALGO is relatively easy to use, can all the pieces of the puzzle.
manage parallel searches and has a toolset for
the analysis of models. Another partner has
developed methodologies for biologically-driven

21
ACRONYM Contract number: LSHC-CT-2006-037559
Starting date: 1 January 2007
CancerGrid
www.cancergrid.eu
SUMMARY
In the three years of this multidisciplinary
research project, the 10-member Consor-
tium plans to develop and refine methods
for the enrichment of molecular libraries
to facilitate discovery of potential anti-
cancer agents. Using grid-aided computer
technology, the likelihood of finding
anti-cancer novel leads will substantially
increase the translation of basic knowledge
to application stage.
In particular, through the interaction with
novel technologies and biology, the R&D
consortium aims at:
• developing focused libraries with a high
content of anti-cancer leads;
• building models for prediction of disease-
related cytotoxicity and of kinase/
HDAC/MMP and other enzyme (i.e. HSP90)
inhibition or receptor antagonism using
HTS results;
• developing a computer system based on
grid technology, which helps to accelerate
and automate the in silico design of
libraries for drug discovery processes,
and which is also suitable for future
design of libraries for drug discovery
processes that have different biological
targets (the result is a new marketable
technology).
| EC contribution: € 2 804 075
Grid-aided computer system
for rapid anti-cancer drug design
Background
After the completion of the sequencing stage of
the human genome project, the major focus of
discovery efforts turned to the identification of
the ‘druggable’ portion of the genome that is
linked to pathological states and is able to inter-
act with the drug-like chemical space, restoring
normal functions.
Apparently, the druggable genome is a subset of
the 30 000 genes in the human genome that
express proteins and represent, in many ways, an
unprecedented gift and exceptional opportunity for
drug discovery scientists and for patients who are
hoping for therapies of diseases currently uncured.
That subset (estimated as ca. 3 000 proteins) is
able to bind drug-like molecules as characterised
by the Lipinski’s rule-of-5 criteria.
In order to find more rapidly small molecule mod-
ulators to the newly emerging validated targets,
the high-throughput screening provides a reason-
able solution to screen large compound libraries.
However, it seems most of the targets can be clas-
sified into large target families such as kinases
and GPCRs: thus, development of target focused
libraries could dramatically increase the hit rate
as well as open the way to identify selective
inhibitors/antagonists within the target families.
The idea of ‘focused libraries’ or ‘targeted
libraries’ of molecules emerged in recent years
as a ‘compromise’, or as an attempt to bridge
between two seemingly conflicting approaches
to drug discovery:
• High Throughput Screening (HTS), by which
hundreds of thousands of compounds, mainly
in big pharma, were tested against a (hopefully
validated) biological target such as a protein or
a cellular system. The basic assumption of HTS
is that large numbers and diversity should
cover chemical space well enough to find, at
22
| Duration: 36 months
least, ‘hits’ (that are active in micromolar con-
centrations) which may subsequently be trans-
formed to ‘leads’ (with affinities in the
nanomolar range and with reasonable drug-like
properties) and finally to drug candidates.
Combinatorial chemistry has also been on the
side of HTS, presenting the ability to synthesise
huge amounts of derivatives based on specific
‘scaffolds’.
• Rational drug design approaches such as struc-
ture-based design and ligand-based design.
The first takes into consideration the detailed
atomic structure of the target and the possibili-
ties for forming physical interactions (i.e.,
hydrogen bonds, Van der Waals interactions,
electrostatic complementarity, hydrophobicity,
etc.) between small molecules and specific
sites on the targets, while the second depends
more on properties of known active molecules
and uses similarity ideas (including ‘pharma-
cophore’ searches) to discover new active mole-
cules. The substantial reduction in discovering
new chemical entities by big pharma in recent
years has been in part attributed to the fail-
ures due to very low hit rate in both the HTS and
Combichem, on the one hand, and on the
inability to properly taking into account the
pharmacokinetic (ADME/Tox) effects as well as
for entropy, solvation and target flexibility in
structure- and ligand-based designs.
A landmark in introducing pharmacokinetic con-
siderations to drug design and development
has been the ‘Rule of 5’ of Lipinski. This idea,
which is now less than a decade old, also pro-
vided an immediate tool to reduce the size of
combinatorial libraries and of HTS candidates by
‘filtering’, i.e., requiring that all molecules must
pass the Lipinski rule (three out of four conditions
for the limiting of molecular weight, calculated
lipophilicity, and the numbers of H-bond donors
and acceptors) in order to be in the proper
bioavailability range.
Key words: bioinformatics,
?? pharmacology, grid technology, library design, in-silico prediction of drug-like properties,
prediction of ADME parameters, predictive toxicology, creation of virtual libraries

ROLE OF SMEs |A
Inte:Ligand (Austria) will provide in silico screening of compound databases of commer-
cially available small drug-like molecules, consulting in compound profiling, and decision
support tools for medicinal chemistry. The company will generate virtual libraries for the
consortium partners and will distribute its library generation software tools to the members
of the consortium. Inte:Ligand will also market the enhanced versions of its software and
exploit its enlarged competences in ligand target interaction modelling.

GKI Economic Research Co. (Hungary) gained experience in leading international consortia
by acknowledging the importance of interactivity and proactive communication in facilitat-
ing projects with a variety of key actors. In CancerGrid, a similar approach will be taken.
From the social science standpoint, it is also important to raise awareness towards the
objectives and anticipated results of CancerGrid. With this in mind, GKI will prepare and
publish a case study of the project, targeting a wide audience beyond the direct stakehold-
ers. GKI will also be responsible for organising the involvement of direct or indirect stake- |B
holders in the area of CancerGrid (such as healthcare providers and physicians, industry,
regulatory authorities, experts in ethics, law and social sciences, health economics, public
health, patient organisations, policy-makers etc.) as appropriate.

DAC (Italy) is a biopharmaceutical company, founded in 2004, specialized in the identifi-

cation of new anti-tumour drugs. In particular, DAC is developing new proprietary small-
molecule compounds with inhibitory activity against chromatin remodeling enzymes
(histone deacetylases) and against HSP90, key players in cancer and non-cancer diseases.
As a partner of the CancerGrid consortium, DAC will initially develop target-based assays
in order to perform screenings of compounds previously identified as hits in the cell-
based screening. Moreover, DAC Srl will design, synthesize and weigh-out a focused
library (1500 compounds) for which the target based screening will be repeated.

The molecules that passed the Lipinski filter were
thus targeted on oral bioavailability, and their
numbers were much smaller than those for the ini-
tially planned experiments. The idea of ‘filters’
thus gained momentum, and additional filters
such as those of Veber (limiting the number of
rotatable bonds and the size of polar surface
area), also for bioavilability, were suggested.
Both Lipinski and Veber rules did not consider
directly any conformational aspects (3-dimen-
sional descriptors of the molecules to be tested,
but pharmacophore searches (ligand-based
design) and virtual docking and scoring (structure
based design) serve as subsequent filtering
processes in 3D that cover the ‘affinity’ part of
drug action, while the other filters mostly deal
with ‘drug transport’ issues.
These two properties are, to a large extend, orthog-
onal. Thus, one may regard the filtering process as
beginning with huge numbers of molecules, which
are reduced to a smaller set by chemical descrip- | A Typical fold of matrix metalloproteinases
tors. This smaller set may then be studied with structured in 3 α-helices (red) and 4 parallel and
1 antiparallel β-sheets (yellow). The binding site
more detailed conformations at the pharma-
is represented by a white surface while the zinc
cophore level, reducing it further to a group of ion is shown as a light-gray sphere and the three
molecules which may be docked virtually to the catalytic histidines are rendered as ball-and-stick.
assumed target, finally leaving a small set of sub-
stantially ‘focused’ or ‘targeted’ lead candidates. | B Coordination between zinc and the three
catalytic histidines and the phosphonate group of
The main ‘focusing’ activity has been however the ligand extracted from the 1ZS0 is highlighted.
concentrating on molecular scaffolds that are use-
ful for probing families of targets such as GPCRs,
tyrosine kinases, MMPs etc.
But, even that approach suffers from many draw-
backs. Lipinski and Veber rules can not distin-
guish well between drugs and non-drugs, and are
clearly not appropriate indicators of ‘drug-like-
ness’. Neural networks have been applied specif-
ically to this problem and managed to distinguish
properly between drugs and non-drugs, but have
the disadvantage of ‘hidden layers’ which do not
enable to plan and design novel molecules.

23
ACRONYM
CancerGrid
A drug-like index has been suggested but is based
on fragment identification and therefore limited in
its ability to discover novel structures. Structure-
based approaches can consider small molecule
flexibility, but are still inappropriate for dealing with
the flexibility of the protein targets, especially with
the flexibility of backbone and of larger loops. The
scorings in docking methods have recently been
exposed to much criticism. Using single conforma-
tions in pharmacophore searches is clearly inappro-
priate, because it has been shown that small
molecules bind to proteins in conformations that
are higher in energy than their global minima.
Toxicity predictions have not yet reached enough
reliability to prevent major toxicity threats by drugs.
The need for selectivity has not yet been properly
addressed in the preparation of focused libraries.
Therefore, although many companies nowadays
are offering focused libraries for kinases, GPCRs
and other families of molecules, there is a great
need to improve the production of such libraries
in order to shorten the time for discovery and to
save enormous expense. A main stumbling block
on the way to solving such issues is the complex
combinatorial nature of the problem of library
construction and drug design.
In this proposal, we include methods that deal
directly with the combinatorial nature of the prob-
lems, that have been shown to solve combinatorial
problems in a highly satisfactory manner, that dis-
cover the global minimum in most cases and
retain a large set of best results, many of them
excellent alternatives to the global minimum.
Expected results
Novelties and added values of the IT part of the
project:
• virtual focused libraries of anti-cancer agents;
• potential anti-cancer agents;
• HTS technology;
• data for model building purposes;
• models able to predict anti-cancer properties;
• CancerGrid System: a grid-based computer aided
tool that able to provide anti-cancer candidates
faster and in a more efficient way, also suitable to
develop candidates for other targets.
Potential applications
The models developed within the frame of this
project can be used for filtering large discovery
libraries to find anti-cancer drug candidates,
and to design anti-cancer focused libraries. The
CancerGrid computer system will be able to sup-
port the design of lead compounds in general, not
only in the anti-cancer field, but in any other
activity area. Thanks to its grid-based architec-
ture, the system will be able to predict molecular
descriptors for compound libraries, containing
a large number of molecular structures, in a short
time. When calculating 3D molecular descriptors,
the system will take all major conformers into
account. This enables the calculation of informa-
tion-rich molecular descriptors, and the develop-
ment of reliable linear and non-linear models.
The system will also be able to apply these mod-
els to predict the biological activity or chemical/
physical property of the compounds.
24
 Scientific coordinator
György Dormán
Assistant Director of Science and Technoloy
AMRY Hungary
Zahony u. 7 Budapest HU 1031, Hungary
gyorgy.dorman@amriglobal.com
www.amriglobal.com

Project manager
István Bágyi
Manager, Grants & IP
AMRY Hungary
istvan.bagyi@albmolecular.hu

Partners
Thierry Langer
Inte:Ligand Software-Entwicklungs
und Consulting GmbH
Maria Enzersdorf, Austria
www.inteligand.com

Mati Karelson
Tallinn University of Technology
Tallin, Estonia

Mart Saarma
| Workflow Scheme of Computer Aided Drug Discovery in CancerGrid. University of Helsinki
Helsinki, Finland

Balazs Borsi
GKI Economic Research Co.
Budapest, Hungary
www.gki.hu/en/index.html

Peter Kacsuk
Computer and Automation Research Institute
Hungarian Academy of Sciences
Budapest, Hungary

Amiram Goldblum
University of Jerusalem
Jerusalem, Israel

Saverio Minucci
DAC S.R.L.
Milano, Italy
www.genextra.it/dac.html
| Grid Based IT Support for Drug Discovery. www.dacresearch.it

Angelo Carotti
University of Bari
Bari, Italy

Ferran Sanz
University Pompeu Fabra
Barcelona, Spain

25
ACRONYM Contract number: LSHC-CT-2006-037251
Starting date: 1 January 2007
CAPPELLA
www.cappellabio.eu
SUMMARY
The inhibition of protein:protein inter-
actions (PPI) is one of the most prom-
ising approaches to the development
of novel cancer therapies. This project
brings together some of Europe’s leading
biotech SMEs and several highly recog-
nised academic institutes. By combining
five distinct chemical approaches and
testing them on three different targets
(all from different partners) a series of
innovative small-ligand tools and libraries
that allow new approaches to the inhi-
bition of PPI in cancer will be devel-
oped. The project is a unique opportunity
to integrate novel in silico, chemical,
genetic and ADME-based approaches to
the design, synthesis and optimisation
of libraries and compounds.
| EC contribution: € 3 361 300
Combating cancer through novel approaches
to protein: protein interaction inhibitor libraries
Background
Most protein:protein interactions occur within
the cell and thus can only be targeted by small
molecules. Furthermore, PPI differ structurally
from more classic drug targets such as enzymes
and receptors, and consequently existing com-
pounds have generally delivered disappointing
results. Therefore, new approaches are needed
to develop novel small molecules which inhibit
PPI in cancer.
Aim
The objective of this project is to develop a series
of innovative small-ligand tools and libraries that
allow new approaches to the inhibition of protein-
protein interactions in cancer. A key theme is the
utilisation of structural motifs found in natural
PPI-inhibitor compounds. This is coupled with
high content testing of the resultant structures on
three distinct PPI targets relevant to different
types of cancer, to allow compound rule-sets to
be developed and improved. We want to develop
small-ligand libraries focused on PPI inhibitors
of relevance to cancer. Furthermore, we will
develop innovative tools that allow improved
library design in this area by integrating in silico
approaches, bio-informatics, new approaches to
compound synthesis and pharmacology. The proj-
ect will also cover the scientific areas such as in
silico prediction of drug-like properties, predic-
tion of ADME parameters, predictive toxicology
and creation of virtual libraries.
| Duration: 36 months
Expected results
Innovative tools for designing PPI inhibitors
• Five different PPI-inhibitor library creation tools,
based on five complementary approaches:
– in silico;
– genetic chemistry;
– advanced natural product technologies;
– retro-synthesis of natural scaffolds and;
– ADME improvement.
• Cross-fertilisation of approaches so that each of
the five approaches learns lessons from the oth-
ers and incorporates relevant leanings into its
approach.
• Three high-content assay systems for three
important PPI cancer targets (p53-Mdm2, Beta
catenin-TCF4, BRCA2-RAD51).
• Design rules for PPI inhibitor compound libraries
(mass, diversity composition, lipophilicity, com-
pound class etc.) generated from 15 complementary
data sets.
Novel small-ligand libraries and
pre-clinical candidates
• Several ‘PPI inhibitor’ compound libraries.
• Different candidate compound families from
within these libraries that can subsequently be
taken forward into pre-clinical testing by the
SME partners.
26
Key words: identification of novel compounds, natural products, inhibition of protein:protein interactions, high throughput screening

ROLE OF SMEs Scientific coordinator

Sanne Jensen
Evolva S.A.
There are five SMEs within the CAPPELLA project consortium. Generally speaking, the SMEs Hagmattstrasse 6
provide very specific scientific know-how and technological platforms to the project, with- 4123 Basel, Switzerland
out which the project would be rendered incoherent. SMEs bring to the project the results of Project manager
their in-house developments. By combining the know-how of these different companies, the
project has made a pharmaceutical development which would not have been possible by Tanja Thybo
one of the companies acting alone. info@cappellabio.eu
www.evolva.com

With regard to the SMEs involved in the CAPPELLA project: Partners

PharmaMar is a pharmaceutical company specializing in the detection and development of Jens Peter Muller
AnalytiCon Discovery GmbH
pharmaceutical products from extracts obtained from marine organisms. The company pos- Posdam, Germany
sesses a huge collection of marine specimens from which previously unknown natural com- www.ac-discovery.de/english/go.html
pounds are extracted and characterized. Structural data on such new natural compounds act
Karsten Kristiansen
as a very important database for the CAPPELLA project. BioLigands ApS
Odense, Denmark
Analyticon is a provider of methods for the fractionation and analysis of highly complex
extracts from biological samples and concomitantly a provider of computer-based methods Thierry Langer
Inte:Ligand Software-Entwicklungs
for the processing of data obtained. und Consulting GmbH
Vienna, Austria
Inte:Ligand contributes to the project with a computer-based in-silico analysis of potential www.inteligand.com
pharmaceutically relevant drugs. The analysis will permit the prediction of drug behaviour Birger Lindberg Moller
in toxicological or pharmacokinetic studies and will allow the computer-based evaluation of Royal Veterinary & Agricultural University
potential drug analogues. University of Copenhagen
Copenhagen, Denmark
BioLigands is the provider of a highly efficient in vitro assay for the interaction between Simon Munt
a tumor suppressor protein and its antagonist. The screening assay provides compound PharmaMar S.A.
data which will be incorporated into a computer-based drug evaluation. Madrid, Spain
www.pharmamar.com/language.cfm

Evolva contributes its chemical evolution platform, which permits chemically evolved meta- Ashok Venkitaraman
bolic pathways to be expressed in yeast. It is expected that chemically evolved expression University of Cambridge
Cambridge, United Kingdom
libraries will give access to new pharmaceutically active small molecular weight com-
pounds. The elucidated chemical structure obtained from such compounds will be passed Ariel Ruiz i Altaba
through the in-silico development procedure developed by Inte:Ligant. University of Geneva
Geneva, Switzerland

Juhan Sedman
University of Tartu
Tarku, Estonia

27
ACRONYM Contract number: LSHG-CT-2006-037462
Starting date: 1 October 2006
ChILL
SUMMARY
The objective of this project is to develop
and validate a new technology based on
the Chromatin Immuno-Linked Ligation
(ChILL) method that will transform the
way the molecular analysis of chromatin
is performed and will not only facilitate
analysis of very small sample sizes, such
as early embryos or diagnostic samples
from patients suffering from a range of
diseases, but also radically improve the
resolution of the epigenetic marks.
| EC contribution: € 1 800 480
Chromatin Immuno-linked ligation:
A novel generation of biotechnological
tools for research and diagnosis
Background
The sequence of an organism’s genome does not
directly determine how the genome is used to
build the organism. A second, more complex reg-
ulatory code – the epigenetic code – is encrypted
in the chromatin structure and the 3D nuclear
organisation of chromosomes. Epigenetic infor-
mation is encoded in DNA modifications (namely
methylation), chromatin composition and modifi-
cation, and nuclear topology, or the dynamic
organisation of the genome within the nucleus.
Epigenetic information not only provides the first
cue to allow a cell to interpret the genome, it can
also be heritably transmitted through cell divi-
sion to maintain cellular identity. Moreover, while
many heritable disorders in humans are caused
by DNA sequence changes (mutations) that abol-
ish gene expression, a number of diseases are
caused by inappropriate gene silencing, brought
about by epigenetic modifications. Indeed, most
cancers involve the epigenetic silencing of genes
that normally control cell proliferation. The princi-
pal forms of epigenetic modification are DNA and
histone methylation.
A challenge that is central to modern biology is the
identification of the spatial and temporal dynamics
of epigenetic factors in a number of physiological
situations. The Chromatin Immuno-Precipitation
(ChIP) assay has played a pivotal role in decipher-
ing patterns of epigenetic marks that govern gene
transcription. Besides 'classical’ ChIP, several sim-
ilar techniques have been described in the litera-
ture. Recently, new technologies designed to
improve on the existing ChIP and native ChIP
(NChIP) technologies, have emerged.
In addition, low resolution and reproducibility prob-
lems are often encountered. These severe limita-
tions of the ChIP method are overcome by the
Chromatin Immuno-Linked Ligation (ChILL) method,
which could provide the foundation for a new gen-
eration of biotechnology tools and methods.
28
| Duration: 36 months
Aim
The objective of this project is to develop and
validate a new technology which has the potential
to replace the various ChIP technologies, and to
transform the way the molecular analysis of
chromatin is performed. The ChILL technique has
been patented by one of the partners of this proj-
ect, leaving the consortium free to operate with
regard to intellectual property rights. The ChILL
method is based on specific ligations which occur
between DNA stretches under diluted conditions.
In this environment, ligation partners can only
interact if they are in close proximity.
This proximity is created by new oligonucleotide-
antibody conjugates (nucleoproteic probes, or
oligo-ab), which physically place the target DNA
in contact with the oligonucleotide reporter
sequences. The ligation products are then ampli-
fied by the polymerase chain reaction and analysed
with real-time instruments and/or classical gel
electrophoresis.
Due to the ligation step taking place under diluted
conditions, the ChILL method will generate data
comparable to those obtained with ChIP, but with
increased sensitivity and a simplified protocol
that omits the tedious immuno-precipitation step.
As a proof of principle, the ChILL method has
already been shown to be at least 100 times more
sensitive than the regular ChIP assay.
ChILL will not only facilitate analysis of very small
samples, such as early embryos or diagnostic
samples from patients, but will also radically
improve the resolution of the epigenetic marks.
In addition, strong detergents used in the ChILL
assay open up the chromatin structure, rendering
it more accessible to antibodies than in conven-
tional ChIP assays.
Another major advantage of ChILL will be its abil-
ity to interrogate several parameters in a single
sample. For this purpose, a variant of ChILL called
Key words: chromatin remodeling, transcription regulation, epigenetic, ChIP assay, histones, DNA methylation

ROLE OF SMEs Scientific coordinator

Didier Allaer
Diagenode S.A.
For the ChILL project, Diagenode has three main objectives: Avenue de L’Hopital, 1 Tour Giga B34
4000 (Sart Tilman)
Liège, Belgium
• First, as coordinator of the research project, the company aims to create strong scientific didier.allaer@diagenode.com
synergies among the participants. www.diagenode.com

• As the SME participant, Diagenode ensures that research is oriented towards possible Partners
final commercial applications. In the case of ChILL, the interest is concerned with better Rolf I. Ohlsson
understanding of how an innovative technology can be translated into a diagnostic tool. Uppsala University
Dept. of Development & Genetics
Evolution Biology Centre
• Last but not least, one of Diagenode’s roles is to create ‘added value’ within the SME, Uppsala, Sweden
by gaining scientific experience and know-how in a ‘high-tech’ field. The new scientific
expertise created by the EU funded research projects is also recognised and accepted Henk G. Stunnenberg
outside the company, by the scientific community and, in a broader sense, by the Radbout University Nijmegen
Dept. of Molecular Biology
commercial community. Nijmegen, The Netherlands

combinatorial ChILL will be developed. This will
represent a major breakthrough, because it will
mean that several epigenetic marks can be col-
lected from a single tube, making it easier to build
up what might be called an ‘epigenetic profile’ of
the biological material in question.
Expected results
The Chromatin Immuno-Precipitation (ChIP) assay
plays an absolutely pivotal role in deciphering
patterns of epigenetic marks that govern gene
transcription. While the ChIP assay is a versatile
tool, it suffers from low resolution and low sensi-
tivity. These strong limitations of the ChIP method
are overcome by the Chromatin Immuno-Linked
Ligation (ChILL) method. ChILL will not only
facilitate analysis of very small sample sizes, such
as early embryos or diagnostic samples from
patients suffering from a range of diseases, but
also radically improve the resolution of the epi-
genetic marks. The ChILL approach also offers
F. Fuks
Université Libre de Bruxelles
Faculty of Medicine Laboratory
opportunities to examine simultaneous co-locali- of Molecular Virology
sation of two or more factors on the same chro- Brussels, Belgium
matin template, and the epigenetic marks will be
D. Clark
resolved in unprecedented detail. GeneSys Ltd.
Camberley, United Kingdom
The expected results of the programme would
be to make ChILL technology accessible to all
European research laboratories via validated pro-
cedures, reagents or kits. The project also expects
to launch diagnostic kits using ChILL technology
for the diagnosis of diseases linked to epigenetic
disorders.
Potential applications
The immediate impact of ChILL will be a better
understanding of the epigenetic code. The longer
term commercial impact of the ChILL method
might also be very important for Diagenode with
possible development of tools for the research or
diagnostic market.

29
ACRONYM Contract number: LSHP-CT-2007-037304 | EC contribution: € 1 271 664 | Duration: 36 months
Starting date: 1 January 2007

CILMALVAC

SUMMARY
This STREP, co-ordinated and led by an
The Tetrahymena system as an innovative
SME, will focus on the development of new approach to malaria antigene expression
malaria vaccine candidates with the aim of
taking at least one product to the stage of
pilot scale. Products showing most promise,
once expressed in the Tetrahymena system
(or Ciliate system), will proceed to antigen
testing in vitro and in vivo, to assess their
structure and antigenic integrity. At least
Background Expected results
one product is expected to reach lead opti-
misation, safety and toxicology testing.
Malaria kills over one million children in Africa The main objective of this STREP is to produce
alone each year, with an addition of up to 500 mil- within three years at least two candidate vaccine
Combining the expertise of the two aca-
lion episodes of clinically significant illness due to antigens against the blood stage of the malaria par-
demic malaria research laboratories with
malaria annually. Worldwide deaths are esti- asite Plasmodium falciparum, ready to use for pre-
the novel Ciliate-based expression sys-
mated at between 2 and 3 million per annum. Few clinical evaluation. The candidate antigens (MSP-1
tem under development by the SME will
other infectious diseases place such a burden on and VAR2CSA) will be expressed by the novel
generate recombinant Tetrahymena ther-
the social, economic and healthcare systems of expression platform Tetrahymena thermophila,
mophila strains expressing malaria anti-
developing countries. Therefore there is a press- a free-living Ciliate, which expresses Plasmodium
gens based primarily upon MSP-1 and the
ing need for the development of a vaccine against falciparum antigens efficiently. Partial results will
var2CSA genes of Plasmodium falciparum.
malaria, to ease at least part of this overwhelming be: vector constructs that are suitable for expres-
To utilise the capabilities of the partici-
burden on the continent of Africa, which suffers sion; appropriate reproducible lab scale purifi-
pants to greatest efficiency, this STREP
the majority of the deaths and illness caused by cation protocols; optimised host strains; a first
will comprise, besides the Project
the malaria parasite. up- and downstream process up to pilot scale; and
Management, work packages dealing
implementation of the first steps of a quality man-
with the generation of antigen expressing
Ciliate strains, pilot scale production and
Aim agement for potential later GMP production.
purification of the antigens and the test-
The aim of this project is to use an innovative new
ing and validation of candidate vaccines.
expression platform based on the Ciliate Potential applications
Tetrahymena thermophila in conjunction with two
This STREP application, co-ordinated by
novel malaria vaccine candidates, as a method of There are no effective vaccines for malaria cur-
Cilian AG, will provide an expression plat-
advancing these antigens to pre-clinical testing, rently available. Vaccination trials conducted in
form that can easily combine antigens to
prior to testing in humans. It will produce novel humans with existing candidates have been met
develop new combination vaccines that
Tetrahymena organisms expressing Plasmodium with limited success. This stresses the need for
may be more promising than vaccines cur-
falciparum antigens at pilot-scale production lev- continuing efforts towards testing novel candi-
rently under development. Ciliate-based
els. The two antigens selected are novel yet prom- dates. This project offers a novel biotechnological
expression of Plasmodium falciparum
ising candidates based on the N-terminal region approach to vaccine development and responds
proteins in secreted, membrane bound or
of MSP-1 and the Var2 CSA variant of the PfEMP-1 to the demands of developing countries, non-
cytosolic forms will complement the work
antigen family. profit organisations and charity foundations, to
done under the larger European malaria
technologically contribute to actions targeted at
vaccine development project.
the major poverty-related diseases, including
malaria. One goal of the approach is to apply the
underlying technological concept of this project to
the later industrial development and production
of new and highly effective vaccine candidates
against malaria.

30
Key words: Malaria, Plasmodium, vaccines, Ciliates, Tetrahymena, MSP-1, VAR2CSA, biotechnology, bioproduction

ROLE OF SMEs Scientific coordinator

Marcus Hartmann
Remco Brandt
This project is driven by the coordinating German SME Cilian AG which has developed Cilian AG
a novel protein expression platform based on recombinant eukaryotic ciliate cells which Johann-Krane Weg 42
D-48149 Muenster, Germany
excrete the desired product either membrane-bound or in cytosolic form. Under this project cilmalvac@cilian.de
the quality and immunogenicity of the secreted proteins will be tested for two current www.cilian.de
malaria vaccine antigens. The project will thus allow the SME to validate the utility of their
novel expression system and, at the same time, deliver GLP scaled-up processes for two Partners
promising malaria vaccine candidates, provided by the European partners of the project. David Cavanagh
Institute of Cell, Animal
and Population Biology
University of Edinburgh
Edinburgh, United Kingdom
homepages.ed.ac.uk/eang15

Thor Theander
Centre for Medical Parasitoolgy
University of Copenhagen
Copehagen, Denmark
www.euromalvac.org/profiles/
theander.htm

© Shutterstock

31
ACRONYM Contract number: LSHM-CT-2006-037950 | EC contribution: € 3 000 000 | Duration: 36 months
Starting date: 1 Janvier 2007

cNEUPRO

SUMMARY
Alzheimer’s Dementia (AD) is one of the
Clinical Neuroproteomics
most common brain diseases in the elderly. of Neurodegenerative Diseases
Dementias pose a major health problem in
European countries, with currently 5.7 mil-
lion affected dementia patients in the EU25.
No curative therapies are currently avail-
able for these dementias; however, first
disease-modifying treatment strategies
such as Aβ-immunisation have entered
Background Aim
clinical trials. These novel treatments will
be most effective if they are offered at
Europe has to face a threatening increase in the cNEUPRO is designed to discover innovative pro-
a very early dementia stage. Currently,
prevalence of the most common dementia, i.e. tein biomarkers and to develop novel CSF and
however, the reliable clinical differential
Alzheimer’s Dementia (AD). There is an urgent blood multiplex assays for the accurate early, dif-
diagnosis of very early dementia stages is
need for novel disease- modifying treatments, ferential and possibly predictive diagnosis of AD.
not satisfactory. Here, recent research has
which will be most effective if offered at a very Moreover, cNEURPO will develop first European
clearly demonstrated that multipara-
early dementia stage, preferentially as preventive SOPs for CSF-based NDD.
metric neurochemical dementia diagnos-
therapy during the prodromal stage of mild cogni-
tics (NDD) in cerebrospinal fluid (CSF)
clearly improves the early and differential
tive impairment (MCI). However, the reliable clini- Expected results
cal differential diagnosis of very early AD is not
diagnosis of dementias.
satisfactory and conventional diagnostic tools do cNEUPRO consists of two R&D modules:
not offer predictive diagnostics for AD. Here,
cNEUPRO will apply advanced proteomic
recent research has clearly demonstrated that Module I is dedicated to the discovery of novel
tools to discover novel neurochemical
multiparametric neurochemical dementia diag- protein biomarkers, the generation of high-affin-
dementia markers (BIOMARKERS) in blood
nostics (NDD) in cerebrospinal fluid (CSF) clearly ity ligands and the implementation of biomarkers
and CSF for the improved early, as well as
improves the early and differential diagnosis of into novel ELISA or Multiplex Assays. The discov-
predictive, diagnosis of AD. A predictive
AD. Moreover, recent studies have also indicated ery of biomarkers is differentiated into the devel-
dementia diagnosis is essential in order
that incipient AD can be predicted several years opment activities: definition of high-quality
to optimise the effectivity of forthcoming
prior to dementia onset. However, these promis- samples, identification of candidate biomarkers
preventive therapeutic strategies. Our
ing results of CSF-based NDD need to be validated in blood and CSF by multi-dimensional state-of-
initiative will establish European standard
by additional studies. Furthermore, additional the-art proteomics, and validation of the candi-
operating procedures (SOPs) for current
neurochemical biomarkers have to be identified date biomarkers (¡ biomarker). The validation of
neurochemical dementia diagnostics
for the improved early differential diagnosis of a biomarker comprises its protein chemical (struc-
(NDD) and we will establish the first NDD
dementias and, most importantly, first assays tural) validation by advanced mass spectrometry
reference centres in Portugal and Hungary.
for blood-based NDD need to be developed. and its clinical validation within a re-test study.
Moreover, only blood-based NDD will allow
A strong methodological impact is placed
a widely applicable monitoring of therapy efficacy. For validated biomarkers we will devise novel
on the quality of pre-analytical sample han-
poly- and monoclonal antibodies as well as high-
dling and clinical phenotyping, which has
Meanwhile, CSF-based NDD has entered neuro- affinity molecules. The latter highly stable small
been neglected in industry-driven discov-
chemical routine diagnostics of dementias in binding proteins are designed using a proprietary
ery studies. cNEUPRO integrates innovative
European expert centres. However, there is technology and may possibly also be used as
biotech and bioinformatic companies with
a strong need to develop first standard operation therapeutic tools or scaffolds for molecular neu-
leading clinical and proteomic dementia
procedures (SOPs) for CSF-based NDD, which sig- roimaging. Finally, the biomarkers will be inte-
research centres. cNEUPRO will also sup-
nificantly depends on the quality of preanalytical grated into novel ELISA and, most importantly,
port the discovery of new diagnostic targets
sample handling, storage conditions and sample Multiplex-Assays. Applying advanced bioinformat-
and, furthermore, will provide a promising
storage. It is noteworthy that the success of this ics tools (proprietary technology), cNEUPRO will
approach to identify novel scaffolds for
novel approach for the improved diagnosis of design a prototype predictor system for AD.
advanced molecular neuroimaging.
very early dementias has also stimulated strong
research activities in the US.
Accordingly, cNEUPRO will contribute
considerably to the welfare, health and
quality of life in Europe, and concomitantly
it will reinforce the competitiveness of the
European biotech industry.

32
Key words: Alzheimer’s Dementia, biomarker, neurochemical dementia diagnostics, cerebrospinal fluid, medical proteomics,
blood-based bioassays, multiplex assays, predictive diagnostics for preventive therapy, quality control

ROLE OF SMEs
The SME Protagen (Germany), Farallone Therapeutics B.V. (The Netherlands), MicroDiscovery
(Germany) and Matrix Advanced Solutions (Germany) are partners in cNEUPRO. They con-
tribute commercially tuned management skills, as well as specialist scientific experience to
assist in mass spectrometry-driven candidate biomarker identification (Protagen), develop-
ment of high-avidity and highly stable small binding proteins (Farrallone Therapeutics B.V.)
and sophisticated multidimensional bioinformatic data analysis (Microdiscovery, Matrix
Advanced Solutions). In several areas of the project’s research SME involvement is crucial
since it provides unique proprietary technology, which is essential to the success of the
research initiative. The cNEUPRO project has realised a close and synergistic network
between the SME and academic partners of the research initiative. Moreover, the SME partners
are centrally involved in the scientific management of the consortium.

| Core facility mass spectrometry unit of one of the

laboratories of cNEUPRO partners for identification of
biomarkers.© 2007 Dr. Oliver Ratajczak – strukturwelt.de

Scientific coordinator Edgar F. da Cruz e Silva (Proteomics),

Module II is dedicated to improving the perform- Odete A.B. da Cruz e Silva (NDD reference
ance of current CSF-based NDD, by defining Jens Wiltfang center Portugal)
European SOPs for pre-analytical sample han- University of Erlangen-Nuremberg University of Aveiro
Schwabachanlage 6 Aveiro, Portugal
dling, sample storage and assay conditions. As
D-91054 Erlangen, Germany
part of module II, CSF quality surveys will be con- jens.wiltfang@psych.imed. Laszlo Vescei
ducted, ‘gold standard’ CSF samples devised, and uni-erlangen.de University of Szeged
we will establish two new NDD reference centres www.uni-erlangen.org Szeged, Hungary
in Hungary and Portugal. Partners Johannes Schuchhardt
MicroDiscovery GmbH
Potential applications Sylvain Lehmann Berlin, Germany
Centre Hospitalier Universitaire de Montpellier www.microdiscovery.de
Montpellier, France
• Improved early and predictive diagnosis of Lucilla Parnetti
Alzheimer’s Dementia. Kaj Blennow University of Perugia
• Development of first blood-based NDD for Sahlgrenska Academy at Göteborg University Perugia, Italy
Mölndahl, Sweden
dementia diagnostics and therapy monitoring. Helmut E. Meyer, Katrin Marcus
• Identification of potential therapy responders Charlotte Teunissen Ruhr-Universitaet Bochum
by indicative biomarker phenotypes. VU University medical centre Bochum, Germany
• Discovery of novel scaffolds, which may possi- Amsterdam, The Netherlands
Michel Bergh
bly also be used as therapeutic tools or scaf- Connie Jimenez Farallone Therapeutics B.V.
folds for molecular neuroimaging. Vrije Universiteit Amsterdam Amsterdam, The Netherlands
Amsterdam, The Netherlands www.farallone.com
• Elucidation of the molecular mechanisms involved
in AD. Markus Otto Carsten Korth
• Implementation of first European SOPs for CSF- Universitätsklinik Ulm Heinrich Heine University of Duesseldorf
based NDD. Ulm, Germany Düsseldorf, Germany

David Burn (clinics), Tuula Pirttila

Chris Morris (proteomics) University of Kuopio
University of Newcastle upon Tyne Kuopio, Finland
Newcastle, United Kingdom
Luc Buee
Martin Wiesenfeldt Institut de la Santé
Matrix Advanced Solutions Germany GmbH et de la Recherche Médicale
London, United Kingdom Lille, France
www.matrix-as.com
Stefan Müllner
Protagen A.G.
Dortmund, Germany
www.protagen.de

33
ACRONYM Contract number: LSHB-CT-2007-037730 | EC contribution: € 2 985 102 | Duration: 36 months
Starting date: 1 March 2007

COBRED
www.cobred.eu

SUMMARY
COBRED aims at discovering colon cancer
Colon and breast cancer diagnostics
(CRC) and breast cancer (BC) biomarkers
for patient follow-up (monitoring markers),
by exploiting the capacity of three state-
of-the-art high-throughput technologies in
an integrated systems biology approach.
The specific RTD objectives are to:
• design a clinical protocol for prospective
clinical CRC and BC collections that fit
Background There is ample, but only circumstantial, evidence
the needs of the three high-throughput
deriving from survival data of patients with early
‘omics’ technologies used, namely trans-
An apparent paradox of current cancer epidemiol- stages of cancer, suggesting that earlier diagno-
criptomics, proteomics and metabolomics;
ogy is that while new therapies and diagnostics sis would allow a 10-20 % survival rate increase. In
• identify biomarker candidates (metabo-
improve survival rates in common cancers, e.g. fact, the potential benefits of early CRC and BC
lites, proteins, PBL derived mRNAs)
colon and breast cancer, the incidence rates are diagnosis are so high that a wide range of com-
capable of detecting and assessing the
also increasing and thus the net effect is negative. munity and governmental efforts have been
status of minimal residual disease,
implemented for population wide screening.
metastases and recurrence after surgery
Colorectal cancer (CRC) is the third most common
and chemotherapy;
cancer type worldwide; in the year 2000 the Biomarkers are substances found in the blood,
• develop a centralised database to inte-
global incidence was around 1 million, close to other bodily fluids (e.g. urine) or tissues that either
grate the data generated by the three
10 % of all cancers, resulting in about 0.5 million alone or in combination may signal the presence of
technology platforms, to include the clini-
deaths, totalling almost 8 % of all cancer mortal- cancer or the risk of cancer. Diagnostics based on
cal and pathological information on the
ity (1). Lifetime risk of developing colorectal ade- biomarkers have the potential to significantly
collections;
nocarcinoma is one of the highest of all cancers, improve current cancer diagnostic means, provid-
• discover biomarkers with better speci-
approximately 6%, and of colorectal adenoma, ing a higher sensitivity (i.e. much smaller tumours
ficity and sensitivity, using cross-platform
the benign but precancerous lesion, is approxi- can be detected), more easily, faster and at a much
advanced data-mining techniques on the
mately 50%. The risk of CRC rises with age, partic- lower cost (5).
combined data from the consolidated
ularly after the age of 60.
database; and
Biomarker discovery and validation, in the same
• validate the biological relevance and diag-
Breast cancer (BC) is the most common cancer way as drug discovery and validation, is a long
nostic potential of the identified biomark-
among Western women. In these patients, it is not process with a high rate (60-80%) of attrition of
ers by testing their specificity on tissue
the primary tumour, but rather its distant metas- candidate biomarkers along the major steps of
arrays and in relevant preclinical models.
tases that are the main cause of mortality. The qualification that ultimately ends in the approval
yearly incidence rate is over 0.5 million (630 000 by the Food and Drug Administration (FDA) in the
COBRED gathers the expertise and RTD
new breast cancer cases) which result in around US and the European Agency for the Evaluation of
resources of three biotech SMEs, leading
0.2 million deaths. Recently, the rates of metasta- Medicinal Products (EMEA) in the EU. Often,
academic partners and two leading cancer
sis and mortality in BC patients have decreased as seemingly good candidates that have been identi-
treatment centres renowned for their
a result of early diagnosis by mammographic fied and found valuable in one study do not show
expertise in BC and CRC treatment. After
screening and the implementation of systemic the expected predictive values in the second
3 years, COBRED will deliver a set of bio-
adjuvant therapy similarly to CRC. However, as study. In fact, the number of new diagnostics
marker candidates verified in preclinical
the population ages, the incidence of breast can- approved per year is decreasing, in sharp contrast
studies and ready for large scale clinical
cer increases (2). to the intensifying efforts to discover biomarkers.
validation and further development for
Therefore, despite having the highest potential
commercialisation by the respective SME
Continuous improvements in the treatment of value, COBRED chose not to pursue the discovery
partners. Furthermore, COBRED will have
another major life threatening illness, namely of screening markers because of economic and
demonstrated the potential to explore
cardiovascular disease, leads to an increase in logistic impracticalities of a large scale screening-
consolidated data resulting from different
the overall life expectancy. This contributes to marker validation in BC and CRC. Instead, the proj-
high-throughput technologies and clinical
the increase of the incidence rate, in CRC and BC ect focuses on the second largest clinical need,
profiles with advanced data mining tech-
among others, due to population ageing. The namely the improvement of patient follow-up,
nologies for enhanced biomarker discov-
speed of population ageing is higher than the through the discovery of monitoring markers,
ery. Although within the project scope,
decreased mortality due to the accumulated which are expected to report relapse, metastasis
COBRED focuses on biomarkers for fol-
treatment benefits from new cancer diagnos- and minimal residual disease at earlier stages,
low-up diagnostics, which have the poten-
tics (3) and therapies (4) thus leading to a para- which are more amenable to surgical and
tial to evolve into early cancer detection &
doxically negative net effect. chemotherapy treatment, and which are more
screening tools.
likely to improve cancer patient survival.

34
Key words: cancer, biomarker, monitoring markers, breast, colon, transcriptomics, proteomics,
genomics, metabolomics, datamining

ROLE OF SMEs Scientific coordinator

Laszlo Takacs
BioSystems International S.A.S.
BioSystems International, a French SME, is the coordinator of COBRED. 4 rue Pierre Fontaine,
91058 Evry cedex, France
laszlo.takacs@biosys-intl.com
The three SMEs involved (BioSystems International, Biocrates Life Sciences and Ipsogen) www.biosys-intl.com
are research-intensive SMEs who play leading roles given their expertise in ‘omics’
(genomics, proteomics and metabolomics) technologies, an issue which is at the heart of Partners
the COBRED project and the technological basis for the achievement of the project’s objec-
Klaus Weinberger
tives. The targeted project results are clearly of interest and potential benefit to SMEs, since Biocrates Life Sciences A.G.
business opportunities will be created for them in the field of diagnostic tools and methods Innsbruck, Austria
(and related IPR). www.biocrates.com

Fabienne Hermitte
A fourth SME (ARTTIC) is responsible for the project management. Ipsogen
Luminy Biotech Entreprises
Marseille, France
www.ipsogen.com
Aim Potential applications
Xavier Sastre-Garau
COBRED aims at discovering colon cancer and Diagnostic kits for BC and CRC patient follow-up. Institut Curie
Paris, France
breast cancer biomarkers for patient follow-up www.curie.fr
(monitoring markers) by exploiting the capacity of
three state-of-the-art high-throughput technolo- References David Malka
gies in an integrated system biology approach. (1) Midgley R. et. al. Nat Clin Pract Oncol. Jul; 2(7):364-9 (2005); Institut Gustave Roussy
Villejuif, France
The goal is to identify biomarker candidates (2) Parkin D.M, et. al. Int J Cancer 1999; 80: 827-841. (1999),
www.igr.fr
(metabolites, proteins, PBL derived mRNAs) capa- Elmore J.G. et. al. JAMA. 293:1245-1256 (2005); (3) Shen Y, J et. al.
Natl Cancer Inst. 17;97(16):1195-203 (2005); (4) Nygren P et. al. László Fésüs
ble of detecting and assessing the status of mini-
Acta Oncol. 44(3):203-17. (2005); (5) Baker M. Nat Biotechnol. University of Debrecen
mal residual disease, metastases and recurrence Debrecen, Hungary
23(3):297-304. (2005).
after surgery and chemotherapy. www.unideb.hu

Andras Guttman
Expected results Universität Innsbruck
Innsbruck, Austria
COBRED will deliver candidate protein, metabo- www.hlbs.org
lite and mRNA biomarkers tested in preclinical
Jaak Vilo
studies, ready for large-scale clinical validation University of Tartu
and further development for commercialisation Tartu, Estonia
by the respective SME partners: Ipsogen for biit.cs.ut.ee
mRNA derived markers, BioSystems International Bruno Cucinelli
for protein markers and Biocrates Life Sciences ARTTIC S.A.S.
for metabolomics markers. Paris, France
www.arttic.com
Specific project results will include:
• sets of biomarkers (gene signatures, proteins,
metabolites, or a combination of these) that will
be considered clinically relevant for early diag-
nosis of primary BC and CRC and relapses;
• central repository system hosting the results
from the technological platforms and the rele-
vant clinical data;
• prospective clinical collection of BC and CRC;
• clinical validation for the diagnostic potential of
subsets of the identified biomarkers in compari-
son to existing biomarkers and to currently
available imaging techniques;
• preclinical models for the biomarker evaluation
and biological studies.

35
ACRONYM Contract number: LSHB-CT-2006-037575 | EC contribution: € 3 189 385 | Duration: 36 months
Starting date: 1 January 2007

COMICS
comics.vitamib.com

SUMMARY
A battery of reliable and validated in vitro
Comet assay and cell array for fast
assays is needed to test for genotoxic and and efficient genotoxicity testing
cytotoxic effects of chemicals, without
resorting to animal experiments. The
comet assay, a sensitive indicator of DNA
damage, will be combined in this project
with the Cell Array system, to establish
and validate high capacity assays suitable
for chemical testing. Up to 800 cell sam-
Background • to increase the speed of scoring of comets;
ples will be processed for comets on a sin-
gle microscope slide. Arrays will use cells
The comet assay for DNA damage is widely used, • to use lesion-specific enzymes and inhibitors to
with different metabolic capabilities, with
but has a major drawback as it is labour-intensive, measure different kinds of DNA damage;
data on cytotoxicity obtained in parallel
and therefore can be used only in studies in which
with DNA damage. A medium-throughput
the numbers of samples are relatively small. The • to develop and compare methods for measuring
assay will also be developed. Comet
development of high-throughput variants will DNA repair activity;
analysis by differential staining of dam-
increase its applicability in both genotoxicity test-
aged/undamaged DNA using established
ing and population biomonitoring. DNA damage is • to develop an approach to measure gene-spe-
and novel dyes combined with automated
a good marker of exposure to genotoxic chemi- cific DNA damage and repair;
image analysis will be faster and more
cals; measuring cellular repair of this damage
reliable than at present. A crucial aspect
gives additional information on the mode of • to validate the comet assay in its various forms;
of the cellular response to DNA damage is
action of genotoxic agents and on individual sus-
DNA repair; variations between people
ceptibility to carcinogens. • to develop reference and internal standards for
can affect cancer risk, while genotoxic
use in the comet assay;
chemicals can act by interfering with
repair. Two methods for measuring repair,
Aim
• to make the various innovative products avail-
one based on the comet assay, the other
The overall objective is to develop reliable and able for use by companies and researchers
using a ‘Repair Chip’ approach, will be
tested genotoxicity and cytotoxicity assays that, investigating DNA damage and repair.
compared. In addition, fluorescent probes
combined, will reduce the need for animal experi-
which lock onto the DNA after hybridis-
ation (‘padlock probes’) will be applied
ments in assessing the safety of chemicals. Expected results
Specific aims include:
to study gene-specific DNA repair. The
Validated assays for DNA damage and repair that
modified comet assay methods will be
• to increase the throughput of the comet assay will be accepted by regulatory authorities for use
assessed for reproducibility and sensitiv-
up to 20-fold; in genotoxicity testing and will thereby reduce
ity in an inter-laboratory prevalidation
reliance on experimental animals.
trial, using a coded set of standard chem-
• to develop further the cell array system as a par-
icals, to satisfy regulatory bodies, as well
as industrial users of the technology. The
allel assay for cytotoxicity; Potential applications
result will be robust, validated, high-
• to seek optimal cell types for use in genotoxicity Commercial genotoxicity testing, biomonitoring in
throughput in vitro genotoxicity tests.
and cytotoxicity testing; human population studies, basic research in DNA
This proposal brings together academic
damage and repair.
partners and SMEs, together with a large
industrial concern, and the European
Centre for the Validation of Alternative
Methods (ECVAM). Dissemination through
professional and trade publications, regu-
latory channels, and scientific conferences
will lead to widespread adoption of the
new methods.

36
Key words: DNA damage, DNA repair, genotoxicity, comet assay, biomonitoring

ROLE OF SMEs Scientific coordinator

Andrew Collins
Department of Nutrition
Out of the seven industrial participants to this project, five are SMEs and they contribute to University of Oslo
the key activities in the project, devising new software for image analysis as required by the PB 1046 Blindern
0316 Oslo, Norway
novel methods of scoring of comets (IMSTAR); providing suitable cell lines (Biopredic); pro- a.r.collins@medisin.uio.no
viding custom-made DNA-damaging chemicals for calibration purposes (Severn Biotech);
providing dyes for differential staining of intact and damaged DNA plus running training Partners
workshops (TATAA Biocenter); pre-market product development and testing (Thistle).
Brigitte Fouque
Commissariat à l’Énergie Atomique
Grenoble, France

Françoise Soussaline
IMSTAR S.A.
Paris, France
www.imstarsa.com

Thomas Hartung
Joint Research Centre
Ispra, Italy

Gunnar Brunborg
Norwegian Institute of Public Health
Oslo, Norway

Christiane Guillouzo
Institut National de la Santé
et de la Recherche Médicale
Rennes, France

Katarina Volkovova
Slovak Medical University
Bratislava, Slovakia

Jon Eigill Johansen

Chiron AS
Trondheim, Norway

Neven Zoric
| The principle of the ‘padlock probe’. The probe TATAA Biocenter AB
(left panel) has at its ends sequences complementary Göteborg, Sweden
to adjacent parts of the target DNA. After hybridisation, www.tataa.com
these ends are ligated and the probe thus locked onto
the target. These probes can be designed to lock onto Elizabeth Martin
defined gene sequences, and so permit an examination AstraZeneca
of damage and repair in those specific genes. Macclesfield, United Kingdom
[Figure provided by Prof. Mats Nilsson.]
Galen Milne
Thistle Scientific Limited
Glasgow, United Kingdom
www.thistlescientific.co.uk

Andrew Smart
Severn Biotech Ltd.
Kidderminster, United Kingdom
www.severnbiotech.com

Christophe Chesne
Biopredic International
Rennes, France
www.biopredic.com

Mats Nilsson
Uppsala University
Uppsala, Sweden

Karel Angelis
Institute of Experimental Botany
Prague, Czech Rep.

37
ACRONYM Contract number: LSHM-CT-2006-037227
Starting date: 1 August 2006
CVDIMMUNE
www.cvdimmune.com
SUMMARY
The CVDIMMUNE project aims at: Investi-
gating novel risk markers for CVD in
European patient cohorts of in about
15 000 patients including unique cohorts as
the Swedish Twin registry, the MORGAM-
study and SLE. Investigating immunomod-
ulation as a therapeutic strategy for of
CVD. Developing documentation for regis-
tration of diagnostic ELISA kits in EU and
the US. Developing proof of concept for at
least one pharmaceutical product candi-
date. Providing a strong research foundation
and knowledge on mechanisms.
| EC contribution: € 2 700 000
Immunomodulation and autoimmunity
in cardiovascular disease and atherosclerosis
Background
Cardiovascular disease, mainly caused by athero-
sclerosis, is the main cause of death in the
Western world and also increasingly in develop-
ing countries. Even though progress has been
made in prevention of the disease, the inflamma-
tory and immunological nature of atherosclerosis
is not reflected by available diagnostic measures.
Furthermore, treatment has been improved by
lipid lowering drugs, e.g. statins, but novel treat-
ment modalities aiming at the pathological
inflammatory and immune reactions characteris-
ing atherosclerosis are yet to be developed.
Likewise, the understanding of the mechanisms
leading to atherosclerosis and causing the immune
reactions are poorly characterised. This applies to
the general population but also to SLE, an autoim-
mune disease where the risk of CVD is very high.
Aim
Atherosclerosis, the major cause of cardiovascu-
lar disease (CVD) is an inflammatory disease,
where the immune system plays an important
role. Autoantibodies as protection or risk mark-
ers, and therapy through immunomodulation
could be a major advance in the prevention and
treatment of CVD and is a focus of this project.
One type of antibodies are natural antibodies
against phosphorylcholine (aPC), an antigen
exposed in some bacteria and in phospholipids
with platelet activating factor (PAF)-activity, e.g.
in oxidised LDL. The project’s clinical and experi-
mental studies indicate that aPC, mainly of IgM
type, are protection factors against human ather-
osclerosis and CVD. The project’s plan is therefore
to develop aPC as a diagnostic tool, which will be
tested in several unique cohorts, including
healthy individuals and high risk individuals. The
project also thinks aPC could represent a novel
therapeutic modality, where both polyclonal and
monoclonal aPC are possibilities. Both kinds of
aPC antibodies will be developed and tested in
mouse animal models for atherosclerosis.
| Duration: 36 months
In contrast to natural antibodies (which are germ
line encoded), antiphospholipid antibodies (aPL)
are risk markers for both arterial and venous
thrombosis, and the main focus is novel types of
aPL against platelet activating factor (PAF) or PAF-
like lipids (aPAF). These novel risk markers (aPAF)
will be tested in the same cohorts as aPC and, in
both cases, robust kits will be developed. The
genetic background of aPC and aPAF will be stud-
ied, e.g. in the Swedish Twin Registry. In a proto-
typic autoimmune disease, namely SLE, where the
risk of CVD is very high, such aPL are raised.
Annexin A5 is a plasma protein, interfering with
phospholipid surfaces and acting as an anticoag-
ulant. The project has demonstrated that aPL
inhibit Annexin A5 binding to endothelium, an
effect neutralised by intravenous immunoglobu-
lins (IVIG) and that Annexin A5 is present in ather-
osclerotic lesions, especially at sites prone to
rupture. Based on these findings, the project has
hypothesised that raising Annexin A5 binding,
either by administration of neutralising antibod-
ies from IVIG in individuals with high aPL levels, or
by administration of Annexin A5 per se, could
prevent plaque rupture and atherothrombosis.
Taken together, the project combines diagnostic
and therapeutic projects and is focused on the
role of the immune system, especially autoanti-
bodies, in atherosclerosis and atherothrombosis.
This project combines academic and industrial
expertise and objectives, aiming at developing:
• a novel protection marker for atherosclerosis,
natural IgM antibodies against phosphoryl-
choline (PC) and novel risk markers, IgG autoan-
tibodies against phospholipids (aPL): platelet
activating factor (PAF) and PAF-like lipids (aPAF);
• these markers will be investigated in unique
patient cohorts. Documentation for registration
of diagnostic ELISA kits in EU and the U.S. will be
developed;
• novel immunomodulation therapy against ath-
erosclerosis and CVD in direct association with
these factors will be developed, along with the
38
Key words: atherosclerosis, atherothrombosis, natural antibodies, antiphospholipid antibodies, SLE, immunomodulation

ROLE OF SMEs Scientific coordinator

Johan Frostegård
Department of Medicine,
SMEs play a pivotal role in CVDIMMUNE. Athera Biotechnologies AB is in collaboration with Karolinska University Hospital, Huddinge
Karolinska Institutet, the originator of the majority of the project ideas and product candidates Center for Infectious Medicine
and Rheumatology Unit,
explored in the project. Athera develops the two diagnostic risk markers and therapeutic candi- 141 86 Stockholm, Sweden.
dates to be investigated. Furthermore, Athera is the main party responsible for the commercial- johan.frostegard@medhs.ki.se
isation of the results of these efforts. The second SME in the project, IsoSep AB, plays an integral
role by developing the chemistry solutions vital to several of the programmes in the project. Project manager
Narinder Gautam
narinder.gautam@medhs.ki.se
administration of atheroprotective aPC and the • Establishment of in vitro and in vivo models for
increase of Annexin A5 binding to endothelium studies of aPC and Annexin A5 relating to ather- Partners
through the neutralisation of aPAF and other aPL osclerosis and atherothrombosis. Hans Grönlund
or administration of Annexin A5 per se, a plasma Athera Biotechnologies AB
protein that may prevent rupture of atherosclerotic • In vivo data for drug candidates for atheroscle- Stockholm, Sweden
www.athera.se
plaques and CVD; rosis and atherothrombosis and data compiled
• proof of concept for at least one of these phar- to submit an IND application from one of the Peter Sever
maceutical product candidates. drug candidates investigated in the project. Imperial College London
London, United Kingdom
Expected results Potential applications Stefan Blankenberg
Johannes Gutenberg-University Mainz
• Development of robust and quantitative test kits The project expects its novel protection and risk Mainz, Germany
in ELISA format for analysis of IgM antibodies to markers to reflect inflammatory and immunologi- Ewa Ninio
PC and IgG antibodies to PAF or PAF-like lipids in cal factors in plaques and to be useful as tools for Institut National de la Sante et
serum. risk assessment for CVD, as a complement to clas- de la Recherche Medicale, U525
sical risk factors as dyslipidemia, hypertension, Paris, France
• Epidemiological data on aPC and aPAF from sev- diabetes, and smoking. The project also proposes Paul Quax
eral well characterised and, in several cases, that treatment relating to these factors could be TNO Netherlands Organization for
unique cohorts of healthy and high-risk individuals. a major step forward, in addition to established Applied Scientific Research
Leiden, The Netherlands
ones such as lipid lowering drugs.
• Assessment of genetic variability of aPC and Marta E. Alarcón-Riquelme
aPAF and identification of candidate genes. Uppsala Universitet
Uppsala, Sweden

Thomas Norberg
IsoSep AB
| Resting levels of EC intracellular calcium before leukocytes were allowed to interact Tullinge, Sweden
with ECs is shown in individual cells through continuous registration of fluorescence www.isosep.com/home.shtml
intensity with a widefield microscope. Endothelial cell borders are shown by labelling
ECs with Alexa 488-conjugated anti VE Cadherins antibodies. ECs (GREEN) were Wouter Jukema
loaded with Calcium sensitive probe.
Leiden University Medical Center
Leiden, The Netherlands

Jörg Blaeser
| Leukocytes, freshly isolated from venous blood of healthy donors on Ficoll/Hypaque Phadia GmbH
gradients were allowed to settle on the monolayers at 37 °C were allowed to transmi- Frieburgh, Germany
grate through IL-1 β treated EC at 37 °C. Leukocytes,labeled (Red) and are at different
www.phadia.com
stages of diapedesis process.

| Changes in EC intracellular calcium were measured during leukocytes extravasation

on individual cells through continuous registration of fluorescence intensity with
a widefield microscope. Leukocytes were allowed to transmigrate through IL-1 β
treated EC monolayers at 37 °C. A transient increase in Enthothelial cells- [Ca2+]i is
shown. ECs (GREEN) were loaded with Calcium sensitive probe. Localized increase in
EC Calcium in individual cells is shown (GLOWING GREEN).

39
ACRONYM Contract number: LSHC-CT-2007-037834 | EC contribution: € 3 640 293 | Duration: 36 months
Starting date: 1 March 2007

DEPPICT
www.deppict.eu

SUMMARY
Protein:protein interactions (PPI) are cen-
Designing Therapeutic Protein:Protein Inhibitors
tral elements in cellular processes and for Brain Cancer Treatments
important targets for selective therapeu-
tic agents. They constitute a rich area for
discovery of novel small ligand-based
therapies. This proposal seeks to utilise
such interactions, in particular those fea-
turing a α-helix binding groove such as
p53-MDM2, or more novel targets, e.g.
Background Aim
nm23-prune, to develop targeted small-
molecule libraries with physico-chemical
Amongst the range of cancer types, brain and The main objective of the proposed project is to
properties appropriate for therapeutic
perhaps pancreatic cancers are especially lack- provide more effective anti-tumour therapies by
effect against various tumour types such
ing in effective treatments. In particular brain developing targeted small ligand libraries with
as the brain cancers of glioblastoma and
tumours are: appropriate physico-chemical properties for ther-
medulloblastoma.
• the leading cause of death from childhood can- apeutic effect targeted against protein:protein
Combination of the concepts below should
cers among persons under 19; interactions implicated in various tumour types.
provide an opportunity to unlock the poten-
• the second leading cause of cancer-related The research activities will concentrate on knowl-
tial of protein interactions as key compo-
deaths in males aged 20-39; edge-based approaches supporting translational
nents in signalling pathways via design
• the fifth leading cause of cancer-related deaths research aimed at bringing basic knowledge
of selective small-molecule modulators
in women aged 20-39. through to applications in clinical practice and
targeting the kinase-effector interaction
public health. The project will thus focus on pro-
instead of the ATP active site.
Although onset of disease varies with tumour viding small molecule ligands with minimal side
• Develop an understanding of the ele-
type, it can occur at a relatively young age causing effects as treatments for the brain tumours
ments controlling selectivity in protein:
additional and significant social and economic glioblastoma (GBM) and medulloblastoma.
protein signalling networks by develop-
problems for both patients and their families.
ing approaches for design of small mole-
cules that target α-helix binding groove
Expected results
Current standard treatments include surgery,
interactions through use of structure-
radiation therapy and chemotherapy. These may The successful integration of the various aspects
based and fragment-based approaches.
be used either individually or typically in combi- of this proposal will provide a robust knowledge-
• Data-mining of ADME and drug-drug
nation. Brain cancers however present unique based strategy for exploiting protein:protein
interactions to build a predictive data-
problems due to the location of the tumours: sur- interactions as drug targets in the treatment of
base for library design.
gery and radiotherapy carry considerable risk to brain tumours. The strategy should however be
• Develop quantitative structure/property
the patient and resection is not always possible. sufficiently generic to be transferable to other dis-
relationships, with an emphasis on CYP-
Chemotherapy is faced with the problem of pene- ease areas, especially within the CNS, where pro-
mediated metabolism, ABC transporters
tration of drugs across the blood-brain barrier tein:protein interactions provide an entry point
at the blood/brain and brain/tumour
(BBB) and of lack of specificity. The focus for into disease-modifying therapies.
interfaces, mutagenicity, solubility, pKa,
these patients is therefore on more effective ther-
and passive permeability, and predictive
tools for mutagenicity and other genetic
apies to prevent relapse, and on more efficient Potential applications
screening and diagnosis to halt the disease at an
toxicology end-points.
early stage. The design of selective small molecule modula-
• Develop predictive PK and PBPK models
tors of protein:protein interactions should pro-
to improve understanding of BBB and
vide the basis for developing new therapeutic
tumour penetration.
strategies against brain cancers. They will allow
• In vitro and in vivo PK/PD and TK/TD char-
for improving current libraries and for building
acterisation of compounds, to increase
predictive databases for library design of new
understanding of their mechanism of
specific drugs and therapeutic agents with high
action and reduce the use of laboratory
central nervous system penetration, necessary to
animals.
reach a higher efficacy, selectivity, responsiveness
Such knowledge-based approaches will
and lower toxicity. In addition these approaches
also be applicable to design of small mol-
will represent a powerful system for preclinical
ecules for other protein:protein interac-
data collection, leading to an optimisation of
tions utilising a α-helix binding groove
clinical trials setting and development.
both for peripheral tumours and other
therapeutic areas.

40
Key words: protein:protein interactions, small molecule inhibitors, knowledge driven drug design, blood/brain, tumour penetrant

ROLE OF SMEs Scientific coordinator

Graeme Robertson
Siena Biotech S.p.A.
The project is specifically designed to increase SME efforts towards research and innova- Fiorentina, 1
tion, to encourage collaborations between SMEs and to expand their scientific and techno- 53100 Siena, Italy
grobertson@sienabiotech.com
logical knowledge base. The four SMEs involved in the project, Sienabiotech S.p.A. (SIBI), www.sienabiotech.it/index/index.jsp
Molecular Discovery (MD), Crystax (Crystax), and Aureus Pharma (AUR) take leading roles
in driving and managing the planned library design and drug discovery programme. The Partners
active and serious involvement of a SME working in drug discovery such as SIBI guarantees
Gabriele Cruciani
the rapid application of the research results. Specifically, SIBI researchers will be involved Molecular Discovery Ltd.
in library design, construction of in silico paradigms, setting up of experimental metabolism Pinner,Middlesex, United Kingdom
models and screening of libraries for ADME attributes. Molecular Discovery will provide www.moldiscovery.com/index.php
high quality software tools and chemoinformatics procedures aimed at the prediction of the Massimo Valoti
physicochemical profiling of the investigated compounds with potential anti-tumour activity. University of Siena
Crystax will perform all the necessary processes (cloning, expression, purification and crys- Siena, Italy
tallisation) to obtain the 3D structure of the pharmacological targets proposed in this proj-
Juan Aymami
ect. This will allow the correct characterisation of the active sites, where small molecules Crystax Pharmaceuticals S.L.
can bind and have a pharmacological effect. The Aureus Pharma team will set up a database Barcelona, Spain
from scientific literature in order to perform data-mining of ADME and drug-drug interac- www.crystax.com
tions to build predictive tool sets; design and implement predictive models based on Roberto Pellicciari
datasets from the knowledgebase developed; and collect pertinent data from literature to University of Perugia
build predictive toxicology models and filters. In combination, the four SMEs carry out crucial Perugia, Italy
roles in the DEPPICT project. Sophie Ollivier
Aureus Pharma
Paris, France
www.aureus-pharma.com

Prof. Herbie Newell

University of Newcastle
Newcastle, United Kingdom

| Iterative Research Cycles where data will be used to construct robust

testable hypotheses in the context of the pathophysiology of brain
tumours. To achieve this it is necessary to look for trends – Structure
Activity Relationships. The discovery and exploitation of site/mechanism
of action and developing knowledge at multiple levels – Target, Cell,
and Pathway will be key to achieving this.

41
ACRONYM Contract number: LSHB-CT-2007-037303 | EC contribution: € 3 189 400 | Duration: 36 months
Starting date: 1 January 2007

DeZnIT

SUMMARY
The objective of DeZnIT is to develop and
Design of zinc metalloenzyme targeted drugs
apply new methodology for the rational using an Integrated Technology approach
and accelerated design of novel drugs tar-
geted against zinc-containing enzymes.
These enzymes are key modulators of
many serious human diseases including
cancer, glaucoma, obesity, and rheuma-
toid arthritis. Despite some successes,
many major technological challenges
Background Expected results
remain in the development of effective
drug therapies against this enzyme family.
Zinc-containing metalloenzymes have a wide DeZnIT is highly focused on the identification of
range of specific biological activities. They are novel and more effective drug candidates, which
DeZnIT will address these challenges by
implicated in several types of diseases such as will be further developed for serious human dis-
developing and integrating key technolo-
cancer, atherosclerosis, neuronal degenerative eases. The other outcomes of DeZnIT are improved
gies from pharmacogenomics, computer
diseases, glaucoma and inflammation. In this pro- methods for computational drug design and other
modelling, structural and molecular biol-
posal, the project concentrates on the therapeuti- platform technologies such as crystallography,
ogy and chemistry, combined with drug
cally important zinc-containing enzyme families of molecular biology (including development of bio-
discovery infrastructure and expertise. In
carbonic anhydrases, histone deacetylases and the markers) and chemical synthesis. The success of
particular, highly novel computational
ADAM (A Disintegrin And Metalloprotease domain) DeZnIT would lead to significantly reduced costs
approaches taken from the field of com-
family of proteinases, in particular ADAM17, also and timelines for drug discovery processes, with
puter science will be applied to drug
known as TACE (TNF-α Converting Enzyme). consequent health and economic impacts.
design for the first time.

The consortium members combine all the

Whilst many computer-assisted drug design Potential applications
methods have been developed over the past sev-
necessary competencies to achieve the
eral decades, their application to the medicinally In addition to the specific applications outlined
goals and objectives of DeZnIT.
important class of zinc-containing enzymes has above in the area of zinc metalloenzymes, any
been challenging. The nature of the interaction methods developed during the course of DeZnIT
between the potential drug molecule and a metal may be applicable to other classes of metal con-
such as zinc requires a very time consuming cal- taining enzymes of therapeutic importance.
culation and obtaining accurate results is difficult
to achieve in a real-world setting.

Aim

• To develop modern, sophisticated comput-

erised methodology for high-throughput drug
screening in silico, focussing on Zn-containing
enzymes.

• To isolate and characterise target proteins within

the Zn-containing enzyme families (including
newly identified members) for the screening of
more efficient drugs.

• To design and create new classes of enzyme

inhibitors.

42
Key words: zinc metalloenzymes, drug design, computer-assisted drug design, cancer, inflammation

ROLE OF SMEs Scientific coordinator

Paul Finn
InhibOx Ltd.
There are three SME participants in DeZnIT, each playing a key role. One of the SMEs, Pembroke house
InhibOx, is the project co-ordinator and, in addition, will focus on the delivery of novel com- 36-37 Pembroke street
Oxford OX1 1BP, United Kingdom
putational methodology. KeyDP will provide molecular and structural biology expertise, paul.finn@inhibox.com
whilst TopoTarget will provide drug screening technology. Together, the SMEs provide sig- www.inhibox.com
nificant expertise in the commercial development of small molecule therapeutics in a highly
synergistic manner with the academic partners. Partners
Steven Butcher
TopoTarget A/S
Copenhagen, Denmark
www.topotarget.com

Flip Hoedemaeker
Key Drug Prototyping B.V.
Amsterdam, The Netherlands
www.keydp.com

Peteris Tapencieris
Latvian Institute of Organic Synthesis
Riga, Latvia

Seppo Parkkila
University of Tampere
Tampere, Finland

Andrea Scozzafava
University of Florence
Florence, Italy

William Graham Richards

University of Oxford
Oxford, United Kingdom

| A detail from the crystal structure of carbonic anhydrase II, a key enzyme of interest to the project
and the first crystal structure produced by the consortium.

43
ACRONYM Contract number: LSHB-CT-2006-037212 | EC contribution: € 2 499 999 | Duration: 36 months
Starting date: 1 January 2007

Diagnosis

SUMMARY
Infectious diseases continue to be a seri-
Development of new and cost effective methods
ous burden around the world, in both for non-invasive diagnosis of human pathogens
developing and industrialised countries.

The main objective of DIAGNOSIS is to con-

tribute to the above need by developing
a novel easy to use, low cost, mostly non
invasive biotechnological platform for the
detection of infectious diseases. The chal-
Background Expected results
lenging aim is to reach a short and efficient
sample treatment implemented into exist-
Infectious diseases are a global concern. Of the Novel technologies
ing and newly developed portable PCR lab-
annual 12 million deaths attributable to infectious • New principles for NA separation and
oratory for multiplex fluorescent pathogen
diseases on the planet, 95% occur in the developing purification
detection. The concept will be proven on
world, particularly in the most impoverished areas • New sorbent methods and materials
human critical pathogens but will be
where individual and general hygiene standards • Protocols for sample preparation
applicable also for animals, and plants
remain very low and prevention policies are non- • Protocols for samples target concentration
pathogens. The concept will be applica-
existent, poorly adapted or insufficiently funded. On • Chemistry for oligonucleotides synthesis
ble for samples taken from affected
the other hand, economic and industrial develop- • Multiplex PCR
organisms as well as from food/feed and
ment also accounts for the emergence of infections, • Protocols for diagnostic assays
environments (water, air, soil etc.).
such as food-borne pathogens that take advantage • Protocols for POC (point of care) sample
of the increasing industrialisation of the food chain, preparation
The scientific and technological objec-
nosocomial infections in the increasingly complex
tives will include the development of:
hospital environment and travel-related infections. New products
• new principles of nucleic acids sorption/
In addition, the demographic trend towards an • Kits for ultra-rapid separation and purification
desorption;
ageing population in Europe enhances the risk of of DNA and RNA
• innovative concentrating methods and
increasing infection as elderly people are prone to • Kits for separation and purification of NA from
materials for the enrichment of viruses,
invasive medical procedures and are, in general, difficult (inhibitor rich) samples
micro-organisms and nucleic acids;
more susceptible to infectious diseases. • Kits for separation of different classes of NA
• the adaptation of the phosphoramidite
European science must play a major role in this fight • Kits for non-cultural enrichment of
chemistry to alternative fluorescence
to curb infectious diseases, particularly through micro-organisms
dyes in order to broaden the labelling
the establishment of a stronger and more coher- • Kits for diagnostic assays of critical pathogens
assortment for multiplex PCR analyses,
ent surveillance and control system and through • Prototype instrument for fluorescent detection
a portable non-dependent on external
a substantially increased investment in research • Portable PCR laboratory
power supply PCR laboratory;
to underpin this endeavour. • Kits for sample preparation outside the
• exemplary demonstration of the whole
Only with this investment will Europe be able to laboratory
technological chain on several groups
manage infectious diseases within its own bound-
of human pathogens, including the
Mycobacterium complex, the periodontal
aries. In addition, Europe will also be able to help Potential applications
prevent the emergence and spread of infections
pathogens, the causal agents of popula-
prevailing elsewhere on the globe and to pursue The application workpackage will concentrate but
tion shifts within the intestinal microflora
its historical tradition of giving assistance to the not limit its activities to the following groups of
associated with inflammatory bowel
poorest countries. pathogens and critical sample sources for multi-
diseases and Fungal skin infections,
plex PCR systems with fluorescence detection,
completed by the diagnosis of main
representatives of food-born pathogens.
Aim thus approving and demonstrating the broad
and beneficial universal applicability of the tech-
The main strategic objective of DIAGNOSIS is to con- nological development in the work packages
tribute to the above need by developing a novel, technological work packages:
easy to use, low cost and non invasive biotechnol- • mycobacterium complex:in sputum;
ogy for infectious diseases diagnosis, i.e. pathogens • difficult culturable fastidious periodontal
detection. pathogens in gingival crevicular fluid;
The challenging aim is to reach a short and efficient • predominant food-borne human pathogens;
sample preparation followed by highly sensitive, • gut flora pathogens in stool samples for analyses
accurate, cost efficient multiplex diagnosis imple- of intestinal microbiota associated with inflam-
mented i.a. into a portable PCR fluorescent labora- matory bowel disease;
tory. The concept will be proven on human critical • fungal pathogens in hair, skin and nail samples.
pathogens but will be applicable also for animals,
plants and environmental, and food samples.

44
Key words: infectious diseases; diagnosis; nucleic acids, sample preparation, monolithic sorbent; DNA, RNA, PCR,
real-time; fluorescence detection; multiplex PCR; phosphoramidite chemistry; portable instrument; Mycobacterium;
gingival crevicular fluid, food-born pathogens; gut flora Pathogens; Fungal pathogens

ROLE OF SMEs Scientific coordinator

Robert-Matthias Leiser
Agrobiogen GmbH
DIAGNOSIS is enhancing the competitiveness of Europe’s biotechnology industry by the Thalmannsdorf 25,
development of fast and reliable nucleic acids separation and purification, new methods for Larezhausen
86567 Hilgertshausen, Germany
separation from inhibitor enriched samples and new instruments and kits for fast and cost matthias.leiser@agrobiogen.de
effective detection of critical human pathogens. www.agrobiogen.de

Most of the partners are industrial partners, thus taking the outcome of the project directly Partners
to the European biotechnology industry. Denis Rebrikov
DNA-Technology jsc
• The consortium consists of 73 % SMEs, all of which are based on innovative technologies Moscow, Russia
www.DNA-Technology.com
and research, with 67 % of the budget allocated to SMEs. The main idea is to promote their
technologies and develop new products by enhancing their business plans. Claus-Detlev Bauermeister
Labor Dr. Bauermeister & Co
• The project management is undertaken by two SMEs: one an expert with the technologi- Moers, Germany
cal work, and the other an expert in administrative management and coordination of EU Radovan Haluza
founded projects. This company is led by a woman. Generi Biotech s.r.o.
Hradec Kralove, Czech Republic
www.generi-biotech.com
• DIAGNOSIS is allocating one WP to exploitation and dissemination by its SMEs partners,
including internal workshops and staff exchange between the relevant entities. A detailed Camilla Giammarini
plan of staff exchange will be implemented during the project. DIATHEVA Srl
Fano, Italy
www.diatheva.com
• International Cooperation is assured through the participation of 3 partners from INCO
countries (Russia and Armenia); one of which is a Russian SME (DNAT), while the other Martin Gehri
two are research institutes which will provide essential know-how for the project. PreentTec AG
Fribourg, Switzerland
www.preentec.ch

Ronald Arthur Bosch

Hilbrands Laboratorum B.V.
Wijster, The Netherlands
www.hlbbv.nl

Sergey Zavriev
M.M. Shemyakin-Yu.A.
Ovchinnikov Institute of Bioorganic
chemistry of RAS
Moscow, Russia
www.ibch.com

Hamlet Balayan
Institute of Fine Organic Chemistry of NAS
Yerevan, Republic of Armenia
www.sci.am/resorgs.php?oid=14&langid=1

Ulf Goebel
Charité – Universitätsmedizin Berlin
Institut für Mikrobiologie und Hygiene
Berlin, Germany
www.charite.de/imh

Pnina Dan
OSM-DAN Ltd.
Rehovot, Israel
www.osmdan.com

45
ACRONYM Contract number: LSHB-CT-2007-036644
Starting date: 1 October 2006
DIALOK
SUMMARY
The DIALOK consortium consists of two
SMEs (based in The Netherlands and
Hungary) and five academic participants
(based in The Netherlands, Germany and
Spain) and is dedicated to the develop-
ment of innovative drugs that display
a restricted action within specific target
cells or organs. Such locally acting drugs
will have an improved safety and effi-
cacy, as side-effects in other tissues will
be prevented.
| EC contribution: € 1 978 070
Development of Innovative Assays and Locally
acting therapies aiming at critical Kinases in
hepatic and renal fibrosis
Background
Kinases are a class of enzymes that play a key role
in intracellular responses to stress and growth
factors. Kinases catalyse the transfer of phos-
phate from ATP to proteins, which may either be
other kinases, transcription factors or other regu-
latory proteins. As such, the activation of kinases
leads to a cascade of activating signals that regu-
late many physiological processes, e.g. cell divi-
sion and differentiation. Aberrant kinase activity
is associated with many diseases such as cancer,
diabetes, and chronic inflammatory disorders.
Kinases have been identified by the pharmaceuti-
cal industry as important targets for drug devel-
opment, with major investment having been made
in basic research and drug design in this area,
estimated at 20 % of the total R&D budget in the
pharmaceutical industry. Over 500 kinases have
been identified in the human genome and many
new kinase inhibiting drugs will be developed in
the coming decades. Indeed, some of the most
successful drugs introduced in the past years are
kinase inhibitors, such as Gleevec and Irresa.
Within the development of this class of highly
potent drugs, some critical problems have arisen.
For example, even kinase inhibitors with high
specificity for a specific kinase sometimes have
adverse effects that prevent the further develop-
ment of safe drugs. This problem is inherent to the
class of compounds, since kinases often play an
important role in both pathophysiological and
normal physiological processes.
46
| Duration: 36 months
Aim
The DIALOK consortium is dedicated to the
development of innovative drugs that display
a restricted action within specific target cells or
organs. Such locally acting drugs will constitute
improved safety and efficacy, since side-effects in
other tissues will be prevented. The project will
investigate this therapeutic strategy for kinase
inhibitors, a class of drugs that has tremendous
therapeutic potential but that is also associated
with unacceptable side effects. Kinase inhibitors
will be conjugated in two classes of carrier sys-
tems, directed towards either the liver or kidney.
In this way, the project will develop locally acting
drugs for the treatment of either hepatic or renal
fibrosis, aiming to prove this concept in experi-
mental animal models.
An important novel aspect of the project is the
linker used for coupling the drug to the carrier.
DIALOK will employ Kreatech’s Universal Linker
System (ULS), a novel patented drug-linker which
enables straightforward coupling with most
kinase inhibitors (broadly applicable) without
changing the original drug structure. Another
unique property of ULS is that it provides con-
trolled release of the conjugated drug over
a period of days, which is of great importance
for effectiveness of the delivered drug.
In parallel to development of locally acting kinase
inhibitors, DIALOK will develop novel assays for
detecting activation of kinases. Such assays will
be of great value to the project, accelerating and
strengthening the validation of kinase inhibitor-
based therapeutics. Kreatech’s ULS-based (fluo-
rescent) reporter molecules are particularly
suitable for the detection of phosphorylated
kinase substrates, and therefore enable broadly
applicable, non-radioactive detection of activated
kinases, as compared with traditional kinase
activity assays, which use radiolabeled ATP or
phosphoaminoacid-specific antibodies.
Key words: drug delivery, kinase inhibitors, kinases, liver disease, renal disease, drug safety, inflammation, fibrosis

ROLE OF SMEs Scientific coordinator

Jack Veuskens
KREATECH Biotechnology B.V.
There are two SMEs in this project, namely Kreatech and Vichem Chemie. They are experts, Vlierweg 20
respectively, in linking bio-organic molecules based on coordinative chemistry, and in the 1032 LG Amsterdam, The Netherlands
j.veuskens@kreatech.com
design and synthesis of kinase inhibitors. Taken together, new cell specific therapeutic com- www.kreatech.com
pounds are developed to be tested for specificity and effectiveness by the RTD partners
of the consortium. Kreatech also plays a key role in managing the project as a whole and Partners
safeguarding intellectual property rights.
K. Poelstra
Groningen University Institute
for Drug Exploration
Dept. of Pharmacokinetics
and Drug Delivery
Expected results Potential applications Groningen, The Netherlands

The DIALOK consortium proposes the improved
safety and efficacy of kinase inhibitors by means
of local drug delivery. By restricting the activity of
the inhibitor to the diseased tissue only, the bal-
ance between therapeutic effects and side-
effects can be altered dramatically (Fig. 1). Since
the locally delivered drug will provide adequate
drug levels within the targeted organ, in combi-
nation with much lower levels in the other parts
of the body, the safety and efficacy of the drugs
will be improved.
G. Kéri
In this project, participants will explore the deliv- Vichem Chemie Ltd.
ery of kinase inhibitors for the treatment of both Budapest, Hungary
liver and renal fibrosis, since no adequate phar- www.vichem.hu
macotherapy yet exists for these types of dis- M. Templin
eases. The technology will be also applicable to Natural and Medical Sciences Institute
the treatment of other diseases in which kinases at the University of Tuebingen
Reutlingen, Germany
play an important role, e.g. cancer, or inflammatory
diseases such rheumatoid arthritis. R. Bataller
IDIBAPS (Institut d’Investigacions
Biomèdiques August Pi i Sunyer)
Laboratory of Liver Fibrosis
Barcelona, Spain

M. Ruiz
University Autonoma Madrid
Vascular and Renal Research Laboratory
Local diseases require local drug treatment. Madrid, Spain
This can be effectuated by drug delivery.
RJ Kok
Utrecht University
Dept. of Pharmaceutics
Utrecht, The Netherlands

| Fig. 1 Schematic depiction of how we

want to improve the safety and therapeutic
efficacy of kinase inhibitors.

47
ACRONYM Contract number: LSHB-CT-2006-037681 | EC contribution: € 2 977 400 | Duration: 36 months
Starting date: 1 December 2006

DiaNa
www.diana-eu.fi

SUMMARY
DiaNa combines the accumulated expert-
Predictive diagnostics for diabetic
ise from the previous FP5 EU project, nephropathy – Novel nanotechnology
Mechanisms of Proteinuria (QLG1-2000-
00691) and the FP6 project, ADDNET
based test platforms
(LSHB-CT-2003-503364). The latest know-
ledge on the pathophysiology of diabetic
nephropathy and newly identified uri-
nary markers are utilised to develop
predictive diagnostic tests to follow dis-
Background Aim
ease progression. By using metabolomic
approaches, the project aims to find
Diabetic nephropathy is the main cause of end- The ultimate goal of the project is to develop
additional markers from diabetic urine.
stage renal failure in the Western world. The novel diagnostic tests, based on the best molec-
In parallel, two separate approaches will
World Health Organization (WHO) estimates that ular understanding reflections in urine to reveal
be used to develop diagnostic tests, one
currently there are over 200 million people with the early diabetic damage during the pre-
based on nanobead technology, and the
diabetes worldwide. The prevalence is constantly microalbuminuric stage of the disease.
other on a multiplexing platform allow-
rising and estimated to reach over 300 million by
ing the combination of several parame-
ters in a single test. This will translate
the year 2025. Overall, up to 40 % of diabetic Expected results
patients will develop debilitating kidney compli-
into early identification of patients at
cations. Diabetic nephropathy is becoming not The ultimate goal of the project is to develop
high risk of rapid loss of kidney function.
only a severe health problem for individual novel diagnostic tests based on the best molec-
After validation with clinical material,
patients, but also a major economic burden of all ular understanding reflections in the urine to
subsequent steps will include transfer of
societies. The project aims to achieve a better reveal the early diabetic damage during the pre-
the test into patient use by an SME. This
understanding of the pathophysiologic mecha- microalbuminuric stage of the disease.
approach, which directly aims at devel-
nisms underpinning the development of diabetic
oping a clinical urinary test, will be sup-
ported by extensive basic research on
nephropathy, a major complication shared by Potential applications
both type I and type II diabetes.
the mechanisms/biomarkers of diabetic
The applications will include novel magnetosen-
nephropathy.
sors for the detection of diabetes-diabetic kidney
damage.

48
Key words: kidney, cardiovascular disease, diabetes, urinary markers, rapid diagnostics, magnetosensors, disease management

ROLE OF SMEs Scientific coordinator

Harry Holthofer
Haartman Institute
Three SMEs are involved, plus a subsidiary of a large company: Haartmaninkatu 3
University of Helsinki
FI-00014 Finland
• Philogen SpA utilising their expertise to extract antibodies specific for the molecules harry.holthofer@helsinki.fi
involved in the pathogenetic sequelae of diabetic nephropathy and used for diagnostics; www.Helsinki.fi

National Centre for Sensor Research/

• Future Diagnostics B.V. combining the antibodies produced to novel test platforms, including BioAnalytical Sciences
the appropriate packaging into existing and to-be-developed concepts; Dublin City University
Dublin 9, Ireland
• United Laboratories Ltd. developing and screening for appropriateness of the platforms harry.holthofer@dcu.ie
www.cbas.ie
developed for daily routines with incoming patient samples; and
Partners
• Philips Electronics Netherlands B.V developing novel magnetosensors for detecting low
amounts of target molecules in patients’ urine. Per-Henrik Groop
Samfundet Folkhälsan
Helsinki, Finland
In addition, market analysis and surveys, IPR strategies, and competitor analysis will be www.folkhalsan.fi
provided by an additional party as a subcontractor of project partner, University of Helsinki.
Rob van der Heijden
Universiteit Leiden
Leiden, The Netherlands
www.leidenuniv.nl

Dario Neri
Swiss Federal Institute of Technology
Zurich, Switzerland
www.ethz.ch

Reinerio Gonzales
Philogen SpA
Siena, Italy
www.philogen.it

Menno Prins
Philips Electronics Nederland B.V.
Eindhoven, The Netherlands
www.philips.com

Mike Martens
Future Diagnostics B.V.
Wijchen, The Netherlands
www.future-diagnostics.nl

Jussi Vilpo
United Laboratories Ltd.
Helsinki, Finland
www.yhtyneetlaboratoriot.fi
© Shutterstock

49
ACRONYM Contract number: LSHB-CT-2006-037739 | EC contribution: € 1 834 331 | Duration: 36 months
Starting date: 1 January 2007

Drop-Top

SUMMARY
The management of patients with superfi-
Integration of DNA, RNA and protein markers
cial bladder cancer is difficult. No reli- in a tool for the prognosis and diagnosis
able means exist to determine whether
a tumour will progress towards an infil-
of human disease
trative form, which requires radical sur-
gery (cystectomy), or whether it will
remain superficial, which requires only
conservative surgery (resection). In addi-
tion, no dependable marker exists to
Background Aim
predict whether a primary tumour will
reappear or not during the years follow-
With an ever increasing incidence, cancer is the DRoP-ToP has two major objectives, one techno-
ing surgical resection, forcing patients
second major cause of death in the Western logical and one scientific. Regarding the former,
to undergo constant revisions that reduce
world. Although advances in our understanding of the project proposes to develop a tool for multi-
their quality of life and overburden health
the mechanisms of tumour onset and progression parametric analyses (mRNA levels, large genetic
care systems.
have been enormous, major impact on survival rearrangements, genetic mutations, genetic poly-
has been mainly restricted to sertain kinds of morphisms, protein levels and post-translational
Studies have identified biomarkers with
tumours. Besides advances in different therapies, modifications) of biological samples, to better
potential for the prognosis (progression
the improvement in survival can also be attributed predict tumour progression and recurrence. The
and recurrence) of superficial tumours.
to improvements in diagnosis and the identifica- evaluation of such heterogeneous parameters
However, the analyses have often been
tion of high-risk groups, which allow for earlier will be performed on a single microarray: the
limited to a single type of marker (e.g. pro-
and better treatment selection. triple microarray, an oligonucleotide microarray
tein or genotypic markers) or even to
In contrast to therapies and diagnosis, the overall for simultaneous DNA, RNA and protein assess-
a single marker. To the best of the pro-
prognosis of the most common cancers, such as ment). The triple microarray constitutes the test
ject’s knowledge, no study has attempted
lung, colon, prostate, breast and bladder cancers surface of a workstation that integrates technol-
to integrate different types of markers for
remains poor, particularly when the tumour can- ogy for the hybridization, scanning and detection
an increased predictive power.
not be cured by surgery. The ‘post-genomic era’ of biomarkers. Its simplicity should facilitate
has brought many promises that this situation will a wide implementation of this tool in the clinic.
The main scientific goal of DRoP-ToP is to
change, but it has also given the emphasise to the As scientific objective, the project proposes to
identify a set of markers (at protein-, RNA-,
need to make appropriate and better use of infor- identify a set of biomarkers with power for the
and DNA level) with high predictive power
mation, technology and clinical resources. The prediction of clinical behaviour of bladder cancer.
for tumour progression and recurrence. In
project believes that resources are often wasted Selection of such set of biomarkers will be the end
addition, DRoP-ToP pursues an ambitious
because of inappropriate approaches and inade- point of a five-phase endeavour:
technological challenge: the development
quate collaboration between clinical, academic • identification of candidate biomarkers for blad-
of a prognosis microarray, based solely on
and industrial partners. der cancer progression and recurrence from the
nucleic acid probes, for the detection of
Transcriptome analysis by DNA microarrays has scientific literature and from existing data gen-
the above mentioned predictor set.
been successfully used for the identification of bio- erated by two DRoP-ToP partners specialised in
markers of tumour progression. However, due to bladder cancer;
various inconsistencies from study to study, their • pre-selection of biomarkers on the basis of the
application to common clinical practice has not yet strength of their association to tumour behav-
taken place. The DRoP-ToP project intends to over- iour and on the scientific and technical quality of
come these limitations by a two-fold approach: the study;
• prospective validation of the information • measurement and validation of said candidate
acquired through retrospective studies. For this, biomarkers in a set of samples from patients
a collaborative multicentre effort is essential; with a detailed clinical record and follow-up;
• integration of biomarkers from genome, tran- • application of bioinformatics and biostatistics
scriptome and proteome analysis in a single pre- tools for the identification of a set of biomarkers
dictor set. Even though each of these three with a strong association to tumour behaviour.
analyses by itself will likely contribute, it is
expected that the combination of biomarker The DroP-ToP strategy should be applicable to the
types will result in an enhanced predictive study of any tumour type, and more generally to any
power. disease with a genetic or gene-expression compo-
nent. However, and as a proof of concept, the
project proposes to apply it to bladder carcinoma
because it represents a paradigm of the need for
useful biomarkers in the clinical setting:

50
Key words: urology,
?? clinical analysis, anticancer therapy, prognosis, microarray

ROLE OF SMEs
The DRoP-ToP consortium is made of 8 multi-disciplinary partners coming from 3 European
Member States (France, Spain, and Germany), 2 Associated States (Israel and Switzerland),
and one INCO Country (Former Yugoslav Republic of Macedonia).

Among the partners, the participation of 3 European High-Tech SMEs (Progenika Biopharma,
Genewave and NuAce Technologies) must be noted. Progenika Biopharma is the coordinator
of the DRoP-ToP consortium.

Progenika is a leading company in Functional Genomics and has wide expertise in microar-
ray technology, which is critical to the success of the project. The company disposes also of
a relevant know-how in genomics technology and has gained an outstanding level of expe-
rience in sample preparation from almost all human, plants and animal models, in microarray
processing and data mining, both in Expression and Genotyping projects. In particular,
beside acting as coordinator for the DRoP-ToP project, Progenika is committed to lead the
work on the design, validation and optimization of gene specific probes (for mRNA expres-
sion analysis) as well as allele specific probes (for genotyping). Progenika is also responsible
for the mRNA expression analysis and protocol optimization for the to-be developed probes.
The SMEs Progenika and Genewave are together responsible for the production of the final
chip functionalized with the three different detection probes.

Genewave is developing and commercializing new biophotonic instruments and systems for
genomic, proteomic and post-genomic applications. Conscious that the sensitivity of detec-
tion constitutes one of the major hurdles preventing biochips from reaching mass applica-
tions, Genewave has developed an amplifying substrate for biochip (AmpliSlide™) based
on an original optical design and its associated high-throughput reader (AmpliReader™).
Within the scope of this project, Genewave will further develop and optimized these tech-
nologies with a main goal to obtain highly sensitive substrates with a coating chemistry
optimized for the efficient simultaneous binding of RNA, DNA and Aptamers and integrated
instruments dedicated to the use in clinical diagnostics (integrated microarray analysis
station). This will represent a major advance as such a tool will allow much more powerful
diagnostics than available today aiming at less invasive, screening and diagnostic tests.

NuAce has developed a unique technology for synthesizing Dinucleotide-based Aptamers

(DBAs), which can be employed as target-specific binders for genomic, proteomics and
therapeutics applications.

The DBAs are highly suitable for creating protein recognition agents that can be used in pro-
tein chips. NuAce’s expertise will support the project in building up its basic concept, and
provide technological components including the task to generate DBAs to be immobilized
on the chip that specifically detects protein markers identified within the project.

51
ACRONYM
Drop-Top
• it is one of the best models of tumour progression;
• its incidence ranks fifth among all cancer types
(the fourth most common in males and the ninth
in females);
• despite widely variable outcome, the diagnosis
and prognosis tools used in the clinic are few and
the same, and they are invasive even for asymp-
tomatic patients (cystoscopy);
• it is the most expensive cancer type, as it can recur
many times after treatment;
• its evolution is very difficult to predict, whereas
the therapeutic approach for its two forms is com-
pletely different: when invasive at the time of
diagnosis, it has a poor prognosis and requires
aggressive surgery (cystectomy); when non-inva-
sive, prognosis is favourable and it only requires
conservative surgery (resection);
• its recurrence is also difficult to predict, which
leads to unnecessary visits and cystoscopies for
about 50% of patients, whose tumours will never
recur;
• a number of highly promising biomarker candi-
dates have already been identified and reported
in the literature.
Expected results
Cancer is the second leading cause of death world-
wide. In the year 2002 there were 10 million new
cases of cancer in the world, 6 million deaths and
approximately 22 million people living with cancer
worldwide. It is estimated that by year 2020 there
will be 15 million new cases per year, and 10 millions
deaths. Bladder cancer is a highly common neopla-
sia, mainly among men, and its incidence is rising in
several countries in Europe. Approximately 125 000
new cases with bladder cancer are diagnosed each
year in the EU.
Despite continued interest in the development of
novel tests to better predict bladder cancer progno-
sis, there has been very limited progress. This is in
part due to the fact that all tests developed until
present are based on the detection of only one type
of biomolecule (i.e. RNA, DNA or protein). Our
approach is radically different: from a systematic
review of current knowledge on biomarkers of blad-
der cancer and existing research results of the par-
ticipating academic partners, we propose to
develop a microarray that can detect the 3 major
types of molecules in human biological samples.
This should provide a much more solid basis to
identify molecular predictors of the disease.
The DRoP-ToP proposed technology will bring
about three main improvements:
• the number of invasive tests will be strongly
reduced, leading to a reduction in costs by
decreasing hospital admissions and the number
of occupation hours lost;
• reduction in the number of invasive tests will also
diminish morbidity and improve the quality of life
of patients;
• a better prognosis will allow more adequate choice
of treatment i.e. avoiding therapy to patients who
do not need it and applying more aggressive ther-
apy to patients at risk.
While most patients develop bladder tumours with
a relatively good prognosis in terms of survival,
their management is very expensive because of the
multiple recurrences that most patients suffer, the
need for invasive follow-up procedures, and the fre-
quent hospitalisations. Overall, bladder cancer
patients generate the highest cost/patient and life-
time among patients with cancer. In conclusion,
bladder cancer generates very high costs to society.
At the present time, there is no test recommended
or approved to help establish the prognosis of
patients with bladder cancer. Over the past 10 years
several products have been approved by the FDA
for use in the early detection of bladder cancer
recurrence (i.e. nmp22, BTA, Diagnocure Immunocyt,
Vysis). However, none of these tests is yet used
routinely in the clinical setting because they do not
provide a substantial benefit. Therefore, there is
a tremendous need for better tests.
Patients with bladder cancer develop multiple (up
to 30) tumour recurrences, thus requiring contin-
ued follow-up after the initial diagnosis. For this
reason, most patients undergo at least two med-
ical visits over the first few years after diagnosis.
Subsequently, the frequency of medical examina-
tions varies according to the evolution of the dis-
ease. Therefore, a test that would allow the early
detection of recurrences and an improved estab-
lishment of prognosis would be applied very fre-
quently to the patients. The DRoP-ToP proposed
test could even be used more commonly than cys-
toscopies are performed today, given that it would
not be invasive. Its availability would allow demon-
stration of the concept that early detection of
tumour recurrence is associated with improved
overall outcome.
Potential applications
Diagnosis and prognosis for the bladder cancer
and other diseases.
52
 Scientific coordinator
Gorka Ochoa
Progenika Biopharma, S.A.
Parque Tecnológico de Bizkaia
Edificio 801 B
Derio-Vizcaya
48160, Spain
gochoa@progenika.com
www.progenika.com

Partners
Francois Radvanyi
Institut Curie-CNRS
Paris, France

Nuria Malats
Institut Municipal d’Investigacio Medica
| Triple microarray and Integrated station for improved Universitat Pompeu-Fabra
multiparametric analysis of biological sample. Barcelona, Spain

Gordana Cerovic
Genewave S.A.S.
Palaiseau Cedex, France
www.genewave.com

| Comparison between a standard glass slide and an Melanie Hilanio

AmpliSlide™. In a standard glass slide a large portion of University of Geneva
the emitted fluorescence by substrate-attached fluorophores Geneva, Switzerland
escapes into the glass substrate. Constructive interference
allows AmpliSlide™ to amplify and redirect this emitted
Zivko Popov
University Cyril and
fluorescence towards the reader’s optics. This amplification,
Methodius-Faculty of Medicine
up to a 20-fold increase in signal, results in enhanced
Department of Urology
sensitivity. (Top and middle: illustration and computerised Skopje, Former Yugoslav Republic
simulation of light emission from fluorophore placed on of Macedonia
the slide. Bottom: side by side comparison of images from
scanned slides hybridised under identical conditions). Hader Kless
NuAce Tecnologies, Ltd.
Rehovot, Israel

Joerg Hoheisel
Deutsches Krebsforschungszentrum
Heidelberg, Germany

53
ACRONYM Contract number: LSHM-CT-2006-037870
Starting date: 1 December 2006
EACCAD
www.cdiff.nl
SUMMARY
Clostridium difficile-associated disease
(CDAD) has become the most frequent
nosocomial infection in many European
hospitals. In 2004, the situation was
exacerbated by the arrival in Europe of
a new hypervirulent strain (PCR ribotype
027) previously confined to N. America,
where it has been responsible for a mas-
sive increase in CDAD incidence and
associated deaths. Central to the control
of epidemics are the deployment of
assays able to rapidly diagnose and
monitor the presence and spread of the
organism. No such tests currently exist
for these new hypervirulent C. difficile
strains. It is the overall objective of this
proposal to develop the urgently
required rapid, diagnostic assays in
close collaboration with 3 SME’s.
| EC contribution: € 1 771 000
European approach to combat outbreaks of
clostridium difficile associated diarrhoea by
development of new diagnostic tests
Background
C. difficile is resistant to various antibiotics and
capitalises on the ensuing disruption of the nor-
mal intestinal flora to colonisation and cause dis-
ease. The spectrum of disease ranges from
asymptomatic carriage to a fulminant, relapsing,
and increasingly fatal colitis. The effects of CDAD
are devastating, both in terms of morbidity/mor-
tality and the high costs of disease management.
Presently, C. difficile may only be treated with
either metronidazole or vancomycin. A number of
factors have contributed to the worrying escala-
tion in the incidence of CDAD. The elderly and
immuno-compromised are particularly at risk
(80 % of cases occur in the over 65s). The propor-
tion of the population in these high-risks groups
is rapidly rising. Strains exhibiting greater viru-
lence are also beginning to emerge, which in some
instance has been attributed to the production of
additional virulence factors, e.g. binary toxin. The
situation has now been exacerbated by the arrival
in Europe during 2004 of a new hypervirulent
strain and antibiotic resistant strain (ribotype
027, toxinotype III) previously confined to Canada
and the USA. The occurrence of this strain is asso-
ciated with an excessive use of cephalosporines
and quinolone antibiotics, and has been responsi-
ble for a massive increase in CDAD incidence in N.
America and associated deaths, e.g. the propor-
tion of patients with CDAD who died within
30 days after diagnosis rose from 4.7 % in 1991-92
to 13.8 % in 2003. This epidemic strain isolated
in Canada, USA, UK, Belgium, France and The
Netherlands was characterised as toxinotype III,
North American PFGE type 1, restriction-endonu-
clease analysis group type BI and PCR-ribotype
027. The strain produces toxins A and B and con-
tains a 18 bp deletion in the toxin regulator gene
TcdC. It is imperative that an overall strategy to
combat this and similar novel variant(s) is
devised. Central to control of epidemics by such
new C. difficile strains with increased virulence is
a strategy that will include not only a rapid detec-
tion but also a specific recognition of virulent
strains. Diagnostic assays for CDAD rely either on
the detection of C. difficile products (toxins),
| Duration: 36 months
C. difficile genes, or the culture and toxin testing of
the isolates. Toxins can be detected either by their
biological properties (cell cytotoxicity assay) or by
immunological methods (latex agglutination,
immunoassay). The cell cytotoxicity test is the
‘gold standard’. However, there are significant
drawbacks. Laboratories must have access to cul-
tured monolayers, and results vary according to
the cell line, dilution factors, reagents used and
storage conditions. Additionally, the turnaround
time is very slow. Enzyme immunoassaysconsist
of conventional enzyme immunoassays and mem-
brane immunochromatographic tests. The sensi-
tivities and specificities of enzyme immunoassays
are within 85-95 % of the cell cytotoxicity test, and
numerous commercial kits are available. However,
their performance relative to each other has not
been subjected to a rigorous meta-analysis.
Immuno-chromatography tests are extremely sim-
ple, can be performed at the bedside and give
a result within 30 minutes. This may be of crucial
importance in an epidemic situation to recognise
infected patients. DNA-based tests are focussed
on the detection of the C. difficile genes encoding
16S RNA, GDH or the toxin genes (tcdA & tcdB).
Aim
The recognition of suitable targets and devel-
opment of a commercial rapid test that will dis-
tinguish variant hypervirulent and antibiotic
resistant strains from ordinary C. difficile strains is
the main aim of this project. The objective will be
achieved through the complementary skills of
a consortium composed of 3 SMEs and 4 public
sector institutes, each experts in their fields.
There will be a close collaboration in the form of
subcontractors with the European Study Group of
C. difficile (ESGCD). Suitable diagnostic markers
(DNA- and antigen-based) will be identified using
a combination of targeted approaches (focusing
on toxin and antibiotic resistance determinants),
and empirical approaches (DNA arrays and HT-
AFLP) to identify unique strain differences. Assay
development will be led by the SMEs, using pro-
prietary technologies. Clinical validation will be
performed in a certificated reference laboratory.
54
Key words: clostridium difficile, hypervirulent type 027, CDAD, diagnostics, outbreaks

ROLE OF SMEs Scientific coordinator

Ed J. Kuijper
Department of Medical Microbiology
The consortium consists of a balanced mix of public sector scientists that have worked on Leiden University Medical Center
C. difficile for most of their professional careers (taken from four institutes), together with PO Box 9600, 2300 RC
Leiden, The Netherlands
three SME’s with highly developed technology on bacterial toxin preparation, molecular ejkuijper@gmail.com
diagnostics and enzyme-immunoassays. Therefore, complementary expertise, and ‘state-
of-the-art’ technology is supplied by partners specialised in diagnostics, epidemiology, Partners
genomics and drug susceptiblity screening.
Maja Rupnik
The three SMEs participating in the project, tgcBiomics, PathoFinder and Coris BioConcept, Dept. Med. Microbiol. Immunol.
will mainly contribute to the development of molecular tests and rapid membrane University of Maribor
immunoassays for detection of the target in patient material and in bacterial isolates. Maribor, Slovenia

The programme outputs will allow the formulation
of a European strategy to combat the consider-
able threat now being posed to European quality
of life by C. difficile.
Expected results
• Recognition of targets for new diagnostic tests
by characterisation of hypervirulent and drug
resistant C. difficile strains. The targets are based
on toxins, toxin coding regions, or unique other
genes of C. difficile.
• The availability of molecular tests and rapid
membrane immunoassays for detection of the
target in patient material and in bacterial isolates.
• Validation of new developed tests for clinical
diagnostics and strain characterisation. The new
molecular tests and rapid membrane assays will
be investigated in faeces samples of patients
with various forms of C. difficile associated diar-
rhoea. The newly developed tests will also be
used to recognise hypervirulent isolates and
antibiotic resistance of clinical isolates obtained
by prospective surveillance studies in Europe.
Potential applications
Nigel Minton
Institute of Infection
and prevent an outbreak. The genomic approaches Immunity and Inflammation
(DNA Array and HT-AFLP) will provide fundamen- University of Nottingham
Centre for Biomolecular Science
tal information on the genetic make-up of hyper- Nottingham, United Kingdom
virulent C. difficile strains and will lead to greater
insight into pathogenesis which will in turn allow Paola Mastrantonio
Istituto Superiore di Sanità, ISS
the development of more effective therapeutic Rome, Italy
countermeasures and IPR spin-offs. Additionally,
European guidelines will be formulated to diag- Cristoph von Eichel-Streiber
nose CDAD and to combat outbreaks. The intro- tgcBiomics GmbH,
Mainz, Germany
duction of these tests and European guidelines www.tgcbiomics.de
increase the awareness of CDAD as an important
nosocomial infection and will be of help to pre- Thierry Leclipteux
Coris BioConcept
vent the development of large outbreaks by new Gembloux, Belgium
hypervirulent variants, as currently occur in USA www.corisbio.com/index.asp
and Canada. Application of the new tests and
Guus Simons
updated guidelines will contribute to insights in Pathofinder B.V
the epidemiology of CDAD and will be of general Maastricht, The Netherlands
support to prevent over-prescription of antibiotics www.pathofinder.nl
in hospitals. Application of the new developed
tests will provide a platform for automation of
diagnosis. A further stimulant for effective DNA- | Toxin A (TcdA) and toxin B (TcdB) are
based diagnostic tests is to extend testing on encoded on large chromosomal region
the same faecal sample for other non-bacterial PaLoc, which encompasses two toxin
causes of infectious diarrhoea, such as viral diar- genes (tcdA and tcdB) and three
additional genes coding for regulatory
rhoea and parasitic diarrhoea. It is possible to auto- and putative transport function
mate nucleic acid extraction and use a common (tcdR,E,C). In nontoxigenic strains,
extraction for all subsequent analyses. PaLoc is replaced by 115 bp sequence.

The new diagnostic tests will overcome the lack

of sensitivity and specificity of current diagnostic
tests. The new immunoassay offers an alterna-
tive for those laboratories which lack capability
in molecular biology. Recognition of variant 027
is not possible with the currently available diag-
nostic tests. Rapid recognition of CDAD and its
variant 027 will result in appropriate patient
treatment and specific measures to prevent noso-
comial spread and the development of outbreaks.
The rapid molecular test will provide the first indi-
cation of the presence of type 027, allowing ade-
quate infection control measures to be undertaken

55
ACRONYM Contract number: LSHB-CT-2006-037545
Starting date: 1 August 2006
ENLIGHT
www.olink.com/content/Enlight/Enlight.html
SUMMARY
The ENLIGHT project aims to develop
analytical procedures with the sensitivity
and specificity required to study individ-
ual nucleic acid and protein molecules,
and also interacting molecules, in their
normal context in cells and tissues (in
situ) and in tissue lysate microarrays.
A spectrum of reagents will be developed
for the analysis of specific markers of par-
ticular interest in oncology. Furthermore,
software and algorithms will be estab-
lished for automatic user-independent in
situ image analysis of single molecule-
events. These methods and algorithms
will be applied to evaluate candidate bio-
markers of special relevance for tumour
biology and cancer pathology.
| EC contribution: € 2 978 810
New molecular methods and image analysis tools
for analysis of cancer biomarkers in situ
Background
In situ analysis of cells and tissues has been an
essential part of pathological research and diag-
nosis primarily within cancer for many years, and
a number of specific biomarkers of predictive
and prognostic value for various cancers have
been identified. In situ analysis of nucleic acid
sequences is dominated by in situ hybridisation,
while in situ analysis of proteins is dominated by
immunohistochemistry where sections of tissues
are tested for the presence of proteins by specific
antibodies. Due to limitations in these technolo-
gies there is a significant need in the scientific
community for new efficient techniques and pro-
cedures for more advanced analyses. A major
challenge is to develop improved means for
more detailed studies of biomolecules in situ, in
order to determine their abundance, sub-cellular
localisation, and secondary modifications, as
well as how they interact with other molecules
and participate in signalling and control of cellular
function.
Aim
The first aim is to develop new molecular methods
and assays for the analysis of individual DNA and
protein molecules in situ. The project is based on
two fundamental technological inventions, pad-
lock probing and proximity ligation. These are the
first technologies to offer the sensitivity and speci-
ficity required for studies of single bio-molecules
in situ. The padlock probe technology is used to
interrogate nucleic acids and to distinguish closely
similar sequence variants, while the proximity lig-
ation assay (PLA) is applied to analyse individual
proteins, interactions between proteins, and post-
translational protein modifications.
Secondly, the project will develop automated
image analysis procedures to complement the
molecular methods. The objective is to achieve
quantitative information about what molecules or
molecule complexes are present in the sample
and their tissue or sub-cellular localisation (i.e. in
which cellular substructures).
| Duration: 36 months
Finally, the new methods and image analysis
procedures will be used to clarify the role of
molecular biomarkers in tumourigenesis, prima-
rily concerning the AP-1 and HER protein families
and for mitochondrial DNA. The methods will also
be tested in a high-throughput microarray analy-
sis system. The cancer biomarker will primarily be
investigated in a research setting, but the utility of
the markers for diagnostic analyses will also be
explored.
Expected results
This project is expected to provide new means to
study biomarkers for oncogenesis, and to gener-
ate novel insights in cancer biology. It is expected
that the in situ techniques developed in this proj-
ect, and the scientific knowledge created, in the
longer run will lead to improved disease preven-
tion, more rapid and accurate cancer diagnosis,
and better treatment opportunities.
New analytical means will be developed to analyse
cancer biomarkers in situ. Relative to state-of-the-
art procedures, these methods are expected to
provide significantly improved in situ analyses in
terms of specificity, sensitivity (single molecule
detection), possibility to study biomarker localisa-
tion, analysis of protein interactions and protein
modifications, and an opportunity for simulta-
neous analysis of multiple markers (multiplex
analysis). Automated image analysis procedures
will be developed, i.e. software-based classifica-
tion of molecules and their localisation in tissues
or cells. The software will provide a rapid way to
analyse many samples as well as user-independent,
unbiased data classification.
Potential applications
Cancer biology and diagnosis.
56
Key words: cancer, biomarker, in situ analysis, technology development, proximity ligation, padlock probing

ROLE OF SMEs Scientific coordinator

Björn Ekström
Anders Alderborn
This project is centred around three European SMEs with high future potential. The SMEs Olink AB
are brought together with academic scientists and one large established company, Dako Dag Hammarskjölds väg 54A
751 83 Uppsala, Sweden
Denmark, to enable the development of new efficient technical solutions for the analysis of bjorn.ekstrom@olink.com
individual molecules in tissues or in single cells. The results from this project are expected anders.alderborn@olink.com
to provide important new commercial opportunities for products addressing significant mar- www.olink.com
ket needs, thereby allowing the participating European SMEs to build sustainable busi- Partners
nesses at the forefront of biotechnology. To ensure that the outcome of the project will be
advantageous for the SMEs, one of them, Olink AB, has the role as project coordinator. Mats Gullberg
DakoDenmark will, as a non-SME, have a role as advisor to the SMEs in matters such as Olink AB
Uppsala, Sweden
product requirements and market needs. www.olink.com

Ulf Landegren
Ewert Bengtsson
Uppsala University
Uppsala, Sweden
www.uu.se

Henrik Winther
Dako Denmark A/S
Glostrup, Denmark
www.dako.com

Anders Larsson
Immunsystem I.M.S. AB
Uppsala, Sweden
www.immunsystem.com

Niels Foged
Visiopharm A/S
Hørsholm, Denmark
www.visiopharm.com

Olli Kallioniemi
VTT Technical Research
Centre of Finland
Turku, Finland
www.vtt.fi

John Bartlett
The University of Edinburgh
Edinburgh, United Kingdom
www.ed.ac.uk

Anton Raap
Hans van Dam
Leiden University Medical Center
Leiden, The Netherlands
www.umc.nl

| Microscopic examination of tissue sections.

57
ACRONYM Contract number: LSHP-CT-2006-037651 | EC contribution: € 2 400 000 | Duration: 36 months
Starting date: 1 January 2007

EPIVAC

SUMMARY
More than 40 million people are currently
Development of a multi-step Improved Epidermis
infected with HIV1, mostly coming from Specific Vaccine Candidate against HIV/AIDS
developing countries resulting in an urgent
need for effective and affordable treatment
of HIV1 infections. The main objective
of the project is to develop an efficient
genetic vaccine candidate for therapeutic
and preventative use against HIV/AIDS.
Background Based on this knowledge, the EPIVAC Project pro-
The vaccine planned should be capable of
poses the concept of combining the advantages of
inducing cell-mediated and humoral
The Human Immunodeficiency Virus (HIV) induces various vaccines by engineering them into single
immunity against the virus and virally
chronic infection in patients, eventually leading to vectors, i.e. by designing plasmids that harbour the
infected cells in different phases of the
deterioration of the immune system and the onset genetic code necessary for the production of recom-
viral life-cycle.
of immune deficiency. HIV induces significant cell- binant viral particles, which further target the skin
mediated and humoral immune responses, which as a preferential site for genetic immunisation.
DNA vaccines could fulfil these require-
considerably reduce viral titre after initial burst of
ments if rendered more efficient. To this
end, a combination of complementary
the HIV1 replication and spread in the body. These Aim
naturally induced immune responses only partially
technologies by four SMEs will be used.
control HIV spread and in fact there are no clearly EPIVAC aims to generate a multi-step, improved,
The novel DNA vaccination technology
documented cases of true clearance of the viral efficient and affordable DNA-based preventative
will combine:
infection. Nevertheless, it is possible that the trig- and therapeutic vaccine against HIV.
• the restricted expression of the multi-
gering of additional immune responses, notably
epitope/multivalent HIV antigens in
through the presentation of modified HIV anti- The first goal of EPIVAC is the development of
specific cells of the epidermis;
gens, could generate different types of immune a reliable, reproducible and robust delivery sys-
• a micro-needle array-based injection
responses that could contribute towards better tem. This will include micro-needle arrays and
device for reproducible and efficient
control of the infection and thus improve clinical an injection device for the controlled delivery of
delivery into the epidermis;
evolution and reduce viral transmissibility. the GTU®-based vector system and for cell-type-
• EPI-GTU® technology that allows
specific epidermal expression of the genes of
strong and long-term expression using
The quality and intensity of the humoral or cellu- interest in epidermal differentiating keratinocytes,
segregation/partitioning function of
lar immune responses required for efficacious Langerhans cells and melanocytes.
the Bovine papillomavirus type 1;
preventative or therapeutic vaccinations vary,
• Plasmo-VLP® technology that allows an
depending on the target infectious agents. The plasmids and genes of interest used in these
expression of the immunogens within
Preventative vaccines against acute viral infec- studies will allow for the quantitative evaluation
and onto virus-like-particles;
tions often rely on strong neutralising antibody of the efficiency and kinetics of delivery of plas-
• the adjuvant effect of different cytokines.
responses, while therapeutic vaccines against mid DNA into the epidermis and epidermal cells.
chronic infectious diseases often rely on cytotoxic Further, to follow the process of diffusion, degra-
The step-by-step combination of these
responses capable of eliminating infected cells. dation and intracellular up-take and onset of bio-
technologies will be evaluated at the labo-
logical activity of the delivered expression system
ratories of the three academic partners by
Most antiviral vaccines in current use are based in specific cells of the epidermis will be assessed.
using state of the art methods. The initial
on homologous inactivated or attenuated viral The plasmids used will carry the site-specific fluo-
evaluation of vaccine efficacy will be per-
particles, i.e. attenuated measles virus for rescent labels for the monitoring of DNA delivery
formed on mice and pigs and will be ulti-
measles vaccination. This establishes that pack- into the epidermis as well as the diffusion and
mately validated in Cynomolgus monkeys.
aging antigens in/onto particles is one of the most degradation of the plasmid.
efficient ways of triggering efficient antiviral
EPIVAC aims to conduct its preclinical
immune responses. Some of the most promising The second goal of the EPIVAC project will be to
development up to the GMP production
new vaccines have been designed and developed analyse the effect of different HIV1 antigen
phase. Testing of numerous vector batches
in the field of DNA vaccination. DNA vaccines are expression in different cells of the epidermis on
will be aimed towards having enough
low in cost, stable and easy to produce, whilst the nature and breadth of the induced immune
suitable material ready for evaluation in
offering the possibility to combine several anti- response.
clinical trials.
gens when required. However, it appears that
DNA vaccination, typically induces cellular immu- One major problem in developing an AIDS vaccine
nity, but rarely or inefficiently neutralising anti- is the lack of knowledge regarding immune mech-
bodies that often play a major role in protection anisms for protection against HIV1 infection and
against viruses (1). for removing the virus from the body. Another

58
Key words: vaccines, DNA Therapy, epidermal genetic vaccination, HIV infection and AIDS

Scientific coordinator
ROLE OF SMEs Ioana Stanescu
FIT Biotech Plc
Biokatu 8, 33520
EPIVAC comprises four SMEs among the seven partners, including the coordinator FIT Tampere, Finland
Biotech Plc., SILEX Microsystems, ESTLA Ltd. and EPIXIS s.a. ioana.stanescu@fitbiotech.com
www.fitbiotech.com
FIT Biotech will contribute its GTU® (Gene Transport Unit) platform technology and the appli- Partners
cations based on it, including novel vectors, self-replicating vectors for DNA immunisation
against HIV, AIRE (immunological mechanisms) and DNMT3L (immune diseases, new genes). Henrik Hellqvist
Silex Microsystems AB
Sweden
SILEX will bring to the table extensive expertise from the development and production of www.silexmicrosystems.com
Micro-Electro-Mechanical-System (MEMS) components. SILEX personnel and the fully
equipped MEMS production facility provide an excellent environment for quick prototyping, Evgeny Berik
development and production of microneedles that will be used in this project. The produc- Estla Ltd.
Tartu, Estonia
tion of microneedles is an area of specific manufacturing expertise based on previous work www.estla.com
for various diagnostic and drug delivery applications.
Charlotte Dalba
EPIXIS S.A.
ESTLA Ltd. develops, produces and supplies accessories for research organisations (optics, Paris, France
fine mechanics, special instruments for biophysics), special lasers (excimer, dye, copper www.epixis.com
vapour) and laser-based systems for science, medicine, industry and entertainment. The
David Klatzmann
company will contribute to the EPIVAC project through studies of the injection process and University of Pierre and Marie Curie
vaccine distribution by optical methods, and by the design and fabrication of the specialised Paris, France
instruments needed for injections with microneedle chips. www.upmc.fr

Mart Ustav
EPIXIS s.a. is dedicated to the development of preventive and therapeutic vaccines against Tartu University Institute of Technology
infectious diseases. The company’s proprietary pseudotyped virus-like particle (VLPs) have Tartu, Estonia
the unique property to express the pseudotyped viral envelops in their native conformation, www.tuit.ut.ee
and can likewise efficiently induce broadly neutralising antibodies. EPIXIS will contribute to Roger Le Grand
EPIVAC with pseudotyped VLPs produced in vivo by vaccination with ‘plasmo-VLPs’. French Atomic Energy Commission
Paris, France
www.cea.fr

goal of this project is to contribute towards the Potential applications

identification of some immune correlates of pro-
tection during the evaluation of vaccine efficacy in
non-human primates. The induced immune
response triggered by the vaccination will be char-
acterised qualitatively and quantitatively towards
every viral target protein. The immunised animals
will be challenged after immunisations with the
hybrid SHIV, and analysed for control, clearance
and protection.
Expected results
• Epidermal genetic vaccinations; Improved treat-
ment of HIV infection and AIDS by using nano-
technology.
• Improved standards for vaccination in large ani-
mals, notably by using swines that are not often
used in vaccine development and which could
become interesting alternatives to the use of
non-human primates for challenge experiments.

• New devices and modalities for DNA delivery to References

the epidermis. (1) Tuteja et al., 1999.

• Generate improved DNA-based vaccines com-

bining the advantages of GTU vectors for long-
term expression and plasmo-VLP vectors for the
presentation of antigens onto VLPs.

• Generation of new proprietary HIV antigens

based on the EPIVAC optimised vector.

59
ACRONYM Contract number: LSHB-CT-2007-037283 | EC contribution: € 1 887 160 | Duration: 36 months
Starting date: 1 February 2007

EURO-PHARMACO-GENE

SUMMARY
The project outlines the development of
Design of targeted Gene Pharmaceutics
a novel Gene Pharmaceutics prototype using self-assembling functional entities
through translational research. This can
be accomplished by the combined efforts
of three research-intensive biotech com-
panies, together with two academic
groups, representing state-of-the-art skills
and proprietary technologies in comple-
mentary areas. These include nucleic acid
Background Expected results
analogue chemistry, short interfering RNA
(siRNA) technology, gene transfer and
During the last years, developments in genomics The project combines research with technological
gene therapy, as well as imaging instru-
have enabled an unprecedented acquisition of implementation in the development of new Gene
ment manufacturing, and methods for self-
new knowledge with relevance for human dis- Pharmaceutics. Obtaining pharmacologically sat-
assembling supramolecular complexes.
ease. In parallel, the biotech industry has isfactory gene drug delivery systems has the
This will lead to the design of new self-
invented novel ways of generating drugs in order potential to impact positively on a range of both
assembling Gene Pharmaceutics and bring
to meet the demands from the healthcare sector. common and rare healthcare burdens within
them to the clinical grade stage.
Europe and beyond. Strategies targeting hepatitis
The aim is to develop plasmid and siRNA-
The development of new pharmaceutics in the B and C, and haemophilia are presented in the
based drugs that target the liver, since this
field of genomics and biotechnology is likely to be current proposal. The expected result of the pro-
organ is affected in many disorders involv-
successful, provided that there is an optimal inte- posal would thus be efficient and productive
ing a genetic component. Three diseases
gration of multidisciplinary efforts from both aca- progress in the development of clinically-potent
have been selected for this purpose,
demia and industry. This is a major challenge, and cost-effective pharmacological formulations
namely hepatitis B and C infections and
since new concepts need to be explored and com- of gene-based medicines.
an inherited form of bleeding disorder,
bined into commercially viable innovations. The
haemophilia A (Factor VIII deficiency).
development of a drug from the lab bench to The market for gene drugs is potentially very
Moreover, many aspects of this platform
a clinical grade product is very costly, involving large, although it is dependent upon the develop-
technology are likely to be applicable to
many translational steps and often in excess of ment of safe and pharmaceutically acceptable for-
essentially any liver disorder and may also
one hundred million euros. Only major pharma- mulations and protocols. This project, through the
be transferable to other organ systems.
ceutical companies have the financial resources expertise of the partners, aims to prove that this
Fully developed, this technology will result
to accomplish this task. This means that small and technology possesses the appropriate properties
in new, safer and more rational drugs.
medium sized enterprises (SMEs) need to develop for successful application.
Gene Pharmaceutics technology is based
novel drug concepts to a stage where the proof of
upon the addition of functional entities to
nucleic acids. The schematic representa-
principle can be evaluated by the big pharmaceu- Potential applications
ticals, in order to bring the therapy to the clinic.
tion (Fig. 1) shows three different func-
The potential applications of the drug-delivery
tional entities (blue squares, orange
circles and red triangles, or different grey-
Aim technology proposed here are much broader
and could include cancer, vaccine approaches to
shades, when printed in black and white)
The project has the following objectives: infectious disease, arthritic disorders, tissue
linked to peptide-nucleic-acid (PNA)
• generation of new forms of DNA-binding syn- engineering, and various inherited syndromes
anchors, which are glued onto the plasmid
thetic compounds, which will serve as genetic which, while less common, nevertheless impose
through hybridisation to PNA anchoring
glues; huge burdens on patients, their families and
sequences (green, yellow and light blue
• enhancing linking chemistry for biologically active healthcare providers. The success of this proposal
regions, or different grey-shades, when
entities coupled to DNA binding compounds; will create a new pharmaceutical platform and
printed in black and white) in the plasmid.
• optimising the assembly of Gene Pharmaceutics demonstrate its potential for treatment, which
Other nucleic acid analogues, such as
by in vivo experimental studies; would have a strong impact on public health and
LNA, or derivatives thereof, can also be
• developing standard operating procedures related expenses.
used as anchors. The marked sequence in
for the manufacturing and assembly of Gene
the lower portion of the plasmid repre-
Pharmaceutics according to good manufacturing
sents the transferred gene. This could be
procedures.
a reporter gene, a therapeutic gene, such
as the one encoding Factor VIII, which is
defective in haemophilia A, or a short hair-
pin RNA expression cassette, in which the
shRNA is directed against a component of
hepatitis B or C virus.

60
Key words: gene therapy, hepatitis, haemophilia A, siRNA, PNA, nucleic acid analogues

ROLE OF SMEs Scientific coordinator

C. I. Edvard Smith
Clinical Research Center
Of the five participants to this project, two are academic and three are SMEs. The academic Department of Laboratory Medicine
research lab from Karolinska, in addition to coordinate, will perform assembly and biolog- Karolinska Institutet at Novum
Hälsovägen 7
ical testing of the tool kit for gene transfer. These tools can be described as novel self- SE-141 57 Huddinge, Sweden
assembling supramolecular complexes. While the academic research lab in Denmark will edvard.smith@ki.se
concentrate onnew chemistry, in particular on novel nucleotide analogue chemistry and Website: www.ki.se
nucleic acid functionalisation, especially based on the locked-nucleic-acid (LNA) platform Partners
technology.
Jesper Wengel
The key role of the SMEs is highlighted below: Eurogentec focuses on advanced, peptide- University of Southern Denmark
Department of Physics and Chemistry
based synthesis, development of optimised coupling procedures for peptides and nucleic Odense M, Denmark
acid analogues. The company is an SME based in Belgium. www.sdu.dk

Biospace provides state-of-the-art imaging solutions for monitoring of the biological effects Daniel Marechal
Ivo Rudloff
of Gene Pharmaceutics. It is an SME based in France. EUROGENTEC S.A.
Seraing, Belgium
Avaris concentrates on development of novel pharmaceutics, in particular providing trans- www.eurogentec.com/eu-home.html
lational research which brings non-viral gene transfer systems from the research lab bench Serge Maitrejean
to the clinic. It is an SME based in Sweden. BIOSPACE S.A.
Paris, France
The strength of this consortium is in the diversity and complementarity among partners, Mats Lake
combining basic research with the applications to human health. AVARIS AB
c/o Karolinska Innovations
Stockholm, Sweden
www.avaris.se

| Fig. 1 Schematic representation of technology. | Fig. 2 Interaction and complementarity among partners. The arrows
indicate reciprocal relationships, i.e. partners connected will provide
know-how, experience or products bi-directionally.

61
ACRONYM Contract number: LSHB-CT-2006-037168 | EC contribution: € 2 173 492 | Duration: 36 months
Starting date: 1 October 2006

EXERA
www.altaweb.eu/exera

SUMMARY
The objective of the EXERA project is to
Development of 3D in vitro models
develop novel 3D in vitro models of mouse of estrogen-reporter mouse tissues for the
tissues from five major organs for the phar-
maco-toxicological analysis of Estrogen
pharmaco-toxicological analysis of Estrogen
Receptors-Interacting Compounds (ER-ICs): Receptors-Interacting Compounds (ER-ICs)
liver, skin and bone (non reproductive sys-
tems), ovary and testis (male and female
reproductive systems).
Background • Conventional cell cultures often do not express
This objective will be pursued through
suitable easy-to-assay quantifiable markers or
a work programme which allies an inte-
Industries from different fields (Pharmaceuticals, they need transfection procedures that increase
grated scientific approach between inno-
Chemicals, Cosmetics, Foods and Toxicologicals) variability of the data.
vative technologies such as the 3D-culture
need reliable, fast and economic in vitro models,
device, known as ‘Rotary Cell Culture
which are alternative to animal testing and can • The systems used for the in vitro and in vivo
System’ (RCCS Technology adapted to the
provide predictive data on the actions of NR-ICs analysis of NR-ICs (mainly estrogens and andro-
needs of this project), established trans-
and in particular ER-ICs (Estrogen Receptors gens) are generally composed of cells derived
genic mouse lines (estrogen-reporter
Interacting compounds). from reproductive tissues. The recent knowl-
mice, here called MOUSE-1) and genomic
edge of the widespread distribution of nuclear-
platforms for ER-ICs characterisation.
The need for appropriate in vitro models which receptors (in particular steroid receptors) in all
can reproduce features and reactivity of specific the tissues of the organism and their involve-
The strategy is planned around five main
mammalian target tissue/organs to ER-ICs is thus ment in several diseases, makes the available
points including, besides the mentioned
becoming an imperative research priority. The sci- systems inadequate to assess the effects of
technologies, multiple cell cultures quality
entifically, economically, socially and ethically rel- NR-ICs on the whole physiology (Villa R, 2004).
controls, immortalisation control, cell bank-
evant stakes are therefore considerable.
ing and the use of specific markers of estro-
• The available models do not easily provide infor-
genic action and cell differentiation/health,
The tissue- and organ-specific in vitro models mation on the effects of compounds at different
in order to obtain estrogen -responsive 3D-
which have been built so far have several serious developmental stages.
cultures of well differentiated mouse cells.
limitations:
The corresponding work programme will
Aim
• Most of the available cell lines of mammalian
be ensured by an important involvement
origin are derived from tumours or have a trans- EXERA’s original approach is based upon power-
of the whole partnership and by a high
formed phenotype. Their functional and struc- ful evidences:
degree of coordination between 6 private
tural features do not mirror the original tissue.
and 3 public institutions.
Use of the transgenic MOUSE-1: This estrogen-
• When mammalian-derived in vitro models are reporter mouse model represents a new strategy
available, they consist of primary cell cultures or that allows studying estrogen receptors-medi-
of isolated tissue slices: their in vitro survival is ated gene regulation in vivo and in derived in
limited (time-course and dose- response stud- vitro systems. The numerous studies performed
ies are very difficult). Moreover, if of human on this animal model in several laboratories
origin, they have the disadvantage of depend- have demonstrated its reliability and suitability
ing on regular supply from available clinical to the study of molecules acting through estrogen
sources. receptors.

• 2-Dimensional culture conditions may be not
optimal for tissue-like organisation and cellular
functions (e.g. polarised cells of a parenchymal
tissue, which normally require complex cellular
interactions, and cannot behave physiologically
when adhering to solid substrates, as in the
case of conventional culture conditions).
3D cultures: Cell-cell and extracellular matrix-
cell interactions play a fundamental role in
maintaining the function of numerous organ
systems. Hence, tissue engineering represents
a good way to overcome limits of monolayer cul-
tures and to maintain tissue-like architecture
and functionality.

62
Key words: estrogen
?? receptors, endocrine disruptors, estrogenic drugs, transgenic estrogen-reporter mice,
in vitro assays, 3D-cultures, in vivo imaging

ROLE OF SMEs
Industrial participation is important (some 70 % of the EU contribution will go to SMEs) and
diversified. It is composed of 5 SMEs and one industry. One SME (ALTA S.r.l.) will be involved
in this project for administrative management. The fact that SMEs from different but comple-
mentary fields take part in this consortium, not only implements the recommendation of the
6th FP, but represent an added value since it ensures the strong commitment of the partici-
pants to the success of the study and will guarantee the future exploitation of the project’s
results ensuring the eventual transition from discovery to the market.

Specific role description:

BIOSERV: Establishment of Sertoli, Leydig, peritubular and corresponding Granulosa cell

lines from tissue isolates of the estrogen reporter model ERE-Luc.
Development of fully functional micro test systems in which cells are maintained in chip
based micro-culture environment.

CELLON: Cellon will provide the 3D cell culture systems, Rotary Cell Culture Systems (RCCS).
Cellon will benefit from the new application of this technology to pharmaco-toxicological
testing of hormonal chemicals and will promote the diffusion and applications of the RCCS
in Europe and worldwide.

HORMOS MEDICAL: Hormos operates in the project as an implementation and validation

arena, to provide the consortium with data on different compounds with varying SERM and
| Optical imaging on the estrogen reporter mouse
NR related activity in different tissues. Hormos can adapt the cellular systems ‘in house’ and ERE-Tk-Luc. The mouse was exposed for 6 hours
validate the cell lines under development with selected compounds, which have known tis- to 5 μg/kg of 17ß-estradiol.
sue selectivity and different pharmacological estrogen profiles in tissues eg. bone, uterus,
breast and liver, ovaries.

DNAVISION: The main task of DNAVision is to produce gene expression profiling (by DNA
microarrays) of the cell systems generated by the other partners of the consortium and
compare the data to the in vivo situation (from tissues of the ERE-Luc mouse).

BioUetikon Ltd.: BioUetikon will provide the technical expertise to manufacture and quality
control cryopreserved cell banks of up to twenty immortalised mouse cell lines supplied
to BioUetikon by the consortium.

ALTA: Working in close contact with the Coordinator, ALTA’s specific contribution to this
project will be:
• to check the progress of the administrative work;
• to co-ordinate the administrative bodies of the different participants’ institutions; | Cell-medium interface of Sertoli cell aggregates
• to organise technology transfer and follow IPR issues. cultured in RCCS. Cells are strain with DAPI
(Mag 40X).

63
ACRONYM
EXERA
Techniques and methodologies: The steps to
reach the proposed objectives will involve sev-
eral complementary techniques and partner
expertise: cell isolation, conditional immortalisa-
tion, cell banking, 3D-cultures, whole genome
expression profiles, in vitro imaging, in vivo
imaging, and application of 3D-cultures devices
(RCCS Technology).
Cell isolation from tissues of MOUSE-1: Reliable
protocols available inside the partnership will
be applied so as to isolate well differentiated
cells from liver, skin, bone, testis and ovaries
of MOUSE-1 and establish cell cultures with ‘phys-
iological’ estrogen-dependent phenotypes for
immortalisation.
Conditional Immortalisation: This step will be per-
formed by transfection methodologies in 3D and
by using suitable commercially available vectors,
made inducible by specifically modified antibi-
otics devoid of hormonal actions. The immortalis-
ing gene will be switched on for cell production,
and off for characterisation and testing.
Constitution of a cell bank: Immortalised cell cul-
tures that will satisfy the following parameters
will be expanded and controlled for banking.
3D-cultures adapted to grow cells with an unal-
tered estrogen-dependent phenotype: Estrogen-
dependent pathways will be characterised in
3D-cultures. Comparison between hormone stim-
ulation in vitro and in vivo will be performed with
the use of the transgenic marker (luciferase) and
gene expression profiles. Data on the activity of
selected ER-ICs will be produced in each specific
cell line.
Assessment of the 3D-culture systems for the
pharmaco-toxicological characterisation of ER-ICs.
64
Expected results
The corresponding work programme will be
ensured by the important involvement of the
whole partnership and by a high degree of coordi-
nation between 6 private and 3 public institutions.
The expected results that will be scientifically,
socially and economically relevant are as follows:
• the application/adaptation of new 3D-culture
technologies to cell cultures devoted to the
study of ER-ICs;
• the constitution of a cell bank;
• a battery of differentiated 3D cell-based sys-
tems derived from estrogen-reporter mice for
basic and applied research (e.g. pharmacology
and toxicology), public use and industrial use.
Potential applications
The EXERA project seeks to overcome the limita-
tions of conventional in vitro approaches to the
risk assessment of endocrine active compounds.
In addition to scientific and regulatory advances,
EXERA will also promote technological innova-
tions by including research on the applicability of
novel cell based methods and novel end-points to
the assessment of the estrogenic action of ER-ICs.
The developed cell-based systems will become
very useful tools in investigating tissue specific
regulatory pathways and hormone-dependent
physiological processes.
This project is the first attempt to apply the RCCS
technology performance to the systemic analysis
of hormone-dependent pathways. This will be
obtained by using different cell types in standard-
ised conditions. Its possible adaptations to indus-
trial screening procedures will be intensively
exploited. The expected achievement is to fulfil
the need of additional practical, new and easily
standardisable end-points for all the estrogen
hormone target organs.
 Scientific coordinator
Diego Di Lorenzo
Laboratorio di Biotecnologie
Ospedale Civile di Brescia
P.le Spedali Civili 1
25123 Brescia, Italy
dilorenzodiego@yahoo.it
www.spedalicivili.brescia.it
www.med.unibs.it

Partners
Adriana Maggi
Center of Pharmacology
and Biotechnology
University of Milan
Milan, Italy

Kalervo Väänänen
University of Turku
Turku, Finland

Paul Tomkins
Bioserv Ltd.
Athlone, Ireland

Richard Fry
CELLON S.A.
Bereldange, Luxembourg
www.cellon.lu

Mikko Unkila
Hormos Medical
| The RCCS (Rotating Cell Culture System) culturing liver fragments from ERE-tk-Luc mice. Oy Pharmacity
Turku, Finland

Jean-Pol Detiffe
DNAVision S.A.
Charleroi, Belgium
www.dnavision.be

John Milne
BioUetikon Ltd.
Dublin City University
Dublin, Ireland

Aldo Tagliabue
ALTA SRL
Siena, Italy
www.altaweb.eu

65
ACRONYM Contract number: LSHP-CT-2005-037912 | EC contribution: € 1 217 800 | Duration: 36 months
Starting date: 1 December 2006

FASTEST-TB

SUMMARY
It is widely accepted that rapid, cost-
Development and Clinical Evaluation
effective diagnosis of high sensitivity and of Fast Tests for Tuberculosis Diagnosis
specificity is a prerequisite for the pre-
vention and control of tuberculosis (TB);
a global disease in humans, killing more
than 3 million people annually. Methods
and devices currently in use do not meet
these requirements.
Background Aim
New strategies are urgently needed for
combating the problems of TB diagnosis.
The current methods of diagnosis (microscopy, To develop and evaluate high-speed, POC tests
First-generation detection tests using
culture, chest x-ray, PPD, PCR) are inadequate for based on the detection of antibodies and antigens
a novel, high-speed device for quantita-
the diagnosis of tuberculosis, as these are either in body fluids, e.g. whole-blood, serum, urine, spu-
tive measurement of antigens in sputum
too slow, not sensitive enough or too expensive. tum or saliva for the diagnosis of both pulmonary
and urine of TB patients have recently
The usual means of diagnosing TB in the majority and extra-pulmonary TB.
been developed. The device also enables
of developing countries where culture facilities
simultaneous measurement of antigens
and antibodies within 20 minutes. The
are not available is by the detection of acid fast Expected results
bacteria in sputum by direct microscopy. But this
main objectives of this proposal are to:
test is laborious and insensitive as only 40-60 % The outcome of this project will lead to new inex-
• Identify novel antigens using genomic
of all adults with pulmonary TB can be identified pensive and fast diagnostic tests that can be per-
and proteomic approaches.
by the current smear test using Ziehl-Neelsen formed on site without the requirement of any
• Purify sufficient quantities of antigens
staining. complicated or expensive instruments. The tests
and raise antibodies.
will provide results within 15-20 minutes and shall
• Optimise immobilisation conditions for
In low-resource TB endemic countries, poor access be preferably non-invasive.
the specific antigens and antibodies on
to high-quality microscopy services and/or pau-
different Carriers.
• Manufacture and evaluate different, fast
cibacillary nature of pulmonary TB in HIV positive Potential applications
patients results in even lower rates of sensitivity
tests using approximately 6 000 clinical
of AFB (acid fast bacilli) detection. Potential applications of this project results are:
specimens (sputum, saliva, serum, urine)
from TB patients at study sites in Asia,
Thus, the two main problems concerning TB diag- • The new Fast tests shall enable accurate TB
Africa, America and Europe.
nosis are: diagnosis on the spot within 15-20 minutes.
• sputum microscopy, currently the most widely
Such tests and devices would be a major
used method to detect tuberculosis, which is • Inexpensive TB diagnosis shall be feasible in
breakthrough in the early diagnosis and
cumbersome and insensitive, leaving many low-resource settings highly suitable to TB
prevention of tuberculosis. The Coordi-
patients undetected and; endemic countries.
nator (LIONEX, an SME) in co-operation
• bacterial culture, the gold standard, is more sen-
with a WHO centre, a lung hospital in
sitive, but which takes 4-6 weeks to complete, • Antigen detection Fast tests will have consider-
Germany and additional expert scientists
and is too complex for most settings where TB is able advantages over current methods especially
from low-resource, TB-endemic countries
endemic. when dealing with HIV positive populations,
(India, Turkey, Nigeria, Mexico) shall in this
which show reduced immune response.
project, evaluate the clinical potential of
The HIV pandemic has led to a resurgence of TB as
antigen and antibody detection using the
a major public health problem. Immunodeficient • Additional significant advancement shall be
high speed, cost-effective Point of Care
HIV-positive patients are particularly vulnerable made by developing dual HIV-TB tests which are
(POC) tests, with which results can be
to TB and are even more difficult to diagnose than urgently needed in endemic countries in Africa
obtained on site within 20 minutes. Finally,
those who are diagnosed HIV negative. and Asia where HIV infection is increasing daily.
the project also aims to develop TB-HIV
dual antibody detection POC Fast tests.

The outcome of this project will lead to

new inexpensive and fast diagnostic tests
that can be performed on site without the
requirement of any complicated or expen-
sive instruments. The tests will provide
results within 15-20 minutes and shall be
preferably non-invasive.

66
Key words: Tuberculosis, TB diagnosis, serology, antigen discovery, TB-Fast test development, clinical evaluation

ROLE OF SMEs Scientific coordinator

Mahavir Singh
LIONEX Diagnostics & Therapeutics GmbH
The project is coordinated by LIONEX GmbH, an SME dedicated to the prevention and con- Inhoffenstraße 7
trol of TB. The project’s efforts are focused towards the development of completely new and 38124 Braunschweig, Germany
info@lionex.de
fast tests for the diagnosis of TB, which shall be of particular use in developing countries www.lionex.de
where several million people are infected with TB each year. Several of the project’s partners
come from developing countries. The coordinating SME will have a pivotal role in enhancing Partners
the communicating with endemic countries.
Françoise Portales
Institute of Tropical Medicine
Antwerp, Belgium
www.itg.be

Helmut Bloecker
Helmholtz Centre for Infection
Research (previously GBF)
Department of Genome Analysis
Braunschweig, Germany
www.genome.gbf.de

Harald Hoffmann
Institute of Microbiology
and Laboratory Medicine
WHO-reference laboratory for
Tuberculosis and Mycobacteria
München-Gauting, Germany
www.asklepios.com/Gauting

Olcay Yegin
Akdeniz University Medical School
Department of Pediatric Immunology
Antalya, Turkey
www.akdeniz.edu.tr

P. R. Narayan, Alamelu Raja

Tuberculosis Research Centre
Chetput, Chennai, India
www.trc-chennai.org

Gertrud Biersack
Sacred Heart Hospital
Lantoro, Abeokuta
Ogun State Nigeria
www.geocities.com/sacredheartabeokuta

Jürgen Knobloch
Institut für Tropenmedizin
Universitätsklinikum Tübingen
Tübingen, Germany
www.med.uni-tuebingen.de/
tropenmedizin/index.html

Iris Estrada
Dept. of Immunology
National School of Biological Sciences
Santo Tomas, Mexico
© Shutterstock

67
ACRONYM Contract number: LSHG-CT-2006-037683
Starting date: 1 January 2007
FGENTCARD
www.fgentcard.eu
SUMMARY
The focus of the consortium project is
to define biomarkers and novel diag-
nostic tools for risk factors for coronary
artery disease (CAD) (glucose intoler-
ance, insulin resistance, hypertension,
dyslipidaemia and obesity), using func-
tional genomic and genotyping technolo-
gies along with the wealth of knowledge
arising from mammalian genome annota-
tions. The consortium is preparing innova-
tive infrastructure of both techniques and
materials that provide strategic support
for CAD quantitative genetic studies in
animal models and humans. FGENTCARD
is using state of the art functional
genomic and genetic technologies includ-
ing NMR metabonomic and automated
proteomic profiling of biofluids and organ
biopsies, microarray based gene tran-
scription profiling and original technolo-
gies for identifying disease susceptibility
loci. Results from this research will pro-
vide resources for extension and valida-
tion of CAD biomarkers in other models
and human cohorts, and will exemplify
multidisciplinary strategies which can be
applied to other disease areas.
| EC contribution: € 3 000 000
Functional GENomic diagnostic Tools
for Coronary Artery Disease
Background
The completion of the genomic sequence of
many mammalian species and progress in high-
throughput genotyping and gene expression
profiling technologies are amongst the most sig-
nificant recent advances in biomedical science.
With the growing number of cohorts for case-con-
trol genetic studies, these resources and tools
have a wide range of applications for localizing
chromosomal regions associated with disease
susceptibility, identifying disease causative DNA
variants and characterizing mechanisms regulat-
ing gene expression in health and disease. A par-
ticularly important application is in tackling the
genetic cause of increasingly frequent disorders
in western society, including CAD, a growing
health and societal concern in the general popu-
lation. The genetic causes of CAD risk factors,
which associate diabetes, hypertension, dyslipi-
daemia and obesity, will be addressed through
the definition of biomarkers derived using func-
tional genomic and genotyping technologies
applied in animal models of CAD and large cohorts
of patients.
Aim
The general aim of FGENTCARD is to apply func-
tional genomic and genotyping technologies
along with the wealth of knowledge arising from
mammalian genome annotations to defining
novel diagnostic tools for risk factors of glucose
intolerance, insulin resistance, hypertension, dys-
lipidaemia and obesity, which are key pathophys-
iological elements in CAD. FGENTCARD results
utilize the power of functional genomic technolo-
gies to tackle these increasingly frequent and
prevalent inherited diseases. The proposed stud-
ies will ultimately generate fundamental knowl-
edge on the impact of functional genomics to
identify disease biomarkers and test their use for
disease prediction.
68
| Duration: 36 months
Expected results
FGENTCARD will deliver technological and ana-
lytical tools applied to the definition of CAD bio-
markers through genetic studies in clinical
cohorts and rodent crosses, which will be used to
map CAD susceptibility loci and genes providing
targets for gene cloning and entry points for drug
development. A set of standard operation proce-
dures will be developed for the detection of CAD
biomarkers for genetic and clinical studies in
other cohorts and other disease areas. This pro-
gram will design and utilize methods for multi-
modal gene expression profiling and subsequent
data integration that can maximize the power of
genetic linkage and association analyses.
Potential applications
Advancement in knowledge, technological plat-
forms and analytical tools will contribute to a bet-
ter understanding of genetic systems that
underpin multifactorial diseases. Progress in this
area will play a key role in providing the essential
tools for the development of strategies to identify
genes for epidemiological important disorders
and targets for the generation of novel therapies.
Overall, the potential wealth of information
obtained on gene expression represents novel
challenges in quantitative genetics and ultimately
significant advances for disease diagnosis and
prevention. Knowledge of the effects of genetic
variations on metabolic processes and metabo-
type regulation will have an important impact in
the field of polypharmacology.
Key words: functional genomics, atherosclerosis, metabonomics, nuclear magnetic resonance,
transcriptomics, proteomics, rat, mouse

ROLE OF SMEs Scientific coordinator

Dominique Gauguier
University of Oxford
The project provides SMEs with original biological material and data from collections of The Wellcome Trust Centre
case control cohorts and genetic crosses between animal models. These can be used to for Human Genetics
Roosevelt Drive Oxford OX3 7BN
test their technologies in deriving disease biomarkers and CAD susceptibility genes. An United Kingdom
important aspect of the research project lies in the application of a multidisciplinary gdomi@well.ox.ac.uk
approach, allowing SMEs, specialised in technologies designed to test a specific level of www.well.ox.ac.uk/~gdomi
gene expression control, to obtain data from a comprehensive screening of patterns of
gene expression regulation in health and disease, ranging from genetic polymorphism, to Partners
transcriptome, proteome and metabonome. This approach is designed to promote efforts
towards research and innovation and to facilitate collaborations between SMEs and Pierre Zalloua
American University of Beirut,
between academic groups and SMEs. The two SMEs involved in the project, namely Department of Internal Medicine
Metabometrix Ltd. and IntegraGen S.A., combine very different expertise in metabo- Faculty of Medicine
nomic technologies (Metabometrix) and disease gene mapping (IntegraGen), which will Beirut, Lebanon
synergistically be applied to the chromosomal mapping of CAD biomarkers.
Mark Lathrop
Centre National de Genotypage
Metabometrix is a spin-off company built on the skills of the world’s pre-eminent Evry, France
metabonomics research team at Imperial College, London, and experienced scientists
Jeremy K Nicholson
from the UK and US pharmaceutical industries. The group’s portfolio of intellectual and Imperial College
technical advances is unique and underpins a substantial lead in the field. The company Chemical and Molecular Systems Biology
has a proprietary platform of metabonomics technologies for generating, classifying and London, United Kingdom
interpreting metabolic information from biological fluids and tissues. Ulla Grove Sidelmann
NovoNordisk A/S
Methods that IntregraGen has developed for the purpose of genome-wide linkage studies Malov, Denmark
are particularly well adapted to the research of the genes predisposing to CAD pathophysio-
Jorg Hager
logical components, namely late onset multifactorial diseases. The techniques will be IntegraGen S.A.
properly used for the identification of the genes predisposing individuals to CAD and Evry, France
related phenotypes. The company will be in the best possible position to estimate the www.integragen.com
relevance of the results obtained and implement the pertinent molecular diagnostic tests. Frank Bonner
In combination, the two SMEs play crucial and synergetic roles in the FGENTCARD project. Metabometrix Ltd.
London, United Kingdom
www.metabometrix.com

| The consortium utilises

modern functional genomic
and genetic technologies to
map etiological biomarkers
of coronary artery disease in
animal models and humans.

69
ACRONYM Contract number: LSHB-CT-2006-037661 | EC contribution: € 2 793 724 | Duration: 36 months
Starting date: 1 November 2006

GLYFDIS
www.glyfdis.org

SUMMARY
Developing effective tools to screen for
Glycans in Body Fluids- Potential
cancer is an important endeavor and there for Disease Diagnostics
is much research taking place to develop
these tools. GLYFDIS project’s objective is
to develop methods for earlier diagnostic
and effective disease screening of stomach
and pancreatic cancer that will lead to bet-
ter treatment outcomes. Early diagnosis of
cancer is of far greater prognostic impor-
Background Aim
tance than any attempts to treat the dis-
ease in its late stages. Even in cases where
Cancer is a significant burden on individuals, fam- GLYFDIS’ main objectives are:
the eventual outcome cannot be changed,
ilies and society. The economic impact of cancer is
treatment is simpler and quality of life
substantial. In 2002, the overall cost of cancer, as • To optimise high-throughput methods of glycan
improved for those cases where early
published by the National Cancer Institute, was analysis for the diagnosis of stomach and
diagnosis is achieved. For this purpose,
172 billion US dollars. This does not account for pancreatic cancer by the analysis of glycans
GLYFDIS proposed a method of a simple
the psychological toll that it takes on individuals in blood.
noninvasive blood testing. Accurate
and families.
monitoring of a cancerous state following
• Identifying cancer associated glyco-markers in
diagnosis can significantly contribute
Early detection and diagnosis of cancer is based serum samples of stomach and pancreatic
to prognosis determination and on-line
on the observation that treatment is more effec- cancer patients.
evaluation of therapeutic regimens.
tive when the disease is detected earlier in its
natural history, prior to the development of symp- • Developing and validating protocols for lectin-
The most widespread and diverse post-
toms than in an advanced stage. Diagnosis of can- based microarrays intended for large scale
translational modification is glycosylation.
cer in the early stages of the disease influences screening of cancer associated glyco-markers
The location and variation of glycans place
many aspects of life. It can significantly decrease in serum samples.
them in a position to mediate cellular
cancer-associated morbidity and mortality and to
and intracellular signalling events, as
well as participate in different biological
relieve the burden from patients, their families Expected results
and the society. Accurate monitoring of a cancer-
processes including pathology states such
ous state following diagnosis can significantly • To identify biomarkers using glycomic and pro-
as cancer. Therefore, the project proposes
contribute to prognosis determination and on-line teomic methods together with computer based
to use analyses of glycans for identifying
evaluation of therapeutic regimens. Developing algorithms.
novel biomarkers that can be used for
effective tools to screen for cancer is an important
the diagnostics and monitoring of cancer.
endeavour and there is much research taking • To develop a non-invasive, modest, diagnostic
place to develop these tools. The goal is to detect kit that will identify specific markers for cancer
the cancer when it is localised to the organ of ori- in the blood.
gin without invasion of surrounding tissues or
distant organs. • Constructing a website and a glycome bio-bank
integrating GLYFDIS results and serving as basis
The GLYFDIS project will make use of glycans. for a continuously growing public glycome data-
Their diversity, compared to genome or proteome, bank.
makes the glycans ideal for diagnosis and moni-
toring of cancer. Cancer-associated changes in the • Dissemination of the information to the scientific
glycome of the tumoural tissue are very frequent. community and community at large.
Currently one of the main obstacles is the lack of
sufficient technology. Glycome-analysis technolo- Potential applications
gies today fall behind the rapidly developing
genome- and proteome-analysing technologies. The project will generate knowledge relevant for
non-invasive diagnosis of cancerous states with
The group hopes to identify biomarkers that can the effort in developing a standard protocol for
be used to develop a non-invasive method for the diagnosis of serum samples.
early diagnosis of stomach and pancreatic cancer
based on glycan analysis.

70
Key words: diagnostics, glycome, blood, glycan, mass spectrometry, disease markers

ROLE OF SMEs Scientific coordinator

Angel Porgador
Ben-Gurion University of the Negev
RNTech Beer-Sheva, Israel
RNTech is an SME specialising in early stage diagnosis of digestive tract cancers with spe- angel@bgu.ac.il
www.bgu.ac.il
cial focus on colorectal and pancreatic cancer. The company operates a dedicated biobank
of biological samples selected from patients that have undergone surgery for the removal of Partners
digestive tract solid tumour.
Rakefet Rosenfeld
Procognia Ltd.
RNTech’s role in GLYFDIS has three facets: Ashdod, Israel
• providing biological samples collected from pancreatic and stomach cancer patients and www.procognia.com
healthy control subjects for the discovery and validation phases of the project;
Pauline Rudd
• contributing to the project database by providing genomics data on pancreatic cancer NIBRT
patients as well as clinical data on all selected patients and healthy subjects and partici- Dublin, Ireland
pating in the bio-statistical and bio-informatics treatment of such data and research www.nibrt.ie
results;
Jasna Peter-Katalinic
• providing with its network of clinical oncologists and cancer biology specialists to the Muenster University
validation of identified potential biomarkers. Muenster, Germany
www.uni-muenster.de/en
As any other partner, RNTech will also contribute to the management and the dissemination Julien Taieb
plan of the project. RNTech Diagnostics SPRL
Charleroi-Gosselies, Belgium
Procognia www.rntech.com
Procognia has developed a lectin-array based technology for rapid analysis of glycosylation
profiles of intact glycoproteins. The array contains 25-30 well-characterized lectins (carbo-
hydrate binding proteins) with overlapping specificities. The binding of a glycoprotein to the
array results in a characteristic fingerprint that is highly sensitive to changes in the protein’s
glycan composition. The large number of lectins, each with its specific recognition pattern,
ensures high sensitivity to changes in the glycosylation pattern. Automatic algorithms were
constructed for deconvoluting these signals into a glycan profile output. The major advan-
tages of this technology in comparison to traditional methods of glycoanalysis are its short
analysis times, the relatively low protein amount needed for analysis, the possibility to
analyse multiple samples in parallel, and the relatively low costs compared to the classical
analysis methods (HPLC/MS).

A highly sophisticated, automated platform (GlycoScope) was first developed for use in the
biopharmaceutical industry for the analysis of recombinant glycoprotein drugs. By tailor-
ing algorithms for various protein families, this product provides accurate, quantitative
glycoanalysis for single proteins.

In addition, Procognia is developing a line of products for the life science and academic | Vision of MALDI-TOF-MS. © Danny Machlys, BGU.
research market. The products are a line of off-the-shelf kits for glycoanalysis, distributed
by QIAGEN. The first product, Qproteome™ GlycoArray, launched in 2006, provides a rapid
and simple tool for glycoanalysis of glycoproteins. This kit can be used without sophisticated
equipment, and generic interpretation algorithms provide semi-quantitative glycoanalysis
for purified glycoproteins.

The second product will be launched in 2007 for analysis of global glycosylation patterns of
membrane protein extracts. The kit is intended for analysing global changes in glycosyla-
tion patterns in extracts of cell membrane proteins of cultured mammalian cells, with the
aim of enabling characterisation of glycosylation-related biological effects.

As a partner in GLYFDIS, Procognia will optimise the existing technology for analysis of
global glycosylation pattern to allow the characterisation of complex protein mixtures in
serum from healthy donors and donors with pancreatic or stomach cancer.

71
ACRONYM Contract number: LSHC-CT-2006-037737 | EC contribution: € 1 715 000 | Duration: 36 months
Starting date: 1 March 2007

HI-CAM
www.hi-cam.org

SUMMARY
The purpose of the project is the develop-
Development of a high-resolution Anger camera
ment of a compact and high-resolution for diagnosis and staging of cancer diseases
Anger camera to be used in clinical and
research environments and which allows
based on state of the art detector technology
earlier and more reliable diagnosis and
therapy planning of cancer diseases in
specific applications where high overall
spatial resolution (less than 3 mm) and
system compactness (less than 10x10 cm2
field of view) are required.
Background higher than 20cpm/uCi. Pinhole collimators will
be also realised;
The state-of-the-art in the field is represented by • a very compact geometry of the detection mod-
The gamma camera is based on the well-
a range of commercial systems, usually having ule, based on a thin substrate where the SDDs
established Anger architecture, where
large field detectors (~ 40x50 cm2). These sys- array and VLSI readout circuits will be assem-
a collimator acts as a mechanical sieve for
tems are best exploited while performing whole- bled, and a single CsI(Tl) crystal (potentially
incoming gamma photons, a continuous
body SPECT studies since their large, heavy substituted by the more recently introduced
scintillator uses the energy of each selec-
PMT-based detector heads and bulky gantries LaBr3:Ce) will be coupled to the photodetector
tively passed gamma photon to generate
present difficulties in operating close to the array;
visible photons, and an array of photode-
patient’s skin for dedicated studies of specific, • the introduction of a thermoelectric system to
tectors emits electric signals in response
small tissues such as in parathyroid imaging, attain moderate cooling (~ -20 °C) during opera-
to the absorption of the visible photons.
brain scanning or investigation of kidney cancer tion of the gamma camera;
The improvement of performances is
in infants. In a realistic clinical setting, at an • the development of dedicated VLSI electronics
based on the use of a particular type of
imaging distance usually rather greater than for amplification and filtering of the detector sig-
photodetector, the Silicon Drift Detector
20 cm, the overall effective spatial resolution is nals, followed by processing electronics based
(SDD), which has recently demonstrated
typically 10-16 mm (7-10 mm for brain studies). on FPGA for the event reconstruction;
its ability to provide better performanc
When a single detector head is used for dedi- • the design of a compact assembly of the com-
with respect to the commonly used
cated scintigraphic studies of small organs, per- plete Anger Camera. The compactness of the
photomultiplier tubes.
mitting a closer imaging distance, the overall assembly will allow ease of positioning of the
effective spatial resolution is limited by both the instrument close to the patient’s body surface;
The camera is intended for use both sin-
intrinsic spatial resolution of the system and the • the realisation of image-reconstruction algo-
gle-handedly for planar scintigraphic stud-
collimator. rithms and user interface software running on
ies and inserted in an annular holder
a common personal computer.
(gantry) of small diameter for SPECT imag-
ing. Thanks to its compactness and high
Aim
spatial resolution, it offers potential appli-
Expected results
The aim of the project is therefore the develop-
cations in early diagnosis of cancer dis-
ment of a new compact and high position resolu- • Development of large-areas low-noise Silicon
eases affecting areas of the human body
tion (< 1 mm) gamma camera based on the new Drift Detectors.
which can be hardly imaged with the large
SDD photodetector technology. The first techno-
and heavy imaging heads and gantries of
logical objective is the development of an • Development of high-resolution collimators.
commercial Anger cameras. The camera
extended array of SDDs with large cell size (1 cm2),
to be developed in the present project
characterised by high detection efficiency to the • Development of a high-resolution and compact
also offers promising perspectives of inte-
scintillation light and low electronic noise. The Anger Camera based on state-of-the-art tech-
gration at the system level with MRI
low noise level is a result of specialised advanced nologies.
instrumentation, thanks to the relative
semiconductor processing, as well as of the inte-
insensitivity of the SDD photodetectors
gration of an on-chip JFET in the detector chip, • Improved diagnostic capabilities thanks to the
to large magnetic fields.
which allows us to fully exploit the intrinsic low use of the camera.
capacitance of the SDD, by the minimisation of
The research activity will be organised as
follows: the first two years of the three-
parasitic capacitances of the connection between Potential applications
detector and electronics.
year project will be dedicated to the
• Improved possibility to implement an effective
development of the SDD-based Anger
The other key technological objectives addressed therapy with higher capability to detect as small
camera, while the third year will be dedi-
by the project are: as possible concentrations of tumour cells.
cated to the experimentation of the cam-
• the realisation of a high-resolution collimator.
era in selected imaging applications
The aim is to obtain a parallel hole collimator • Effective imaging on reduced volume of the
related to cancer diagnosis and research.
whose spatial resolution equals ~2 mm at an biological tissues: less than 10 x 10 cm2 area of
imaging distance of 5 cm with a sensitivity kept the planar view (in scintigraphic investigations

72
Key words: technological sciences, health sciences, physical sciences, medical imaging

ROLE OF SMEs Scientific coordinator

Carlo Fiorini
Politecnico di Milano
Two SMEs, L’accessorio Nucleare S.R.L. and Nuclear Field Holland B.V., are involved with Via Golgi 40
key technical aspects of the development of the HICAM gamma camera. 20133 Milano, Italy
carlo.fiorini@polimi.it
www.elet.polimi.it
L’ACN is a company currently operating in the market of instrumentation for nuclear medi-
cine and will be particularly involved with the development of the gamma camera instru- Partners
mentation, taking as a start-point the gamma-ray detector developed by the other partners.
Carla Finocchiaro
Adapting the technology currently employed to the results of the present project, L’ACN will CF consulting Finanziamenti
be ready to release a commercial system within a very short time for planar scintigraphy Unione europea srl
applications. Milano, Italy
www.cf-consulting.it
The HI-CAM project will also produce a potential development and market impact for the Leonardo Pepe
Nuclear Field Holland (NUFI) company, which is particularly interested in launching a very L’accessorio Nucleare S.R.L. (L’ACN)
high resolution (VHR) collimator, similar to the one developed within HI-CAM, onto the Cerro Maggiore (MI), Italy
www.acn.it
world market for use in diagnostic medical imaging. With the potential to create an intrinsic
resolution of 1 mm, which is the aim of the HI-CAM project, the goal of NUFI is to create Pieter van Mullekom
a 0.5 mm hole collimator which would suit the resolution of the HI-CAM camera. In doing so, Nuclear Fields International B.V.
Vortum Mullem, The Netherlands
the project will develop the next generation commercial, low cost collimators, giving OEM www.nuclearfields.com
companies the possibility to move in this direction and begin redesigning their systems.
Lothar Strüder
Max-Planck-Gesellschaft zur Foerderung
der Wissenschaften eV
Münich, Germany
with one single imaging head); less than 10 cm • Thyroid cancer, particularly differentiated carci- www.mpg.de
total extent on the coronal plane of the patient’s nomas, with 99mTc-perthecnetate.
Brian Hutton
body being imaged by the acquired scans (after University College London
appropriate rotation of the camera/s on the • Parathyroid cancer with 99mTc-sestamibi for London, United Kingdom
annular holder in the tomographic arrangement). preoperative localisation of parathyroid ade- www.uclh.nhs.uk
nomas with the aim of surgical planning in Ugo Guerra
• Measurements on anatomical sites of the target MIP interventions (minimally invasive parathy- Ospedali Riuniti di Bergamo
which usually lead to severe space constraints roidectomy). Bergamo, Italy
during acquisition of the scan. www.ospedaliriuniti.bergamo.it
• Breast cancer with 99mTc-labelled lipophilic Ignasi Carrió
• Improved use of imaging instrumentation in cations (SestaMIBI or tetrofosmin). The most Institut de Recerca de l’Hospital
those conditions where the patient’s age, condi- promising application of the proposed system de la Santa Creu i Sant Pau
Barcelona, Spain
tion or physical disabilities (e.g. patient on concern its use in preoperative or postoperative www.santpau.es
wheelchair) prevent an effective use of large sites.
detector heads and gantries without compro- Giovanni Lucignani
mising patient comfort. In addition, the project offers innovative Università degli Studi di Milano
Milano, Italy
approaches to the diagnosis of tumours in infants www.unimi.it
• Brain tumours. and children.

| Principle scheme of the Anger camera

based on Silicon Drift Detectors technology
developed in HICAM.

73
ACRONYM Contract number: LSHC-CT-2007-037642 | EC contribution: € 3 635 200 | Duration: 36 months
Starting date: 1 March 2007

HighReX
www.sectra.se/medical/mammography/highrex

SUMMARY
Breast cancer is currently the most com-
High Resolution X-Ray Imaging for Improved
mon cause of death from cancer for Detection and Diagnosis of Breast Cancer
women below seventy years of age and
currently over 100 million European
women are screened every year for early
detection through mammography. The
objective of the proposal is to increase
the efficiency in detection and diagnosis
of breast cancer and thus to decrease the
Background their age, are significantly more radiation sensi-
mortality in breast cancer. To achieve this,
tive compared to older women. Due to the limi-
we will develop novel imaging methods
The incidence of breast cancer currently increases tations of the current technology, in many EU
based on recent results in the research
in all European countries and according to the countries breast cancer screening is presently
fields of nanotechnology, x-ray optics,
European Breast Cancer Network (EBCN), every only offered to women older than 50.
detector technology and integrated
year 50 000 women are diagnosed with breast
electronics. The new modality will be
designed by leading European industry
cancer. Around 40 % of these women will die from Aim
the disease, making it the second most common
and SMEs in these areas and develop the
cause of death for women between the age of 20 The HighRex project intends to solve the current
only commercially available European
and 70. The most efficient weapon against breast dilemma in mammography by increasing the
detector platform for digital mammogra-
cancer is currently early detection through mam- image quality in terms of contrast and spatial res-
phy today into a leading technology plat-
mography screening. An early detection makes olution while lowering the radiation dose. This will
form for tomorrow. The novel method will
the subsequent therapy more successful and also be achieved by using results from fundamental
provide significantly increased contrast
mitigates bi-effects and facilitates breast con- research in nano-technology, x-ray optics and
and spatial resolution compared to cur-
serving surgery in contrary to mastectomy. There detector technology obtained during the last
rent state-of-the art breast imaging
is currently scientific evidence for a decrease of years. The currently only European detector plat-
through elimination of noise from elec-
mortality between 30 and 40 % in the screened form commercially available for digital mammog-
tronics as well as from overlapping tissue
population. raphy will be drastically improved and developed
and by way of utilizing the signal more
into a detector system for the next generation
efficiently through fast single photon
Currently, film is the most common image recep- breast imaging equipment.
counting integrated circuits. To make
tor in mammography, but this is now being
sure that the project targets the right
issues in breast imaging, experienced
replaced by digital mammography. Expected results
mammography doctors from several
In mammography screening 70-90 % of the can- An increase in breast cancer detection rate in
European breast imaging centres are
cers are detected. The undetected cancers are screening of just 1 % in Europe would mean that
involved in the project and they will also
mainly in women with dense breasts where the an amount of cases in the order of 500 otherwise
test and evaluate the new imaging sys-
contrast resolution of state-of-the-art equipment undetected cases would be diagnosed annually,
tem and compare it to current state-of-art
is limited by overlapping tissue. Recent results with a potential of 100 to 300 lives saved. It may,
mammography as well as ultrasound and
from the so called ACRIN trial show that this chal- however, be expected that the increase in detec-
MR imaging of the breast. The clinical tri-
lenge can to some extent be met with the advent tion rate is significantly higher than 1 %, maybe
als will involve an enriched population
of digital mammography. The improvements are, even exceeding 10 %.
of symptomatic women and the poten-
however, modest and the problem remains. What
tial impact on European screening for
and diagnosis of breast cancer will be
makes the problem worse is that the risk for Potential applications
breast cancer is almost a factor three higher for
estimated from the results.
women with dense breasts. Competitiveness of the Highrex European tech-
nology platform will manifest itself stronger in
One way of solving the problem would be to the second generation of mammography and the
increase the radiation dose to increase contrast proposed project will be able to deliver a stan-
resolution. However, in dense breasts, this would dard for 3D mammography that will be unsur-
also increase the noise caused by overlying tis- passed for quite some time. reason to believe
sue. Moreover, the radiation dose in mammogra- that the photon counting advantages in mam-
phy is a growing concern, and increasing the mography would also be beneficial in other imag-
radiation dose would mean an increased risk for ing applications such as CT and chest x-ray
radiation induced cancers. This is particularly true imaging, and this project has the potential to pro-
for women below the age of 50 who on average vide the example needed for the technology to
have much denser breasts and who, because of spread also to those areas.

74
Key words: mammography, breast imaging, photon counting, tomosynthesis, contrast mammography, breast cancer, dual-energy

ROLE OF SMEs Scientific coordinator

Mats Danielsson
Sectra Mamea AB
The three participating SMEs, Detection Technology (DEETEE), Silex Microsystems AB Kistagången 2
(SILEX), and Artinis Medical Systems (ARTINIS) will be heavily involved in the design and SE-164 40 Kista, Sweden
Mats.Danielsson@sectra.se
assembly of every crucial part of the proof-of-principle prototypes. DEETEE will be respon- www.sectra.com/medical
sible for designing the required application specific circuits as well as the X-ray sensors;
SILEX will design the X-ray optics while ARTINIS will design phantoms for evaluation of Partners
the prototypes. If the proposed research is successful, the proof-of-principle prototypes
Mikko Juntunen
will be developed into real products and the participating SMEs will be in an excellent Detection Technology Inc.
position to take part in volume production as well as in continuous development of the Ii, Finland
product. The competitiveness of the SMEs will further be strengthened through the www.deetee.com
increased capacities developed within the project, as well as through the international Edvard Kälvesten
contacts created and a network that will facilitate problem solving in the future and form Silex Microsystems AB
a basis for other cooperation projects. The know-how gained in the project is likely to be Järfälla, Sweden
sufficiently generic to have the possibility of being applied also in other areas, e.g. in www.silexmicrosystems.com/pages
developing imaging modalities for other examinations than mammography. Roeland van der Burght
Artinis Medical Systems B.V.
Zetten, The Netherlands
www.artinis.com

Matthew Wallis
Addenbrooke’s Hospital
University of Cambridge
Cambridge, United Kingdom

Kenneth Young
Royal Surrey County Hospital NHS Trust
Guildford, United Kingdom

Walter Heindel
Münster Universität
Münster, Germany

Ulrich Bick
Charité Universitätsmedizin Berlin
Humboldt University
Berlin, Germany

Brigitte Séradour
Association pour la Recherche
et le Dépistage des Cancers du Sein
Marseille, France

Nico Karssemeijer
Radboud University
Nijmegen, The Netherlands

Ruben van Engen

| Vision of clinical application for breast
cancer detection with 3D photon counting
tomosynthesis based on research in the
Highrex project.
Stichting Landelijk Referentie
Centrum voor Bevolkingsonderzoek
Nijmegen, The Netherlands
Karin Leifland
Capio Diagnostics Radiology Sweden
Stockholm, Sweden

Ulf Strand
Avalon Product Development
Helsingborg, Sweden

75
ACRONYM Contract number: LSHP-CT-2007-037760 | EC contribution: € 1 103 505 | Duration: 36 months
Starting date: 1 April 2007

HIVResInh

SUMMARY
HIV-1 can develop multidrug resistance in
Preparation and Identification of New HIV
patients receiving various combination Reverse Transcriptase Inhibitors Targeted Against
chemotherapies. This is one of main prob-
lems in anti-HIV/AIDS chemotherapy. To
HIV Strains Resistant to anti-HIV/AIDS drugs
identify compounds active against HIV-1
drug-resistant strains, project partners
plan to synthesise and investigate the
structure, conformation and selected
physicochemical and biological proper-
Background Aim
ties of a range of new and known, modi-
fied 2’, 3’-dideoxynucleoside analogues.
Human immunodeficiency virus (HIV) encodes for The general aim of this project is to identify and
an RNA-dependent DNA polymerase (reverse prepare and identify new potential drugs from the
Compounds of this type should act as
transcriptase, RT), but not the specific enzymes class of new modified 2’,3’-dideoxynucleosides,
competitive drug-resistant reverse tran-
required for the phosphorylation of 2’,3’-dideoxy- active against HIV-1 drug-resistant laboratory and
scriptase (RT-Res) inhibitors. Slow releas-
pyrymidine and purine nucleosides. To exert clinical strains.
ing forms of these compounds (prodrugs)
antiviral activity, these analogues must undergo
will also be prepared. Drug-resistant
reverse transcriptases will be obtained
a three-step phosphorylation by host cell kinases Expected results
and/or be metabolised by other enzymes. Their
from engineered HIV-1 drug-resistant
5’-triphosphates act as RT competitive inhibitors To obtain new modified 2’,3’-dideoxynucleosides
mutants, as well as by recombinant tech-
and/or DNA terminators. Since RT is essential to and their phosphates, highly active drugs against
niques. Interactions of synthesized com-
HIV replication, the development of RT inhibitors drug-resistant HIV strains, and to detect their
pounds with the wild type HIV-1 RT, as
is a key strategy in the fight against AIDS. physico-chemical and biological properties. Results
well as with HIV-1-Res RT, will be investi-
However, drug resistance emerges rapidly with will be disseminated through patenting.
gated and potent inhibitors will be sub-
these nucleoside-based inhibitors (NRTIs).
jected to antiviral activity determinations
in cell cultures and in vitro cytotoxicity.
Potential applications
At present, the emergence of HIV-1 variants resist-
ant to standard drugs is one of the major obsta- After obtaining positive biological results,
Structure-activity relationships will be
cles to chemotherapy of HIV-1 infection. HIV-1 can patents and publications will be submitted to
performed and selected RT inhibitors will
develop multidrug resistance in patients receiving a pharmaceutical firm (SME) for further investiga-
be subjected to determination of com-
various combination chemotherapies. Therefore tions in animals and in the clinic, allowing poten-
plete cross-resistant profiles in labo-
the development of novel compounds especially tial outlicensing of the above-mentioned drugs.
ratory and clinical HIV-1 strains from
modified 2’,3’-dideoxynucleosides, which are
documented clinical context of resistance.
active against wild-type as well as multidrug-
resistant variants, is urgently needed.
Investigation of in vitro viral escape will
also be determined. Long-term anti-
retroviral therapy often results in toxic
adverse events attributable to mitochon-
drial damage due to the inhibition of DNA
polymerase γ synthesis and the reduction
of cellular energy production.

The toxicity of the new drugs will be evalu-

ated by determining the inhibitory proper-
ties (IC50 ) and insertion and exonucleolytic
removal of new nucleoside analogues by
DNA polymerase γ. Finally, selected active
compounds with low in vitro cytotoxicity will
be subjected to in vivo (in mice and/or rats)
pharmaco-toxicological investigations.

76
Key words: chronic diseases, virology, anti-HIV and AIDS drugs

ROLE OF SMEs Scientific coordinator

Tadeusz Kulikowski
Instytut Biochemii iBiofizyki PAN
This project comprises one SME, InPheno AG, which plays a key scientific role in the project. 5a Pawinskiego Street
Researchers at InPheno have a solid background in pre-clinical profiling of anti-HIV drugs. 02-106 Warsaw, Poland
tk@ibb.waw.pl
InPheno will mainly contribute to the determination of a complete cross resistance profile www.ibb.waw.pl
of new HIV inhibitors in laboratory strains and variants from clinical context, as well as
investigating whether the new inhibitors provoke viral escape in vitro. InPheno expertise is Partners
centred around preclinical profiling of HIV resistance in diagnostics and drug discovery,
Kazimierz Kita
which will provide an important contribution to the critical mass of the project. Instytut Przemyslu Organicznego
Oddzia w Pszczynie
Pszczyna, Poland
www.ipo.pszczyna.pl

Marek Figlerowicz
Instytut Chemii Bioorganicznej PAN
Poznan, Poland
www.ibch.poznan.pl

Patricia Laquel-Robert
UMR 5097 CNRS/Université Bordeaux 2
Bordeaux, France
www.cnrs.fr

Andrzej Piasek
Instytut Medycyny Doswiadczalnej
i Klinicznej im. M. Mossakowskiego PAS
Warsaw, Poland
www.cmdik.pan.pl

Francois Hamy
In Pheno AG
Basel, Switzerland
www.inpheno.com

Kazimierz Kita
Instytut Przemyslu Organicznego
Oddzial w Pszczynie
Pszczyna, Poland
www.ipo.pszczyna.pl

© Shutterstock

77
ACRONYM Contract number: LSHP-CT-2007-037301 | EC contribution: € 2 250 000 | Duration: 36 months
Starting date: 1 January 2007

HIVSTOP

SUMMARY
The Acquired Immunodeficiency Syndrome
Development of an Effective RNA
(AIDS) caused by infection with the human Interference-Based Anti-HIV-1 Therapy
immunodeficiency virus type 1 (HIV-1) is
a pandemic continuing to grow at an
Using an SV40-Derived Vector
alarming rate, despite the availability of
highly active anti-retroviral chemotherapy
(HAART). The World Health Organisation
(WHO) and European Union (EU) therefore
launched a co-ordinated action program to
Background Aim
combat poverty-related communicable
diseases, including AIDS.
HAART can be effective; however, resistant viral To develop a novel therapy for the treatment of
strains do emerge. Eventually, these resistant individuals infected with HIV-1. This therapy
In this project a novel therapy for the
variants can cause AIDS in treatment-resistant involves the application of RNA interference
treatment of individuals infected with
patients. A novel therapy that involves the appli- (RNAi) to prevent productive infection of new cells
HIV-1 is to be developed. This therapy
cation of RNA interference (RNAi) to prevent pro- with HIV-1 and so eventually cure infection.
involves the application of RNA interfer-
ductive infection of new cells with HIV-1 and thus
ence (RNAi) to prevent productive infec-
eventually cure infection is the aim of this project. An SV40-based vector will be used, and the costs
tion of new cells with HIV-1 and therefore
So far, RNAi-based inhibition of HIV-1 replication and complexity will be kept low. Therefore a pro-
eventually cure infection. An SV40-based
has been accomplished through the introduction ducer cell line will be generated, to produce viral
vector will be used to transfer the thera-
of virus-specific, synthetic short double-stranded vector particles at high titres and focus on
peutic anti-HIV-1 sequence to T-cells of
RNAs. These are short interfering RNAs or DNA a single-administration, long-lasting therapeutic
HIV-1 infected individuals in order to
constructs encoding short hairpin RNAs. However, molecular vaccination.
result in long-lasting improvements of
their use as therapeutic antiviral against HIV-1 is
their condition. SV40 vectors are intrinsi-
cally safe, transfecting both non-dividing
limited because of the rapid emergence of virus Expected results
escape variants.
and dividing cells. In order to use this
• Proof of safety and efficacy of the developed
therapy in developing countries it is
In order to solve this durability problem, DNA con- therapeutic vaccine tested in vitro and subse-
essential to keep the costs and complex-
structs encoding virus-specific long hairpin RNAs quently in vivo using mouse and simian immun-
ity low. A producer cell line will therefore
(lhRNAs) were developed. It was demonstrated odeficiency virus (SIV)/Cynomolgus macaque
be generated in order to produce viral
recently that expression of such lhRNAs in target models.
vector particles at high titres and focus
cells provides durable, sequence-specific and
on a single-administration, long-lasting
broad-spectrum inhibition of HIV-1 replication. • A producer cell line to produce viral vector parti-
therapeutic molecular vaccination.
cles at high titres.
The safety and efficacy of the developed
therapeutic vaccine will be tested in vitro
Potential applications
and subsequently in vivo using mouse
Therapeutic anti-HIV-1 Vaccine.
and simian challenge models.

78
Key words: therapeutic molecular vaccination, HIV-1, AIDS, SV40-Vector and RNA interference

ROLE OF SMEs Scientific coordinator

Gerrit-Jan van Holst
Viruvation B.V.
The SME involved in this project, Viruvation B.V., will be responsible for the co-ordination Wassenaarseweg 72, PO box 1048
of the project. Viruvation is a young biotechnology company which focuses on RNAi-based 2302 BA Leiden, The Netherlands
gerritjan.vanholst@viruvation.com
antiviral strategies and will be responsible for the development of SV40 production tech- www.viruvation.com
nology. The company will further contribute with know-how on virology and proprietary
technology of importance for the project’s core tasks. Partners
Ben Berkhout
Academisch Medisch Centrum (AMC)
Amsterdam, The Netherlands
www.amc.nl.

Puri Fortes
Fundación para la Investigación
Médica Aplicada (FIMA)
Pamplona, Spain
www.cima.es

Neil Almond
National Institute for Biological
Standards and Control (NIBSC)
Potters Bar (Hertfordshire), United Kingdom
www.nibsc.ac.uk

© Shutterstock

79
ACRONYM Contract number: LSHB-CT-2006-037319
Starting date: 1 December 2006
IBDchip
SUMMARY
The IBDchip Project will develop an easy
to use DNA array and accompanying inno-
vative chip reading device. The IBDchip
will be a non-invasive tool with the
capacity for the simultaneous analysis of
around 100 relevant mutations to predict
the clinical evolution, the risk of develop-
ing IBD-related complications, and the
likelihood of responding to certain drugs
for each IBD patient.
| EC contribution: € 2 467 314
Usefulness of a new DNA array (IBDchip) to predict
clinical course, development of complications and
response to therapy in patients with inflammatory
bowel disease (IBD)
Background
Inflammatory bowel disease (IBD) includes Crohn
disease (CD) and ulcerative colitis (UC). Both are
increasingly common, chronic illnesses, currently
affecting nearly 1 million patients in Europe. CD
and UC affect patients early in life, seriously
impairing their quality of life and resulting in enor-
mous personal, social, and economic costs.
There is evidence suggesting that genetic factors
play a key role in IBD pathogenesis, pointing
towards a polygenic mode of inheritance for CD
and UC. However, to date studies have only
addressed the influence of single mutations on
IBD, resulting in a poor prediction of clinical course
or response to therapy in individual patients.
Aim
The main aim of this project is to provide doctors,
for the first time, with a non-invasive, predictive
tool to optimise treatment in IBD patients, thus
resulting in better clinical outcomes and improved
cost-effectiveness of treatment.
Expected results
• A fully validated innovative prototype IBDchip
which will give doctors vastly improved capaci-
ties to make more accurate individualised pre-
dictions of clinical outcomes of IBD and choose
the optimum and most cost effective therapy for
each patient.
• A new DNA array reader which will be faster and
one fifth of the price of existing machines to
optimise the reading of the IBDchip and help
make it ubiquitous.
| Duration: 36 months
• A clear understanding of the pathways to clini-
cal service, ethical and legal issues, and cost-
effectiveness of the IBDchip, which will result
in maximum uptake of the IBDchip in routine
clinical practice.
• The results for the academic partners will be
new knowledge derived from the research
undertaken in the project and published in
a range of leading academic publications.
Potential applications
The IBDchip will have very wide application across
the EU and beyond. The team has the working
objective of the IDBchip being used for 15 % of
both UC and CD patients (a total of approximately
320 000 people) within three years of the end
of the project (i.e. in 2011). These illnesses are
increasing and the project team expects that the
IBDchip and new reader will be embedded as
a routine part of treatment over the coming decade.
It is also probable the IBDchip project R&D
processes and the resulting technologies can be
adapted to address problems in the prediction
and treatment of other polygenic inflammatory
conditions such as rheumatoid arthritis. The team
intends to use the consortium and its work over
the next three years as the foundation for future
projects to explore other potential applications of
the technology.
80
Key words: inflammatory bowel disease, IBD, Crohn’s disease, ulcerative colitis, genetic factors, DNA array, scanner,
pathways to clinical service

ROLE OF SMEs Scientific coordinator

Miquel Sans
Gastroenterology Department
Progenika Biopharma S.A., one of the two SMEs involved in the project, has been the main Hospital Clínic/IDIBAPS
project driver, having originated the idea, identified and engaged the partners and will per- Barcelona, Spain
msans@clinic.ub.es
form tasks that use a major part of the EC contribution to the budget. Building on develop- www.idibaps.ub.edu
ment work done for their existing products, Progenika will use this project to validate new
technology and knowledge and create a prototype IBDchip that has been tested in clinical Partners
use and, therefore, is close to final commercialisation. The innovative prototype chip will
Marta Artieda
give Progenika a clear advantage over competitors in becoming first to market with their Progenika Biopharma S.A.
new knowledge intensive product. Derio, Spain
www.progenika.com
Innopsys is the second SME involved in the project and will develop a slide reader to be Stéphane Le Brun
commercialised alongside the IBDchip, which will be smaller and much cheaper than exist- Innopsys S.A.
ing machines and will take the company into a new market place (the reading of DNA arrays) Carbonne, France
while reinforcing their scientific and technological capacity for future innovations. www.innopsys.fr

Derek Jewell
University of Oxford
Nuffield Department of Medicine
and Oxford GKP
Radcliffe Infirmary
Oxford, United Kingdom
www.ndm.ox.ac.uk
www.oxfordgkp.org

Severine Vermeire
The University Hospital in Leuven
Leuven, Belgium
www.kuleuven.be

Salvador Peña
The Laboratory of Immunogenics
Department of Pathology
VU University Medical Center
Amsterdam, The Netherlands
www.vumc.nl

Stefan Schreiber
University Hospital Schleswig-Holstein
The Institute for Clinical
Molecular Biology (ICMB)
Kiel, Germany
www.uk-sh.de

Milan Lukas
The University Hospital in Prague
Prague, Czech Republic
www.cuni.cz

Silvio Danese
Istituto Clinico Humanitas
Rozzano
Milan, Italy
www.humanitas.it

81
ACRONYM Contract number: LSHM-CT-2006-037400 | EC contribution: € 2 500 000 | Duration: 36 months
Starting date: 1 January 2007

IMMUNATH

SUMMARY
The immune system has a major role in ath-
Translating innate immune receptor function
erosclerosis and its innate and adaptive into diagnostic and therapeutic applications
arms jointly and separately co-determine
atherosclerotic disease initiation and pro-
for atherosclerosis
gression. The search for approaches to
modulate the inflammatory response in
atherosclerotic disease is still in its infancy.
Inflammatory diseases like rheumatoid
arthritis (RA) have much longer been rec-
Background also by immunisation in mouse models. In ath-
ognized as immune disorders and hence
erosclerotic mice, it has been shown that the
are much ahead in development of thera-
Atherosclerotic cardiovascular disease remains vaccination approach may also be applied to
peutics targeting inflammation. A multi-
as number one killer of the aging population in atherosclerotic disease. A successful vaccina-
disciplinary approach will stimulate the
Western Society and numbers of cardiovascular tion strategy to prevent adverse outcomes due
discovery of immune modulating com-
events are strongly increasing in developing to atherosclerotic disease will have enormous
pounds to treat atherosclerotic disease.
countries. Worldwide about 17 million deaths are impact on healthcare.
Thereto, the current project joins forces of
caused by this inflammatory disease and the
three SMEs owning unique proprietary
complementary technology together with
costs for health care and loss of productivity Aim
exceeds $ 169 billion Euro a year in Europe.
four academic groups, which are actively
Fortunately, increasing knowledge on the mecha- General project objective: to develop and validate
involved in the field of cardiovascular dis-
nisms of atherosclerotic disease resulted in pre- therapeutic approaches that modulate the innate
ease and immune modulation. Research
ventive strategies and a subsequent decrease in and adaptive immunological responses in athero-
groups’ work is dedicated to SMEs to
rate of mortality in industrialized countries since sclerotic disease.
develop new and test pre-existing lead
1950. However, the increasing prevalence of type
compounds that modulate the innate or
II Diabetes in developed and developing coun- This general objective can be specified according
adaptive immune response and subse-
tries deserves careful consideration since this to 4 Work packages:
quent atherosclerotic disease. In addition,
will surely influence morbidity and mortality rates
diagnostic markers will be exploited that
due to cardiovascular disease. Improvement of WP 1 – Receptors. To identify targets for interven-
reflect the severity of atherosclerotic dis-
our understanding of the mechanisms that lead tion and test antagonizing compounds in the sig-
ease based on innate receptor ligands and
to atherosclerotic disease has resulted in innova- nalling cascade of the innate receptors, TLR and
responsiveness, focused on TLR and NOD
tive modalities that may help diagnose, prevent NOD, to inhibit atherosclerotic lesion development.
receptors.
and treat this life threatening disease.
WP 2 – Ligands. To identify endogenous ligands
In work packages (WP) 1 and 2, targets for
We now know that atherosclerosis is an inflam- for TLR and NOD that are involved in athero-
intervention that have been discovered
matory disease and that the body’s immune sys- genesis and assess diagnostic value of ligand
using an integrated genomics or pro-
tem plays a central role in the initiation and expression and receptor responsiveness following
teomics approach, will be validated and
progression of atherosclerotic lesion develop- ligation.
antagonists constructed using both small
ment. The recent insights in how the immune sys-
molecule and antibody technology. WP 1
tem recognizes endogenous and exogenous WP 3 – Innate Immunity. To inhibit atherosclerotic
will focus on innate receptor signalling,
ligands and how ligation of innate immune recep- lesion progression by leading compounds, target-
WP 2 will address the therapeutic and
tors results in a local inflammatory response, has ing TLR ligation or signalling and TNFalpha that
diagnostic value of TLR ligands and
opened exciting new therapeutic avenues which have been developed and licensed by participat-
responsiveness. In WP 3 and 4, the prop-
we would like to implement. Atherosclerosis ing SMEs.
erties of therapeutic lead compounds and
bears many similarities to other inflammatory dis-
diagnostic modalities that are based on
eases like rheumatoid arthritis or Crohn disease. WP 4 – Adaptive immunity. To inhibit atherosclerotic
modification of the innate and adaptive
Experimental studies revealed that such diseases lesion progression by immunisation targeting
immune response will be assessed using
may be treated by different approaches in humans: lipoproteins that have been shown to induce a vas-
state of the art in vitro and animal model
blockade of innate immunity (anti-TNFalpha) and cular inflammatory response and plaque formation.
systems. This STREP will significantly
advance the position of three SMEs based
on a multidisciplinary approach, and will
promote therapy and diagnosis for a dis-
ease with high socio-economic impact.

82
Key words: Atherosclerosis, immune system, toll like receptor, vaccination

ROLE OF SMEs Scientific coordinator

Gerard Pasterkamp
University Medical Center Utrecht
Three SMEs will participate in this consortium: OPSONA (Dublin), Bio-Invent (Lund) and Experimental Cardiology
Alloksys (Utrecht). All three companies have specific expertise that does not overlap: pro- Room G02-5123
Heidelberglaan 100
duction of TLR agonists/antagonists, immune-therapy based on passive immunisation and 3584CX Utrecht
Toll Like receptor ligand recognition, respectively. These companies will provide tools and The Netherlands
compounds that will be used in experimental models in order to examine applicability to g.pasterkamp@umcutrecht.nl
www.vascularbiology.nl
treat atherosclerotic disease. In addition, the academic institutes will search for new lig-
ands and proteins that play a role in TLR signalling in atherosclerotic disease. The SMEs will Project manager
then try to develop antagonising therapies to prevent or stabilise atherosclerotic disease.
These will be evaluated in experimental models in the participating academic centres. Arnold Heijkamp
Interuniversity Cardiology
Institute of The Netherlands
Postbox 19258
3501 DG Utrecht
The Netherlands
arnold.heijkamp@icin.knaw.nl
Expected results Potential applications www.icin.knaw.nl

It is expected to detect: • Therapeutical interventions based on immuno Partners

• molecules/proteins that serve as a therapeuti- modulation that may prevent initiation of and
Mark Heffernan
cal target in atherosclerotic disease; complications by pre-existent atherosclerotic Chrisopher Locher
• targets that may serve as surrogate endpoints disease. OPSONA Therapeutics Ltd.
for adverse cardiovascular events in clinical tri- Dublin, Ireland
www.opsona.com
als or as a prognostic marker for clinical events • Prognostic measures that may help diagnosing
due to atherosclerotic disease; the patients prone to develop acute myocardial Marc Feldmann
• therapeutic interventions to prevent initiation or infarction. Claudia Monaco
progression of atherosclerotic disease by: Kennedy Reserach Institute
Imperial College
– antagonising receptors, London, United Kingdom
– antagonising ligands,
– altering receptor response, R. Carlsson
Bo Jansson
– immunisation. Bioinvent International AB
Lund, Sweden
www.bioinvent.com
Medium TNF10 ng/ml TNF + Remicade Sups + Remicade
J Nilsson
Harry Bjorkbacka
University of Lund
Lund, Sweden

G. Hansson
Zhong-Qun Yan
Sups IL-1 10 ng/ml IL-1 + IL-1 Ra Sups + IL -1 Ra Karolinska Institute
Stockholm, Sweden

Jon Daniel Laman

Erasmus University
Rotterdam, The Netherlands

Ruud Brands
Alloksys Lifescience B.V.
| Monaco C. et al, 2007 (unpublished data). Utrecht, The Netherlands
www.alloksys.eu/php/index.php

Gerard Pasterkamp
Dominique de Kleijn
Utrecht University Medical Centre
Utrecht, The Netherlands

83
ACRONYM Contract number: LSHC-CT-2006-037489
Starting date: 1 October 2006
Immuno-PDT
www.immunopdt.net
SUMMARY
Photodynamic therapy of cancer, i.e. the
generation of reactive oxygen species in
the tumour environment which follows
the irradiation of suitable photosensitiz-
ing molecules, is an attractive modality
for the selective ablation of inoperable
superficial neoplastic lesions. This Proj-
ect puts together a network of academic
research groups and companies for the
development of antibody-based targeted
photodynamic therapy modalities. The
planned research activity starts with the
synthesis of novel photosensitizing mol-
ecules suitable for conjugation to anti-
bodies, and with the identification of
novel human monoclonal antibodies,
capable of a selective targeting of the
tumour neovasculature for immuno-PDT
applications. Following an extensive in
vitro characterisation of the most prom-
ising antibody-photosensitizer conju-
gates, the therapeutic potential of the
best conjugates will be tested in rodent
models of cancer, paving the way for
future clinical applications.
| EC contribution: € 3 000 000
Immunophotodynamic therapy
of cancer: concepts and applications
Background
Cancer chemotherapy is generally accompanied
by severe side effects, mainly due to unspecific
cytotoxicity of classic antineoplastic treatments.
Photodynamic Therapy contributes to a signifi-
cant efficacy in the treatment of neoplastic
and abnormal tissues, using a combination of
photosensitizer, such as porphyrin, chlorin, bac-
teriochlorin or phthalocyanine derivatives, and
tissue-penetrating visible laser light. Laser light
promotes the photosensitizer into its excited
state. The photosensitizer, in turn, interacts with
molecular oxygen and returns to its ground state,
resulting in the generation of the highly localised
cytotoxic agent, singlet oxygen, which ultimately
affords tumour destruction.
PDT is a modality of cancer treatment that causes
cytotoxic action only locally in the region of expo-
sure to laser light with a specific wavelength
matching the absorption profile of the photosen-
sitizer, thus leading to very site specific toxicity.
The targeted delivery of photosensitizers to suit-
able neoplastic sites is likely to increase the scope
and the efficacy of PDT therapy still further. The
antibody-mediated targeted delivery of photosen-
sitizers to the tumour neo-vasculature mediates a
rapid occlusion of blood vessels, thus depriving
tumour cells of oxygen and nutrients and trigger-
ing an avalanche of tumour cell deaths. As an
additional benefit, lower doses of photosensitizer
can be administered, thus reducing problems of
skin photosensitivity.
Aim
The present project has as objectives the synthe-
sis and conjugation of novel infrared photosensi-
tizers to the most promising antibodies against
vascular tumour antigens obtained by human
antibody technology, the immunohistochemical
characterisation, the biodistribution and imaging
targeting in vivo, in order to select the best anti-
body-photosensitizer conjugates to be taken for-
ward into clinical trials as a final objective.
| Duration: 36 months
In detail, the objectives are:
• the synthesis of novel infrared photosensitizers
with sufficient water solubility (i.e., not sticky to
unwanted cells and tissues), which absorb in
the near-infrared light spectrum and which effi-
ciently generate singlet oxygen and/or other
reactive oxygen species;
• screening of phage display libraries to find the
most suitable antibodies for the project;
• investigation of a novel method for the conjuga-
tion of the antibody and photosensitizer mole-
cules. The project proposes to investigate the
coupling of photosensitizers to antibodies,
based on the non-covalent but stable interac-
tion of photosensitizing molecules with specific
antibody fragments or suitable single domain
binders;
• evaluation of the conjugates in vitro and in vivo.
The project’s novel PDT agents will be exten-
sively tested in vitro, in order to ascertain
whether non-covalently bound photosensitizers
can retain singlet oxygen production activity
upon irradiation.
The agents will be tested in rodent models of can-
cer and, if successful, will open novel therapeutic
opportunities for the selective treatment of super-
ficial tumours in accessible body cavities.
Expected results
Most importantly, there is a reasonable expecta-
tion of a medical benefit for cancer patients stem-
ming both directly and indirectly from this Project:
• directly, since immuno-PDT procedures promise
to be invaluable for the selective ablation of
inoperable superficial neoplastic lesions, such
as certain head and neck, gastrointestinal, uro-
genital and gynecological tumours;
• indirectly, since the knowledge generated by
the validation of novel antibodies for vascular
targeting applications is likely to have an impact
in other forms of immunotherapy, including the
use of full IgGs and antibody-cytokine fusions
for cancer therapy.
84
Key words: photodynamic therapy, antibody-photosensitizer conjugates, tumour neovasculature

ROLE OF SMEs Scientific coordinator

Chiara Falciani
Reinerio Gonzalez
Immuno-PDT has put together a network of academic research groups and companies for Philogen S.p.A.
the development of antibody-based targeted photodynamic therapy modalities. The three Siena, Italy
chiara.falciani@philogen.it
SMEs – Philogen, Photobiotics and Trojantec – are crucial partners in Immuno-PDT and reinerio.gonzalez@philogen.it
share 52 % of the budget. www.philogen.it

Philogen (Italy) will produce antibodies against vascular tumour antigens by human Partners
antibody technology, with the final aim of selecting the best antibody-photosensitiser Ross Boyle
conjugates to be taken forward into clinical trials. University of Hull
Hull, United Kingdom
Photobiotics (UK) will contribute with the synthesis of novel photosensitizing molecules, Gokhan Yahioglu
suitable for conjugation to antibodies. The wide range of immuno-conjugates made will have Photobiotics Ltd.
differing physico-chemical properties, which may lead to different internalisation rates. London, United Kingdom
www.photobiotics.com
Trojantec (Cyprus) will use low levels of cell permeating peptides (antennapedia) co-coupled to Luciano Zardi
antibody fragments to enhance cellular delivery. This technology will be used to supplement Centro Biotecnologie Avanzate
photosensitiser delivery to tumour cells, by facilitating photosensitiser delivery to tumour cells Genova, Italy
www.biotecnologie.it
surrounding the targeted vasculature.
Dario Neri
The collaborations will establish the feasibility and biomedical potential of a novel class of Swiss Federal Institute of Technology
targeted PDT applications, and will provide invaluable information about their anti-cancer Zurich, Switzerland
www.pharma.ethz.ch/people/nerid
potential for selective destruction of tumour neo-vasculature. The three SMEs will ensure
that all necessary expertise and resources are in place, to assist translational activities such Peter Vajkoczy
as patent filing, Material Transfer Agreements, licensing deals, GMP manufacture activities University of Heidelberg
Heidelberg, Germany
and clinical development. www.uni-heidelberg.de/index_e.html

Potential applications
When considering immuno-PDT applications in
oncology in a strict sense, the potential market is
directly determined by the incidence of inopera-
ble superficial neoplastic lesions, such as certain
head and neck, gastrointestinal, urogenital and
gynecological tumours, which would benefit from
a PDT-based ablation.
Mahendra Deonarain
Imperial College London
London, United Kingdom
www3.imperial.ac.uk
In a broader sense, discoveries in terms of new
tumour targets, new antibodies, new coupling Christina Kousparou
Trojantec
methodologies, and new photosensitizers will Nicosia, Cyprus
benefit several areas of biomedical development, www.trojantec.com
including non-oncological indications such as
potentially-blinding angiogenesis-related ocular
disorders (such as age-related macular degenera-
tion, diabetic retinopathy, etc.).

85
ACRONYM Contract number: LSHM-CT-2006-037050
Starting date: 1 December 2006
INDABIP
SUMMARY
The INDABIP project aims to identify
biomarkers for the early diagnostics of
Parkinson disease. Biomarkers are any
type of biological molecules that are
present in people suffering a specific dis-
ease, even when the symptoms are mild,
but that are not present in people free
from the disease or suffering from other
diseases. The identification of the early
indications of the development of a neu-
rodegenerative disease is the basis for
preventive treatment strategies, which
aim to control the disease at early stages
rather than when irreparable neurological
damage has been caused.
| EC contribution: € 1 600 000
Innovative diagnostic approaches
for biomarkers in Parkinson disease
Background
Parkinson disease (PD), a specific type of
a group of neurodegenerative disorders called
synucleinopathies, is the second most common
neurodegenerative disorder worldwide. Many
neurodegenerative disorders are preceded by
a pre-symptomatic phase, probably lasting years,
during which degeneration and death of neurons
occurs before any clinical symptoms appear. One
major challenge of clinical research is to improve
early detection of these diseases by developing
tools to move diagnosis backward in the neurode-
generation temporal course. Thus, the central
objective of this INDABIP proposal is the identifi-
cation of molecular markers that hallmark the
onset of a cellular dysfunction in the brain areas
involved in PD, and that enable to identify at-risk
groups, both for disease onset and progression
during the pre-clinical period.
Aim
While biomarkers can take many forms, the IND-
ABIP project aims to identify relevant proteins,
mRNA, miRNAs, differentially matured RNAs and
methylated DNA, whose analysis can be trans-
formed in diagnostic tests. The brain damage in
Parkinson disease and other neurodegenerative
diseases is progressive and, by opening a window
for therapeutic treatment and prevention, the early
detection of biomarkers may help to identify indi-
viduals that have started to develop the disease.
While most biomarkers are mere reporters of the
disease state, others may actually be key factors in
the processes that lead to the onset and develop-
ment of the disease. The second aim of the INDABIP
project is therefore to identify these key factors and
to evaluate their potential as drug targets.
| Duration: 36 months
To study the development and evaluate potential
targets and therapies for Parkinson disease, bio-
logical models are needed, in which the events
that occur in the patient are mimetized. A target is
any molecular entity (transcript, protein, …) that
can be interfered with to interrupt the chain of
events leading to the onset or development of the
disease. We will develop novel in vitro models for
Parkinson disease based on cell cultures for the
development of a high throughput screening plat-
form, and use these for in vitro target validation
experiments.
Finally, we will initiate a screen for potential drugs
interacting with selected molecular targets.
Expected results
The INDABIP project aims to deliver an early diag-
nostic assay for Parkinson disease validated in
three independent laboratories. We will work
closely together with Parkinson disease Patients
Organizations to discuss and promote the possi-
ble future implantation of this diagnostic assay in
the national health systems.
Potential applications
Early diagnostics becomes really helpful when
appropriate treatments become available that
can prevent the further development of the incip-
ient disease. The INDABIP project will therefore
develop the tools to screen for drugs that can pre-
vent the further development of Parkinson disease
and initiate the process of drug development.
86
Key words: Parkinson disease, diagnostics, drug target identification

ROLE OF SMEs Scientific coordinator

Tamara Maes
C. S. O. Oryzon genomics
INDABIP is a SME driven and SME coordinated project. Two companies with complemen- Oryzon genomics S.A.
tary interests will receive about 50 % of the project financing: Oryzon Genomics, a biotech Parc Cintífic de Barcelona
José Samitier 1-5
company based in Barcelona (Spain) and Genfit, a biopharmaceutical company located in 08028 Barcelona, Spain
Lille (France). Oryzon Genomics contributes to the Project with experience in DNA chip tmaes@oryzon.com
technologies and bioinformatics applied to the discovery of biomarkers in neurodegener- www.oryzon.com
ative and oncological diseases. Oryzon Genomics will perform analysis of gene expres- Partners
sion, splicing and methylation analysis in the project. Genfit has solid knowledge in the
field of gene regulation. The Company has gained a solid experience in the analysis of the Sakina Sayah-Jeanne
family of transcription factors known as ‘nuclear receptors’ and has developed innovative Genfit S.A.
Lille, France
strategies to screen for drug candidates that target and modulate these receptors. Genfit www.genfit.com
will also bring its experience in animal models to the project. Both companies believe in
the power of the symbiosis between academic and SME partners and are determined to Isidro Ferrer
add a long term product-oriented vision to the project. Fundació Privada Institut d’Investigació
Biomèdica de Bellvitge
Bellvitge, Spain

Hans Kretschmar
Ludwig-Maximilians-University of Munich
PD DLBD
Zentrum für Neuropathologie
und Prionforschung
Münich, Germany

Irina Alafuzoff
Kuopio University
Department of Neurology
and Neuroscience
Kuopio, Finland

Regis Bordet
Department of Pharmacology
Faculty of Medicine, UL2le
University Hospital
Lille, France

Lewy bodies: optical and e.m.

| LEWY BODIES
Spherical intracytoplasmic inclusions with
concentric eosinophilic core and peripheral
unique or multilayered narrow, pale-stained,
hallo. Diameter ranging from 8 to 30 μm.
May bwe unique or multiple. The core is
composed of densely packed filaments and
granular material. The hallo is formed by
radially-arranged 7-20 nm intermediate
filaments associated with granular electron-
dense coating material and vesicular structures.

87
ACRONYM Contract number: LSHP-CT-2006-036871 | EC contribution: € 2 000 000 | Duration: 36 months
Starting date: 1 January 2007

INNOVAC

SUMMARY
The INNOVAC project comprises seven
Highly innovative strategies for vaccination
partners, three of whom are SMEs. The to poverty related diseases
consortium will develop three platform
technologies that will be used for novel
and highly innovative methods for vacci-
nation against two of the most important
poverty-related diseases, namely tuber-
culosis (TB) and malaria. An important
aspect to this project is the inclusion of
Background Expected results
a vaccine-producing SME, Vabiotech,
from a developing country. The three
The partners have a background in vaccine It is not expected that a ‘ready-to-go’ vaccine will
R&D platforms are:
development (Cutting; Cobra Biomanufacturing & be developed during the lifetime of this project.
• bacterial spores. Robust and heat-stable
Nano-S), vaccine manufacture (Vabiotech), malaria The aims are more realistic, namely the valida-
bioparticles with proven efficacy as
(Heussler) and tuberculosis (Manganelli and tion of one or possibly more of the platform tech-
mucosal vaccines;
Delogu). They have formed a collaborative group- nologies in development. In principle, the project
• intracellular & Invasive bacteria includ-
ing through which they will exploit novel intellec- may generate encouraging results with one or
ing E. coli strains and Mycobacterium
tual property (IP) with the aim of demonstrating more vaccine candidates against either malaria
bovis (rBCG);
proof of principle and commercial feasibility. or TB. This could lead to preclinical studies and
• S-layer protein conjugates and S-layer
long-term clinical studies, in collaboration with
protein coated liposomes.
Aim industrial partners.
INNOVAC will focus on discovery activi-
ties including proof-of-principle studies
The aim of this project will be to develop new and Potential applications
novel vaccines that could be developed for vacci-
to show Ag expression, testing of vac-
nation against malaria and/or TB. Proof-of- Heat stable vaccines are of particular interest to
cines in vitro as well as challenge experi-
principle that can enhance the value of existing IP developing countries enabling more stable and
ments in vivo. The project will test and
will be the primary aim. The technologies under robust products. Invasive delivery systems, if
evaluate highly innovative strategies for
development are particularly novel and include validated, could be efficient at targeting and
vaccination using recombinant systems,
heat-stable bacterial spores for antigen delivery preventing infection of not only Plasmodium
some in their infancy and others at a more
as well as bacterial systems that can deliver anti- and M. tuberculosis but also other intracellular
advanced stage of development. This
gens inside the host cell (intracellular delivery). pathogens.
project will include construction of vac-
Malaria and TB are of concern to both developing
cine vehicles, their evaluation in animal
and developed countries. One of the partners in
models, challenge experiments and
the project, Vabiotech, is a commercial partner
finally safety tests, where appropriate, in
with a long history in vaccine production from
order to take potential vaccines to the
a developing country, namely Vietnam. It is
stage of clinical evaluation. Inclusion of
expected that this company will facilitate the
a partner SME from Vietnam will enable
development of novel vaccine technology for
technology transfer to disease-endemic
developing countries.
countries.

88
Key words: Bacillus, bacterial spores, spore vaccines, heat-stable vaccines, 2nd generation vaccines, mucosal vaccines,
oral vaccines, edible vaccines, malaria, tuberculosis, nanobiotechnology, S-layers, M. bovis, M. tuberculosis

ROLE OF SMEs Scientific coordinator

Simon M. Cutting
School of Biological Sciences
The INNOVAC consortium carries 2 SMEs, Nano-S, and Cobra that have IP rights to novel vac- Royal Holloway University of London
cination strategies, vectors and strains. A further SME is Vabiotech in Hanoi, Vietnam, who Egham, Surrey,
TW20 0EX, United Kingdom
will collaborate with the European partners. Its inclusion is important to introducing and s.cutting@rhul.ac.uk
transferring technology rights to disease-endemic countries. www.rhul.ac.uk

Cobra, will manage pilot scale production of spore vaccines. This will include the design and Partners
production of GM spores that are unable to proliferate; GMP production methods for spore Rocky Cranenburgh
production and optimised methods for large scale production. Cobra Biomanufacturing plc
Keele (Staffordshire), United Kingdom
www.cobrabio.com
Nano-S will be responsible for optimisation of S-layer vesicles for mucosal immunization.
Alexander Matis
Nano S Biotechnologie GmbH
Vienna, Austria
www.nano-s.com

Riccardo Manganelli
Department of Histology
Microbiology and
Medical Biotechnologies
University of Padova
Padova, Italy
www.unipd.it

Giovanni Delogu
Istituto di Microbiologica
Facolta’ di Medicina e Chirurgia “A. Gemelli”
Universita Cattolica del Sacro Cuore
Roma, Italy
www.unicatt.it

Volker Heussler
Bernhard Nocht Institute
for Tropical Medicine
Department of Molecular
Parasitology
Hamburg, Germany
www.bni-hamburg.de

Nguyen Thu Van

Vabiotech
National Institute of
Hygiene & Epidemiology
Hanoi, Vietnam
www.vabiotechvn.com
© Shutterstock

89
ACRONYM Contract number: LSHM-CT-2006-037965 | EC contribution: € 1 299 697 | Duration: 36 months
Starting date: 1 November 2006

INTELLIMAZE
www.intellimaze.org

SUMMARY
Behavioural change is the most sensitive bio-
High-throughput, fully automated and cost-effective
logical end-point signalling any alteration in behavioural phenotyping of normal, clinical and
the organism of a mouse. However, large-
scale bio-assays of behaviour face limita-
genetic mouse models
tions: outdated technology, need for space
and specialised manpower, lack of standard-
isation, and increasing legal demands on ani-
mal husbandry. This has limited the use of
behavioural methods to specialised labora-
Background • there is limited knowledge about the behav-
tories, also limiting the market.
ioural biology of mice;
In order to advance scientific progress and
Too many mice. During the past 15 years, molecu- • species-pecific functions of structures in the
expand the market, 2 SMEs and 1 academic
lar biology and ENU mutagenesis programmes mouse brain are poorly known;
partner will combine their existing expert-
have led to an explosion of mouse models, many • the development of clinical mouse models for
ise and products for behavioural pheno-
of them needing behavioural characterisation. psychopathology faces problems in recognising
typing to generate a compact modular
Behavioural characterisation (‘phenotyping’) of how a behavioural impairment relevant to the
system, INTELLIMAZE, based on a recently
laboratory animals is an established tool in neu- human disorder would manifest itself in a mouse;
developed technology of in-cage testing of
robiology and neuropharmacology, but may find • all these problems are compounded by the lack
microchipped mice, INTELLICAGE. This sys-
much wider application in drug development, eco- of standardisation and comparability of test
tem should fit into a single small mouse
toxicology and other fields of biomedicine dealing results.
room, where it will:
with changes in body physiology. However, there
• assess home cage activity and learning of
is no appropriate technology to deal with the large Animal welfare. For behavioural testing, mice are
transponder-tagged mice living in social
number of mice. High-throughput behavioural often kept isolated over prolonged periods. Yet,
groups;
phenotyping (HTBP) would be needed, either for mice are social animals and isolation in an impov-
• automatically analyse social behaviour;
mass screening of mice, or, equally importantly, erished environment can cause many physiological
• guide individual mice to a battery of tra-
for the application of numerous tests to selected and neurochemical changes producing con-
ditionally used tests;
samples. founded results. Moreover, European legislation is
• show ongoing learning on-line to a super-
likely to ban animal housing under isolated condi-
visor working in his office;
Simplistic technology. Traditionally, animals are tions. This calls for social in-cage alternatives in
• analyse data according to expert knowl-
subjected manually to a battery of tests designed behavioural testing.
edge-based rules;
for demonstrating changes in spatial or fear-
• provide a web-based analysis of results
for user groups.
related memory, motivation, exploration or learn- Aim
ing abilities, thought to reflect the operation of
The bottleneck of such technological devel-
specific brain system. In addition, tests have been This SME project allies three SME’s and four aca-
opment is functional validation and compar-
designed to model processes observed in human demic partners for developing and validating
ison with traditional tests. Three reputed
diseases of the CNS. Thus, every laboratory spe- a compact, economic and fully automated modu-
academic partners will use the novel tech-
cialising in behavioural analysis must maintain an lar platform, INTELLIMAZE, that will permit both
nology for:
expensive collection of test set-ups, all of them high-throughput and detailed behavioural char-
• generating new mouse models of depres-
being conducted with single mice. acterisation of current and future mouse models
sion;
in biomedicine. In accordance with legislative
• profiling malfunctions of specific brain sys-
Economic limits. A standardised preliminary behav- trends in Europe, the system will operate with
tems; and
ioural screen of a knockout mouse requires testing mice living in social groups in a home cage.
• monitoring the effects of age-dependent
of about 100 mice in 4-6 different tests, equalling
neurodegeneration in existing and new
three person-months; a more detailed characteri- The technical development will be done by two
mouse models. Finally, an SME partner in
sation requires up to 6 person-months, even when SMEs (NewBehavior, and Frank Buschmann Inter-
need of efficient behavioural phenotyping
using highly standardised procedures and auto- national) and one academic partner (Laboratory
will validate the novel systems for drug dis-
mated data analysis. Thus, the main obstacles for of Systemogenesis at the Anokhin Institute of
covery and development.
high-throughput behavioural phenotyping are Normal Physiology of the Russian Medical Academy
It is expected that the availability of simpli-
costs in terms of space, salaries and expertise. of Science).
fied, rapid and thorough behavioural testing
of mice without need for specialised per-
Hidden problems in mouse testing. Traditional The commercial objective is to obtain a significant
sonnel will open new and much larger mar-
behavioural characterisation of mice faces a num- market share of the developing market of auto-
kets for the SMEs. Moreover, significant
ber of problems well known to experts but rarely mated test systems, expand the present market to
scientific discoveries in the fields of drug
discussed publicly: include new categories of customers, and to tailor
development, psychopharmacology, neu-
• mice are far less cooperative than rats and other such systems for small biotech SMEs in need of
rodegeneration, neural plasticity and repair,
laboratory animals; behavioural characterisation.
and genetic engineering are predicted.

90
Key words: mouse phenotyping, testing apparatus, high-throughput testing, transponder technology, automation,
Alzheimer’s disease, depression, anxiety, brain lesions, neurology, transgenic mice

ROLE OF SMEs Scientific coordinator

Hans-Peter Lipp
NewBehavior AG
Three SMEs, sharing 45 % of the project budget, are key players of the project. NewBehavior Hardurmstrasse 76
acts as coordinator and is responsible for the development of hard- and software for novel CH-8005 Zürich, Switzerland
hp.lipp@newbehavior.com
automated systems evolving from current products centred on automated assessment of
behaviour and learning in home cage systems. Frank Buschmann International adds comple- Project manager
mentary expertise in construction of behavioural apparatus of single animal testing, together
with expertise derived from its products in web-based management of experimental protocols Toni Lipp
t.lipp@newbehavior.com
and mouse colony supervision. Thus, the resulting INTELLICAGE and INTELLIMAZE system will www.newbehavior.com
not only operate in a single laboratory but can be used for parallel multi-user testing in
European projects and large pharmaceutical companies. Finally, the company Evotec, acting Partners
as a validating user, brings its experience in industrial drug development and testing. This will
Frank Buschmann
ensure that the developed systems do comply with both the needs of academic research lab- Frank Buschmann International GmbH
oratories and those of pharmaceutical and biotech companies. It is anticipated that this Bochum, Germany
approach will substantially enlarge the market for behavioural testing systems for mice. www.fbiscience.com

The joint scientific objectives of the academic
partners are validation of this novel technology
and inter-laboratory standardisation. According
to their expertise, they will also implement the
novel technology specifically for:
• in-depth behavioural profiling of brain lesions in
mice, focussing on hippocampus, striatum and
prefrontal (University of Zurich);
• development of novel behavioural paradigms
for mouse models of anxiety and depression
(Istituto Superiore di Sanita in Rome);
• monitoring the progress of brain malfunction in
mouse models of Alzheimer’s disease and pre-
mature ageing (EVOTEC Hamburg and NEUROTEC
at Karolinska Institute Stockholm).
Expected results
What is proposed here is almost a dream for mouse
behavioural biologists: a fully automated behav-
ioural test system for mice inside a home cage, and
outside in traditional test arenas, working without
supervision, and outputting data in familiar format
Enrico Alleva
Istituto Superiore di Sanità
and ready for statistics. Scientifically, it will permit Dipartimento di Biologia
to conduct almost all those studies that should Cellulare e Neuroscienze
Roma, Italy
have been done but were never realised. Moreover,
cross-laboratory standardisation is achieved with Abdul Mohammed
minimal efforts, and animal welfare guaranteed. Karolinska Institute
Department of Neurobiology
Commercially, it will certainly penetrate the market, Health Care Sciences and Society (Neurotec)
and has the potential of opening new markets in Karolinska University Hospital
biotechnology and pharmaceutical industry having Stockholm, Sweden
been hesitant in using costly behavioural assess-
David P. Wolfer
ment. Finally, as the products combine state-of-the- University of Zürich
art technology with expert behavioural knowledge, Institute of Anatomy
it will offer a sustainable perspective for the SMEs, Division of Functional Neuroanatomy
Zürich, Switzerland
providing a technological edge over the US, and
keeping production competence in Europe. Konstatin Anokhin
Russian Academy of Medical Science
Anokhin Institute of Normal Physiology
Potential applications Department of Systemogenesis
Moscow, Russia
It is expected that these systems will be employed
by the pharmaceutical industry, by small biotech Antje Willuweit
EVOTEC Neurosciences GmbH
companies producing and testing their own com- In vivo Pharmacology Group
pounds, by companies offering phenotyping Hamburg, Germany
services for mice, and by academic behavioural
research laboratories.

| Assessing learning abilities of individual

transponder-tagged mice in an automated
home-cage (INTELLICAGE). Each cage house up
to 16 mice and contains 4 operant conditioning
units allowing for assessment of spatial,
temporal and operant learning abilities.

91
ACRONYM Contract number: LSHB-CT-2007-037636
Starting date: 1 January 2007
InVitroHeart
er-projects.gf.liu.se/~invitroheart
SUMMARY
Invitroheart seeks to establish stable cell
lines that reliably reflect human cardiomy-
ocyte properties through the develop-
ment of models derived from human
embryonic stem (hES) cells. Its aim is to
deliver reliable in vitro models that could
be used by the pharmaceutical industry
to replace experimental animals in:
• investigations on pharmacological toxi-
city and safety of compounds in the drug
discovery and development processes;
• the testing of toxic effects of chemicals
according to the new system of the Com-
munity on the Registration, Evaluation
and Authorisation of Chemicals (REACH).
The Invitroheart consortium is composed
of nine participants and four of them are
SMEs. The SMEs contribution is crucial to
the project as regards the generation of
cells and assay technologies, and as
experts in life science and micro-sensor
technologies, they are the key providers
of state-of-the-art technology.
| EC contribution: € 2 701 611
Reducing Animal Experimentation in Drug Testing
by Human Cardiomyocyte In Vitro Models Derived
from Embryonic Stem Cells
Background
In the pharmaceutical industry, reliable in vitro
cell models would contribute to replace current
techniques with animal experimentation in the
selection and optimisation of lead compounds
and in documentation of a selected drug candi-
date before it enters clinical phases. In the toxic-
ity testing of chemical substances, replacement of
animal testing methods can be attained as well.
The means to accomplish the objective, in addi-
tion to new stable hES cell derived cardiomy-
ocytes, are as follows:
• state of the art methods for electrophysiological
cardiac cell monitoring;
• optical micro-sensor monitoring in micro-culti-
vation systems for in vitro screening;
• a multi-micro-bioreactor platform for high-
throughput screening of drugs and chemicals.
Invitroheart will carry out comparative studies of
cardiomyocytes derived from hES cells with
established in vitro models in order to validate the
new models and methods. The outcome of the
project is new efficient in vitro pre-validation
models which will significantly reduce the use of
animal experimentation for cardiotoxicity testing
by 60-80 %. Furthermore, it will strengthen the
possibility for the participating SMEs to market
new potential products in the areas of in vitro
assay methods and in vitro compound screening.
Studies of toxicity and safety pharmacology in
general, and cardiotoxicity in particular, are key
activities throughout the drug discovery programs
in the pharmaceutical industry. Such activities are
initiated to detect detrimental compound effects.
For example, electrophysiological changes such as
QT prolongation, which leads to delayed ventricu-
lar repolarisation and cardiac arrhythmia, are
induced by a vast range of chemical entities for
multiple therapeutic areas. Unintended QT effects
of new drugs are the most common cause of drug
withdrawal from the market and delays in or lack
of regulatory approval for marketing.
92
| Duration: 36 months
Clinical cardiotoxic effects are defined as symp-
toms of clinical heart failure, and subclinical car-
diotoxic effects such as cardiac abnormalities
detected in asymptomatic persons by means of
various methods. One of the problems is the avail-
ability of preclinical models able to screen rapidly
a large library of substances and to provide
rational bases for clinical trials. A significant bot-
tleneck in the development of novel assays has
been the lack of research purposes. Animal mod-
els have been invaluable for risk assessment of
compound safety; however, critical limitations
remain in these models for robust prediction of
certain toxic outcomes in humans.
Aim
The overall aim of the project can be summarised
as follows:
• to replace animals with human cell culture sys-
tems in preclinical pharmaceutical development
and chemical substance toxicity testing;
• to support the predictability of the drug discov-
ery and development process of cardiovascular
pharmaceuticals by allowing more reliable and
relevant testing in the preclinical phase and
hinder weak lead candidates to enter clinical
phases with innovative human cardiomyocyte
cell systems;
• to deliver an in vitro testing system with adja-
cent methodology pertinent for validation in
GLP/SOPs environment for cardiac safety;
• to deliver in vitro testing systems with adjacent
methodology pertinent for chemical substance
toxicity testing within REACH;
• ultimate aim: to reduce or even totally abolish
the use of animals in drug and chemical sub-
stance testing, refine the model system under
consideration and to replace the animal models
currently used.
Specific technology related objectives:
• to establish relevant hES cell derived cardiomy-
ocytes cultures that allow a more predictable pre-
clinical lead testing program to be carried out;
Key words: embryonic stem cells, cardiomyocyte, animal experimentation, safety assessment, in vitro models,
cardiac toxicity, electrophysiology, QT prolongation, optical sensor, high-throughput screening, bioassays

ROLE OF SMEs Scientific coordinator

Carl-Fredrik Mandenius
Linköping University, IFM, SE-581 83
Out of nine partners in Invitroheart, four are SMEs (Cellartis, Multi Channel Systems, Linköping, Sweden
Pharmacelsus and PreSens) and their share of the requested funding from the Commission cfm@ifm.liu.se
www2.ifm.liu.se/biotech/
amounts to 59 %. They provide state of the art expertise in key research activities.
Project manager
In particular:
Magnus Fredriksson
magfred@ifm.liu.se
Cellartis brings to the project a strong expertise in the field on hES cells. They will establish
appropriate protocols for the production and characterisation of cardiac cells, for quality Partners
control of these cells according to GMP-standards, and for development of innovative cell
preservation methods. They will provide to partners well characterised human cardiomy- Peter Sartipy
Cellartis AB
ocytes for the planned research. A future goal is to investigate in detail differentiation Göteborg, Sweden
processes and to provide large quantities of cardiomyocytes to customers. www.cellartis.com

Thomas Meyer
Multi Channel Systems (MCS) provides functional electrophysiological monitoring during Multi Channel Systems GmbH
the development of the hES cell derived cardiomyocytes. Furthermore, MCS will develop Reutlingen, Germany
a hardware platform optimised for cardiomyocyte electrophysiology screening, including www.multichannelsystems.com
development of software to automate the data acquisition and analysis. Also, a prototype of
Christine Batzl-Hartmann
an integrated automated screening system will be manufactured. MCS provides access to Pharmacelsus GmbH
the worldwide distribution network to market the complete assay. Saarbrücken, Germany
www.pharmacelsus.com
Pharmacelsus will design and build new in vitro assay systems for hES cell derived car- Christian Krause
diomyocytes in order to support predictive in vitro models of the consortium. Furthermore, PreSens GmbH
Pharamacelsus will provide its scientific experience of a broad range of in vitro models for Regensburg, Germany
pharmaceutical testing and will integrate consortium knowledge in statistical validation www.presens.de
into the developed new assay systems. Pharmacelsus’ excellent in-house facilities for Morten Laursen
analysis (Fluorimetry, Spectroscopy, HPLC, LC-MS/MS) will support partners to carry out Lundbeck A/S
specific assay testing with the different systems developed. Dept. of Safety Pharmacology
Valby, Denmark
www.lundbeck.com
PreSens will integrate chemical optical sensors for pH and oxygen measurements in the
assay technologies developed, adapt existing sensors and develop new sensors accord- A. Lindahl
Göteborg University
ing to the special demands of the new methods. PreSens will integrate optoelectronic Dept. of Clinical Chemistry/
instruments based on its sensor technology and will deliver these to the partners of the Transfusion Medicine
consortium. Furthermore, it will investigate the implementation of fluorescence intensity Göteborg, Sweden
measurements in the existing instruments and will give support in data interpretation. www.biomedicine.gu.se/avdelningar/
avdelning_4

• to develop a real-time sensor based in vitro
model for short-term studies of cardiac side-
effects that mimics the function and complexity
of the cardiomyocyte tissue in vivo;
• to develop a real-time sensor based in vitro
model for long-term studies of cardiac side-
effects that mimics the function and complexity
of the cardiomyocyte tissue in vivo;
• to establish a versatile cell lab platform based
on the developed cell lines and cultivated in
advanced miniaturised bioreactor systems with
non-invasive measurement techniques for in
vitro testing of cardiotoxicity.
Elmar Heinzle
Expected results Saarland University
Dept. of Biochemical Engineering
Saarbrücken, Germany
Successful results of the project will, if adopted by www.uni-saarland.de
the European pharmaceutical community, lead to:
• the preservation of significant numbers of Susanne Bremer
ECVAM (European Centre for
experimental animals; the Validation of Alternative Methods)
• reduced work carried out during pharmaceuti- Joint Research Center
cal drug discovery and development in the Institute for Health and
Consumer Protection
preclinical and early clinic phases; Ispra, Italy
• improved predictability of quality of lead candi- ecvam.jrc.it/index.htm
dates increases the chances for passing the
entire clinical trials process;
• reduced total development time of leads;
• attainment of better quality and safety in docu-
mentation filed to regulatory bodies.

93
ACRONYM Contract number: LSHC-CT-2006- 037852 | EC contribution: € 1 902 150 | Duration: 36 months
Starting date: 1 October 2006

LIGHTS
www.lights-EU.org

SUMMARY
Ovarian cancer is the fifth most common
Small ligands to interfere with Thymidylate
cause of death from cancer in women. The synthase dimer formation as new tools for
standard first-line treatment is a combina-
tion of paclitaxel and carboplatin (DDP) or
development of anticancer agents against
carboplatin alone. In the case of progres- ovarian carcinoma
sive disease or drug resistance treatment
with platinum, either alone or in combi-
nation, especially investigational com-
pounds should be used. The mechanisms
Background medicinal chemistry issues that can critically influ-
behind acquired resistance to cDDP and
ence the time schedule for obtaining an investiga-
its derivatives are not clear yet, although
Ovarian cancer is the fifth most common cause of tional drug candidate. Nevertheless it is also
it is evident that the process is multifacto-
death from cancer and the most common cause of expected as a byproduct of the project that poten-
rial, including enhanced DNA repair. In the
death from gynecologic cancer in women of all tial drug candidate(s) with high quality in vitro
human ovarian carcinoma cell line A2780,
ages in the Western world. Single-agent carbo- activity profile can be obtained ready for in vivo
a 3-fold-DDP-resistance was associated
platin (cDDP) has been considered a reasonable pharmacology profiling.
with cross-resistance to the thymidylate
option for first-line chemotherapy for ovarian can-
synthase (TS) inhibitor 5-fluorouracil and
cer. However, the occurrence of resistant cell pop- In particular LIGHTS objectives are:
to methotrexate, a 2.5-fold increase in TS,
ulations in the tumour, limiting the usefulness of • derivation of small-ligand libraries with ligands
and an increase in the intracellular pools
the platinum drug represents a growing problem. design to bind to the Thymidylate synthase
of the TS cofactor 5, 10-methylentetrahy-
Resistant cells often became refractory to the ini- monomer/monomer interface affecting dimer
drofolate and of tetrahydrofolate. The ulti-
tially used drugs and extremely difficult to eradi- formation and TS- TSmRNA interactions;
mate goal of LIGHTS is to directly halt
cate. Therefore the use of drug combinations is • validation of the integrated, multidisciplinary
tumour progression and the development
necessary. The combination of cDDP and antifo- drug design strategy necessary to achieve
of drug resistance upon treatment with
lates such as azidothymidine (AZT), a deoxythymi- objective 1, which poses a highly challenging
platinum derived drugs, by inhibiting the
dine analogue, or more recently pemetrexed design problem. The strategy including protein
protein regulatory function of monomeric
(Alimta), which inhibits three enzymes in the de cysteine SH-labelling to identify low-affinity
TS through small molecule cellular per-
novo purine and pyrimidine pathways, has been ligands, peptide mimetic design, and filtering
turbation. The scientific and technological
shown to synergistically affect the growth of for ADME properties;
objectives will be to design small-ligand
human ovarian carcinoma cells resistant to DDP. • identification of small-ligands identified in
libraries to bind to the TS monomer (dimer
Due to the role played by the enzymes of DNA a chemical-biology approach as effective per-
interface) and thereby disrupt TS. The
synthesis and repair in the occurrence of cDDP- turbing agents to investigate the mechanism
strategy will include systems pathway
resistance, it seems of great priority to develop of resistance against a panel of cis-platinum
analysis, protein SH-labelling to identify
clinical reagents designed to limit the intracellu- resistant ovarian carcinoma cell lines;
low-affinity ligands, peptide mimic design
lar level of TS protein, which is associated with • provide potential drug candidate(s) with new
& synthesis, and filtering for ADME prop-
clinical resistance, thus sensitising even resist- mechanism of action for further development as
erties. The multidisciplinary approach will
ant cells to the effects of anticancer drugs. The safer therapeutic agent(s) for the treatment of
be carried out by a consortium integrating
ultimate aim of LIGHTS is to directly halt the ovarian carcinoma.
Molecular modelling, Chemistry, Chemoin-
tumour progression and interfere with the devel-
formatics, Structural Biology and Pharma-
cology, and will apply the knowledge
opment of drug resistance upon treatment with Expected results
platinum derived drugs by inhibiting the protein
being created by genomics and other
regulatory function of TS through small molecule The project provides the integration of different
fields of basic research to the problem of
cellular perturbation. scientific areas that are culturally well separated into
discovery of anticancer agents. The con-
more established medical approaches to impact
sortium consists of six groups from five
different countries, including three SMEs.
Aim health determinant in ovarian cancer disease.

The project is clearly oriented to directly halt the
progression of ovarian cancer and interfere with
the development of drug resistance upon treat-
ment with platinum-derived drugs by inhibiting the
protein regulatory function of monomeric TS. The
intermediate objectives are based on employing
novel medicinal chemistry strategies to identify
potential drug candidates with new mechanisms of
action. LIGHTS specifically addresses early phase
It supports the discovery of new potential anti-
cancer drugs with non-cross resistance profiles;
the new potential drug candidate will be ready to
enter the pharmacological phase. If the new identi-
fied molecules will be moderately/very active with
good bioavailability in vitro against ovarian cancer,
these products will be very interesting to larger
pharmacompany and could provide a successful
technological transfer outcome.

94
Key words: ovarian cancer, thymidylate synthase, drug resistance, drug discovery, protein-protein interaction

ROLE OF SMEs Scientific coordinator

Costi Maria Paola
Institution, University of Modena
Out of the 6 partners, three are SMEs, highly committed to the project research objectives and Reggio Emilia, Italy
and outcome. In fact, the involvement of the SME Naxospharma, Molecular Discovery and Via Campi 183
41100 Modena, Italy
EML provide expertise in discovery and synthetic chemistry support, lead development, costimp@unimore.it
intellectual property issues, searching for out-licensing and/or co-operative opportunities cdm.unimo.it/home/dipfarm/
for the inventive aspects of the project. costi.mariapaola

Partners
In particular:
Rebecca Wade
EML Research will contribute by setting up and simulating biochemical network models for EML Research GmbH
Heidelberg, Germany
the cycles involving TS, protein design, protein structure-based ligand and peptide design, www.eml-r.org/english/index.php
ligand optimisation, and mechanistic studies of effects of ligands on TS dimerisation and
RNA binding. Paolo Lombardi
Institution, Naxospharma srl
Cesate (MI), Italy
Naxospharma encompasses discovery and synthetic chemistry support, lead development, www.naxospharma.com
intellectual property issues, searching for out-licensing and/or co-operative opportunities
for the inventive aspects of LIGHTS. Hannu Myllykallio
Institut de Génétique et Microbiologie
Université Paris-Sud
Molecular Discovery will provide high quality software tools and chemoinformatics proce- Orsay, France
dures aimed at the prediction of the physicochemical profiling of the investigated com- www.igmors.u-psud.fr/MYLLYKALLIO/
pounds with potential anti-tumour activity. This data is crucial for the discovery planning MYLLYKALLIO-eng.htm
and flow-chart LIGHTS. IT procedures, models building and applications will be the main Massimo Baroni
task of Molecular Discovery. The software will be developed and implemented by intro- Molecular Discovery Ltd.
ducing the data obtained by the other partners in LIGHTS. Particular focus will be given Ponte San Giovanni (PG), Italy
www.moldiscovery.com
to ADMEtox profiles.
Robert Stroud
UCSF-Genentech Hall, UCSF
San Francisco, USA
msg.ucsf.edu/stroud

The proposed research could provide the technical

developments and innovation, which could have
a large impact on Biotech industry. The selection of
the participating SME partners guarantees that the
new knowledge (methods, potential drug(s) candi-
date(s)) might be transformed into new technology
and new products.

Potential applications

The proposed research could lead to technical

developments and innovation, which could have
a large impact on Biotech industry. The selection
of the participating SME partners guarantees
that the new knowledge (methods, potential
drug(s) candidate(s)) might be transformed into
new technology and new products. The consor-
tium, in addition to its contribution to the pro-
ject’s basic research by providing a suitable
discovery chemistry programme, will be respon-
sible for further development of the selected
promising new chemical entities comprising
intellectual property protection, chemical and
pharmaceutical development. | Detail of the X-ray source of the European Synchrotron Radiation Facility (ESRF), Grenoble, France.

95
ACRONYM Contract number: LSHB-CT-2006-037499 | EC contribution: € 2 933 291 | Duration: 36 months
Starting date: 1 January 2007

liintop
www.liintop.cnr.it

SUMMARY
The main aim of the project is to optimise
Optimisation of liver and intestine in vitro models
and provide established protocols and for pharmacokinetics and pharmacodynamics studies
experimental in vitro models for testing
intestinal and liver absorption, metabo-
lism and toxicity of molecules of pharma-
cological interest. The added value of the
project, with respect to the existing
experimental approaches in this field, is
to provide optimised sequential proce-
Background from industrial enterprises. In vitro systems comply
dures, easily amenable to validation
with the request of reducing animal experiments,
studies for screening and testing of new
In Europe, three Directives regulate the testing thus satisfying a widely shared ethical concern. On
drugs, possibly by miniaturised and
of chemicals: Council Directive 67/548/EEC and the other hand, they offer economic advantages in
automated technology. A consortium of
its subsequent amendments; Council Directive terms of reduced time consumption and lower costs
15 participants includes seven compa-
88/379/EEC and subsequent amendments, and in safety assessment of novel drugs.
nies, out of which six are SMEs. The
Council Directive 76/769/EEC. Moreover, the
direct participation of SMEs in the
research activities will assure that those
Council Regulation No. 793/93 on the evaluation Aim
and control of risk of existing substances also
procedures will meet the requirements of
deals with the same topic. The main new aspect is The main aim of the project is to optimise and pro-
industrial application.
that a distinction has been made between the new vide established protocols and experimental in
substances notified since 1981, and those notified vitro models for testing intestinal and liver
The project is, therefore, articulated in
before then. For the latter (about 100 000), it has absorption, metabolism and toxicity of molecules
different approaches, which will integrate
been estimated that insufficient data are available of pharmacological interest. Moreover, from a sci-
at various levels. A first basic approach
concerning their safety. Thus, the White Paper pro- entific point of view, the project represents
will be the optimisation of in vitro liver
poses a harmonisation of testing requirements for a unique effort to link, by an in vitro approach, dif-
and intestinal models for their use in
new and existing substances, by introducing a new ferent systems (i.e. gastrointestinal tract and
transport and toxicity of structurally
system for the Registration, Evaluation and Authori- liver) and pathways involved in vivo in the absorp-
diverse reference drugs chosen with the
sation of new and existing Chemical Substances tion and metabolism of orally ingested sub-
help of a steering committee of relevant
(REACH) (COM-2001/88 Final; COM-2003/644). stances. This kind of approach is important for
stakeholders. A parallel approach will
further development of tests for chronic exposure
deal with the identification of the trans-
This implies, on the one hand, a cumbersome plan in which the interrelation between different
port and metabolic pathways and possi-
of testing, and on the other hand, the use of organs is a key factor and where at present nearly
ble cytotoxic effects of these drugs, in
a huge number of animals. The European Centre no in vitro data are available. Such integrated
order to develop appropriate monitoring
for Validation of Alternative Methods (ECVAM) models will be developed to the point of entering
procedures. New advanced technologies
has already addressed the possibility of using pre-validation procedures to be submitted to
(genomics, proteomics, metabolomics)
alternative methods, according to the 3Rs model, regulatory boards.
will be used in order to develop high
in order to reduce this number, or at least the ani-
throughput models related to the specific
area of intestine-liver absorption and
mal suffering associated with certain kind of tests. Expected results
The EU has addressed this issue in the directive
biotransformation. Each approach will
86/609. The use of non-validated alternatives has • To provide standardised cellular models of
take care of the reliability of the protocols
also been suggested based on the ‘weight of evi- human hepatocytes and enterocytes reliable
used and of the relevance of the whole
dence’, i.e. widely used and well consolidated pro- for prediction of drug absorption, metabolism
procedure to the in vitro/in vivo extrapo-
cedures. This project may well contribute to those and toxicity. Sequential procedures, easily
lation of drug effects. To this end, a unit in
aspects, by providing new procedures submitted amenable to validation studies, possibly by
charge of computer-based studies will
to optimisation. miniaturised and automated technology will be
support and pilot the project throughout.
developed.
A successful outcome of the project, in fact, will
have a strong and diversified impact on social and • To obtain on these models a database concern-
economic issues. The main effect will be related to ing in vitro absorption, metabolism and toxicity
the expanded use of in vitro systems, meeting of selected drugs including the characterisation
existing expectations from the public at large and of the regulation of relevant genes.

96
Key words: in vitro human hepatic and intestinal models, metabolism, absorption pharmacokinetic and pharmacodynamics,
in silico modelling

ROLE OF SMEs
Among the 15 consortium participants, seven are industrial companies, namely six SMEs
plus a large company, NV Organon. This project presents a strong contribution from high-
tech SMEs, like Biopredic International, Advancell, Siena Biotech that will convey into the
project leading and innovative core technologies and services. Their direct participation in
the research activities (particularly on transporters and metabolites identification) will
assure that the optimised sequential procedures, for screening and testing of new drugs will
meet the requirements of industrial application.

This proposal addresses an issue of great relevance in the drug discovery process, i.e.
absorption and entero-hepatic bio-disposition of drugs, which presently still relies on | In vitro intestinal cells, immunostained with
in vivo experimentation. The development of integrated in vitro predictive tools capable of a thight junctions marker.
addressing these issues, possibly sustained by miniaturised and automated technology,
will have a positive outcome in competitiveness and success of pharmaceutical industry,
since decisions taken on partially characterised compounds (or with questionable human
relevance) may lead to great economic losses at later stages.

Scientific coordinator Maria Laura Scarino

Istituto Nazionale di Ricerca
• To develop prediction mathematical models of Flavia Zucco per gli Alimenti e la Nutrizione (INRAN)
CNR, Istituto di Neurobiologia e Medicina Molecolare Roma, Italy
pharmacokinetics and pharmacodynamics based www.inran.it
Via del Fosso di Fiorano 64
on the available in vivo data and on the in vitro 00143 Roma, Italy
data from the cellular models used in the project. f.zucco@inmm.cnr.it Vera Rogiers
www.cnr.it/sitocnr/home.html Vrije Universiteit Brussel
Dept. Toxicology
Best case scenario: Partners Brussels, Belgium
www.vub.ac.be/english/index.php
• to transfer the best hepatocyte and enterocyte Pascale Anderle
Ente Ospedaliero Cantonale/Istituto Jouko Uusitalo
models and relevant testing procedures to the Novamass Analytical Ltd.
Oncologico Svizzera Italiana (EOC/IOSI)
industrial setting for high throughput applica- Bellinzona, Switserland Oulu, Finland
tions in the development of new drugs; www.eoc.ch/ www.novamass.net
• establishing the relevance of the proposed in Sjeng Horbach
Jose V. Castell
vitro models to human in vivo situation. Dep.de Bioquímica Fac. Medicina/ NV Organon
Centro de Investigacion Department of Pharmacology
Oss, The Netherlands
Potential applications Hospital Universitario La Fe
www.organon.com/authfiles/index.asp
Valencia, Spain
www.fundacionlafe.org/indexE.htm
Optimised sequential procedures and reference Dr. Karen Rowland -Yeo
standards concerning in vitro models of hepa- Christophe Chesne Simcyp Limited Blades Enterprise Centre
BIOPREDIC International Sheffield, United Kingdom
tocytes and enterocytes, easily amenable to www.simcyp.com
Rennes, France
validation studies will allow a new molecule of www.biopredic.com
pharmacological activity to be tested for: Ugo Zanelli
SienaBiotech SpA
• potential toxicity at the level of the intestinal Andrè Guillouzo
Drug Profiling – Metabolism
mucosal barrier; INSERM U62O
Faculté de Pharmacie, Université de Rennes 1 Siena, Italy
• intestinal absorption; Rennes, France www.sienabiotech.com/index/index.jsp
• metabolic modification in the intestinal cells; www.inserm.fr/en/home.html
Myriam Fabre
• absorption and metabolism in the hepatocytes; Advancell
Jouni Hirvonen
• hepatotoxicity; Faculty of Pharmacy, University of Helsinki Barcelona, Spain
• optimal pharmacokinetic behaviour. Helsinki, Finland www.advancell.net/index.html
www.helsinki.fi/university/index.html
Peter Krajcsi
Brian Houston SOLVO
School of Pharmacy and Pharmaceutical Sciences Budaörs, Hungary
University of Manchester www.solvo.hu
Manchester, United Kingdom
www.manchester.ac.uk

97
ACRONYM Contract number: LSHM-CT-2006-037957
Starting date: 1 October 2006
MagRSA
www.MagRSA.org
SUMMARY
Methicillin-resistant Staphylococcus aureus
(MRSA), a virulent organism resistant
to many drugs, is responsible for most
nosocomial and community-acquired
infections. It can cause life-threatening
disease, and treatment options are lim-
ited. Effective diagnostics is a strategic key
element in the campaign against the
spread of MRSA, allowing better infection
surveillance and control measures as well
as more efficient patient treatment and/or
isolation options. The MagRSA project
aims at the development of a new diag-
nostics platform that will provide a fast,
simple and accurate identification of MRSA
from clinical samples.
| EC contribution: € 2 095 800
Fully Automated and Integrated Microfluidic
Platform for Real-Time Molecular Diagnosis
of Methicillin-Resistant Staphylococcus Aureus
Background
Methicillin-resistant Staphylococcus aureus (MRSA),
an organism resistant to many drugs, is seen with
increasing frequency in hospitals and long-term
care facilities. It can cause life-threatening disease,
and treatment options are limited. MRSA infections
are indeed associated with a 40 % mortality when
found in the blood of patients suffering from
severe staphylococcal infection. According to the
World Health Organization (WHO), resistance of
Staphylococcus aureus (Staph A) to methicillin, its
usual antibiotic, increased from 2% in 1975 to 60%
today and no new antibiotic is expected on the mar-
ket for many years. Whereas MRSA is considered as
a nosocomial pathogen, recent reports showed an
increasing number of outbreaks in the community,
despite the absence of known risk factors (prior
hospitalisation, antibiotic use or household con-
tacts from the healthcare system). Indeed, a rela-
tively large spread of MRSA strains within the gay
community was recently reported in several
European countries and the United States. Such
atypical MRSA is known to produce a potent toxin
causing severe skin infections and necrotising
pneumonia in both immunocompromised and
immunocompetent individuals.
With such critical health issues, an early detection
of MRSA carriers is crucial for infection control
strategies but also to take appropriate therapeutic
decisions, avoiding non-appropriate utilisation of
last barrier antimicrobial agents. Strategies to fight
MRSA transmission are indeed well-documented,
and can efficiently reduce subsequent colonisation
and infection. However, for cost issues and better
patient management, these strategies need to be
focused on patients with confirmed MRSA and
defined resistance phenotype.
98
| Duration: 36 months
Aim
The MagRSA project aims at the development of
a new diagnostics platform that will provide a fast,
simple, automated and accurate identification of
MRSA from clinical samples.
The diagnostic protocol that is proposed relies on
a new and clinically validated procedure that con-
sists of a direct one-step enrichment of MRSA
present in either nasal or inguinal swabs, followed
by DNA extraction of immunocaptured bacteria
and their identification by multiplex sequence
amplification, using real-time quantitative PCR.
This protocol will be implemented with a simple
‘hands-off’ system based on:
• novel strategies for the integration of full opera-
tions required for the entire nucleic acid analy-
sis chain in a microfluidic platform; and
• advanced microfluidic magnetic nanoparticles
manipulation technology allowing efficient cap-
ture and extraction of target bacteria and
nucleic acids. The separate steps of sample
preparation, signal amplification by multiplex
PCR, and simultaneous detection of multiple
genes, will be performed as one single step
using a ready-to-use disposable fluidic chip.
In light of the above, this project aims to provide
hospitals and care units with a fast, easy and
automated test for the rapid diagnostic of MRSA.
Moreover, the simplicity of the proposed technol-
ogy concept, integrating cost effective and widely
available components, allows for the provision of
low cost systems, a prerequisite condition for the
large adoption of molecular tests by hospitals.
Key words: magnetic nanoparticles, microfluidics, quantitative PCR, antimicrobial resistance, MRSA, molecular diagnostics

ROLE OF SMEs Scientific coordinator

Jacques Schrenzel
Geneva University Hospitals
The MagRSA project Consortium is composed of 6 partners, among which are 3 high-tech Division of Infectious Diseases – Genomic
SMEs with complementary expertise. Ademtech is an established company with large Research Lab
Rue Micheli-du-Crest 24
expertise in magnetic nanoparticles manufacturing for in vitro diagnostics and life sci- CH-1211 Geneva, Switzerland
ences applications; Spinomix is a start-up company specialized in the development of fully jacques.schrenzel@genomic.ch
automated and miniaturized solutions based on a proprietary magnetic nanoparticles www.genomic.ch
handling technology – termed MagPhase™ – in a micro fluidic environment. The tech- Project manager
nology offers cost-efficient, rapid, automated and compact sample handling systems for
multitude of applications in life-science and in vitro diagnostics (IVD) market; and TATAA is Kirsten Leufgen
a leading service provider in tailor-made real-time quantitative PCR (RT-qPCR) gene SCIPROM
rue du Centre, 70
expression analysis in Europe. CH-1025 St-Sulpice, Switzerland
info@sciprom.ch
The project presents therefore a strong contribution from high-tech SMEs with leading www.sciprom.ch
and innovative core technologies and services. With complementary competencies and
Partners
core activities, all SMEs expect from this project to expand further their technologies and
activities portfolio. Moreover, these SMEs consider the project as a technological and Amar Rida
commercial opportunity that may open large market perspectives to their existing core Spinomix S.A.
technology and products. Lausanne, Switzerland
www.spinomix.com
amar.rida@spinomix.com
In addition another SME, a young Swiss company called SCIPROM, takes care of the project
management. Neven Zoric
TATAA Biocenter AB
Göteborg, Sweden
www.tataa.com
neven.zoric@tataa.com

Felix von Stetten

Expected results Department of Microsystems Engineering
Faculty of Applied Sciences
The MagRSA project measurable and quantifiable Laboratory for MEMS Applications
Freiburg, Germany
objectives can be classified in three categories: www.imtek.de
• new molecular diagnostics protocol allowing felix.von.stetten@imtek.uni-freiburg.de
efficient and reliable MRSA diagnostics and
Manuel Gaboyard
genotyping; ADEMTECH S.A.
• new assay reagents including magnetic nanopar- Pessac, France
ticles for sample preparation and quantitative www.ademtech.com
PCR (Q-PCR) related reagents; gaboyard@ademtech.com
• fully automated systems, mainly based on
advanced microfluidics and nanoparticles han-
dling technologies, for MRSA diagnostics and
genotyping.

Potential applications
| Staphylococci growing on agar plates (yellow
The MagRSA project will address the unmet need colonies are Staphylococcus aureus, and white
for new diagnostics tools for management and ones are Staphylococcus epidermidis).
control of antimicrobial resistance in general
and Methicillin-resistant Staphylococcus aureus
(MRSA) in particular. Moreover, MagRSA project
will provide a diagnostics platform with poten-
tial applications in molecular diagnostics as the
most growing segment within the global in vitro
diagnostics market.

99
ACRONYM Contract number: LSHC-CT-2006-037555 | EC contribution: € 2 500 000 | Duration: 48 months
Starting date: 1 January 2007

MAMMI
evalin12.ific.uv.es/ep_mammi

SUMMARY
The proposed project focuses on the
Mammography with molecular imaging
development of a PET prototype dedi-
cated to the examination of breast can-
cer, using a gamma ray sensor based on
an innovative design and the new gener-
ation of photo-detectors and scintillating
crystals. The innovative features of the
PEMT (Positron Emission MammoTomo-
graphy) system proposed will imply
Background Expected results
a high resolution (pushed to the physical
limit), higher sensitivity and lower costs.
Breast cancer is the most common non-skin can- MAMMI proposes a new PET device specifically
It includes integrated analogue and digi-
cer and the leading cause of cancer death in designed for breast cancer diagnosis and evalua-
tal electronics through the design of an
women. The best condition for successful breast tion of therapy response. The dedicated breast
ASIC chip. The main application will be
cancer treatment is early detection. Some stud- cancer PET camera will improve the position reso-
early breast cancer diagnosis and evalua-
ies indicate that early breast cancer detection lution of current whole-body PET cameras (about
tion of chemotherapy response. New
has reduced the disease mortality by about 5mm) and will push it to the physical limit (slightly
radio-tracer molecules will be searched
29 %. The ability to define the extent of disease, below 1mm).
for the detection and visualisation of
to monitor response, and to predict tumour
the pharmacokinetics of breast tumours,
behaviour in patients with breast cancer are The new detector design will also have the ability
more specific than glucose (FDG) for
therefore important public health problems. of detecting the depth of interaction of the gamma
breast cancer, and based on human amino
ray interactions within the crystal with a resolu-
and fatty acids. Phase I Clinical trials will
Conventional methods for breast cancer imag- tion better than 3mm. This is an essential feature
be performed with the new radio-tracers.
ing like X-ray mammography, ultra-sound and since it allows for an improvement of the final
A clinical multi-centric validation will be
Magnetic Resonance Imaging (MRI) produce mor- image resolution by almost eliminating the paral-
performed for the PEMT prototypes.
phologic and structural images, show lesions lax error present in current PET detectors. This is
(like micro-calcifications), but not cancers. On the essential in the case of breast examination since
contrary, imaging methods based on Molecular the detector cameras are placed close to the
Imaging show functional images, metabolism. body, to increase the sensitivity.
This implies that they are much more sensitive
and hence these devices can be used to detect The advantages of the new generation of photo-
and locate malign tumours at an early stage. For detectors (silicon photo-multipliers), such as
instance, PET (Positron Emission Tomography) is their compactness, will be explored. The design
a powerful tool for non-invasive molecular imag- of the electronics, including an ASIC, will allow an
ing diagnostic based on gamma ray (emitted by acquisition rate capability of the order of 1 MHz,
an isotope compound, previously administered with minimum dead time, to cope with the higher
to the patient) detection. sensitivity.

Aim Moreover MAMMI will develop and study more

• Design and development of a dedicated low cost
PET camera prototype for breast examination
with an intrinsic resolution of less than 1 mm,
high sensitivity, and tomographic 3D recon-
struction.
specific than FDG radio-tracers for breast cancer
diagnostic and therapy monitoring, based on
human amino acids (such as FLT) and fatty acids
(such as FAS).
Potential applications

• Study of new and more specific radio-pharma-
ceuticals for breast cancer detection and ther-
apy monitoring (FLT, FAS, etc.). Perform phase I
clinical trials of the radio-tracers.
• Clinical multi-centric validation of the new PEMT
prototype.
The main application will be early breast cancer
diagnosis and evaluation of chemotherapy
response. New radio-tracer molecules will be
searched for the detection and visualisation of the
pharmacokinetics of breast tumours, more spe-
cific than glucose (FDG) for breast cancer, and
based on human amino and fatty acids.

100
Key words: PEMT, PET mammography, molecular imaging, breast cancer diagnosis, chemotherapy

ROLE OF SMEs Scientific coordinator

Jose Ma Benlloch
Consejo Superior de Investigaciones científicas
Each of the three SMEs participating in MAMMI, namely General Equipment for Medical IFIC- Instituto de Física Corpuscular
Imaging S.L. (GEM-Imaging), DIGI UTOPIKA Ltd. (DUT) and Ray Therapy Imaging AB (C-RAD), Edificio Institutos de Investigación
46071 Valencia, Spain
brings specific expertise into this consortium, complementing and strengthening the over- benlloch@ific.uv.es
all group. GEM-Imaging has experience in the construction of gamma ray detectors and is ific.uv.es
therefore crucial to the overall project. It will not only help constructing the prototype, but
also be instrumental in the eventual exploitation at the end of the project. For this purpose, Partners
GEM-Imaging has already conducted a market research study and set up a preliminary Sibylle Ziegler
business plan. C-RAD is involved in the manufacturing of associated electronic parts and Klinikum Rechts der Isar
plays an important role in the building of the prototype. DUT has extensive experience with der Technischen Universität München
Munich, Germany
software development, and bring this knowledge to bear on the project for tailor-made portal.mytum.de/navigation_view
software solutions essential for the operation of the final machine.
Angels Bernabeu
General Equipment for
Medical Imaging, S. L.
Paterna, Spain
www.gem-imaging.com

Johann Hauer
Frauhnofer-Institut für
Integrierte Schaltungen (IIS)
Erlangen, Germany
www.iis.fraunhofer.de

Pedro Branco
DIGI-UTOPIKA Ltd.
Lourinhã, Portugal
www.utopika.net/utopika/EN

Norberg Gunnar
C-Rad Imaging AB
Frösön, Sweden
www.c-rad.se

Anders Brahme
Karolinska Institutet
Stockholm, Sweden
ki.se

Renato A. Valdês Olmos

Netherlands Cancer Institute
Amsterdam, The Netherlands
www.nki.nl
© Shutterstock

101
ACRONYM Contract number: LSHE-CT-2006-037899 | EC contribution: € 2 914 000 | Duration: 36 months
Starting date: 1 January 2007

MANASP
www.manasp.org

SUMMARY
• The goal of the project is to develop
Development of novel management strategies
new treatment strategies for Invasive for invasive aspergillosis
Aspergillosis (IA) which has become the
major infectious complication of treating
haematological malignancies with inten-
sive chemotherapy or haematopoietic
stem cell transplantation (HSCT).

• Ineffective host immune responses

Background
facilitate fungal invasion of the pul-
monary system and other vital organs
Over the past decade, invasive aspergillosis (IA)
leading to death. In order to redress
has emerged as the most serious life-threatening
this immunological imbalance, it is pro-
infectious complication of intensive remission-
posed that new immunotherapeutic
induction chemotherapy and allogeneic HSCT in
strategies are developed, which will
patients with a variety of haematological malignan-
augment current antifungal treatments
cies. Aspergillus fumigatus is the most commonly
and reduce morbidity and mortality.
isolated species from cases of IA and is the focus of
project research although it is believed that the
• Facilitated by recent publication of the
intended outcomes will act as a paradigm for man-
A. fumigatus (the principal pathogen of
agement of IA due to less common species such as
the genus) genome sequence the project
A flavus and the emerging A terreus. Despite the
will exploit new knowledge and tech-
limited improvements that have been made with
niques in genomics and post-genomics.
preventative strategies and the development
The project will identify the immuno-
of new antifungal drugs, IA has an incidence of
logically important fungal molecules to
10-30 % and is still associated with high mortality
design immunotherapies based on vac-
rates as high as 90 % in some surveys. T lympho-
cines using fungus-primed innate immune
cytes provide a critical secondary defense against
cells, monoclonal antibodies or adoptive
this and other fungal pathogens. Therefore,
transfer of specific T lymphocyte clones.
Aspergillus-specific T-cell immunity, transferred
through the infusion of ex vivo-generated, donor-
• The project will also generate new
derived, Aspergillus-specific T-cells might be bene-
nucleic acid based diagnostic tests to
ficial for recipients of allogeneic HSCT.
inform when and how immunotherapy
can be optimally applied.
There are only raw data regarding immunotherapy
The outcomes will have strong commer-
of patients with invasive fungal infection, and min-
imal data relating to IA. This might be due, at least
cial applications which will be delivered
in part, to the complex antigenic properties of
by three leading European SMEs within
A. fumigatus, which have been less well charac-
the consortium.
terised compared to viruses such as CMV or EBV.
Only a minority of the hundreds of (glyco)proteins
of A. fumigatus reported in the literature have
been characterised at either a molecular and/or
biochemical level.
The diagnosis of IA is a particular challenge.
Conventional microbiological methods fail to detect
most cases so that current diagnostic categories
are based on a combination of clinical, imaging,
and histopathological (often post-mortem) criteria.
There have been some advances with non-culture
techniques based on PCR based amplification of
fungal DNA or detection of Aspergillus antigens in
blood samples. However, these have not been
validated as tools for identifying patients at risk or
for monitoring responses to treatment by deter-
mination of fungal loads.
Aim
The overall goal of this project is to develop more
effective management strategies for IA with the
following aims:
• development of immunotherapeutic strategies for
Invasive Aspergillosis. This will be achieved by
identifying the T-cell clones that react with spe-
cific Aspergillus targets and evaluating their effi-
cacy for prevention and treatment of IA. Success
will be measured by characterisation of the gener-
ated T-cells, and demonstration of their functional
properties against Aspergillus;
• development of improved diagnostic tests for IA
with commercial potential. This will be achieved
by identifying appropriate nucleic acid targets,
extraction and amplification protocols and demon-
strating their sensitivity and specificity in clinical
samples;
• validation of a dendritic cell based vaccine
immunotherapy strategy in animal model to gen-
erate protective immunity against Aspergillus;
• use of genomic and proteomic techniques to iden-
tify new Aspergillus targets that interact with the
host’s immune system.
Expected results
• Identification of different pattern recognition
receptors in response to A. fumigatus and their
role in activating DCs.
• Identification of PAMPs of A. fumigatus useful
for immunotherapy strategies.
• Identification of murine DC subsets capable of
inducing antifungal Th responses.
• Adoptive transfer of manipulated DC into mice
suffering from IA.
• Characterisation of Aspergillus-specific T-cell
response in healthy individuals.
• Identification of a protective T-cell response in
patients surviving IA.
• Development of a clinical protocol under current
cGMP-conditions for treatment of patients with IA.
• Modulation of Aspergillus-specific immune
response by transduced T-cells.
• Preparation of a bank of monoclonal antibodies
against A. fumigatus.

102
Key words: immunotherapy, vaccine, antigens, T cells, dendritic cells, A. fumigatus, PCR diagnostics, monoclonal antibodies,
GMP-conditions, aspergillosis, transplantation

ROLE OF SMEs Scientific coordinator

Hermann Einsele
University of Wuerzburg
MANASP focuses on the commercialisation of assays for molecular diagnosis and immune Medizinische Klinik II
therapy of invasive aspergillosis. Three out of nine partners from the consortium are SMEs, Klinikstrasse 6 – 8
97070 Wuerzburg, Germany
while one Work Package leader comes from an SME. Translational strategies for commercial einsele_h@klinik.uni-wuerzburg.de
exploitation of the results exist, including an IPR Advisory Committee.
Project manager
Cepheid AB, who acquired the diagnostic company Sangtec in 2007, already produces
Juergen Loeffler
molecular diagnostic kits for the detection of viral infections. They have 11 years of experi- loeffler_j@klinik.uni-wuerzburg.de
ence within the field of molecular diagnosis and are certified according to ISO-9001/2000.
Their activities comprise research and development, manufacturing and the sale of Partners
CE-labelled PCR-based molecular diagnostics. Cepheid has many patents relevant to MANASP,
Birger Janssen
including a non-exclusive worldwide PCR license, a non-exclusive license for real-time PCR and Cepheid AB
also a non-exclusive worldwide UDG sterilisation license. Currently, they are working on the Bromma, Sweden
optimisation of different fungal PCR assays and on automated fungal DNA extraction. www.sangtec.com
MAT Biotech is a private biotech company founded in 1999. The company has two activities, Tom Rogers
namely the development of therapeutics and an antibody high throughput screening plat- Trinity College
form. With the former, the company focuses on the development of antibody therapies to Department of Clinical Microbiology
treat haematological cancers. MAT’s product portfolio comprises a 90Y-anti-ferritin poly- Dublin, Ireland
clonal (Ferritarg) antibody to treat refractory Hodgkin’s disease, and a 90Y-AMB8LK mono- Jean Paul Latgé
clonal antibody-radioisotope product to treat refractory Hodgkin’s disease, liver cancer, and Institute Pasteur
pancreas cancer, which is in advanced pre-clinical trials. Currently, they perform screening Unité Aspergillus
Paris, France
assays to identify reactive monoclonal antibodies against A. fumigatus.
Miltenyi Biotec GmbH is a leading, international biotech company in the field of magnetic Luigina Romani
cell separation (MACS®technology). Miltenyi Biotec develops, produces and sells world- University of Perugia
wide magnetic cell separation reagents and equipment for biomedical research and clinical Department of Experimental
Medicine and Biochemical Science
applications, particularly in the fields of haematology and immunology. The CliniMACS® Microbiology Section
system is an automated cell selection device. It is approved for clinical stem cell graft engi- Perugia, Italy
neering using CD34 and CD133 selection and permits large-scale cell isolation of other cel-
Jean Kadouche
lular products such as dendritic cell precursors, NK cells and T-cell subsets. In addition, Monoclonal Antibody Therapeutics (MAT)
pioneering technologies are made available, such as MACSiBead™ particles for activation Evry, France
and expansion of T-cells, or the Cytokine Secretion Assay for isolation of cytokine-secreting www.matbiopharma.fr
cells, e.g. antigen-specific T-cells. Reagents and tools for the GMP-grade generation of den- Axel Brakhage
dritic cells and T cells for immune therapy against invasive aspergillosis are also available. Leibniz Institute for Natural Product
Research and Infection Biology
Jena, Germany

• Selection of the most efficient antibodies by in
vitro and in vivo analysis.
• Development of an assay to detect Aspergillus
DNA with high specificity.
• Development of an assay to detect Aspergillus
RNA with high sensitivity.
• Clinical evaluation to confirm sensitivity in detect-
ing Aspergillus infection using standardised defi-
nitions produced by International consensus and
comparison to different well established assays.
• Commercialisation of the assay into an afford-
able and rapid diagnostic test.
Potential applications
• Surveillance of patients being treated for haema-
tological malignancies by chemotherapy or HSCT
using DNA/RNA based molecular diagnostics.
Georg Rauser
This will generate greater ascertainment of possi- Miltenyi Biotec GmbH
ble and probable cases of IA and earlier therapeu- Bergisch Gladbach, Germany
www.miltenyibiotec.com/en/default.aspx
tic intervention leading to improved survival rates.
• Incorporation of these diagnostic tests into inter- Jean-Marie François
nationally accepted EORTC/MSG criteria for clin- Institut National des Sciences Appliquées
ical application in categorising cases of IA to Département de Génie Biochimique
et Alimentaire
facilitate research trials of new antifungal agents Toulouse, France
or other novel therapies.
• Development of immunotherapeutic strategies
based on demonstrated efficacy against Asper-
gillus in vitro and in animal models. This will either
be through adoptive transfer of donor T-cells, or
administration of monoclonal antibodies tar-
geted against immunologically relevant Aspergillus
antigens/epitopes.
• Wider application of this technology to the treat-
ment of other groups of patients (outside the
Haematological Malignancy field).

103
ACRONYM Contract number: LSHG-CT-2006-037226
Starting date: 1 October 2006
MEGATOOLS
www.cellectis.com/megatools
SUMMARY
The MEGATOOL project aims to develop
a large number of new sequence-specific
endonucleases to recognise and target
almost any possible DNA sequence in
any living cell or organism, as well as to
optimise homologous recombination, to
provide scientists with a powerful tool
to undertake functional genomics.
| EC contribution: € 1 999 962
New tools for Functional Genomics based
on homologous recombination induced by
double-strand break and specific meganucleases
Background
The genome sequence programmes have con-
tributed a huge amount of information, and cre-
ated many possibilities. An exhaustive catalogue
of genes is now available for many organisms,
but the real meaning of this information remains
to be deciphered. Thus, the success of functional
genomics definitively lies in the development of
novel tools breaking through the practical limits it
suffers today. Meganucleases-induced recombi-
nation could provide a practical alternative to cur-
rent approaches.
Meganucleases are, by definition, sequence-
specific endonucleases with large (¡ 14 bp)
recognition sites. However, the inactivation or
modification of any and all known genes, or
genomic sequence, depends on the availability of
Meganucleases that cleave within or in the vicin-
ity of each gene sequences. This issue would be
addressed if it was possible to rapidly engineer
the specificity of natural Meganucleases.
Aim
The first objective of the project is to provide the
means to modify a large number of sequences in
rodent genomes. The second is to develop the
tools to engineer a large number of rodent genes,
for functional genomic purposes.
Since meganuclease-induced recombination rep-
resents an extremely powerful tool for gene alter-
ation, MEGATOOL will focus on the generation of
four kinds of results:
• a large collection of novel meganucleases. This
collection of novel proteins should greatly
enhance the repertoire of natural meganucle-
ases and thus allow for the targeting of a large
number of genes in organisms whose genome
has been sequenced, with a strong focus on
rodent genomes;
• the means to exponentially increase this collec-
tion. The collection of novel meganucleases
should provide a unique database of charac-
terised DNA binders. Structural and statistical
104
| Duration: 36 months
studies should reveal the laws governing these
interactions, and this data could in turn be used
in a predictive way, for the design of novel
meganucleases;
• the methods, procedures and quality standards
to make these meganucleases widely usable as
research tools;
• a refined method to use these meganucleases in
cells. The focus will be on mouse cells for func-
tional genomics, providing a direct validation.
Expected results
• Protein engineering: Partner 1 has established
the basis of a combinatorial process to assem-
ble functional engineered meganucleases. It is
expected that this combinatorial strategy will
provide a functional meganuclease for most
chosen genes.
• Computational biology: The FoldX algorithm
can successfully predict the effect of protein
mutation on the specificity of protein-DNA
recognition specificities. Subsequent versions
of FoldX should allow for more efficient design
of meganucleases combinatorial process.
• Structural Biology: A continuous flow of novel
structures that will contribute to the computa-
tional steps is expected.
• Standardisation of protein storage and use:
An efficient purification and characterisation
process for each engineered protein is expected.
• Validation of the general approach: The whole
approach should eventually be validated by
the use of engineered meganucleases on real
chromosomal targets in rodent cells. A general,
standard protocol for rodent cells is expected.
Potential applications
The possibility of correcting errors in a genome
through targeted homologous recombination or
modifying at will any DNA sequence is clearly
enormously attractive to the scientific community.
Key words: functional genomics, genome engineering, protein engineering, meganucleases,
gene targeting, computational biology

ROLE OF SMEs Scientific coordinator

Frédéric Pâques
CELLECTIS S A
The project involves two SMEs (Cellectis S.A. and Fermentas UAB) and two academic labo- 102 Route de Noisy
ratories (CRG and CNIO). 92 235 Romainville Cedex
France
paques@cellectis.com
Cellectis S.A. is a SME biotech company leading the field of genome engineering. Its unique www.cellectis.com
technology and strong intellectual property are centered on homologous recombination
induced by double-strand breaks using meganucleases and its applications. Its aim is to Partners
develop new tools for functional genomics, gene therapy and genome modification. Centro Nacional de Investigaciones
Cellectis has entered into more than 40 deals with industrial partners using living strains or Oncologicas (CNIO)
organisms in their processes. It is also pursuing applications of its technologies to human Structural Biology – Macromolecular
Cristolography Group
therapy. Cellectis has developed specific skills in the field of genome engineering and pro- Madrid, Spain
tein engineering. One of the great achievements of the company lies in a High-Throughput www.cnio.es/ing
Screening platform. Using cell-based functional assays for the identification of novel
endonucleases, this platform has delivered hundreds of novel meganucleases. MEGATOOLS Centro de Regulacio Genomica
System Biology Laboratory
will allow a broad dissemination of Cellectis’ genome engineering tools to the research com- Barcelona, Spain
munity. As a SME demonstrating very strong innovative activity, Cellectis is at the crossroad www.crg.es
of the upstream research that feed the project and of downstream development steps. As
Fermentas UAB
such, Cellectis has a pivotal role in the development of novel products and process within Vilnius, Lithuania
MEGATOOLS. Cellectis will use its High-Throughput Screening platform to deliver custom www.fermentas.com
meganucleases cleaving sequences in the mouse genome. Cellectis will also contribute its
expertise in the field of genome engineering and, more specifically, in gene targeting and
knock-out rodent genes with a panel of novel meganucleases, thereby validating the gen-
eral approach and refining the methods for using these novel tools for functional genomics.

Fermentas UAB, an ISO09001, ISO140001 certified company, is a world leading SME biotech
company in the discovery, manufacturing and marketing of quality molecular biologicals
and in the providing of services to the international research community. Fermentas has
strong expertise in nucleases and in their production, implementation and enzymology. The
company’s product range consists of approximately 400 different molecular biology prod-
ucts, of which 200 are nucleases. Products under the Fermentas brand name are marketed
via a distributor network covering 74 countries in Europe, North and South America, Asia,
Australia and Africa. The key commercial target for Fermentas in MEGATOOLS is to produce
and to make meganucleases developed during the project available to the research com-
munity. Meganucleases, like other restriction enzymes, perform site-specific cleavage of
double-stranded DNA. In fact, these rare-cutting enzymes could be used in many in vitro
applications where restriction enzymes are commonly used. Meganucleases should con-
form to all quality requirements that are applicable to traditional restriction enzymes. The
primary function of the SME in the MEGATOOLS project is to test whether mutant meganu-
cleases created during the project can be used as molecular tools for the rearrangement of
DNA molecules not only in vivo, but also in vitro. After receiving meganuclease mutants,
Fermentas will follow the traditional implementation route of restriction enzymes, including
preliminary evaluation of properties in crude cell extracts, purification, quality controls,
basic enzymology studies and stability tests. These studies will show if and how these
mutant enzymes could be used as analytical tools.

Although it is clearly valuable to understand how
genomic information is translated into function,
rational modification of the DNA sequence of an
organism has been limited by the time consuming
process it requires, despite the development of
new tools for the construction of targeting vectors.
Thus, the possibility of having new tools that will
allow targeting of any DNA sequence for insertion,
deletion or repair could introduce a new revolu-
tion in the field of functional genomics and could
also bring a new paradigm and a new momentum
to human gene therapy.

105
ACRONYM Contract number: LSHM-CT-2007-037831
Starting date: 1 January 2007
MEMORIES
SUMMARY
Alzheimer’s disease (AD) is a progressive
brain disorder that gradually destroys
a person’s memory and ability to learn,
reason, make judgments, communicate
and carry out daily activities. The disease
is the major kind of dementia affecting
elderly people, and the percentage of
patients is going to increase exponen-
tially over the next few years. Currently, no
aetiology and cure has been found. One
major hurdle in drug screening and target
discovery in AD is the lack of a suitable
animal model, as these fail to fully repro-
duce the characteristics of the disease.
The MEMORIES project aims to develop
new mouse models based on deficit of
neurotrophic signalling, potentially use-
ful for developing new therapeutic tools.
| EC contribution: € 2 374 689
Development, characterisation and validation of
new and original models for Alzheimer’s Disease
Background
Alzheimer’s disease (AD) is a neurological disor-
der and is the most common form of dementia in
later life. It is estimated that, by 2050, the number
of people aged 80 years or older will approach
370 million worldwide and that 50 % of those
aged 85 years and older will be affected by AD.
AD is clinically characterised by short-term mem-
ory loss and cognitive dementia, associated with
language and behavioural impairments. The
pathological hallmarks of AD include the presence
of extracellular amyloid plaques, intracellular
neurofibrillary tangles (NFT), neurodegeneration
and cell loss. One severely affected region of the
AD brain is the basal forebrain (which includes the
nucleus basalis of Meynert, the medial septum
and the diagonal band of Broca), a group of
cholinergic neurons that are connected to areas of
the neocortex and hippocampus and that are
important for learning, memory and attention.
The complex degeneration in AD has been fertile
ground for the formulation of hypotheses on the
pathogenesis of the disorder. Methodological
advances allowedshedding light on alterations of
the various neurotransmitter systems in the AD
brain. The discovery of the degeneration in the
basal forebrain, in the context of experimental evi-
dence for the role of acetylcholine in memory, have
led to the development of a symptomatic therapy
for AD, based on enhanced acetylcholine availabil-
ity determined by cholinesterase inhibitors.
Recently, memantine, an uncompetitive antago-
nist of the N-methyl-D-aspartate receptor, was
approved for the treatment of moderate-to-severe
AD. These agents can benefit some AD patients for
a limited period of time. However, due to the exten-
sive and multifocal nature of AD degeneration, the
effects of these neurotransmitter modulators are
modest and the need of a truly disease-modifying
drug persists. Although there have been significant
106
| Duration: 36 months
advances in understanding the biology and subse-
quent diagnosis of AD, such research has not been
translated into a disease-modifying treatment.
One limit in translating basic research findings
into therapeutical agents is the lack of suitable
animal models fully reproducing the AD neurode-
generation. Having animal models reduces the
risk, and thus the cost, of developing drugs.
In the past decade, AD research has been funda-
mentally influenced by the development of geneti-
cally modified animal models of amyloid-driven or
tau-driven neurodegeneration. These in vivo mod-
els – exploited on the basis of early-onset disease
determined by rare, inherited mutations – are
important in understanding the involvement of amy-
loid or tau in the onset of the disease, but failed to
reproduce the hallmarks of the AD pathology fully.
One other potential pitfall in these transgenic
mice is that these models might not be applicable
to sporadic AD. Indeed sporadic forms of AD,
which account for more than 95 % of the popula-
tion afflicted by AD, are multifactorial diseases,
the progression of which is influenced by gender
and epigenetic factors (such as neuroinflamma-
tion, growth factor deficits, autoimmunity/auto-
toxicity). The use of animal models derived from
the genetic forms of AD to screen drugs, instead
of more appropriate animal models, revealed the
limitations of their use for sporadic AD. Indeed,
the vaccine approach seemed to work well in
mice, but brain inflammation in a few patients
triggered an abrupt halt to the clinical trial.
Aim
The MEMORIES hypothesis-driven project gathers
together eight partners from five different coun-
tries towards the aim of developing, characteris-
ing and validating new animal models that have
a real potential for becoming a gold standard in
the AD field.
Key words: Alzheimer’s disease, transgenic mouse model, neurotrophins

ROLE OF SMEs Scientific coordinator

Antonino Cattaneo
European Brain research Institute
Three European SMEs are partners in MEMORIES, and are based in Italy and France. Rita Levi-Montalcini Foundation
These SMEs will receive approximately 35 % of the project budget. Lay Line Genomics is Via del Fosso di Fiorano 64/65
00143 Roma, Italy
an integrated antibody company, focused on the therapeutic area of neurodegenerative a.cattaneo@ebri.it
diseases, whose mission is the discovery of drugs for Alzheimer’s and other neurological www.ebri.it
diseases, leveraging on a unique antibody based technology platform. LLG has an exclu-
sive licence covering any use of the AD11 anti-NGF mouse model. During the MEMORIES Partners
project, LLG will exploit the AD11 mouse model and produce new antibody based mouse Manuel Gaviria
models with the aim of creating new experimental models, also useful in the develop- Neuréva Inc.
ment of new therapeutic tools for this disease. The involvement of the other two SMEs Montpellier, France
www.neureva.com
will be crucial for the standardisation of the procedures to be used in the different labo-
ratories and the management of the project. Neureva conducts drug discovery and drug Thomas E. Willnow
development for diseases of the central nervous system. Its research activity is centred Max Delbrück Centrum
on anatomical and behavioural characterisation of mouse models for CNS pathologies, Für Molekulare Medizin
Berlin, Germany
the choice of mice models being driven by the availability of a large number of transgenic
mice which allows alternative ways for testing molecular or cellular hypotheses. Neureva Liliana Minichiello
will add competencies to standardised protocols and validate mouse models. ACIES is European Molecular Biology Laboratory
Monterotondo, Italy
expert in managing International Management projects and in optimising the financing
of innovation for enterprises working in various industrial and technical sectors. Since Eero Castren
1990, over 500 major companies, research organisations and very innovative small and University of Helsinki
medium-sized businesses, have put their confidence in ACIES to implement financing Helsinki, Finland
systems, valorise innovation or to set up and manage their International projects. Daniel Constam
ACIES’s methodology, based on the principles of Total Quality Management (TQM), Swiss Federal institute of Technology –
allows managing multidisciplinary consortiums. ACIES will provide high quality manage- “Daniel Constam” École Polytechnique
Fédérale de Lausanne
ment services (including knowledge) throughout the project, in accordance with the Lausanne, Switzerland
ISO 10006 (guidelines for quality management in projects) standard.
David Koubi
ACIES
Lyon, France
www.acies.fr

Anders Nykjaer
NeuronIcon A/S
Expected results Potential applications Aarhus, Denmark

Using a multidisciplinary approach, a panel of
mouse models will be produced and analysed
for the presence of neurodegeneration. AD11 anti-
NGF, which already represent a good model for
sporadic AD, will be crossed to mice in which
pro-convertases or SorLA receptors are knocked
out. Additional mice will be created, expressing
mutated form of pro-NGF or in which knockout
of TrkB, TrkA and NGF will be achieved.
Mice will be analysed using standardised method-
ology for neuroanatomy and behavioural analy-
sis. We anticipate that blocking different
signalling pathways will help in ameliorating the
currently available experimental mouse models,
and will also be useful for developing new thera-
peutic tools for this disease and strengthening
European competitiveness in the war against AD.
The creation of a mouse model that by fully repro-
ducing the hallmarks of the disease, will not only
provide insights into the neurobiology of the dis-
ease, but will also allow the evaluation of the
response to drugs, especially in relation to the
effects on pathology is one of the most challenging
aims of AD research.
The potential medical benefits that will derive from
the production of this mouse model are immense.
The identification of protein linked to specific cel-
lular pathways will provide the possibility to
develop new diagnostic assays and new drug tar-
gets for the treatment of AD. Mouse models will
also make it possible to visualise neural circuits in
their normal and abnormal states, which is likely
to have a large impact on the diagnosis of disease
and the evaluation of the effectiveness of therapy.

107
ACRONYM Contract number: LSHB-CT-2006-037702
Starting date: 1 October 2006
Mimovax
www.mimovax.eu
SUMMARY
Alzheimer’s disease (AD) is characterised
by the abnormal accumulation of amy-
loid plaques in the brain. These plaques
mainly consist of the Amyloid- (A) pep-
tides Aβ40/42 derived from the Amyloid
Precursor Protein (APP). In light of the
characteristics of amyloid composition in
patients, Aβ peptides and its truncated
and modified derivatives are highly
attractive targets providing neo-epitopes
not present on parental APP. A Mimotope-
based AD vaccine targeting truncated
forms of Aβ would therefore induce a safe
antibody response exclusively reacting
with the pathological Aβ molecules but
not with parental APP and would avoid
the induction of autoreactive T-cells. This
vaccine will be evaluated in a preclinical
AD animal model and tested in a clinical
trial in patients. Thus, the MimoVax vac-
cine will provide an innovative, safe, cost
effective and efficient approach to suc-
cessfully treat AD patients and to limit the
severe personal and economic impact of
AD on patients, their families and society.
| EC contribution: € 2 370 155
Alzheimer’s disease-treatment targeting truncated
Aβ 40/42 by active immunisation
Background
Alzheimer’s disease (AD) is the most common
form of dementia in humans. According to the
Alzheimer Association, there are currently 12 mil-
lion patients worldwide with estimated social
costs for every patient reaching € 40 000 per year.
At present, no effective treatment is available to
stop the progressive neuro-degeneration and
associated cognitive decline in AD patients. All
treatment strategies applied today are focusing
on the use of small molecular drugs inhibiting the
activity of Cholinesterase to alleviate disease
symptoms. These drugs however have not proven
to effectively halt or revert disease progression
after prolonged treatment.
AD is characterised by the abnormal accumulation
of amyloid plaques in the brain. These plaques
mainly consist of the Amyloid- (A) peptides
Aβ40/42 derived from the Amyloid Precursor
Protein (APP). In humans, the majority of amyloid
plaque material is formed by Aβ40/42 derivatives
which are frequently truncated and modified. Aβ
peptides are considered to be directly involved in
the pathogenesis and progression of AD.
Immunotherapeutic treatment targeting Aβ led
to amyloid plaque reduction and had beneficial
impact on disease progression in animal models.
However, the first phase II clinical vaccination trial
in AD patients using full length Aβ42 as antigen
had to be discontinued due to severe neuroin-
flammatory side effects including brain infiltration
by autoreactive T-cells.
Similar to full length Aβ, truncated and modified
Aβ peptides also seem to be involved in the
pathogenesis and progression of AD. They are
therefore also a suitable point of attack for novel
treatment strategies, but no relevant develop-
ment programme has been started to date.
108
| Duration: 36 months
Aim
The novel technology presented in the MimoVax
project has been developed to create antigens
mimicking the structure of neo-epitopes which do
not contain sequences of the native Aβ peptide.
A Mimotope-based AD vaccine would therefore
induce antibody responses, exclusively reacting
with the pathological Aβ molecules but not
with parental structures like APP. Furthermore,
Mimotopes do not contain potential T-cell self-
epitopes and avoid induction of detrimental auto-
reactive T-cells. Thus, the goal of the MimoVax
project is the development of a safe and effica-
cious Alzheimer vaccine which is predicted to
avoid the development of immunological compli-
cations due to autoreactive T-cells. The develop-
ment of such innovative AD vaccines targeting Aβ
could therefore be a safe treatment regimen to
efficiently fight AD in patients. In addition, new
diagnostic methods will be developed in the
course of the MimoVax project in order to monitor
treatment efficacy.
Expected results
Successful preclinical evaluation of a Mimotope-
based AD vaccine is expected to demonstrate
reduction of amyloid plaque load and alleviation
of the pathologic hallmarks in the brain of animal
models for AD. Additionally, Mimotope-based AD
vaccines will provide means to target the soluble
oligomers of Aβ which are thought to be a major
cause of the synaptic alterations and cognitive
malfunctions typical of AD.
Once these vaccines have proven their efficacy in
reducing Alzheimer-like pathology in our animal
models, an initial clinical trial will be initiated to
demonstrate safety of the identified peptide vac-
cines in patients. The development of such inno-
vative AD vaccines targeting Aβ could therefore
be a safe treatment regimen to efficiently fight AD
in patients and successful completion of initial
clinical testing will be followed by further product
development.
Key words: Alzheimer’s disease, neurodegeneration, dementia, amyloid plaque, truncated Aβ 40/42, mimotope,
active immunotherapy, preclinical characterisation, animal models, clinical trial

ROLE OF SMEs Scientific coordinator

Markus Mandler
Affiris GmbH
The project consortium is constituted by 5 SMEs and 2 academic institutions. Campus Vienna Biocenter
Viehmarktgasse 2a
1030 Vienna, Austria
MimoVax is coordinated by an SME, AFFiRiS GmbH, expert in the development of vaccines markus.mandler@affiris.com
on the basis of peptides to treat Alzheimer’s and atherosclerosis. It is supported a dedicated www.affiris.com
management partner (Biolution Grünert & co keg) also in charge of knowledge transfer and
public relations. JSW-Research’s competences comprise R&D and contract research as well Partners
as the performance of clinical research complemented by histological and biochemical eval- Iris Grünert
uation methods. Its staff possesses long standing experience with a quality assurance sys- Biolution gruenert & co KEG
tem and behavioural studies. piCHEM has been working in the field of peptide chemistry for Vienna, Austria
www.biolution.net
more than 10 years. This enterprise puts its main stress on developing and producing pep-
tides for all kinds of research purposes worldwide. EuroEspes, S.A. expertise includes Antón Alvarez
regular clinical and lab evaluations of patients as well as clinical trials, preclinical pharma- EUROESPES S.A.
cology and genetic diagnosis. Having focused on biochemical research of disorders of Department of Neuropharmacology
Bergondo
the Central Nervous System, EuroEspes has already performed more than 20 clinical trials A Coruna, Spain
concerning Alzheimer’s disease. www.euroespes.com

Manfred Windisch
The tight collaborations between academia and participating SMEs and the financing of the JSW – Research GmbH
clinical trial will provide the basis for the financial exploitation of any IPR generated within Graz, Austria
the project by participating SMEs and academic institutions and will lead to potential www.jswresearch.com
benefit for the participating SMEs and University Institutes. Fritz Andreae
piCHEM research development
Graz, Austria
www.pichem.at

Potential applications
Currently 12 million patients worldwide are suffer-
ing from AD. This number, however, will increase up
to 22 million by 2025, according to the Alzheimer
Association. There is, however, no effective treat-
ment available to stop the progressive neuro-
degeneration and associated cognitive decline in
human patients, thus creating an enormous social
problem for all European societies as well as for the
rest of the western world.
Richard Dodel
The novel peptide vaccine developed in the Philipps-Universität Marburg
MimoVax STREP therefore aims at the potential Marburg, Germany
www.med.uni-marburg.de/
subsequent use in treatment of Alzheimer’s dis- d-einrichtungen/neurologie
ease in human patients. Vaccination will be a cost
effective and powerful way to reduce the econom- Alexander Drzezga
ical and psychological burden exerted by this dis- Technische Universität München
Klinikum rechts der Isar
ease. It would significantly reduce the high costs Munich, Germany
associated with this disease, which will soon www.nuk.med.tu-muenchen.de
exceed US$ 4 billion annually.

| Amyloid plaque staining in the brain of an AD mouse

One of the hallmarks of Alzheimer’s disease is the
accumulation of amyloid plaques in the brain. These
amyloid plaques can be visualised on sections of these
brains by staining with amyloid specific antibodies. This
staining reaction results in a red amyloid plaque (indicated
by a white arrow) surrounded by blue nuclei of surrounding
cells like neurons or astrocytes. A Mimotope-based AD
vaccine as described in this abstract would induce such
specific antibody responses reacting with the pathological
Aβ molecules and could therefore be a safe treatment
regimen to efficiently fight AD in patients.

109
ACRONYM Contract number: LSHG-CT-2007-037291 | EC contribution: € 2 755 356 | Duration: 36 months
Starting date: 1 April 2007

MODEST

SUMMARY
Devices for ultra high-throughput trans-
Modular Devices for Ultrahigh-throughput
fection and screening of primary cells, for and Small-volume Transfection
use in the study of e.g., immunological,
neuronal and liver disorders shall be
developed. Modification of cells is a cen-
tral topic in pharmaceutical and medical
sciences as well as in basic research. The
dominant consideration for cell manipula-
tion is the type of cells used. Until now,
Background as neuronal disorders and liver metastasis to
most often conventional, immortal cell
facilitate investigations of possible mechanisms
lines, being cultured for years or even
Cell transfection belongs to the well established of intervention.
decades in flasks, have been assigned to
technologies in biological, medical, and pharma-
this specified use, although they are
ceutical research but delivery to relevant cells Expected results
mainly irrelevant in physiological and
such as primary cells and adult stem cells is still
medical respects. The optimal choice
a major bottleneck. While conventional trans- On the basis of the Nucleofector® 96-well
would be primary cells, since they are dis-
fection methods, such as lipofection or electro- Shuttle® device and 96-well Nucleocuvette®
tinctly closer to the physiological situa-
poration, usually yield satisfactory results for plates and modules which were launched by
tion than cell lines. However, primary cells
standard cell lines, many other cell lines as well AMAXA in 2006, the Consortium will develop
until recently were hard or often even
as most primary cells are difficult or even impos- ultrahigh-throughput devices and plates. In par-
impossible to transfect by non-viral meth-
sible to transfect with these methods. Viral vec- allel, protocols for cultivating, differentiation,
ods, and consequently, many researchers
tors – as alternative for DNA delivery – work well nucleofection®, and functional screens of pri-
still hesitate to adopt these cells despite
in some cases, but are labour-intensive, not ver- mary cells in small volumes and with low cells
their unquestionable advantages. With
satile, and remain connected with significant numbers will be elaborated and, in a further step,
the advent of the nucleofection® tech-
safety issues. In consequence, most primary cells adapted to the devices.
nology, a unique method for the highly
were considered non-transfectable, representing
efficient transfection of primary cells
was recently made available to the life
a tremendous disadvantage in highly relevant Potential applications
research areas as primary cells most closely
science community.
resemble the situation in the living organism. Innumerable opportunities, e.g., in discovery of
Unlike cell lines, which often have been cultured new regulatory pathways, novel targets, and
for decades, primary cells are freshly isolated potential drug candidates as well as clarification
from the organism’s tissue, and have not gone of signal transduction are addressed by the
through any transformations, the prerequisite for devices that shall be developed in the frame of
the unlimited growth of conventional cell lines. this project. Researchers will make rapid strides
Against this background, it goes without saying in the analysis of the biology of cells among oth-
that the pharmaceutical industry is highly inter- ers for the development of therapeutics, and new
ested in using primary cells instead of cell lines for types of treatments as well as possible cures for
cell-based screening campaigns in drug develop- a variety of diseases and injuries.
ment. With more predictive screens – in terms of
both the relevance of a target and the pharma-
cokinetics/-dynamics of a drug compound – it
becomes much easier to take adequate decisions
as to which targets or compounds to focus for
further development. Consequently, the use of
primary cells in preclinical R&D will positively
impact attrition rates and reduce the significant
time and capital involved in developing a drug.

Aim

The main objectives are:

• the development of devices for ultrahigh-
throughput nucleofection® of primary cells in
multi-well plates; and
• the application of this technology to the
highly relevant area of immunological as well

110
Key words: nucleofection, primary cells, hard-to-transfect cell lines, RNAi, siRNA, ultra high throughput transfection,
adult stem cells, neuronal cells, apoptosis, lead, gene silencing/knockdown, screening

ROLE OF SMEs Scientific coordinator

Herbert Müller-Hartmann
Amaxa A.G.
SMEs play a major role in MODEST, since five of the eight partners are SMEs. Moreover, the Research & Development
medium-sized enterprise AMAXA acts as co-coordinator of the whole project. Nattermannallee 1
50829 Cologne, Germany
herbert.mueller-hartmann@amaxa.com
AMAXA is the only institution worldwide which has the necessary knowledge and experi- www.amaxa.com
ence to adapt the technical needs of device development to the conditions used for the effi-
cient transfection of primary cells and hard-to-transfect cell lines. After performing an Project manager
extensive market study, AMAXA is responsible for prototype building from concept for the Birgit Nelsen-Salz
devices up to testing of software and hardware specifications. As co-ordinator of the proj- Birgit.nelsen-salz@amaxa.com
ect, AMAXA will ensure that the expertise brought to the table by each partner will enable
the collaboration to achieve the goal of providing powerful new tools for basic research and Partners
drug discovery. Andrej Mantei
Deutsches Rheuma Forschungszentrum
The main emphasis of Fotec is on the development steps in injection molding of the multi- Berlin Immunomodulation/DRFZ/German
Rheumatism Research Centre
well plates. This partner will develop the production process for a micro-plate with 384 wells www.drfz.de
and will develop a process concept for the production process of a micro-plate with
1 536 wells (technical study). Together with another partner (HTP Electronics GmbH), Fotec Jörg Pötzsch
also designs the necessary injection moulds. RNAx GmbH
Berlin, Germany
www.rnax.de/en/index.html
AMAXA will support RNAx, Protobios and Dominion Pharmakine to establish nucleofection
protocols and functional assays for relevant cells, in order to evaluate the devices in Kaia Palm
Protobios Ltd.
respect to nucleofection of small volumes and cell numbers up to single cells, respectively. Tallinn, Estonia
With the expertise of RNAx as a partner of MODEST, RNAi technology will become the ideal
basis for a highly efficient high-throughput validation system for the definition of functions Helmut Loibl
of identified targets. RNAx has extensive experience in the development of automated FOTEC Forschungs- und
Technologietransfer GmbH
RNAi, including the adaptation of the system to various cells and cell lines, as well as in the Wiener Neustadt, Austria
development and adaptation of assays to the RNAx automated platform. www.fotec.at/pages/indexEN.html

Josef Anton Pallanits

Protobios has unique expertise in neural stem cells, nervous system development mecha- HTP Electonics GmbH
nisms and transcription regulation networks. The uniqueness of the input of Protobios lies Wiener Neustadt, Austria
in the competition advantage of the new method of creating human neural stem cells and www.hti-ag.at/de/geschaftsfelder/
kunststoff/beteiligungen/htp_electronics/
influencing them to differentiate into various derivates of the nervous system. Protobios
appraises the devices for ultra-high-throughput application, by contributing large cell Naiara Telleria Garay
numbers of hNCS. Dominion Pharmakine S.L.
Cell Biology and Culture Laboratory/
Dominion Pharmakine
The role of Dominion Pharmakine is to identify new biomarkers related to site-specific devel- Derio, Bizkaia, Spain
opment of metastasis, which may be used as prognosis indicators at the clinics, and to opti- www.pharmakine.com
mise the selection of the most likely successful antimetastic targets among large lists of
Thomas Schaumann
candidate genes, ensured by the knock-down functionality assays. Moreover, Dominion Prevas AB
Pharmakine contributes to the MODEST project by providing high-quality primary cell cultures Instrument Development
and considerable experience in cell culture techniques. Västerås, Sweden
www.prevas.com/product development.html

111
ACRONYM Contract number: LSHP-CT-2006-037200 | EC contribution: € 1 505 702 | Duration: 36 months
Starting date: 1 January 2007

MUNANOVAC

SUMMARY
The MuNanoVac STREP project will assess
Mucosal Nano Vaccine Candidate for HIV
a new vaccine strategy to prevent HIV-1
infection based on a primo-vaccination
using a biodegradable synthetic colloidal
carrier made of poly-lactic acid (PLA)
nanoparticles covered with adsorbed
antigens. The aim is to demonstrate that
PLA nanoparticles are a perfect transcu-
taneous or mucosal vaccine vehicle,
Background properties but also the polymer composition and
immunogenic for both arms of immunity
macromolecular architecture, are critical in induc-
and adaptable to many types of antigens
In order to halt HIV infection spreading, a safe and ing an effective immune response. In this context,
as well as easy and simple to produce.
effective AIDS vaccine for both developing and MuNanoVac aims to assess the proof-of-concept
developed countries is urgently needed. Indeed, of a new vaccine candidate to prevent HIV-1 infec-
Such nanoparticle-based vaccine carriers
HIV is still spreading worldwide with more than tion at portal of entry; based on a primo-vaccina-
will allow targeting dentritic cells or trans-
65 million people infected (source: UNAIDS/WHO, tion using a biodegradable synthetic colloidal
porting the vaccine through skin or
2006) and the number of new infections is rising carrier, made of PLA nanoparticles bearing any
mucosal epithelial barriers. To amplify the
sharply in Asian countries, Eastern Europe and sub- absorbed HIV-1 antigens on their surface.
mucosal immune response, the project
Saharan Africa. The numerous research efforts car-
will investigate the potential use of
immunomodulator molecules associated
ried out in this domain have not yet produced an Expected results
efficient anti-HIV vaccine.
with the comparison of two different
The target vaccine candidates will be intensively
immunisation routes.
Many infectious diseases for which no vaccine is evaluated and optimised to reach the best potential.
available suffer from the absence of a good candi- The project will cover the necessary steps to achieve
Moreover, the MuNanoVac project will
date that allows efficient T and B cell immune a complete proof of concept, including preliminary
contribute to advancing a promising vac-
responses. In the case of HIV-1 mediated infec- process development aspects. MuNanoVac will
cine approach for HIV that could also
tion, the present postulate is that both arms of the contribute towards:
prove versatile enough for application to
immune response (humoral and cellular) should • bringing new knowledge and innovative tech-
other poverty-related diseases such as
be stimulated by any potential vaccine candidate. nologies through the HIV vaccine discovery
tuberculosis. With the proposed vaccine
Moreover, recent data on natural primary HIV-1 process, and;
candidate, the project gives Europe
infection establish that the spreading of the virus • proposing new vaccine candidates for combat-
a tremendous opportunity to gain lead-
in the mucosa is essential for the infection to take ing and preventing HIV/AIDS.
ership in the use of biodegradable
place. Hence, every vaccination strategy should
nanoparticles for vaccine carriers.
be able to elicit a strong mucosal immunity at the Additionally, the project results will be promoted
potential sites of contamination and prevent as a basis for developing vaccine candidates for
spreading of HIV-1 virions. other poverty-related diseases. Indeed, the proj-
ect aims to establish a proof-of-concept in order
A future goal for vaccine design is therefore to to promote the potential of PLA nanoparticle-
increase their efficiency by reaching the highest based compounds as effective vaccine candidates
number of antigen-presenting cells (APCs) possi- to support a new HIV vaccine strategy.
ble and to achieve the high local concentrations
required, inducing a potent immune response. Potential applications
Thus, facilitating vaccine compounds penetration
into immunisation sites that are rich in APCs as MuNanoVacs aims at an efficient vaccine strategy
well as specific migration and activation of APCs for the prevention of HIV infection, with a view to
that would benefit the efficacy of new vaccines in treating also other poverty-related diseases.
the induction of protective immune response. Moreover, the advanced research activities con-
ducted in MuNanoVac will generate novel data on
Aim innovative HIV vaccine vehicles with a view to
improving the efficacy of the proposed vaccine.
Current research in the nanotechnology of bioma- This data is crucial for publishing scientific results,
terials is aimed at using nanosystems as vaccine contributing to sharply estimating the accuracy
carriers able to target dendritic cells (DCs) or and pertinence of such new HIV vaccine candi-
allow transport through skin or mucosal epithelial dates and, therefore, for accelerating vaccine
barriers. Results show that not only the colloidal development.

112
Key words: vaccines, immunology and Infections, HIV/AIDS, immune response, vaccine strategy, mucosa,
skin, poly (lactic acid), PLA, nanoparticle and biodegradable carrier

ROLE OF SMEs Scientific coordinator

Jacqueline Huet
PHUSIS
PHUSIS, as the project coordinator, will be in charge of securing the manufacture of selected Espace Randon, 58 Route du Rivet
poly (D, L-lactic acid) – PLA – nanoparticles, with full quality control of the materials, and for 38330 Saint Ismier, France
jhuet@phusis.fr
the scaling-up of the production process – polymerisation, purification, and drying. PHUSIS www.phusis.fr
will also take the lead in securing an agreement among all the parties involved, so that the
process of PLA nanoparticles preparation can be subsequently marketed. Project manager
Bernard Verrier
Institut de Biologie et Chimie des Protéines
UMR 5086 CNRS/UCBL
7 Passage du vercors
69367 Lyon Cedex 07, France
b.verrier@ibcp.fr
www.ibcp.fr

Partners
Robin Shattock
St George’s Hospital Medical School
London, United Kingdom
www.sgul.ac.uk

Teresa Gallart
Hospital Clínic de Barcelona
Barcelona, Spain

Roger Le Grand
Commissariat à l’Énergie Atomique
Paris, France
www.cea.fr

Milan Raska
Palacky University in Olomouc
Olomouc, Czech Republic
www.upol.cz

Behazine Combadiere
Université Pierre et Marie Curie – Paris 6
Paris, France
www.upmc.fr

Ulrike Blume-Peytavi
Charité Universitätsmedizin Berlin
| Uptake of Poly Lactic Acid Nanoparticles loaded with p24 HIV gag protein.by dendritic cells. Berlin, Germany
Illustration by electron microscopy of sub-cellular location in endosomal compartments. www.charite.de

113
ACRONYM Contract number: LSHM-CT-2006-037833 | EC contribution: € 2 700 000 | Duration: 36 months
Starting date: 1 October 2006

MYASTAID
www.euromyasthenia.eu

SUMMARY
Autoimmune Myasthenia Gravis (MG) is
Development of models to improve management
a rare, chronic and heterogeneous neuro- of Myasthenia Gravis: From basic knowledge to
muscular disease characterised by severe
muscle weakness. In most patients, it is
clinical application
due to auto-antibodies to the acetylcholine
receptor (AChR). The detrimental effects of
the autoimmune attack on the muscle are
not fully understood. The current treat-
ments of MG induce severe side-effects
Background autoantigens? Why is the thymus pathologic in
with no permanent clinical remission. The
most cases? Why are females predominant in the
early-onset patients are mostly females
Acquired Myasthenia Gravis (MG) is a rare autoim- early onset disease? What occurs in the muscle
with thymic hyperplasia, while the existing
mune disease with a prevalence around 0.1/2000. after the autoimmune attack? And – finally – how
experimental model for MG (EAMG) does
This disease is due to autoantibodies directed can therapy of MG be improved?
not present thymic pathology. This project
against components of the neuromuscular junc-
intends to develop models to progress in
knowledge, monitoring, diagnosis and
tion and leading to disabling fatigability of mus- Aim
cles. MG is mainly (85 % of the patients) caused by
therapy of MG:
anti-acetylcholine receptor (AChR) autoantibodies Myasthenia gravis (MG) is a well-defined antibody-
• videomicroscopic models to explore the
and in some patients (about 5 %) by autoantibod- mediated disease, but the pathogenic mecha-
motility of lymphocytes involved in
ies against a muscle-specific receptor tyrosine nisms at the effector organ (the thymus) and at
thymic remodelling in young females;
kinase (MuSK). The remaining population for the target organ (the muscle) are still puzzling. The
• new transgenic models overexpressing
which the autoimmune target is not yet identified aims are to improve knowledge, diagnosis, moni-
the CXCL13 chemokine in the thymus, to
is defined as double negative MG patients. toring and management of MG patients. The main
better mimic the human disease which
scientific and technological objectives of the project
involves thymic abnormalities and
If the muscle is the target organ in this disease, are as follows:
increased thymic CXCL13 expression;
the thymus is clearly involved in the pathogenesis
• mouse model of estrogen deficiency, to
of MG with anti-AChR antibodies. Indeed, 50-60 % 1. To improve knowledge on the mechanisms of
determine the influence of estrogens in
of the patients present a thymic hyperplasia with pathogenicity occurring in myasthenia gravis.
predisposition and progression of MG;
germinal centres (GCs) and around 20 % of the • Mechanisms of thymus remodelling in young
• humanised NOD/SCID mouse model
patients have a thymoma. The titre of anti-AChR is patients. This topic will be addressed by
transferred with human MG thymocytes to
not correlated with the severity of the disease but a genomic approach using cDNA microarrays and
test therapy by human regulatory T cells;
is associated with thymic abnormalities. The a post-genomic approach exploring the role of
• T cell receptor-based signature, for bet-
hyperplastic thymus includes all the components chemokines previously identified as key mole-
ter classification and monitoring of MG
of the anti-AChR response: the autoantigen cules in the development of the disease. New
patients;
(AChR), B cells producing anti-AChR antibodies transgenic models overexpressing CXCL13 in the
• rat EAMG models immunised with
and anti-AChR autoreactive T cells. The thymus is thymus will be established to investigate whether
Torpedo AChR, to test an array of ther-
thus clearly involved in the development of MG germinal centers (GCs) will be generated after
apies (IVIg subfractions, chemokine
and thymectomy is often advised for MG patients inducing the disease in this animal model.
inhibitors, regulatory cells);
improving slowly but efficiently over a few years • Determination of the consequences of the
• rat models immunised with recombinant
their symptoms. The other pharmacological treat- autoimmune attack on the muscle organisation,
human AChR subunits, to determine the
ments proposed are: gene expression and function.
contribution of each subunit to the path-
• symptomatic drugs such as cholinesterase – The transcriptome analysis of muscle biopsies
ogenicity and develop immunotherapies;
inhibitors preventing the degradation of acetyl- should identify a specific signature for the dif-
• monkey models to test protective anti-
choline; ferent subgroups of patients: patients with
AChR antibodies.
• glucocorticoids and immunosuppressor drugs anti-AChR antibodies or with anti-Musk anti-
which are used for many autoimmune diseases bodies, and double negative patients.
Since the research teams involved in this
and act in a global way on the immune response; – Identification of new genes and proteins
programme also participate in a large
• plasmapheresis or intravenous human immuno- deregulated as a result of the autoimmune
‘European MG Network” supported by the
globulins in crisis period. attack by analysis of muscle transcriptome in
EC, interactions between the two networks
MG patients, rat EAMG, and in vitro model.
will promote efficient dissemination of the
Although progress has been made in developing – Investigating the specificity and pathogenicity
obtained knowledge.
therapies for MG, this disease is still incapacitat- of each subunit domain. New in vivo models
ing and treatments are not satisfactory. Many will be created by immunising the rodents
questions remain unanswered: Why is there no with each subunit ectodomain as well as their
correlation between the anti-AChR antibody titer combination to evaluate the pathogenicity of
and the disease severity? Which are the other each subunit.

114
Key words: Myasthenia gravis, rare disease, chemokines, hormones, transcriptome, thymus, muscle,
diagnosis, anti-TCR antibodies, therapy, antibodies, acetylcholine receptor, regulatory cells

ROLE OF SMEs Scientific coordinator

Sonia Berrih-Aknin
Université Paris Sud (UPS)
The MYASTAID consortium includes 6 SMEs which will have a key role in the development of CNRS UMR 8162 Hôpital Marie Lannelongue
new diagnostic and monitoring assays, and in the development of new therapeutics Avenue de la Résistance 133
92350 Le Plessis-Robinson, France
approaches. Therefore, MYASTAID will reinforce the SMEs scientific and technological knowl- sonia.berrih-aknin@u-psud.fr
edge on the validation of innovative solutions. The highly experienced SMEs participating in
this project aim to exploit the RTD findings for commercial markets and its translation to the Partners
clinic. The following table shows the contribution and potential benefits to each of the SMEs.
Socrates Tzartos
Hellenic Pasteur Institute (HPI)
Athens, Greece

• Understanding the female predominance in the
early onset disease by analysing the transcrip-
tome of the human thymus in young normal
males and females and by exploring the influ-
ence of sexual hormones on the susceptibility of
MG disease in animal models.
2. To improve diagnosis and monitoring of
Myasthenias.
• By developing a new diagnostic assay more
easy and to develop a monitoring assay of the
autoimmune and regulatory status.
• By searching for the autoantigen in the anti-
MuSK and anti-AChR negative patients by using
proteomics approach.
• By analysing the complete repertoire of the T cells
and the diversity of the anti-TCR antibodies.
3. To improve therapy for MG using several
approaches all of which are based on modula-
tion of the adverse autoimmune response
and/or activation of the muscle response to the
autoimmune attack in animal models.
Expected results
• Identification of genes involved in MG patho-
genesis.
• Mechanisms of action of germinal centre devel-
opment in the thymus.
• Establishment of transgenic mice overexpress-
ing CXCL13 in the thymus and determination of
the role of CXCL13 in the development of thymic
pathology.
• Identification of genes of predisposition specific
to females.
• Identification of new autoimmune targets in
double negative MG patients.
• Mechanisms of action of anti-TCR antibodies.
• Development of new therapies for MG.
Marc De Baets
Potential applications University of Maastricht (UM)
Maastricht, The Netherlands
This project aims to improve diagnosis and moni-
toring. The collaboration with 6 industrial part- Sara Fuchs
Miry Souroujon
ners included in this project will help developing Tsvee Lapidot
the following clinical applications: Weizmann Institute of Sciences (WIS)
Rehovot, Israel
A new, easier diagnostic assay for anti-AChR anti- Amnon Peled
body titers is expected to be developed. Orly eizenberg
Biokine Therapeutics Ltd. (BKT)
A biological diagnosis is still expected for double Jerusalem, Israel
www.biokine.com
seronegative MG patients. But in that case, the
research proposed in this project aims first to Eugene Boswans
identify this autoantigen. Epsilon Biotech (Ebiot)
Antwerp, Belgium
The use of the technology developed by one of the Paul Parren
project’s industrial partners to analyse the T cell Genmab B.V. (GMB)
Utrecht, The Netherlands
repertoire in MG patients will provide a pioneer- www.genmab.com
ing work as an example for studies in other dis-
eases therefore increasing the existing market for Nicolas Pasqual
immune signatures. This technology is based on ImmunId Technologies (IDT)
Grenoble, France
a genomic approach, exploiting sequences of the www.immunid.com
entire TCR locus.
Orgad Laub
OMRIX biopharmaceuticals Ltd.
The development of a new tool named antiTracKeR, Nes-Ziona, Israel
to analyse the anti-TCR repertoire. www.omrix.com/index.asp
The arrays of therapies to be used in animal mod- Michael Roberts
Regulon A.E.
els and particularly in the humanised mice model Athens, Greece
should result in novel therapeutic approaches. www.regulon.org
| Thymic Hyperplasia in early onset
myasthenia gravis patient.The staining
in red (anti-keratin) represents the
epithelial network all over the thymus,
and the staining in green (anti-CD21)
labels B cells and follicular dendritic
cells visualizing the germinal centers.
The picture was obtained by an original
technique using a scanner for microarray.

115
ACRONYM Contract number: LSHB-CT-2006-037479 | EC contribution: € 2 480 000 | Duration: 36 months
Starting date: 1 December 2006

MYOAMP

SUMMARY
Many groups have used animal models to
Amplification of human myogenic stem cells
investigate the possibilities of using in clinical conditions
autologous cell therapy for muscular dys-
trophies, but these data are dispersed,
not always comparable and little atten-
tion has been focused on the transfer of
this knowledge towards applications for
therapeutic trials.
Background be monitored, as well as a combination of recep-
Data exist on injecting murine cells into
tors known to trigger proliferation, (FGF, IGF1, … ).
mouse muscle, but information regarding
Many clinical trials using muscle cells have been The stability of the parameters initially examined
human cells is sparse. The feasibility of
developed in the past for Duchenne Muscular in non-GMP conditions, will be checked through
autologous myoblast transfer therapy
Dystrophy with very limited success. The recent amplification in various conditions, to allow the
has already been demonstrated for car-
emergence of new therapeutic venues, based definition of both guidelines for GMP production
diac repair, even if in cardiac therapy,
upon post-transcriptional genetic corrections and key-parameters to be followed during the
injected cells were mainly used to coun-
called ‘exon-skipping’, has raised new hope for GMP amplification.
teract the development of fibrosis in
this disease. Using viral transfer approaches it
patients devoid of any defect in skeletal
has given very promising results but cannot reach The number of cells to be injected at each implan-
muscle.
every muscle of the body and trigger an immune tation, which is purely empirical in many clinical
response to the vector. Autologous cell therapy trials, will be tested and optimized in a model of
The fact that pre-clinical trials developed
may bypass this reaction and be used as a com- implantation of human cells in immuno-deficient
in mouse models of muscular dystro-
plement or alternative if the cell type used ful- mice, in order to define the maximum number of
phies have been successful as compared
filled both being an efficient vector and bringing cells to be finally amplified in GMP conditions.
to clinical trials, which used mostly allo-
a functional benefit to the diseased muscle.
genic cells and resulted in very limited
clinical benefit for the patients, illus-
Expected results
Autologous muscle cells cannot be used since
trates the urgent need for pre-clinical
these are already defective in dystrophic muscle, The main expected result is to obtain the final
studies using human cells.
while stem cells from other origins are ideal candi- product, i.e. protocols to obtain amplified human
dates, as long as their myogenic and proliferative stem cells, in a state that will allow an optimized
MYOAMP will aim to define conditions
potentials are ensured. In this perspective mesoan- efficiency in injections in vivo.
and guidelines to produce transduced
gioblasts, which have already been used in
human stem cells as vectors for clinical
a mouse model of muscular dystrophy, and AC133 In addition to basic knowledge on the amplifica-
trials. MYOAMP will synergize expertises
cells have a therapeutic potential as demonstrated tion mechanisms, MYOAMP will bring guidelines
from European leaders in their respective
in the mouse, but very little is known about the con- and standard operative procedures to obtain
field to set up conditions for autologous
ditions required to amplify in GMP conditions these these cells in a reproducible and safe manner that
transfer of human stem cells in GMP con-
stem cells isolated from humans, which is an can be directly transferred to SMEs and clinicians
ditions for the treatment of DMD by
essential step required before any clinical trial. for clinical applications.
exon-skipping. It will ensure that these
conditions and guidelines are transferred
to SME and clinicians, defining efficient
Aim These guidelines will therefore address technical,
ethical and safety issues in a GMP environment.
integration through dedicated partners
MYOAMP will address the question of the amplifi-
within the 3-years duration of this project.
cation of these cells used as autologous cell ther- Potential applications
apy vectors and their safety.
Pre-clinical Protocols, Standard Operating Proce-
The cells transduced with a lentiviral construct dures to characterize, amplify and assess myo-
allowing exon-skipping will be selected and further genic human stem cells for autologous cell
amplified. It should be noted that transduced cells therapy treatments in muscle disease.
may be cloned so that their integration site is deter-
mined), as will be proposed in the part of MYOAMP Ethical and safety procedures to cover the pro-
that focus on safety and ethics. In vitro and in vivo tocols.
approaches will bring understanding on the regula-
tion of proliferation, while the telomere length Specific culture medium with a defined set of
(reflecting the mitotic clock status of the cell) will growth factors.

116
Key words: human stem cells, neuro-muscular diseases, cell proliferation, cell therapy, exon-skipping

ROLE OF SMEs Scientific coordinator

Vincent Mouly
INSERM
3H Biomedical cell provider and responsible for defining standard operating procedures UMR S 787 Myologie
(SOP) for cell handling. Institut de Myologie
105 bd de l’Hôpital
75634 Paris Cedex 13
CELLGENIX development of adapted serum-free culture medium and definition of SOP. France
mouly@ext.jussieu.fr
www.inserm.fr
GENOSAFE development of safety procedures and assays for the process. www.institut-myologie.org

Partners
Luis Garcia
INSERM
Paris, France

Yvan Torrente
University of Milan
Milano, Italy

Giulio Cossu
Fondazione Centro San Raffaele
del Monte Tabor
Milano, Italy

Jenny Morgan
Imperial College
London, United Kingdom

Otto Merten
Généthon,
Evry, France
www.genethon.fr

Mallen Huang
3H Biomedical
Uppsala, Sweden
www.3hbiomedical.com

Roland Bosse
Cellgenix Gmbh
Freiburg, Germany
www.cellgenix.com

Vincent Giuliani
Genosafe S.A.
Evry, France
www.genosafe.com

Anton Ottavi
Inserm-Transfert
Paris, France
www.inserm-transfert.fr

117
ACRONYM Contract number: LSHB-CT-2006-037245
Starting date: 1 January 2007
NanoSense
www.nanosense.eu
SUMMARY
There is a need for high sensitivity non-
separation immunoassay technology for
general clinical chemistry instrument
platforms. This need is particularly evi-
dent for large protein disease markers of
low concentration, such as NT-proBNP,
PSA, and a long list of other plasma pro-
teins, protein hormones and specific
antibodies. Such new technology will sig-
nificantly change the diagnostic industry
and healthcare providers much greater
efficacy.
| EC contribution: € 1 433 600
Moving sensitive immunoassays from
slow and expensive to fast and affordable
nanoparticle-based methods
Background
Traditionally, immunoassays have been separa-
tion based, meaning that the analyte of interest
goes through several steps of antibody binding,
washing and separation before final detection.
This type of assay requires a high use of consum-
ables, which is expensive and time consuming
due to all the steps. On the other hand, in a
non-separation assay no separation steps are
involved and the use of consumables is limited,
making the assay less expensive and with a much
shorter assay time. A non-separation assay will
typically be run on a clinical chemistry platform
intended for high-throughput of analytes, making
homogeneous non-separation immunoassays
a high potential market growth opportunity.
Aim
The aim of the project is to move immunoassays
from slow and expensive methods to fast, high-
throughput super-sensitive nanoparticle based
methods. In addition, the project aims to generate
intellectual property for such technology.
118
| Duration: 36 months
Expected results
To achieve the goal of this project, methods and
techniques will be used to optimise each compo-
nent in the assay. When technology, as described
above, was developed for small molecule markers
15 years ago, a large change in the diagnostic
industry was seen and two small SMEs grew into
big industrial corporations. The project foresees
that similar effects may occur when such technol-
ogy is also developed for large molecule markers.
Potential applications
New high sensitivity high speed assay products
on automated clinical chemistry platforms for use
in laboratories throughout the healthcare system,
for higher throughput and for improved cost-
effectiveness.
Key words: nanoparticles, clinical assays, turbidimetry, high sensitivity

ROLE OF SMEs Scientific coordinator

Guri Skjeltorp
Dalen Diagnostics AS
There are five participants in this project, with three being SMEs. The co-ordinator role is Kolsroedveien 120
undertaken by one of the SMEs, Dalen Diagnostics AS in Norway. In addition to the coordi- 1599 Moss, Norway
email@dalendiagnostics.no
nation, the company possesses the necessary expertise for improved signal generation in www.dalendiagnostics.no/
homogeneous nanoparticle assays. The other two SMEs are: 77 Elektronika Kft in Budapest, dalendiagnostics/vis.php
Hungary, which specialises in the field of medical electronics and manufactures blood glu-
cose meters, urine analysers and rapid test readers; and Getica AB, a small, Swedish biotech Partners
company specialising in bioorganic coupling chemistries and bioprocessing of protein Erling Sundrehagen
conjugates and nanoparticles. Ingrid Hulthén
Getica AB
Tösse, Sweden
In the consortium, there is also a large industrial company, Merck Chimie SAS, Europe’s www.getica.se
largest producer of nanoparticles, and an academic participant, the Groningen
University Medical Centre, which provides a reference laboratory for measurements in Richard Vidal
large epidemiological studies. Cécile Genies
Merck Chimie SAS Estapor
Fontenay-Sous-Bois, France
www.estapor.com

Uzonka Farkas
Péter Jakus
77 Elektronika Muszeripari Kft
Budapest, Hungary
www.e77.hu

Dick de Zeeuw
Stephan J L Bakker
Department of Clinical Pharmacology
University Medical Center Groningen
Groningen, The Netherlands
www.umcg.nl

119
ACRONYM Contract number: LSHM-CT-2006-036534 | EC contribution: € 3 299 809 | Duration: 36 months
Starting date: 15 October 2006

NEOBRAIN
www.neobrain.eu

SUMMARY
NEOBRAIN brings together small and
Neonatal estimation of brain damage risk
medium-size enterprises (SMEs), larger and identification of neuroprotectants
companies and academic groups devoted
to the diagnosis, management and neu-
roprotection in newborns with perinatal
brain damage. The focus of NEOBRAIN is
the prevention of brain damage mainly
observed in pre-term newborns.
Background for interventional neuroprotection. The consortium
The objectives of NEOBRAIN are:
will study, in various established animal models,
• to generate marker profiles of damage in
Prevention of perinatal brain damage is of major the mechanisms that lead to perinatal brain dam-
multiple animal models and in human
importance for public health and obviously for age in order to identify genomic, proteomic and
pre-term infants using genomic/genetic,
individual wellbeing. Both white and grey brain metabolomic biomarkers to generate biomarker
proteomic and metabolomic approaches,
matter are affected in perinatal brain damage profiles. They will also establish biomarker profiles
as well as imaging and electrophysiologic
observed in pre-term infants. Long-term conse- in human newborns in an observational clinical
modalities;
quences of extreme prematurity are devastating, study involving extremely pre-term infants born
• to develop neuroprotective strategies
and perinatal brain damage clearly plays a role in before completion of 28 weeks gestation (normal
by identifying candidate molecules for
this scenario. The current pathogenetic paradigm pregnancy duration: 40 weeks).
intervention in animals;
of perinatal brain damage in pre-term infants
• to implement a platform for an observa-
has multiple interrelated aspects and includes Once identified biomarkers of damage and poten-
tional clinical epidemiologic study in
infection/inflammation, hypoxia-ischemia, exci- tial avenues for neuroprotection, the project will
human infants designed to contribute
totoxicity, and free radicals. It is likely that these start developing an intervention, using multiple
to objective 1 above, and to transfer
mechanisms do not act alone, but in concert. animal models to pursue this goal. Only the most
from the animal to the human level
promising strategies will be considered worthy of
insights gained in objectives 1 and 2;
The absolute number of neurological handicaps being translated from bench to bedside.
• to prepare for drug testing by using the
of perinatal origin is increasing in western coun-
project structure as a platform for initial
tries due to the increasing survival of pre-term Further step of the project will be to implement
steps in clinical testing of potential
infants. The major brain lesions associated with a clinical platform
interventions discovered in NEOBRAIN.
cerebral palsy (CP) and cognitive impairment are • to design a biomarker profile of perinatal brain
white matter damage (WMD), mostly occurring in damage in experimental animals and in human
The project further envisages developing
very pre-term infants (born in less than 32 weeks newborns (see above). Thus, participants will
the clinical platform in such a fashion that it
of gestation), and cortico-subcortical lesions establish a functional network of institutions car-
can serve as the basis for subsequent large-
mostly observed in term infants. For financial, ing for newborns that can serve as the basis for
scale pan-European perinatal neuropro-
technical and ethical reasons, the pharmaceutical such a clinical study, designed to identify human
tective research initiatives (Euro-Neo-Net,
industry has difficulties in making substantial biomarker profiles based on genetic and bio-
EURAIBI).
investments in this area, and this has left perina- chemical markers, electroencephalographic (EEG)
tologists with a limited therapeutic arsenal. At the patterns and magnetic resonance imaging (MRI);
present time, despite major improvements in • the consortium will use and expand this platform
neonatal care, there are no established therapeu- for clinical drug testing both within the 36 months
tic regimens for the prevention or treatment of of NEOBRAIN and thereafter.
perinatal brain lesions that are successful.
Nevertheless, epidemiological and experimental Finally, NEOBRAIN will pave the way for clinical
data have allowed the identification of potential drug development. In essence, the clinical plat-
targets for neuroprotection. New animal models, form will be designed in a way that allows for
such as those employed in NEOBRAIN, clearly quick expansion (i.e. recruitment of further cen-
show the pathophysiology involved in neurode- tres), so that bench-to-bedside translational
generation and will help identify neuroprotective steps (i.e. a clinical trial) can be taken quickly after
strategies in the newborn. NEOBRAIN is finished.

Aim Expected results/potential applications

To help reduce the enormous individual, familial NEOBRAIN provides an obvious potential impact
and societal burden that perinatal brain damage in helping to reduce mortality and stamp out devel-
represents, the first objective of this project is to opmental disabilities associated with perinatal
identify early damage markers and novel pathways brain damage.

120
Key words: newborns, hypoxia/ischemia, inflammation, perinatal brain damage neuroprotectants

ROLE OF SMEs Scientific coordinator

Olaf Dammann
Hannover Medical School
Five companies (three of them being SMEs) play crucial roles in the NEOBRAIN project. Two Carl-Neuberg-Str. 1
SMEs are devoted to develop biomarkers in the field of metabolomics (BIOCRATES life sciences, 30625 Hannover
Germany
Austria) and proteomics (BIOANALYT, Germany). A larger company, NEUROPHARMA (Spain) and dammann.olaf@mh-hannover.de
THERAPTOSIS S.A., an SME (France) are designing and developing innovative neuroprotective
drugs. BrainZ, a New Zealand based company (but not an SME) producing electroencephalogra- Partners
phy (EEG) hard- and software, is interested in the development of EEG-markers of perinatal brain
Medizinische Hochschule Hannover
damage. BrainZ has expertise and services not available in Europe and offers important assis- Hannover, Germany
tance at no cost to the NEOBRAIN project. All efforts of the NEOBRAIN research are directed
towards the development of neuroprotective pharmacological strategies that will be directly BIOCRATES life sciences GmbH
Innsbruck, Austria
exploited by the SMEs participating in the project. The involvement of the companies provides www.biocrates.at
a unique opportunity for using the research results in product development without delay.
BrainZ Instruments Ltd.
New Zealand
www.brainzinstruments.com/index.asp
The most important source of societal suffering tion the participating companies as market lead-
from perinatal brain damage is at the individual ers not only in Europe, but also in the USA, Bioanalyt GmbH
and family level. Four out of five pre-term infants Australia and Asia. Potsdam, Germany
www.bioanalyt.com
are limited in their everyday activities. Moreover,
brain-damage-associated cognitive and learning New multi-parametric biomarker measurement THERAPTOSIS S.A.
difficulties represent a potentially preventable tools will be developed based on metabolomic Romainville Cedex, France
source of suffering. It is NEOBRAIN’s goal to con- and proteomic techniques. These tools, in turn, www.theraptosis.com/english/home/
index.htm
tribute to an improvement of this situation for will help improve clinical diagnostics with regard
future generations. to perinatal brain injury, and this will contribute NEUROPHARMA S.A.
to a greater potential for neonatologists to con- Tres Cantos, Madrid, Spain
www.neuropharma.es
Also the economic burden of prematurity sult with parents and within their therapeutic
immense, taking into consideration cost of hos- teams about the individual child’s prognosis. The University Medical Center Utrecht
pital inpatient admissions plus non-hospital growing medical subdiscipline of ‘neonatology’ Utrecht, The Netherlands
www.umcutrecht.nl/zorg
inpatient health care costs, such as costs is a potential market for tools to be developed
incurred through family practitioners, educational in NEOBRAIN. Göteborgs universitet
and social services, considering that approxi- Goteborg, Sweden
mately 60 000 infants sustaining some sort of Another potential market among sick and pre- www.gu.se
brain injury. term newborns is called ‘theranostics’, the indi- Institut National de la santé
vidualised surveillance of therapy efficacy and et de la Recherche Médicale
In addition to the societal and economic impact, results. NEOBRAIN will contribute to this field Paris, France
www.inserm.fr
the close cooperation and integration of enter- by offering improved strategies for biomarker
prises and academic centres offers the unique measurements, including imaging and electroen- Université de Genève
chance to exploit new business areas and posi- cephalographic markers of infant wellbeing. Hôpitaux Universitaires de Genève
Geneve, Switzerland
www.unige.ch/medecine/index.html

Charité Universitätsmedizin Berlin

Berlin, Germany
www.charite.de

Università degli Studi di Siena

Siena, Italy
www.unisi.it

Lunds Universitet
Lunds, Sweden
www.lu.se

121
ACRONYM Contract number: LSHB-CT-2007-037590 | EC contribution: € 2 981 000 | Duration: 36 months
Starting date: 1 February 2007

Net2Drug

SUMMARY
New high-throughput methods allow the
From gene regulatory networks to drug prediction
generation of massive amounts of molec-
ular biological data. These, mainly phe-
nomenological, data are often difficult to
ascribe to the activation of particular sig-
nal transduction pathways and/or tran-
scriptional regulators. A way to facilitate
data interpretation is to construct gene
regulatory networks that include signal
Background Aim
transduction mediators, transcriptional
regulators and target genes. This is
Complex diseases such as cancer are caused by The main aim of this project is to develop an
a complex task, not only because of the
the disregulation of expression of many different integrated technology, comprising cutting edge
huge number of molecules involved, but
genes, resulting in the malfunction of complex cel- bioinformatics, chemoinformatics and experi-
also because of variations across tissues,
lular process. Every cellular state is characterised mental methods, to study the mechanisms that
developmental stages and physiological
and precisely organised by differential expres- cause complex diseases. Understanding the
conditions. However, these networks hold
sions of specific sets of genes. Gene expression is mechanism of diseases is the key to rationalising
the key to the understanding of the regu-
mainly regulated at transcriptional level through drug development.
latory processes within a cell and, thus, to
sequence-specific binding of transcription factors
most life processes in general. The aim of
this project is, therefore, to develop
(TFs) to their target sites in regulatory regions of Expected results
genes, where the combination of these sites and
a toolbox that combines the different
bound factors provide the required specificity. For The aim of this project is to develop a toolbox that
high-throughput experimental methods
the whole genome, we might expect millions of combines and puts different high-throughput
together under the roof of bio- and
functional sites regulating expression of genes experimental methods together under the roof of
chemo-informatics, to allow the exploita-
under different conditions, of which we have the bio- and chemo-informatics, to allow the exploita-
tion of the full potential of the included
knowledge of only a few per million. Therefore, tion of the full potential of the included methods,
methods, as well as the generated data.
computational methods for the prediction of TF as well as the generated data.
The toolbox will comprise a combination
binding sites in genomes are needed.
of the most innovative bioinformatic
This toolbox shall provide a cost- and time-effec-
techniques, based on databases and
New experimental high-throughput approaches tive, knowledge-based approach that allows iden-
methods of artificial intelligence, mod-
have been introduced to study the gene regulatory tification of signal transduction mediators and/or
ern methods of chromatin structure
(and other molecular) mechanisms of complex dis- transcriptional regulators responsible for certain
analysis, micro-array technologies,
eases. Among them are the ChIP (Chromatin changes or responses of the cell, in particular
transcription factor-binding site identi-
Immuno Precipitation)-on-chip method for the iden- those which lead to diseases, thereby facilitating
fication, as well as chemoinformatics
tification of target genes for various transcription the discovery of new targets and consequently the
methods for computer-aided prediction
factors on a high-throughput scale, and RNAi rational design of target-specific drugs.
of biological activity spectra.
approaches (gene silencing by small double-
stranded interfering RNAs) for the functional eluci- Potential applications
dation of selected genes. Novel computation
methods are needed for the automatic interpreta- Identification of drug targets in breast cancer and
tion of high throughput data in order to formulate other diseases.
a hypothesis of molecular mechanisms of diseases.

122
Key words: transcription factors, ChIP-on-chip method, microarray, analysis of promoters, drug targets

ROLE OF SMEs Scientific coordinator

Alexander Kel
BIOBASE GmbH
A number of SMEs (BIOBASE, Progenika and ISB), particularly from the bioinformatics sec- Halchtersche Str. 33
tor, take part in the project, thereby strengthening the link between basic research and 38304 Wolfenbüttel
Germany
a possible later application of the developed technology, either in the form of a service for alexander.kel@biobase-international.com
the pharmaceutical and biotechnological industry, or as a marketable product. www.biobase-international.com

BIOBASE is a coordinator of the project. Among the tasks carried out are: Partners
• manual annotation of project relevant data into existing databases, namely TRANSFAC®, Progenika Biopharma S.A.
TRANSPATH®, and TRANSCompel®; Derio, Spain
• providing the data collected to the community; www.progenika.com
• DNA sequence analysis: search for putative binding sites for TFs; National Public Health Institute
• development of software for the reconstruction of a gene regulatory network (transcription Helsinki, Finnland
network) from the microarray experiments; www.ktl.fi
• causal analysis of experimental data provided by other partners of the consortium and
Fraunhofer Gesellschaft zur Förderung
computational identification of drug targets; and der angewandten Forschung e.V.
• maintaining the workflow for the chemoinformatics group, providing drug targets for Munich, Germany
further prediction of perspective chemical compounds. www.fraunhofer.de

Universitätsmedizin Göttingen
Progenika carries out the microarray analysis and gene validation by RNA interference. Georg-August-Universität Göttingen
Stiftung Öffentlichen Rechts
ISB is responsible for the visualisation of gene regulatory networks, automatic in silico Gottingen, Germany
www.med.uni-goettingen.de
reconstruction of pathways, and methods of semi-quantitative modelling of gene regula-
tory networks. It is involved in the development of a microarray database format and user Institute of Systems Biology, Ltd.
interface, composite modules, methods of artificial intelligence and data mining, and the Novosibirsk, Russian Federation
prediction of the most promising drug targets and markers for breast cancer. Institute of Biomedical Chemistry
of Russian Academy of Medical Sciences
Moscow, Russian Federation

Karolinska Institutet
Stockholm, Sweden
www.ki.se

National Research Council – CNR

Rome, Italy
www.cnr.it

© Shutterstock

123
ACRONYM Contract number: LSHM-CT-2006-037692
Starting date: 1 December 2006
NPARI
www.npari.org
SUMMARY
The apoE and apoB human proteins have
recently been linked to the innate
immune system. Peptide sequences
derived from these proteins have been
shown to have varied anti-infective prop-
erties which can be modified by small
changes to the core peptide sequence.
Thus, the apoE and apoB peptides
exhibit antibacterial, antifungal and
antiviral properties and present an excel-
lent opportunity to develop novel thera-
peutics and medical device coatings.
Specifically the exploitation of these
novel peptides allows for the potential
development of a new array of agents tar-
geting against the growing problems of
antibiotic resistant microorganisms.
| EC contribution: € 2 800 000
Tailoring of Novel Peptide coatings and therapeutics
derived from a newly identified component of the
human innate immunity Against Resistant Infections
Background
Infectious diseases represent the most common
cause of morbidity in the world (WHO). Over the
last 40 years, major advances have been made in
the development of numerous classes of antimi-
crobial agents to treat serious life threatening
infections. This is particularly true for antibacterial
agents. However, microorganisms are slowly turn-
ing the tide and becoming increasingly resistant to
the agents developed by man. Long term and
indiscriminate use of antibacterials has led to
resistance developing for all the major classes of
therapeutic agents. Increasingly clinicians are
fighting a rearguard action with a dwindling
armoury of drugs to combat serious life threaten-
ing infections. Nosocomial or hospital acquired
infections (HAIs) represent an increasingly serious
problem across Europe and the rest of the world.
Data from the SENTRY Antimicrobial Surveillance
program of 25 European university hospitals high-
lighted the five most common bacterial blood
isolates. The most prevalent organisms (E. coli,
S. aureus, P. aeruginosa and K. pneumoniae) are
also the most prevalent CVC associated infections
(Clin Inf Dis 30; 3). Candida species were also
common organisms isolated from blood and car-
ried a crude mortality rate of up to 40 %. These
organisms are the same organisms where resist-
ance is a major issue. The incidence of resistant
bacterial and fungal nosocomial infections is
high. The European Study Group on Nosocomial
Infections (ESGNI) reports on blood stream infec-
tions indicated 72.8 % of infections were nosoco-
mial and mortality due to bacteremia was 7.1 %.
The most frequently isolated microorganisms
from BSI were S. aureus (15.1 %), E. coli (14.5 %),
S. epidemidis and coagulase negative staphs
(CNS) (17.8 %), P. aeruginosa / K. pneumoniae
(both 5.3 %) and Candida spp and enterococci
(both 4.6 %).(ESGNI-001, ESGNI-002).
124
| Duration: 36 months
Aim
The aims of the NPARI consortium are to fully
exploit the exciting properties of this novel pep-
tide class. Specifically the consortium aims to
target peptide sequences into two areas; coating
agents for medical devices and therapeutics
agents.
A major application for the apoE peptides is as
coatings for medical devices such as catheters.
ApoE derivative peptides are already in develop-
ment as coatings for contact lenses. The project
aims to extend this application to use active pep-
tides as coating agents for catheters. Catheter
related infection causes significant morbidity and
mortality across the EU and resistant bacteria and
fungi are often responsible.
Another focus for the application of apoE peptides
is as therapeutic agents. The project will focus on
targeting specific resistant bacteria and fungi in
order to rapidly establish in vivo efficacy in a vari-
ety of animal models. It will specifically target res-
piratory infections caused by Pseudomonas and
Apsergillus. This will have direct clinical relevance
to the 30 000 European CF patients where resistant
Pseudomonas aeruginosa infections are a major
cause of mortality. Colonisation with Aspergillus is
also a major problem is this patient group.
Expected results
• The design of a small peptide library which will
be tailored to the proposed exploitable applica-
tion of the project.
• Determination of the activity spectrum of active
peptides and the ranking of peptide variants.
• Optimisation and toxicity profiling of active
peptides.
• Efficacy profiles against a panel of resistant
organisms growing as biofilms.
Key words: peptide, resistance, infection antibacterial, antifungal, therapeutic agent, coating agent

ROLE OF SMEs Scientific coordinator

Mike Birch
F2G Ltd.
A vital component of the project is the participation of several SMEs who each have Lankro Way, Eccles
expertise in the field of drug development. This, combined with the academic expertise of Manchester, United Kingdom
mikebirch@f2g.com
the remaining partners, allows for an experienced and focused consortium.
Partners
Nikem Research is an Italian based company who specialise in drug development. Nikem
has developed a wide range of ADMET and toxicological assays which can be applied to Christophe d’Enfert
Institut Pasteur
the project. In addition, Nikem has a range of bioanalytical capabilities which will be Biologie et Pathogénicité Fongiques
employed to monitor the pK/pD profiles of the peptides. Paris, France
www.pasteur.fr/ip/index.jsp
Similarly, F2G has expertise in the discovery and development of anti-infective agents, Jean-Marc Ghigo
specialising in anti-fungals. With a range of HTS screening capabilities, chemistry and Institut Pasteur
pharmacology experience, F2G is able to rapidly assess and develop peptides for use in Groupe de Génétique des Biofilms
therapeutic candidates. CNRS URA 2172
Paris, France
www.pasteur.fr/recherche/unites/Ggb
The focus of Ai2 is on the use of peptides to prevent colonisation of medical devices, which
very well complements the expertise within the consortia. Chiara Bigogno, Giulio Dondio
NiKem Research s.r.l.
chiara.bigogno@nikemresearch.com
www.nikemresearch.com

Niels Høiby
Department of Clinical Microbiology
University Hospital of Copenhagen
• Pharmacological and efficacy evaluation of Copenhagen, Denmark
peptides in a range of models.
Curtis Dobson
Ai2 Ltd.
• Efficacy data for candidate coatings in dynamic Manchester Incubator
biofilm models. Manchester, United Kingdom

Potential applications

The exploitation of this new class of antimicro-

bial peptides offers the potential to develop new
therapeutic against a range of the most resistant
and problematic organisms facing European
Infectious Disease Clinicians.

The rate infection by resistant bacteria is increas-

ing but new chemical agents are some way from
the clinic. This project aims to develop candidate
peptide therapeutics which target the most prob-
lematic organisms and develop them to the point
where they show sufficient potential for further
development.

In addition, the project focuses on the prevention

of infection by the same resistant organisms
through the coating of medical devices with active
peptides.

By preventing the colonisation of catheters by

resistant microorganisms it is expected that serious
life threatening infections can be avoided.

125
ACRONYM Contract number: LSHB-CT-2006-037653 | EC contribution: € 2 320 000 | Duration: 36 months
Starting date: 1 October 2006

OMVac

SUMMARY
Otitis media (OM) is one of the most fre-
Novel prevention and treatment possibilities
quent diseases in childhood and the for Otitis Media through the comprehensive
most common indication for the prescrip-
tion of antibiotics. Due to the poor evi-
identification of antigenic proteins
dence for the effectiveness of this
treatment and widespread drug-resis-
tances, there is a need for a prophylactic
vaccine to reduce the misery of children
by preventing the occurrence of OM
Background Expected results
altogether. This study focuses on the
comprehensive identification of antigen
Approximately 80 % of all children undergo an • Comprehensive identification of antigens from
candidates from two of the main
OM episode by 3 years of age. The main M. catarrhalis and NTHi by screening of bacterial
causative agents of OM, namely non-
causative agents are the bacterial pathogens surface display libraries.
typeable Haemophilus influenzae (NTHi)
Streptococcus pneumoniae, Haemophilus influen-
and Moraxella catarrhalis. The antigenome
zae and Moraxella catarrhalis which colonise the • Characterisation of the membrane proteome
of both pathogens will be identified by
middle ear, often after a primary viral infection. and surface located proteins from both
screening of bacterial surface display
After introduction and widespread use of pneu- pathogens by 2D-PAGE and 2D-LC-MS2 and
libraries with human sera from exposed
mococcal vaccines, there is evidence that the serological proteome analysis.
individuals and complementary pro-
impact of the latter two species increased. Acute
teomic approaches. Selected antigens
otitis media (AOM) is characterised by the pres- • Selection of the most promising vaccine candi-
will be evaluated by testing in animal
ence of middle ear effusion accompanied by the dates by validation in vitro and in animal models.
models, characterisation of their role in
rapid onset of signs of inflammation such as otal-
pathogenesis with special emphasis on
gia, otorrhea or fever. Recurrent OM affects up to • Characterisation of protective antigens with
biofilm formation and study of the natu-
40 % of children and may persist for weeks to respect to their role in pathogenesis of M. catar-
ral immune response. This approach will
months causing symptoms ranging from hearing rhalis and NTHi (including biofilm formation).
enable the project to transfer the most
loss and tinnitus to anorexia or conjunctivitis. As
promising vaccine candidates to clinical
AOM is very painful, it results very often in antibi- • Definition of natural immune responses against
trials for the prevention of OM.
otic treatment although solid evidence is lacking the identified antigens from M. catarrhalis, NTHi
that this therapy alters the course of OM disease and S. pneumoniae using the available sera and
The consortium comprises proven and
in children. Also in case of recurrent OM the fail- Ig preparations.
renowned experts of OM research, pro-
ure rate of antibiotic therapy is quite high, often
teomics/mass spectrometry and vaccine
development. Therefore, this multidisci-
due to antibiotic resistances of the pathogens. Potential applications
Considering also the high direct and indirect costs
plinary approach will go beyond any
of OM, there is an urgent need for an alternative The achievement of the goals will drive the devel-
effort that could be undertaken by a sin-
and effective therapy. opment of a prophylactic vaccine against OM and
gle participant by the complementarity
thereby will have a large benefit for the health of
of the technologies.
Aim children in Europe and beyond. Because NTHi
and M. catarrhalis not only cause OM in children
The OMVac project addresses as main objec- but also other infections of the respiratory tract
tives the identification of vaccine candidates like sinusitis, pneumonia or bronchitis, such
from Moraxella catarrhalis and non-typeable a vaccine could proof useful for prevention of
Haemophilus influenzae (NTHi) to develop a pro- these diseases as well.
phylactic vaccine against OM and the compre-
hensive characterisation of natural immune As the project will contribute to science study-
responses against proteineacous antigens of ing these bacteria and their pathogenesis, it
the major three bacterial pathogens causing might also offer new approaches for alternative
OM. Moreover, the role of selected antigens dur- therapies of OM.
ing pathogenesis and biofilm formation will be
investigated.

126
Key words: Otitis Media, vaccine development, Streptococcus pneumoniae, Haemophilus influenzae,
Moraxella catarrhalis, biofilm formation

ROLE OF SMEs Scientific coordinator

Andreas Meinke
Intercell AG
Intercell AG is an international vaccine company founded in 1998 and located in Vienna, Campus Vienna Biocenter 6
Austria and Livingston, Scotland. Intercell’s current activities include the discovery and 1030 Wien, Austria
ameinke@intercell.com
development of innovative immunological products and technologies for the prevention and www.intercell.com
treatment of infectious diseases. Within the OMVac project, Intercell will lead the antigen
discovery and validation process using proprietary technologies. Moreover, Intercell is Partners
responsible for all project management activities.
Andreas J. Kungl
Institute of Pharmaceutical Sciences
AGOWA GmbH is an internationally acting genomics company founded in 1993 and located University of Graz
in Berlin, Germany. It is recognised as a competent outsourcing partner for customers in pri- Graz, Austria
www.uni-graz.at
vate and public research, with the company offering a broad spectrum of services ranging
from library construction, custom DNA sequencing service, genotyping and bioinformatics Wolfgang Zimmermann
up to the complete analysis of genomes. In the course of the OMVac project, AGOWA will AGOWA GmbH
support the antigen discovery process by high-throughput sequencing. Berlin, Germany
www.agowa.de

Éva Bán
2nd Department of Pediatrics
Semmelweis University
Budapest, Hungary
www.sote.hu

John Hays
Erasmus MC
Rotterdam, The Netherlands
www.erasmusmc.nl

Peter WM Hermans
Laboratory of Pediatric Infectious Diseases
Radboud University
Nijmegen Medical Centre
Nijmegen, The Netherlands
www.umcn.nl

Birgitta Henriques-Normark
Karolinska Institutet
Solna, Sweden
ki.se

127
ACRONYM Contract number: LSHG-CT-2006-037793 | EC contribution: € 2 268 531 | Duration: 36 months
Starting date: 1 December 2006

OptiCryst
www.opticryst.org

SUMMARY
The OptiCryst project aims to provide
Optimisation of protein crystallisation
a support platform for Europe’s Structural for european structural genomics
Genomics initiatives. The project aims
tohelp such initiatives take a leap forward
scientifically and commercially, in order
to obtain high-quality crystals of proteins
which are currently proving difficult to
crystallise.
Background Expected results

The wealth of information obtained by Structural
Genomics has allowed protein structure-based
drug design to complement screening and combi-
natorial chemistry to provide more efficient drug
development. Ultimately, this approach will reduce
the time of production cycles and therefore cost
per drug.
Structural Genomics has coincided with the era of
high-throughput, resulting in major advances in
the automation of protein preparation and X-ray
crystallographic analysis, and in automating and
miniaturising crystallisation trials (thousands per
day). Despite this, the success rate in going from
cloned gene to high-resolution protein structure
is still relatively low in all current Structural
Genomics projects, with a major bottleneck situa-
tion from purified protein to diffracting crystals.
This problem clearly needs to be addressed. This
can be done through the production of a design
that will offer new and improved optimisation
methods, in order to turn crystal leads into useful
diffracting crystals.
Moving away from current approaches, and apply-
ing methods based on understanding the funda-
mental principles of crystallisation, the OptiCryst
project will focus on designing techniques to
actively control the crystallisation environment as
the project progresses through its stages.
Potential applications
Structural Genomics is a key discipline in post-
genomic biology, and today the pressure to pro-
duce diffraction-quality crystals that can yield
new protein structures is greater than ever. As
a result, the science of crystallisation is becom-
ing a rapidly developing field and it is gathering
new momentum. The work being carried out by
the OptiCryst project will go a significantly long
way towards addressing the outstanding needs
within that research area.

Aim

The key objective of the OptiCryst project is to

address the critical post-protein production bot-
tleneck area in the field of Structural Genomics.
To date, this area has been consistently ignored
by initiatives worldwide. The project proposes to
enhance the state-of-the-art in protein crystal
optimisation by increasing the success rate of the
production of diffraction-quality crystals from the
current rate of 21 % to at least 40 %.

128
Key words: structural genomics, SME, protein crystallisation, phase diagrams, nucleation, robotics,
high throughput, structural genomics

ROLE OF SMEs Scientific coordinator

Roslyn Bill
Aston University
The OptiCryst consortium is composed of seven SMEs and four academic groups. The role of Dept. of Life and Health Sciences
the SMEs in OptiCryst is to develop new equipment and tools to aid crystallisation. This will Aston Triangle
Birmingham B4 7ET
be achieved by designing new and improved apparatus, based on the joint research results of United Kingdom
the academic partners and the SMEs. These results will be made available to the community r.m.bill@aston.ac.uk
by commercialising the apparatus and turning new techniques into crystallisation kits.
Project manager
Eric Bourguignon
Aston University
Dept. of Life and Health Sciences
Birmingham, United Kingdom
e.bourguignon@aston.ac.uk

Partners
Naomi Chayen
Imperial College
Biological Structure and Function
Biomedical Sciences
London, United Kingdom

Patrick Shaw Stewart

Douglas Instruments Ltd.
Hungerford, United Kingdom

Flip Hoedemaeker
Key Drug Prototyping B.V.
Amsterdam, The Netherlands

Anthony Savill
Molecular Dimensions Ltd.
Newmarket, United Kingdom

Lea Vaiana
Triana Science & Technology S.L.
Armilla, Granada, Spain

Rolf Hilgenfeld
Institute of Biochemistry
University of Lübeck
| OptiCryst Kick-Off meeting at the DESY facility in Hamburg (March 2007). Lübeck, Germany

Marcus Swann
Fairfield Scientific Limited
Crewe, United Kingdom

Juan Manuel Garcia-Ruiz

Consejo Superior De Investigaciones
Cientificas (Csic)
Laboratorio de Estudios Cristalograficos
PT Ciencias de la Salud
Armilla, Granada, Spain

Christian Betzel
PLS Design GmbH
Hamburg, Germany

Lena Gustafson
Gothia Yeast Solutions AB
Gothenburg, Sweden

129
ACRONYM Contract number: LSHM-CT-2007-037669 | EC contribution: € 2 170 000 | Duration: 36 months
Starting date: 1 November 2006

PHECOMP

SUMMARY
Compulsive disorders, including drug
Phenotypical characterisation of animal
abuse and compulsive overeating, rep- models for neuropsychiatric disorders related
resent prevalent neuropsychiatric dis-
eases that have a large health and
to compulsive behaviour
socio-economic impact in the European
population. These disorders are pro-
duced by an alteration of the capability
to control seeking for reward, and seem
linked by common neurobiological sub-
Background European pharmaceutical companies, in order to
strates. However, there is an important
develop new drugs for the treatment of both drug
gap in the availability of reliable behav-
Both drug addiction and food intake disorders con- craving and relapse, core features of the compul-
ioural models in animals that permit to
stitute increasingly serious health care and social sive components of addictive disorders, or for pro-
investigate compulsion towards reward
problems in the EU and are also responsible for the viding new drugs for treating compulsive eating
in the perspective of human pathologies.
loss of millions of working hours every year. leading to obesity and metabolic imbalance.
However, there is still a lack of suitable specific ani-
The present proposal will use new
sophisticated behavioural and neu-
mal models to further elucidate the neurobiologi- Expected results
cal substrate of such disorders. In this context,
roimaging techniques for the characteri-
PHECOMP offers an impact in new animal models The neurobiological bases of compulsive behav-
sation of four new and complementary
for probing these and other related psychiatric dis- iours share common mechanisms, as drug-seeking
animal models of compulsive disorders,
orders and compulsive behaviours. or compulsive food intake promote activation and
allowing to analyse precisely the main
neuro-adaptations within the common neuronal
components of those behavioural alter-
The present proposal is a multidisciplinary project networks. The general strategy of the project is,
ations. The study will be performed in
bringing together new and sophisticated behav- first, to carry out a complete phenotypical charac-
mice and rats, including the transfer of rat
ioural methodologies as well as cutting-edge terisation of four animal models, addressing dif-
models to mice when necessary. The
molecular and imaging techniques which will be ferent components of compulsive disorders that
behavioural and molecular characterisa-
applied to the phenotypical characterisation of tar- are already being studied in partner laboratories,
tion of the models, along with parallel
geted and refined animal models. The characteri- namely:
neuroimaging (PET), will provide a com-
sation of new animal models and their transfer to • the modified conflict model (Dr. Piazza’s group at
plete anatomical and functional illustra-
mice when needed will allow the use of these Bordeaux);
tion of the reward pathways imbalance in
rodent behavioural models for the study of the • the deprivation model (Dr. Spanagel’s group at
the above-mentioned pathological situa-
compulsive components in addiction and related Mannheim);
tions. Novel behavioural paradigms will
psychiatric disorders. • the reinstatement model (Dr. Maldonado’s group
be proposed, tested and validated within
at Barcelona); and
the project, taking advantage of cutting-
edge imaging technologies. Molecular
Aim • the compulsive food-seeking/-taking model (Dr.
Heyne’s group at Reutlingen).
studies will characterise changes induced
There are three main aims of the specific-targeted
in several key elements of the reward cir-
research project: Those models will be transferred from rat to mouse
cuits during these behavioural disorders.
• deliver four phenotypically well-characterised when needed (involving the former groups as well
animal models, namely the modified conflict, the as that of Dr. Dierssen at Barcelona). The proposal
After the full characterisation of the mod-
deprivation and the reinstatement models of will investigate selected genes and proteins
els, they will be used on genetically mod-
compulsive drug intake, and the compulsive (Dr. Przewlocka’s group at Krakow) which could
ified mice for glucocorticoid receptors to
food-seeking/-taking model, addressing differ- play a role in compulsive-derived brain plasticity
ascertain correlations between behav-
ent components of compulsion using rats and and its pathophysiological response. Moreover,
ioural and genetic components of com-
mice; the availability of specific feeding patterns eval-
pulsion in drug addiction and eating
• elucidate the role of selected gene activities and uation tools (Dr. Célérier’s group at Cornellà) and
disorders. Hence, reliable and predictive
protein receptors in the neurobiological mecha- the set-up of potent neuroimaging technologies
animal models will be fully characterised
nisms involved in compulsive disorders; adapted to small experimental animals (Dr. Millán’s
and employed to better understand
• provide complete new structural and functional group at Barcelona) will allow correlating anatomic-
the mechanisms involved in those alter-
illustration of the reward pathways imbalance functional events with behavioural and genetic par-
ations, and to design new therapeutic
found in compulsion, using cutting-edge imaging adigms. Finally, a mechanistically targeted-oriented
strategies in neuropsychiatric disorders
techniques (PET). array of genetically modified mice (Dr. Tronche’s
related to compulsive behaviour.
group in Paris) will be used to specifically address
The ultimate objective of this STREP Project is the elucidation at molecular level of the neurobio-
to provide new knowledge that can be used by logical basis of compulsive disorders, i.e. the role of
the participants, by other research groups or by glucocorticoid receptors.

130
Key words: compulsive disorders, animal models, behavioural paradigms, Positron Emission Tomography (PET),
drug abuse, eating disorders, glucocorticoid receptors

ROLE OF SMEs Scientific coordinator

Rafael Maldonado
Laboratory of Neuropharmacology-NeuroPhar
Three SMEs, leaders in their fields, are crucial partners in PHECOMP and share 42 % of the Universitat Pompeu Fabra
budget. The German company medimod will develop a set of novel tools for preclinical test- Barcelona Biomedical Research Park
c/Dr Aiguader 8
ing of compounds with putative anti-obesity efficacy. The Spanish manufacturer Panlab 08003 Barcelona, Spain
will contribute with an array of technical and software solutions in the precise and accurate rafael.maldonado@upf.edu
analysis of the pattern of eating and drinking behaviours in rodents. Finally, the Spanish
Institute of Advanced Technologies (IAT) will apply current expertise and know-how to Partners
innovation through adaptation of functional PET neuroimaging of small experimental Mara Dierssen
animals to set up new techniques of imaging in mice. Their participation will enable the Centre for Genomic Regulation
consortium to carry out a complete phenotypical characterisation of selected animal Barcelona Biomedical Research Park
Barcelona, Spain
models of compulsive disorders and their transfer from rat to mice when needed, as well
as a fruitful transfer of knowledge to the market. Barbara Przewlocka
Institute of Pharmacology
Polish Academy of science
Krakow, Poland

Potential applications
The optimisation of targeted animal models will
render them suitable for finding new treatment
approaches for these compulsive disorders and
ready-to-use in pre-clinical research to test
putative anti-obesity and anti-addictive com-
pounds. It is recognised that both opioid,
dopamine and cannabinoid systems play key
roles in regulating not only addiction but also
other aspects of limbic and motor function. The
potential for the use of these animals to investi-
gate other CNS diseases as well as to develop
and test new pharmacotherapies is accordingly
very high.
Moreover, PHECOMP offers three SMEs, leaders
in their fields, to take great advantage of partici-
Rainer Spanagel
pating in a project at the European level, thus Central Institute for Mental Health
Mannheim, Germany
enabling the possible outputs of the project to
finally benefit the same (and other) SMEs, thus Pier Vincenzo Piazza
increasing their know-how and commercial com- INSERM u588
petitiveness in and outside Europe. In particular, Paris, France
at the end of the project, medimod (DE) will have Andrea Heyne
a fully-operative food-seeking/food-taking model medimod pharmacology services GmbH
in rat ready for the preclinical search for new phar- Reutlingen, Germany
www.medimod.com/welcome.html
maco-therapeutic solutions in food intake disor-
ders. Also, IAT (ES) will develop and validate new Olga Millán
PET built-in methodologies for neuroimaging Institut d’Alta Tecnologia
Barcelona, Spain
analysis of mice, correlated with behavioural and www.iat-prbb.com/ingles/index.html
molecular data. Finally, Panlab (ES) will set-up
and validate specific devices that will improve the François Tronche
quality and efficiency of animal feeding patterns CNRS (UMR 7148)
Paris, France
evaluation tools.
Evelyne Célérier
Panlab SLU
Barcelona, Spain
www.panlab.com

| Alcohol sensitization and reward are

influenced by circadian genes and
rhythm (Abarca et al., Proc Natl Acad
Sci USA 99, 9026-30, 2002).

131
ACRONYM Contract number: LSHM-CT-2007-037765 | EC contribution: € 2 700 000 | Duration: 36 months
Starting date: 1 January 2007

PHOTOLYSIS

SUMMARY
Flash photolysis is widely applied in cell
Development of flash photolysis for deep
physiology to initiate neurotransmitter uncaging in vivo and high-throughput
and other ligand-receptor interactions in
conditions that are subject to poor diffu-
characterisation of neurotransmitter gated
sional access and receptor desensitisa- ion channels in drug discovery
tion, and for ligands that are particularly
labile. It has the potential to initiate reac-
tions on physiological time and spatial
scales (sub-msec and sub-micron) in com-
Background Aim
plex tissues such as brain slices and in
vivo, and is often combined with electro-
Experimentally it is difficult to separate the con- To develop new photochemical probes and opti-
physiology and optical imaging.
tributions of presynaptic and postsynaptic mech- cal methods in localising and extending the range
anisms to the efficiency and strength of asynaptic of photolysis for use in neuroscience; to adapt
However, this potential is unrealised in neu-
connection. The method of flash photolysis can photolysis to current parallel patch clamp methods
roscience and medicine in several areas:
provide a way of determining the properties of in the development of new medicines.
• photolabile ‘cages’ optimised to make
synapses between neurones in situ that are cur-
use of the localisation achievable with
excitation by the two-photon effect;
rently studied only in recombinant receptors in Expected results
vitro, and would allow the testing of putative
• wavefront modulation of photolysis
mediators of local vasoregulation in the brain. Improved photochemical properties of probes,
light to make z axis location and spot size
These applications of photolysis in neuroscience particularly making better use of the two-
readily changeable;
are impeded by the poor photochemical proper- photon effect for localisation and extending the
• application in high-throughput screening
ties and stability of caged neurotransmitters, by range of synaptic and local messenger systems
for drug discovery of ligands acting at
the unavailability of many mediators in photo- to which the method can be applied. Improved
rapidly desensitising neurotransmitter
labile caged form, and by the unsuitability of methods in drug discovery of ligands active at
receptors in the brain.
present optical methods. brain synapses. Specific therapeutic targeting
of genetically linked channelopathies and appli-
The PHOTOLYSIS consortium comprises
Currently, high throughput screening methods to cations in developing somatic cell replacement
neurophysiologists, photochemists, optical
find ligands acting at brain synapses use conven- therapies.
physicists, specialists in high-throughput
tional perfusion methods to apply the activating
patch clamp screening and ion channel tar-
geted drug discovery, to address these
neurotransmitter or analogue. These methods are Potential applications
too slow to activate receptors on a physiological
areas. New photochemistry of cages com-
timescale because of diffusional access to the cell To investigate neurotransmitter receptors in synap-
bined with new pulsed lasers and new
surface, and for this reason, potential medicines tic transmission in situ. To investigate mediators
adaptive optics will optimise the effi-
that affect the degree of activation of synapses in neurovascular regulation. To improve methods
ciency, depth and location of photolysis
and act in a use-dependent way will not be opti- of deep imaging in vivo. To develop better drugs
in whole brain in vivo and in vitro.
mally detected. The application of this method in acting at synaptic receptors in the brain.
high-throughput screening to test for new medi-
These developments will be combined
cines has the potential to detect use-dependent
with deep imaging to:
ligands acting at the rapidly desensitising amino
• identify mediators and cell types in neu-
acid receptors that mediate neuronal signalling.
rovascular coupling of blood perfusion
to neuronal activity;
• applied to synaptic transmission to study
postsynaptic channels in situ, identify
their role in synaptic plasticities; and
• investigate the interactions between
metabotropic receptors and fast trans-
mitter channels;
• finally, adapt near-UV flash photolysis to
patch clamp HTS technology, in order to
characterise drugs acting at fast activat-
ing and desensitising neurotransmitter
receptors, to study the functional phar-
macology of genetically-linked chan-
nelopathies, and in developing somatic
cell replacement therapies.

132
Key words: photolysis, caged neurotransmitters, synaptic transmission, synaptic plasticity, neurovascular regulation,
wave front engineering, optical imaging, high throughput screening, channelopathies

ROLE OF SMEs Scientific coordinator

David Ogden
CNRS UMR 8118
The three high-tech SMEs in the Photolysis project, Flyion, GeneCraft and Tocris-Cookson, Physiologie Cérébrale
will play three important roles. One is to further develop the library of caged neurotrans- Université René Descartes Paris 5
45 Rue des Saints Peres
mitter ligands available to neuroscience researchers as probes in experiments to investi- F-75006 Paris
gate synaptic transmission and its modification in disease. The second is to develop the France
application of photolysis in drug discovery to improve the detection of ligands that act at david.odgen@univ-paris5.fr
fast-responding neurotransmitter receptors. This will be based on existing parallel patch Project manager
clamp technology modified to introduce a light path for- irradiation with a pulse of near-UV
light to initiate photorelease of the neurotransmitter. Thirdly, through their connections Isabelle Geahel
within the community of drug discovery and ion channel therapies, the SMEs will be Inserm-Transfert
Paris, France
effective in translating the proven power of photolysis in investigating synaptic function isabelle.geahel@inserm-transfer.fr
to the task of identifying potential drugs. www.inserm-transfert.fr

The company Inserm Transfert takes care of the administrative project management. Partners
Serge Charpak
Institut National de la Santé
et de la Recherche Médical
INSERM FR 101
Paris, France

Gail McConnell
John Girkin
University of Strathclyde
Glasgow, United Kingdom

Michael Fejt
Flyion GmbH
Tubingen, Germany
www.flyion.com

Duncan Crawford
Tocris-Cookson Ltd.
Bristol, United Kingdom
www.tocris.com/UK

Ladislav Vyklycky
Dept. of Cellular Neurophysiology
Institute of Physiology
Praha, Czech Republic

Yair Feld
GeneGraft
Israel

133
ACRONYM Contract number: LSHP-CT-2006-037587 | EC contribution: € 2 079 016 | Duration: 36 months
Starting date: 1 December 2006

PlasmodiumdUTPase

SUMMARY
There are around 500 million clinical
Deoxyuridine triphosphate nucleotidohydrolase
cases of malaria each year and about as a drug target against Malaria
1-2 million people die from this debilitat-
ing disease. There is an urgent need for
the development of new drugs because
of drug resistance issues. New drugs
should have novel mechanisms of action
to prevent cross-resistance with existing
drugs. Some novels, drug-like and selec-
Background Expected results
tive inhibitors of the enzyme deoxyuri-
dine triphosphate nucleotidohydrolase
As part of a Framework 5 programme (QLRT-2001- The expected results are compounds that are
(dUTPase) from Plasmodium falciparum,
00305), the project team discovered a novel class advanced leads or preclinical drug candidates for
the causative agent of malaria have been
of inhibitors, which selectively inhibit dUTPase the treatment of malaria.
discovered. The role of this enzyme is to
form Plasmodium falciparum, the causative agent
hydrolyse dUTP to dUMP, maintaining
a low dUTP:dTTP ratio. The aim of this
of malaria. Potential applications
project is to optimise these early lead
molecules to generate late-stage leads
Aim The potential applications of outputs of this proj-
ect are compounds, which could go through to
or preclinical drug candidates.
The aim is to optimise these early lead molecules preclinical development for the treatment of
in order to generate advanced leads or preclinical malaria and if successful proceed to clinical trials.
The project will include:
drug candidates.
• medicinal chemistry activities for the
preparation and optimisation of lead
compounds;
• ADME-Tox assays to ensure that the
compounds have correct ‘drug-like’
properties;
• biological evaluation to determine the
efficacy of the compounds;
• mode of action studies;
• crystallography of inhibitors with the
enzyme active site to assist in the drug
design process.

134
Key words: Malaria, drug discovery

ROLE OF SMEs Scientific coordinator

Ian Gilbert
School of Life Sciences
This project is an exciting collaboration between an SME, the Swedish Pharmaceutical University of Dundee
company Medivir AB and 4 academic institutions. The group has characterized the MSI/WTB/CIR Complex
Dow Street
enzyme deoxyuridine triphosphate nucleotidohydrolase (dUTPase) from the protozoan Dundee DD1 5EH
parasite Plasmodium falciparum, which causes malaria, in an approach to develop novel United Kingdom
antimalarials. The project is a drug discovery project focusing on the optimization and i.h.gilbert@dundee.ac.uk
www.dundee.ac.uk
development of inhibitors of this promising new malaria drug target. Medivir is able to
bring its considerable experience in drug discovery to the project. Medivir is driving the Partners
project towards a preclinical Candidate Drug status and carries a major part of the project
work, including the synthesis of compounds and provision of a large compound library Nils Gunnar Johansson
Medivir AB
for testing as potential inhibitors of dUTPase. For this strong Swedish drug development Huddinge, Sweden
SME, the development of an antimalarial drug targeting dUTPase, may in addition constitute www.medivir.se
a proof of principle for dUTPase as a drug target for treatment of also other diseases.
Dolores González Pacanowska
Instituto de Parasitología
y Biomedicina “López-Neyra”
Consejo Superior
de Investigaciones Científicas
Armilla, Granada, Spain
www.ipb.csic.es

Keith Wilson
University of York
Department of Chemistry
Structure Biology Laboratory
Heslington, United Kingdom
www.york.ac.uk

Reto Brun
Swiss Tropical Institute
Parasite Chemotherapy
Basel, Switzerland
www.sti.ch

© Shutterstock

135
ACRONYM Contract number: LSHB-CT-2007-037933
Starting date: 2 January 2007
POC4life
www.poc4life.eu
SUMMARY
This project aims to improve the health-
care of patients by elaborating a unique
POC diagnosis platform which will help
specialists to deliver an earlier diagnosis
and to decide on appropriate treatment.
The goal is to provide the clinicians with
multiparametric measurement of the
main 4/5 essential markers and to sup-
port decision with a software tool. This
will be a cost-effective breakthrough in
the diagnosis market.
| EC contribution: € 2 497 815
Multiparametric quantum dot bioassay
for point of care diagnosis
Background
Each year 377 000 new European citizens develop
lung cancer and 340 000 die from it. Studies show
that early diagnosis and accurate cancer typing
could save a number of lives. Laboratories nowa-
days have a wide panel of reproducible diagnostic
tests at their disposal: these are mostly routine
tests realised in centralised laboratories. The
needs for early diagnosis, multiparametric analy-
sis of results and quick monitoring of disease
progression or therapeutic sensitivity were pro-
gressively left aside, whereas they could be ful-
filled with using decentralised diagnostic tools,
close to the patient.
Among the possible applications of this new con-
cept, the partners have chosen to work on the pri-
mary diagnosis of the histological types of lung
cancer to help to give an improved initial diagno-
sis and to eliminate the 15-20 % problematic or
late diagnosed cases. The study will pay special
care to women (lung cancer death rates for
women have been still increasing in Europe since
the 1990s and marker patterns may be different).
It will then have a huge impact on health by con-
tributing to the fight against cancer and the devel-
opment of gender dimension in research. For this
purpose, the multidisciplinary project will involve
academic researchers (from Germany, Spain and
France) and SMEs (from Sweden and the UK) gath-
ering around the initiators of the project (the SME
CEZANNE, the University of Strasbourg in France
and the University of Potsdam in Germany) which
have the skills to build a multiparametric device,
to develop immunoassays and to design an inter-
pretation software.
136
| Duration: 36 months
Aim
Objective 1: Elaborate an innovative medical
device: a unique point of care diagnosis platform
which will help specialists to make earlier diagno-
sis and provide more appropriate treatments.
Objective 2: Provide the best possible integration
of parameters by means of a consortium com-
posed of public and private partners such as
research intensive SMEs and academic entities
Europe-wide.
Objective 3: Elaborate the new device for a spe-
cific application: the primary diagnosis of the dif-
ferent types of lung cancer. The project will then
have a huge impact on health by contributing to
the fight against cancer and the development of
gender dimension in research.
The objective of the project is to generalise this
approach to combinations of immuno-assay
measurements to deliver a clear diagnosis of the
disease or monitoring information. The generali-
sation means first that the diagnosis should be
accessible to various types of medical practices
(medical doctor to hospitals) and thus a low cost,
easy to use ‘Point of Care’ (POC) device should
be developed. However, this should not be
done to the detriment of quality and precision.
A homogeneous technology known for high level
precision can therefore be a judicious choice.
Generalisation also means that various patholo-
gies could be addressed: typically from 2 to 4 or 5
immuno-assays. The project therefore aims to
allow the simultaneous measurement of 4 to 5
immuno-assays on the POC device with one draw
of patient sample (1 droplet). Finally, generalisa-
tion means universality of the measurement tech-
nique and of the data reduction process. In this
way, fluorescent measurement based on FRET
(Fluorescence Resonance Energy Transfer) seems
an excellent choice, since it may be extended
in the future to other diagnostics such as DNA
analysis, coagulation, microbiology etc.
Key words: lung cancer, point of care, quantum dots, uv light source, flash lamp, fluorescence, immuno-diagnosis,
multiparameter, blood separation, expert system, molecule coupling, luminescent tags

ROLE OF SMEs Scientific coordinator

Emmanuel Bois
Cezanne SAS
The SMEs will bring to the consortium the complementary and comprehensive expertise 280 allée Graham Bell
required by the other public researchers. Parc Scientifique Georges Besse
30035 Nîmes cedex 1
France
CEZANNE S.A. brings competence in two complementary scientific and technical fields: contact@cezanne.fr
immuno-assay development and scientific instrumentation, which over the years CEZA www.cezanne.fr
managed efficiently to cross-fertilise. Partners
FUJIREBIO DIAGNOSTICS brings competence related to antibody development and Olle Nilsson
characterisation (hybridoma technology, phage display, gene expression analysis, c-DNA Fujirebio Diagnostics
Göteborg, Sweden
immunisation, DNA-shuffling, affinity maturation) and competence in assay development.
Desmond Smith
EDINBURGH INSTRUMENTS brings experience in flash lamps, laser diodes, fluorescence Edinburgh Instruments
spectrometry and a prototype nanosecond plate reader. 2 Livingston
Scotland, United Kingdom

Philippe Pieri
Centre National de la Recherche
Scientifique
Paris, France
Expected results Potential applications
Hans-Gerd Löhmannsröben
The project should attain the following challeng- Multiparametric diagnostics in the following University Of Potsdam
Institut für Chemie und Interdisziplinäres
ing objectives: fields: Zentrum für Photonik
• develop a functional prototype of POC multi- • cancer; Potsdam – Golm, Germany
parametric measurement for immuno assays, • prenatal diagnostics;
Yves Caristan
based on Homogeneous Time Resolved Fluores- • sepsis; Commissariat à l’Énergie Atomique
cence (HTRF), for which main characteristics are: • cardiac. Grenoble, France
equivalent to an A4 sheet of paper, cost of less
Klaus-Dieter Weltmann
than EUR 2 000, works with a sample droplet Eckhard Kindel
deposited on a disposable reagent vessel con- Institute Of Low Temperature
taining dried reagents; Plasma Physics
• define the panel of assays and how to combine Greifswald, Germany
them into a decision making software (to be Rafael Molina
developed). Hospital Clinic Barcelona
Laboratory of Biochemistry
Hospital Clinic C
Barcelona, Spain

Petra Stieber
Institute For Clinical Chemistry
University Hospital Munich-Grosshadern
Munich, Germany

© Shutterstock

137
ACRONYM Contract number: LSHP-CT-2006-037494 | EC contribution: € 2 345 358 | Duration: 36 months
Starting date: 1 December 2006

PRIBOMAL

SUMMARY
Malaria is one of the major public health
Preclinical studies towards an affordable,
challenges in the world, causing more safe and efficacious two-component paediatric
than one million deaths each year. The
disease primarily affects children of the
Malaria vaccine
developing world. The available meas-
ures, such as personal protection or
drugs, have proven to be insufficient to
control the disease. A safe, affordable
and efficacious paediatric malaria vac-
Background countries in sub-Saharan Africa do not have the
cine, which fits in the existing WHO
economic means to purchase expensive vaccines.
Expanded Programme on Immunisation,
It is estimated that more than 300 million individ- The manufacture of rBCG follows the exact same
would alleviate tremendous suffering in
uals suffer from acute disease caused by the protocols and procedures as established for BCG
human kind.
malaria parasite and that more than 1 million peo- and guarantees that sufficient doses of rBCG
ple succumb to this disease each year. Malaria, malaria vaccine can be manufactured at a price
Taking up this challenge, the PRIBOMAL
which is highly endemic in sub-Saharan Africa, per dose similar to BCG. Consortium member
consortium proposes to generate and test
claims its victims predominantly among children Crucell has extensive expertise in adenoviral
in preclinical models the safety and effi-
with the peak incidence of clinical malaria and vaccine manufacturing, employing a mammalian
cacy of an innovative malaria vaccine. The
90 % of malaria deaths in children younger than cell line, coded PER.C6, which can be cultured
vaccine consists of a prime, to be adminis-
5 years. in suspension in large volumes. Therefore, the
tered at birth, of a novel recombinant BCG
PRIMOBAL consortium members consider the pro-
vector carrying preferentially multiple
The challenge faced by the PRIBOMAL consortium posed two-component paediatric malaria vaccine
antigens derived from the Plasmodium
is to design a safe, affordable paediatric malaria to be affordable, thus applicable in developing
falciparum parasite, the cause of malaria.
vaccine that provides long lasting protection countries such as sub-Saharan Africa.
The priming vaccine is followed at week 14
against malaria and that fits within the existing
after birth by a booster vaccination using
industrially developed, recombinant ade-
WHO Expanded Programme on Immunisation (EPI) Aim
so as not to further complicate operational vacci- To demonstrate feasibility (safety and efficacy) in
noviral vector carrying the identical
nation logistics. The first vaccination that children preclinical studies of a novel, affordable, two-
Plasmodium falciparum antigens as the
would receive is at birth with Bacille Calmette- component, paediatric malaria vaccine.
rBCG-based malaria vaccine.
Guérin (BCG) a live and attenuated strain of
Generation of these novel vaccine candi-
Mycobacterium bovis, which is currently the only Expected results
available vaccine against tuberculosis. BCG has
dates, as well as testing in established
been globally used as the TB vaccine for decades The ultimate deliverable of this programme is an
and novel pre-clinical models to deter-
and has proven to be safe in hundreds of millions efficacious paediatric malaria vaccine candidate
mine potency and safety, requires a com-
of children. In recent years BCG receives additional that will eventually be advanced to GMP develop-
bined European effort to bring together
attention as a potential vaccine vehicle. ment and clinical trials. Besides reaching this aim,
the required expertise on basic parasite
the consortium expects that during the execution
biology, malaria epidemiology, disease
The PRIBOMAL consortium considers that a of this programme extensive knowledge will be
onset and progression, recombinant vec-
booster immunisation will be required to achieve gathered regarding immunological features of
tor technology, fundamental immunol-
long-lasting protection. Therefore, a choice was different vaccination schedules, in combination
ogy, advanced animal models, and
made to boost the rBCG.malaria vaccine, given at with information on their protective ability. This
sophisticated proteomics. The interna-
birth either alone or in addition to classical BCG, information will help elucidate correlates of pro-
tional PRIBOMAL consortium bundles all
with a recombinant adenoviral vector, carrying tection and facilitate rational design of future
required experience and as such is well
the identical P. falciparum derived antigens, at malaria vaccines.
positioned to successfully conduct this
14 weeks after birth, thus compliant with WHO EPI
research programme.
schedule. Like rBCG, replication deficient aden- Potential applications
oviral vector has an excellent safety record with
tens of thousands of patients receiving recombi- It can be envisioned that vaccines against other
nant adenoviral vectors in diverse gene therapy disease such as for instance HIV, TB or even can-
and vaccination trials without adverse effects. cer vaccine development can directly benefit
from the PRIBOMAL research. Like malaria these
To ultimately eradicate malaria disease hundreds diseases are considered to require vaccines
of millions of vaccine dosages will need to be that elicit strong humoral and cellular immune
manufactured at low cost per dose, given that responses against a broad range of epitopes.

138
Key words: Malaria, rBCG, rAd35, paediatric vaccine

ROLE OF SMEs Scientific coordinator

Jaap Goudsmit
Crucell Holland B.V.
This project forms part of a wider effort by the coordinating Dutch biotech SME Crucell to Archimedesweg 4
develop a malaria vaccine based on several pre-erythrocytic antigens presented by PO Box 2048
2301 CA Leiden, The Netherlands
a BCG/adenovirus-based prime-boost approach. This FP6-funded project contributes to j.goudsmit@crucell.com
the preclinical testing of this approach in three different animal models, which involves www.crucell.com
a number of European partner groups and thus requires support at European level.
Crucell’s role in the project is very strong, with a large work-share in the generation of the Partners
candidate product but also in all other work packages, underpinning the importance of Stefan H.E. Kaufmann
the project for this SME-based European vaccine development project. Max Planck Institute
for Infection Biology
Berlin, Germany
www.mpiib-berlin.mpg.de

Leif Lindfors
Stockholm University
Department of Immunology
Stockholm, Sweden
www.wgi.su.se

Tom Van der Poll

Academic Medical Centre
University of Amsterdam
Laboratory of Experimental
Internal Medicine
Amsterdam, The Netherlands
www.amc.uva.nl

Ronald Bontrop
Biomedical Primate Research Centre
Rijswijk, The Netherlands
www.bprc.nl

© Shutterstock

139
ACRONYM Contract number: LSHB-CT-2007-037740 | EC contribution: € 2 200 000 | Duration: 36 months
Starting date: 1 March 2007

PRISM

SUMMARY
In this specific targeted research project,
Phospholipid and glycolipid recognition,
cutting-edge nuclear magnetic resonance interactions and structures by magnetic resonance
(NMR) techniques are used to develop
a sensitive, rapid and integrated approach
to understanding the mechanisms of lipid
binding proteins. The project will gener-
alise and accelerate the efforts to charac-
terise a range of peripheral membrane
proteins, thus providing new insight into
Background Expected results
an important class of proteins which play
a key role in regulating complex cellular
Lipids and the proteins that bind them are of sig- The expected goals of this project are the devel-
pathways. Model membranes will be
nificant societal value and medical importance opment and dissemination of biophysical tools
tested to mimic various types of cellular
due to their central roles in health and disease, and structural models for protein membrane
membranes for selected protein mod-
and their relevance to the discovery of novel ther- interactions that can be used by other researchers
ules which will be prepared by specific
apeutic agents. Phospholipids such as phospho- in an industrial or academic environment. The
advanced tailored protein expression
inositides and sphingolipids have crucial roles specific results include:
methods. The generation of lipid libraries
both in cancer development and progression. • tools for studying protein phospholipid inter-
will allow definition of membrane speci-
They act as bioactive lipid mediators, affecting actions;
ficity, and spin labels and micelle-forming
fundamental cellular functions which include pro- • NMR techniques using tags and DNP;
compounds will facilitate the meas-
liferation, differentiation, survival, migration, • efficient preparation of membrane proteins
urement of the angles and depths of
adhesion, invasion, and morphogenesis. These and intracellular probes;
bilayer insertion. These advances in NMR
functions influence many biological processes • protocols for the preparation of membrane
methodology will be complemented by
including neurogenesis, angiogenesis, wound models and lipid systems; and
new computer modelling approaches for
healing, immunity, and carcinogenesis. While ini- • new insights into protein-lipid interactions and
micelle:protein complexes. Predictive
tial discoveries on lipid binding domains have dynamics.
principles of membrane insertion will be
spurred interest among structural biologists, little
used to model membrane orientations of
structures of proteins. To demonstrate
is known about the precise control or specificity of Potential applications
membrane insertion and recognition. This project
the impact for endocytosis, exocytosis
will therefore have effects on public health by aid- The proposed research will be focussed on
and signal transduction, the protocols
ing in the design of new types of agents that bind a selection of model proteins and membrane
and products will be developed and
to membrane interaction sites and provides new types to achieve realistic goals. However, the
tested using the signalling domains and
avenues to modulate target protein activities. results of this project will be of wider importance
modules involved in the trafficking of
due to the provision of basic answers which can
membranes and modification of lipids.
Aim later be applied to other members of the same
class of proteins, and general physico-chemical
Prism project main objectives are: principles can be extrapolated to other lipid inter-
• test and validate model micelle systems to acting proteins. Broad applicability is guaranteed
mimic properties of cellular membranes for by the fact that approximately a third of the pro-
research of membrane-associated proteins; teome and half of the known drug targets are
• develop molecular screening methods in order membrane-associated proteins. The tools and
to define lipid/micelle specificity profiles of results will be used by researchers interested in
protein modules; membrane-associated proteins, lipidomics, func-
• apply dynamic nuclear polarization methods tional and structural genomics, biophysical tech-
and paramagnetic spin label studies for the niques including NMR spectroscopy and DNP
measurement of lipids and protein interactions; applications, and groups interested in membrane
• design, express and screen novel tags and biology and signalling mechanisms.
lipid binding domains involved in membrane
trafficking and signalling;
• test and evaluate new computer modelling
approaches for membrane:protein complexes.

140
Key words: membrane protein, signal transduction, phospholipid, glycolipid, NMR spectroscopy, dynamic nuclear polarization,
structural biology

ROLE OF SMEs Scientific coordinator

Michael Overduin
University of Birmingham
The PRISM project includes two SME partners. Oxford Instruments Molecular Biotools Ltd. Edgbaston, Birmingham, B15 2TT
(OIMBL) offers advanced scientific instrumentation and expert knowledge for biomolecular United Kingdom
m.overduin@bham.ac.uk
analysis. HyperSense™ is OIMBL’s groundbreaking dynamic nuclear polarisation (DNP) www.nmr.bham.ac.uk
polarizer which is capable of amplifying the NMR signal to noise ratio by a factor of up to
10 000. This instrument is the first commercial DNP system, and has been installed at Partners
HWB•NMR. This project provides PRISM with access to DNP-NMR technology for the study
Harald Schwalbe
of proteins and lipids. Johann Wolfgang Goethe-University
BMRZ-Center for Biomolecular
ProtaMAX Ltd. offers bespoke mutagenesis, custom randomisation of protein sequences, Magnetic Resonance
Frankfurt, Germany
and efficient saturation mutagenesis to produce DNA libraries and designer proteins including
biopharmaceuticals. ProtaMAX Platform Technology allows encoding of selected or fully Kai Simons
randomised amino acids, for example, within binding site residues of a protein structure. Max Planck Institute of Molecular
The technology was invented and patented at the University of Aston, UK, and is available Cell Biology and Genetics
Dresden, Germany
to PRISM researchers to obtain and screen for novel protein probes and tags.
Jean Gruenberg
Université de Genève
Faculté des Sciences
Département de Biochimie
Geneva, Switzerland

Gerrit van Meer

Utrecht University
Utrecht, The Netherlands

Andrew Sowerby
Oxford Instruments Molecular
Biotools Ltd.
Oxfordshire, United Kingdom
www.oxford-instruments.co.uk/wps/wcm/
connect/Oxford+Instruments/Internet/Home

John Slack
ProtaMAX Ltd.
Birmingham, United Kingdom
www.protamax.com

141
ACRONYM Contract number: LSHB-CT-2006-036813 | EC contribution: € 2 540 651 | Duration: 36 months
Starting date: 1 November 2006

PROLIGEN
proligen.eu

SUMMARY
PROLIGEN aims to enhance the endoge-
Hypoxic renal proliferation
nous regenerative capacity of injured
kidneys based on information derived
from genomics/proteomics and functional
genomics. The approach of PROLIGEN is:
• to define and identify set of genes/pro-
teins associated with functional recov-
ery from renal injury;
• to build up high throughput test sys-
Background Expected results
tems to follow the basic biological
process involved in regeneration and to
PROLIGEN differs from previous approaches in • Provide new therapeutic tools able to promote
use these read out systems for func-
that it splits the regeneration process into the recovery from acute renal failure (ARF).
tional genomics; and
different main biological process (apoptosis, for-
• to develop biologicals and cell based
mation of pro- versus anti-inflammatory media- • Gain insight into principles of the regeneration.
therapy to foster proliferation.
tors/macrophage phenotype and cell proliferation),
and aims to study regeneration as the result of their • Provide the conceptual basis for the develop-
Currently, studies are focused on evalu-
interdependence. The project takes into account ment of new therapeutic strategies.
ating single factors as growth factors or
that macrophages are at the centre of a complex
stem cell therapy. The project proposes to
enhance regeneration by knowing how
regulatory network receiving and distributing Potential applications
signals from and to all biological process, thus
the genes/proteins that determine dif-
affecting recovery. At variance with previous stud- The resulting gene function and new cell therapy
ferent steps in kidney regeneration are
ies particularly focus is not only on the identifica- information may provide the PROLIGEN consor-
related, and how these settings can be
tion of markers relevant for regeneration rather tium the necessary tools to deliver new biologicals
influenced to improve regeneration. Then,
than the use of functional genomic technology and cell-based therapies for kidney regeneration.
the project will provide new therapeutic
which provide a new network of gene function and
tools able to promote recovery from acute
new platforms to deliver a new cellular based Potential applications of the generated know-
renal failure (ARF) based on functional
therapy strategy. ledge to improve the regeneration in other tissues
genomic studies and cell therapy.
avoiding the use of stem cells may also result.
Aim

PROLIGEN aims to enhance the endogenous

regenerative capacity of injured kidneys based on
information derived from genomics/proteomics
and functional genomics.

142
Key words: acute renal filure, regenerative medicine, kidney regeneration, functional genomics, genomics,
proteomics, macrophage therapy

ROLE OF SMEs Scientific coordinator

Georgina Hotter
Instituto de Investigaciones
The PROLIGEN consortium brings together selected academics, clinitians and industry Biomédicas de Barcelona
experts. Three SMEs play key roles in the research activities of the project, namely Consejo Superior de Investigaciones
Científicas (IIBB-CSIC)
Galapagos NV provides its expertise on functional genomics, Genedata AG takes care of Rosellon 161
bioinformatics and ProtEra s.r.l. contributes to protein synthesis. 08036 Barcelona, Spain
ghcbam@iibb.csic.es
www.csic.es

Partners
Bernhard Brüne
University of Frankfurt – Medical School
Frankfurt, Germany
www.uni-frankfurt.de

Joan Torras
Fundació Privada Institut d’Investigació
Biomèdica de Bellvitge
Lab.4122 Experimental Nephrology
L’Hospitalet de Llobregat
Barcelona, Spain
www.csub.scs.es

Bob. v.d. Water

Leiden/Amsterdam Center
for Drug Research
Leiden University
Leiden, The Netherlands
www.leiden.edu

Jochen Koenig
Genedata AG
Basel, Switzerland
www.genedata.com

Richard Janssen
| PROLIGEN aims to enhance Galapagos NV
the endogenous regenerative Leiden, The Netherlands
capacity of injured kidneys www.glpg.com
based on information derived
from genomics/proteomics Rebecca del Conte
and functional genomics. ProtERA s.r.l.
Sesto Fiorentino
Firenze, Italy
www.protera.it

143
ACRONYM Contract number: LSHB-CT-2006-037293 | EC contribution: € 1 492 500 | Duration: 24 months
Starting date: 1 September 2006

QuAGSIC
www.uni-ulm.de/quagsic/index.php

SUMMARY
The partners will develop methods and
Quantitative analysis of genes in single cells
instruments to analyse the copy number
of nucleic acid sequences down to the sin-
gle cell/single molecule level, with the
goal of developing an early diagnosis sys-
tem for a children’s disease, namely hemo-
phagocytic lymphohistiocytosis (HLH).
The underlying technique is amplification
based counting (ABC), which enables
Background Potential applications
researchers to quantify the copy number
of genetic sequences with a resolution
Many basic questions in Biology and Medicine The technologies developed demand a minimum
of about 100 base pairs in single cells.
demand methods for the analysis of the basic unit amount of material to be analysed. Without
The method provides a resolution which
of life, the single cell. The partners will thus doubt, the single cell is the basic entity of a living
is of a magnitude higher than that of
develop methods and instruments to analyse the organism (or it is even the whole organism).
Fluorescence In Situ Hybridisation, and
genetic content of single cells, with regard to Therefore, applying the methods mentioned
works quantitatively with much lower
quantitative variation of sequences (copy number above to single cells is not only a technological
sample amounts than quantitative PCR. To
variations), as well as qualitative variation of challenge but it is also the major important task
prove ABC’s effectiveness for clinical appli-
sequences (single nucleotide polymorphisms). in system biology over the coming years, partic-
cations, the partners will develop a single
ularly to be able to address medical diagnostics
cell manipulation unit that picks cells from
a solution and transfers them onto an
Aim in the regime of single cells. Single cell analysis
becomes more and more attractive because of lim-
integrated PCR and hybridisation slide
Shortly after the end of the project, QuAGSiC will ited cell population of interest, cell heterogeneity
(AmpliGrid). The AmpliGrid contains dried-
put on the market machines and consumables of samples, or when cells are isolated automati-
on PCR reagents, as well as hybridisation
that allow gene measurements down to the single cally as early dissemination of tumour cells.
probes to detect the presence and speci-
cell level with high precision, in a parallel format
ficity of the PCR products. The single cells
(an Ampligrid can accommodate 48 cells), with It is hoped that the project’s efforts will develop
on the AmpliGrid will then be processed
a high amount of automation. breakthrough analytic tools and systems for pre-
automatically in an integrated PCR and
vention, diagnosis, or monitoring of a broad range
hybridisation machine (AmpliHyb). Clinical
samples will be investigated, in which
Expected results of diseases.
copy number deviations are pathologic as
By the end of the project the partners will be in
in genetic diseases. As a model system,
a position to quickly market systems which allow
QuAGSiC chose HLH which is hard to
gene analysis at the single cell level at low cost,
diagnose and fatal without specific thera-
with high speed, reliability and throughput.
peutic measures, as well as trisomy 21,
which is relevant in prenatal and postnatal
diagnostics.

144
Key words: single cell analysis, hybridization, amplification based counting, AmpliGrid

ROLE OF SMEs Scientific coordinator

Claude Weisbuch
Genewave SAS
The three SMEs in the project have central roles: XTEC – Bâtiment 404
École Polytechnique
91128 Palaiseau
• MMI (Molecular Machines & Industries) is developing an automated cell picker from its France
semi-automatic two dimensional cell selection tool, capillary based cell handling system, claude.weisbuch@polytechnique.fr
to a fully automated three dimensional cell finding and sorting system (cellector 3D). www.genewave.com

Partners
• Adavlytix is using its photolithographically structured microscope slide AmpliGrid™ that
is suitable for performing 48 different 1μl PCR reactions on the same substrate. The Wolfgang Mann
special AmpliGrid™ surface chemistry will be used to define a physical platform for the Advalytix AG
München, Germany
integrated PCR and hybridisation at the single cell level. www.advalytix.de

• Genewave is developing an integrated system which will allow both the PCR and optical Stefan Niehren
detection of hybridisation in an unsupervised single machine. Molecular Machines
& Industries AG (MMI)
Glattbrugg, Switzerland
www.molecular-machines.com

Andres Metspalu
Estonian Biocentre
Tartu, Estonia
www.ebc.ee

Marion Schneider
Clinical Centre,
University of Ulm
Ulm, Germany
www.uni-ulm.de

| Imaging of an Ampligrid.

145
ACRONYM Contract number: LSHM-CT-2006-037846
Starting date: 1 January 2007
RATstream™
www.ratstream.eu
SUMMARY
The RATstream Consortium will concen-
trate on the comprehensive phenotypical
characterisation of rat models of neurode-
generative diseases such as Huntington’s
disease (HD), Parkinson’s disease (PD) and
spinocerebellar ataxia type 17 (SCA17).
Ultimately, the project will deliver a proce-
dure for low-cost automated drug screen-
ing along with a set of data describing the
phenotype for each of the models.
To achieve this goal, automated home cage
systems for behavioural and physiological
phenotyping will be developed by two
SMEs and validated independently by two
academic partners, and individual data will
be incorporated into an integrated data-
base developed by a third SME. In a joint
effort, the groups will develop a compre-
hensive set of behavioural and physiologi-
cal phenotyping procedures, including PET
and DTI technologies, in order to detect
systematically neuropsychiatric correlates
of neuronal dysfunction and disease pro-
gression in rat models of HD, PD, and
SCA17. The resulting set of biomarkers will
lead to a valid set of minimised experi-
ments and markers best suited to provide
read-out parameters in pre-clinical studies
applying novel substances delaying or
preventing neurodegeneration.
| EC contribution: € 3 400 000
European project on the characterisation
of transgenic rat models for neurodegenerative
and psychiatric diseases: Automated home cage
analyses, live imaging and treatment
Background/Aim
RATstream™ is an ambitious European project
that aims to characterise and use three transgenic
rat models of neurological diseases which – in
humans – present with a wide range of neurological
and psychiatric phenotypes:
• transgenic rat model of HD (1);
• transgenic rat model of PD overexpressing
alpha-Synuclein with the A30P mutation; and
• transgenic rat model of SCA17 with 64 expanded
CAG repeats in the TATA binding protein. Such
transgenic rat models are unique worldwide.
The project aims to pursue a completely novel
gene-to-function approach resulting in a compre-
hensive phenotyping process which will comprise
the following components:
• classical phenotyping;
• monitoring of behavioural and physiological
performance in fully automated physiological
and behavioural home cage test systems;
• non-invasive imaging technologies which have
been adapted to small animals;
• neuropathology;
• microarray analysis.
The project will apply this approach to all rat mod-
els in order to achieve comprehensive high-qual-
ity characterisation of models.
Two members of the consortium (TSE, New-
Behavior) aim to develop automated home cage
test systems for rat models which do not exist yet,
but which are imperative in view of the upcoming
large number of transgenic rat models in both indus-
try and academia. Collaboration with the academic
partners FAU and Uni Tübingen will provide an opti-
mal environment for development and refinement
of home cages which are validated via correlation
with data from classical read-outs and by cross
comparison between two experienced academic
partners. Cage systems will be suitable for contin-
uous monitoring of spontaneous, social, cogni-
tive, emotional and physiological measures
(drinking, feeding, metabolic performance/calorime-
try, telemetry for temperature and biopotentials) in
home-cage-like environments for rats.
146
| Duration: 36 months
This phenotyping set up (1-5) will be used to
develop a minimised and essential set of bio-
markers, in order to monitor disease progression
reliably in the transgenic rat models of PD, HD,
and SCA17. Phenotype data are also correlated to
neuropathological features such as protein aggre-
gates, neuronal cell loss, and neurotransmitter
alteration at different disease stages. The pheno-
typing approach will be used to characterise for
each disease model a minimised set of markers
best suited as read-outs in pre-clinical studies,
applying novel compounds delaying or preventing
neurodegeneration.
The objective of this project will be to provide the
proof-of-principle that it is possible in the rat:
• to develop, validate, and use standardised auto-
mated home cage systems, and to adapt in vivo
imaging techniques for phenotyping neurologi-
cal and cognitive function (1st year);
• to harvest large data sets on gene functions and
corresponding phenotypes thereof (2nd year);
• to determine and validate a minimised set of
predictive parameters (2nd year) and experi-
ments as well as of appropriate time slots for
each rat model (low-cost approach); and
• to develop and apply specific quality standards
applicable for phenotyping tools and models
(over the entire project duration);
• furthermore, these rat models will be used
to scrutinise novel experimental, pre-clinical
treatments (year 1-3), chiefly with regard to
effectiveness, side-effects, applicability, and
transferability.
Expected results
• Validated novel automated behavioural and
physiological test systems.
• Behavioural markers derived from correlation
analysis of data from automated and classical
screening for transgenic rats.
• Data on MRI (DTI), PET and Microarray expres-
sion profiling as regards disease progression in
transgenic rats.
Key words: brain research, neurodegeneration, transgenic animal models, comprehensive phenotyping,
automated behavioral phenotyping, in vivo imaging, pre-clinical treatment studies

ROLE OF SMEs Scientific coordinator

Olaf Riess

Four SMEs, sharing 30 % of the project’s research budget, play key roles in the project. TSE Project manager
Systems, based in Bad Homburg, Germany and New Behavior, based in Zurich, Switzerland,
develop cage systems for automated screening for behavioural, cognitive and physiological Holm Graessner
Eberhard-Karls-Universität Tübingen
malfunctions of transgenic rat models. The aim is to identify minimal parameter sets as regards Department of Medical Genetics
number of treated animals, study time and number of parameters to be applied in preclinical Calwerstr. 7
treatment studies. Those systems will be validated against classical methods of screening by 72076 Tübingen, Germany
holm.graessner@med.uni-tuebingen.de
academic partners of the consortium. Trophos S.A., a French biopharmaceutical company, spe- www.uni-tuebingen.de/klinische_genetik
cialising in the discovery and development of drugs for neurodegenerative diseases optimises
two promising drug candidates for preclinical studies and develops respective analytical Partners
methods. CrossLinks, a spin-off company of the Department of Bioinformatics of the
Stephan von Hoersten
Erasmus University Medical Center in Rotterdam, develops, adjusts, implements and hosts Friedrich-Alexander-Universität Erlangen
a data collection, storage and analysis system to support high-throughput (HTP) data col- Germany
lected from automated cages, genomics data and imaging data. One of the crucial aims is the www.fpz.uni-erlangen.de/
Exp_Biomedizin.htm
calculation of the minimised sets of parameters and markers best suited for treatment studies.
Hans-Peter Lipp
NewBehavior AG
Switzerland
www.newbehavior.com
• Full scale phenotyping data for tg rats. Big pharmaceutical companies such as Boehringer
Ingelheim and Novartis have already expressed Silvia Brenda
• Standardised progression features of tg rats. interest in the generated transgenic rat models of TSE Systems GmbH
Germany
PD and HD. With widespread distribution of the www.newbehavior.com
• Minimised parameter sets for pre-clinical trials models and their proven validity for therapeutical
in transgenic rat models. studies, this interest and thus the interest in the Bertrand Tavitian
behavioural test systems will be further increased. Commissariat à l’Énergie Atomique
France
• Power calculation for pre-clinical trials. For instance, based on the publication of the rat HD www-dsv.cea.fr/en/instituts/
model (2), more than 40 academic and pharmaceu- institut-d-imagerie-biomedicale-i2bm/
• Pharmocokinetic and toxicity data for com- tical partners were interested in investigating treat- unites-de-recherche/service-hospitalier-
frederic-joliot-shfj-a-syrota/laboratoire-
pounds to be applied in pre-clinical trials. ment tools (stem cells, drugs, viruses) with the d-imagerie-moleculaire-experimentale-lime
help of this model. With the publication of the PD
• Study reports on preclinical trials. and SCA17 models, an even greater interest is fore- Rebecca Pruss
Trophos S.A.
seeable (for PD because of the limitations of the France
• Data base for phenotyping and treatment stud- mouse models and because of the impact in drug www.trophos.com
ies of transgenic rats. development for pharmaceutical companies).
Ronald Naninga
CrossLinks B.V.
Potential applications For Trophos, the commercial gain consists of The Netherlands
a potential reduction in the risk to further clinical www.crosslinks-it.com
The commercial impact of the project can be esti- development of its drug candidate for the indica-
Annemie van der Linden
mated explicitly for the two SMEs engaged in devel- tion targeted in this STREP, in case the models are University of Antwerp
opment of automated home cage test systems. validated and found predictive of the human dis- Belgium
NewBehavior expects a growing share (10-25 %) in ease. This can lead to significant advantage to webh01.ua.ac.be/biomag
the market for rat behavioural equipment, esti- other commercial competitors, once outcomes
mated to be about € 5 million per annum in Europe can be approved in clinical trials in humans, and
and € 15 million worldwide. TSE expects, in 2008, can point to significant potential earnings.
a share in Europe worth € 1.5 million and, for the
rest of the world, worth € 0.15 million. In 2009, this CrossLinks’ product, namely an integrated data-
is expected to increase up to € 3.75 million in base and software tool for complex phenotyping
Europe and € 1.8 million in the rest of the world of transgenic animals, will bridge a gap in the mar-
respectively. While the market itself is not large in ket. To our knowledge, such a tool does not exist.
comparison with other fields of biotechnology, one
can expect sustainability over a long period, since
automated home-cage testing systems will gradu- References
ally replace existing rat testing equipment in every (1) von Hörsten et al. 2003, Hum Mol Genet 12:617-624.
university and larger pharmaceutical company. (2) Idem.

147
ACRONYM Contract number: LSHP-CT-2006-037276
Starting date: 1 January 2007
RespViruses
medical-surveillance.com/index.html
SUMMARY
The RespViruses project will study the
innate and acquired immune response of
the elderly against the new and known
respiratory viruses. Clinical and basic
research aspects will be addressed
equally, and new diagnostic assays to
evaluate the immune status of the elderly
will be developed.
| EC contribution: € 1 770 361
Immune response to viral respiratory
infections and vaccination in the elderly
Background
During the last few years some new respiratory
viruses (HMPV/hCoV-NL63/SARS/Bocavirus/flu
H5N1) have emerged. In addition to other viruses,
such as RSV, EBV, and Paramyxoviruses, they are
able to induce severe respiratory diseases in
high-risk patients, in particular young children
and elderly.
Aim
The first objective of the project will be to study
the innate and acquired immune response of the
elderly against the new and known respiratory
viruses, both clinical and basic research will be
addressed, in addition, a new diagnostic assays to
evaluate the immune status of the elderly will be
developed. Within the project, an animal model for
the investigation of the elderly’s immune response
will be established. In this model, antiviral agents
will be tested for their ability to support the
patient’s immune response. Up to 40 000 elderly
sera collected during the last 9 years will be tested
for antibodies to emerging respiratory viruses
(HCoV-NL63/HMPV/RSV/EBV/fluH5N1), provid-
ing a wide view of the epidemiology of these
viruses. For a precise view on the elderly’s immune
148
| Duration: 36 months
response to the viruses, a defined and uniform
panel of relevant clinical data related to respira-
tory infections will be collected. Internationally
standardised prospective data mining and a new
multi-lingual software tool will be developed
within the project and used by the partners.
Expected results
The project expects to gain detailed knowledge
on the innate and acquired immune response
to emerging respiratory viruses in the elderly.
A thorough basic investigation of emerging respi-
ratory viruses will provide further handles to
develop antiviral strategies based on siRNA and
external guide sequences (EGSs). Furthermore,
known antivirals will be evaluated with the final
goal to support the elderly’s immune response
whilst reducing mortality in the elderly caused by
respiratory infections.
Potential applications
New diagnostic assays; new antiviral therapies;
optimised treatment and vaccination strategies;
new software tool for surveillance and clinical
data mining.
Key words: new respiratory viruses, immune response of the elderly, mouse models, diagnosis, siRNA, EGS

ROLE OF SMEs Scientific coordinator

Oliver Schildgen
Institute for Medical Microbiology
Three European SMEs are partners in RespViruses, and are based in Belgium, Germany and Immunology, and Parasitology
Spain. These SMEs will receive approximately 50 % of the project budget. Having as partner Department of Virology
University of Bonn
INGENASA skilled in enzyme immunoassays, monoclonal antibodies production, nucleic Sigmund-Freud-Strasse 25
acid cloning and recombinant protein expression will help to develop new prototypes for 53105 Bonn, Germany
diagnostic assay development in respiratory diseases. INGENASA is a SME Biotechnology o.schildgen@medical-surveillance.eu
www1.uni-bonn.de/startseite/jsp/index.jsp
company dedicated to the research, development, production and commercialisation of
products for diagnostic sector with 25 years’ history in this field, mainly for viruses that Partners
affect livestock animals or pets. INGENASA is also active in areas of prevention of animal
diseases (vaccines) and has participated in several funded European projects (BRIDGE, Maria Grazia Cusi
University of Siena
BIOTECH, FAIR, FP5 and FP6 programmes). Siena, Italy
www.unisi.it
The Belgian SME, RNA-TEC, with its profound knowledge and expertise in oligonucleotide
chemistry plays a crucial role in the project by designing and synthesizing suitably stabi- Lia van der Hoek
Academic Medical Center
lized siRNAs and external guide sequences that target highly conserved RNA sequences Amsterdam, The Netherlands
of the respiratory viruses that are the subject of the study. The partners will test these www.amc.uva.nl
compounds in vitro and also in suitable animal models. A long term goal of the project is
Catherine Manoha
to identify potent lead compounds that can be further exploited as potential antiviral University Hospital Dijon
therapeutics using appropriate delivery systems that we can access. Dijon, France
www.chu-dijon.fr
As software developer and consulter in IT departments, SME Mattes Hamann will cover two Matthias Hamann
mean parts during the project. One will be the internal communication and the presentation Hamann
of the project information. In the other part he is responsible for collecting and evaluating Germany
medical data. Therefore MH will develop multilingual software for acquiring relevant www.hamann-software.de
medical data around respiratory disease. SME MH already made some needful experiences Brian Sproat
in surveillance tools. MH will create and develop the project website, a Contact Management RNA-TEC
System and a software tool for acquiring project information. He will also consult any team Leuven, Belgium
www.rna-tec.com
member if necessary.
Beatriz Lazaro
INGENASA
Spain
www.ingenasa.es

Michael Kleines
University Hospital Aachen
Aachen, Germany
www.ukaachen.de/content/
folder/1202162

149
ACRONYM Contract number: LSHB-CT-2007-037241 | EC contribution: € 1 843 427 | Duration: 36 months
Starting date: 1 April 2007

SAGE

SUMMARY
An attractive alternative to the current
SME-led antibody glyco-engineering
state-of-the-art in protein production, is
the use of plant systems for the produc-
tion of pharmaceutical glycoproteins
(including antibodies), given their cost
efficiency and overall safety. The SAGE
project targets an improved plant produc-
tion platform for pharmaceutical glyco-
proteins, to produce large quantities of
Background The partners, part of an international consortium
antibodies for use in cancer diagnostic
of four research organisations, one small and
and therapeutic systems.
The use of plant systems for the production of medium-sized enterprise (SME) and two compa-
pharmaceutical glycoproteins (including antibod- nies, will produce an antibody as a panel of differ-
ies) offers an attractive alternative to the current ent glycoforms, which will be tested for the
state-of-the-art in protein production, given their following:
cost efficiency and overall safety. Producing large • stability;
quantities of antibodies for use in cancer diagnos- • efficacy (e.g. in Fc-receptor binding assays,
tic and therapeutic systems using plant systems tumour cell binding assays and tumour grafting);
could therefore prove a viable and financially • pharmacokinetic properties, such as serum half
sound approach. life and antibody-dependent cellular cytoxicity
(ADCC).
However, the differences in glycan structures
added by plants, in comparison to those found in The project partners will use the results to
humans, pose significant obstacles and in fact develop safer and more active glycoform varieties
researchers recognise that the plant species for therapeutic applications.
used, as well as the tissue and cell type and the
age, have a huge impact on the final glycoform of By using the plant expression systems and BY-2
an antibody. cells to generate the same recombinant antibody,
the consortium targets the production of H10,
Aim a human full-length immunoglobulin G (IgG) that
recognises the CEA.
The SAGE project targets an improved plant pro-
duction platform for pharmaceutical glycopro- SAGE will also conduct a comprehensive, compar-
teins. The partners, a high-calibre team of experts ative study to establish how the structural, func-
in plant-based production technology and tional and clinical properties of the antibody are
immunology, will use four plant-based expression influenced by the glycan structures. The project
systems (including transgenic plants, virus- partners will compare the properties of the H10
infected plants and transformed plant cell lines) antibodies with those of a control H10 molecule
and mammalian cells as a control to generate generated in Chinese Hamster Ovary (CHO) cells.
a therapeutic antibody that recognises the well-
characterised carcinoembryonic antigen (CEA),
as well as their experience and know-how to
launch protein therapeutics on the market.

150
Key words: glycol-engineering, plant-made pharmaceuticals, recombinant antibody, transgenic plants

ROLE OF SMEs Scientific coordinator

Stefan Schillberg
Fraunhofer-Institut für Molekularbiologie
greenovation Biotech GmbH has developed innovative technologies for the production of und Angewandte Oekologie IME
proteins in mosses. The production technology is based on protein secretion into the Department of Plant Biotechnology
Forckenbeckstrasse 6
surrounding medium of mosses which are cultivated under liquid conditions in photo- 52074 Aachen, Germany
bioreactors. Moreover, greenovation has developed expertise in the genetic modification of stefan.schillberg@ime.fraunhofer.de
mosses and in plant glyco-engineering. The SME will produce the H10 antibody in moss www.ime.fraunhofer.de/EN/index.jsp
and the effect of glycan modifications on therapeutic applications will be analysed in vitro Partners
and in vivo.
Yuri Gleba
ICON Genetics
Halle, Germany
icongenetics.com/html/home.htm
Expected results With strong business support, SAGE will convert
any new knowledge or product developed during Gilbert Gorr
The use of advanced plant-based expression tech- the duration of the three-year project directly greenovation Biotech GmbH
Freiburg, Germany
nologies will help SAGE generate innovative thera- into strategic advantage. The project partner www.greenovation.com/english/
peutic and diagnostic antibodies. The consortium Bayer BioScience will utilise IP management index.php
will establish which best plant-based expression support to conduct IP searches and secure extra
Gerben van Eldik
platform should be used to produce therapeutic IP protection, if needed. Bayer BioScience
antibodies, as well as identify the glycan struc- Ghent, Belgium
tures that give antibodies superior properties in SAGE will also transfer the acquired knowledge www.bayer.be/cms/benelux/
a clinical setting. to other scientific groups working in the same byc_cpstd_befr.nsf/
field. Results and information will be dissemi- Dirk Bosch
The team will also determine the effects the vari- nated via electronic mail, peer-reviewed articles, Dion Florack
ous plant-derived glycans have on the physical abstracts and posters. The SAGE consortium Gerard Rouwendal
Plant Research International B.V.
and functional properties of antibodies. This website will also make key findings available to Wageningen, The Netherlands
action will support SAGE’s intention to produce the public. www.pri.wur.nl/UK
improved antibody-based therapeutics with supe-
Eva Stoger
rior performance, as well as to provide treatment University of Natural Resources
for many more people who need it. Ultimately, and Applied Life Sciences
SAGE will be instrumental in improving healthcare Vienna, Austria
for everyone and in bringing down the costs for www.boku.ac.at/home.html
treatment. Hardev S Pandha
University of Surrey
Surrey, United Kingdom
www.surrey.ac.uk

| Regeneration of transgenic
plants producing pharmaceuticals
in petri dishes.

151
ACRONYM Contract number: LSHP-CT-2006-037796 | EC contribution: € 827 313 | Duration: 36 months
Starting date: 1 December 2006

SERO-TB

SUMMARY
There is a great need for simple and
Development of a Specific Serological Kit
robust diagnostic methods for the diag- for the Diagnosis of TB
nosis of tuberculosis (TB). From the
basis of a through-screening process
ten M. tuberculosis antigens have been
identified, exhibiting potential as sero-
diagnostic TB antigens. Two to three of
these antigens will be selected with the
aim of achieving the highest sensitivity
Background Expected results
and specificity in a setting with a high
number of latent TB infections and HIV
Globally, TB is a severe problem, and the rapid By the end of this project, it is expected that the
co-infection. The selection will be based
and accurate diagnosis of active TB is the corner- identification of two or three M. tuberculosis anti-
on evaluating patients with TB, latently
stone of TB control. There is a direct need for: gens, which can form part of a serodiagnostic
infected individuals and symptomatic
• better TB diagnostics methods in developing assay as a tool for detecting active TB in a high
non-TB patients.
countries; and a medium TB incident setting, will have been
• the development of a simple and rapid test based achieved. Furthermore, performance data on the
The selected antigens will be incorpo-
on antibody monitoring, which will be of great ICT prototype are also expected. As a part of this,
rated into an immunochromatographic
importance in controlling the global epidemic. data which highlight the influence of TB incidence
test (ICT) which will be optimised for the
on the performance of an antibody based kit for
detection of M. tuberculosis-specific
There are currently a number of serology-based diagnosis of active TB are expected.
antibodies. Prototypes of the test kit
commercial TB tests available, but none with the
will be produced and in-house proof of
performance data generated. Finally,
required sensitivity and specificity. Potential applications
the performance of this test kit will be
The publications of the genomic regions of differ- The development of the proposed ICT assay
evaluated in a real life scenario in two
ence between M. tuberculosis and M. bovis BCG would lead to an inexpensive and more accessible
independent hospital settings in Turkey
allows identification of genes that are present diagnostic TB tool whilst enabling local and family
and Ethiopia.
only in M. tuberculsosis. From these gene regions physicians in the field to perform the TB diagnosis
100 proteins have been screened, specific for the from the bed-side. This will permit an earlier diag-
M. tuberculosis complex. From these, ten anti- nosis of the disease and therefore an early initia-
gens have been selected, which are frequently tion of the treatment of a contagious disease
recognised by both HIV negative and HIV positive which will lead to a decrease of the transmission.
TB patients. Only by preventing the spread of the disease in
the local community can long-term control of TB
Aim be achieved.

To identify the best combination of two to three

antigens to be incorporated into an immunochro-
matographic test, which will be evaluated for
performance in two real life settings.

152
Key words: tuberculosis, serodiagnosis, antibodies, diagnostics, immunochromatographic test

ROLE OF SMEs Scientific coordinator

Mark Doherty
Statens Serum Institut
The SME role is undertaken by Vircell, a company specialised in infectious diseases and Department of Infectious
more specifically focused on respiratory infections, but which has previously had no TB Disease Immunology
Artillerivej 5, 2300 Copenhagen S
specific activities. This project is regarded as an opportunity to enter the field of TB diagnosis. Denmark
In addition, this project will establish a new collaboration between SSI and Vircell. The tmd@ssi.dk
financial support of this project will allow a SME company like Vircell to undertake a project www.ssi.dk
with the aim of providing developing countries with a diagnostic kit, regardless of the Partners
commercial compensation obtained. Vircell is part of the Work Package (WP) management
team in the project and leads WP 2 “Development of a TB immunochromatographic prototype” Arantxa Cortés
and WP3 “Demonstration of performance of prototype”. VIRCELL P.I.
Granada, Spain
www.vircell.com

Ismail Ceyhan
Refik Saydam National
Institute of Hygiene
Ankara, Turkey
www.rshm.saglik.gov.tr

Abraham Aseffa
Armauer Hansen Research Institute
Addis Ababa, Ethiopia

| Principle of an immunochromatographic test.

© Vircell

153
ACRONYM Contract number: LSHG-CT-2006-037415 | EC contribution: € 2 499 999 | Duration: 48 months
Starting date: 1 December 2006

SMARTER
www.smarter-chromatin.eu

SUMMARY
The identity of a given cell within a meta-
Development of small modulators of gene
zoan organism is primarily defined by the activation and repression by targeting epigenetic
expression pattern of its genes. The acti-
vation and repression of genes is tightly
regulators
regulated by the concerted action of tran-
scription factors that recognise and bind
specific DNA sequences within regulatory
regions.
Background • establishment of histone modification states as
Work done over the last 20 years revealed
standard readouts for drugs that target epige-
this basic mechanism of gene activation
The epigenetic level of gene regulation is being netic modifiers;
and repression, while recent experiments
analysed intensively worldwide. However, the • improvement of known epigenetic modulators
exposed an additional layer of regulation
knowledge gained from these studies has not through medicinal chemistry;
involving modifications of DNA and bound
been transferred to drugs or drug candidates for • identification of target genes that are regulated
histones. These modifications are involved
the treatment of major diseases. Equally, devel- by the SMARTER molecules;
in cellular inheritance of transcriptional
opment of small molecules targeting epigenetic • application of the SMARTER molecules in stan-
states through cell division and develop-
regulators have so far not been the major focus of dard animal model systems to verify their activity
ment, and as they are not coupled to DNA
drug discovery efforts. in living organisms.
sequence, are referred to as epigenetic.

Many factors that impact on epigenetic

To pursue this promising approach it is obviously Expected results
important to further improve understanding how
phenomena are clearly distinct from
the eukaryotic genome in general, and the human Our proposal will thereby promote the develop-
basic transcription factors and are
genome in particular, operates. Therefore knowl- ment and improvement of a new branch of cancer
involved in regulating chromatin struc-
edge about its DNA sequence, its epigenetic con- drugs and as well support validation of new
ture. Modulation of chromatin structure
trol systems and its dynamic structure in relation potential drug target enzymes. Additionally, tools
is frequently achieved by intrinsic enzy-
to gene expression must be integrated. will be generated, which allow new insights in
matic activities that either mark partic-
fundamental mechanisms of gene regulation by
ular regions within the genome for
activity or repression, or use the hydrol-
Aim epigenetic modification.
ysis of ATP to remodel nucleosomal
arrays. This variation of gene expression
The SMARTER project aims at the development Potential applications
and improvement of compounds targeting epige-
patterns in response to external and
netic regulators. These compounds will be tested In the context of human health, an understanding
internal signals has a major influence on
in various assays making it possible to collect of gene regulation is central to our understanding
stem cell differentiation, the mainte-
data sets of several parameters as histone modi- of many medical complaints and conditions.
nance of tissue integrity, and the adap-
fications, chromatin states, gene expression Fundamental aspects of chromatin function are
tation of organisms to environmental
patterns and physiological characteristics in an increasingly recognized as important factor in the
dynamics.
integrative manner for the first time. development of many severe and often untreat-
able diseases. Therefore many proteins that are
Recently, small molecules that target his-
Therefore major objectives are: involved in the regulation of chromatin structure
tone deacetylases (HDAC) have been used
• identification of small molecule inhibitors that are potential drug targets and small molecules
in the treatment of cancer, opening up
target various histone-modifying enzymes; directed against these factors will play an increas-
new avenues in therapeutic research.
• validation of these inhibitors through in vivo ingly important role in treating patients that are
analytics of histone modifications states; affected by one of these maladies.
The SMARTER project aims at the devel-
opment and improvement of such com-
pounds, which is the primary mission of
Chroma, the SME participating in the
consortium.

154
Key words: epigenetics, small molecules, histone deacetylases, chromatin

ROLE OF SMEs Scientific coordinator

Axel Imhof
Histone Modifications Group/
The SMARTER project is specifically designed to strengthen the knowledge base of Protein Analysis Core Facility
Chroma Therapeutics, a privately-held biotechnology company focused on the discovery Adolf-Butenandt Institute
Ludwig Maximilians University of Munich
and development of novel small molecule drugs targeting epigenetic modifiers. The col- Schillerstr. 44
laboration with leading chromatin laboratories will be of great benefit by facilitating the 80336 Munich, Germany
analysis of SMARTER inhibitor molecules that have been and will be discovered by imhof@lmu.de
molekularbiologie.web.med.
Chroma in high-throughput screens. A rapid testing in various biological systems will uni-muenchen.de/groups/imhof
allow Chroma a more directed optimization of the small molecules by their medicinal
chemistry specialists. The new knowledge gained from this project will be efficiently Project manager
translated into new therapies and clinical practice through Chroma’s well-established
Julia Hochstatter
R&D pipeline. Adolf-Butenandt-Institut
LMU
Munich, Germany
Julia.Hochstatter@med.uni-muenchen.de

Partners
Scott Cuthill
Chroma Therapeutics
Oxford, United Kingdom
www.chromatherapeutics.com

Dirk Schuebeler
Friedrich-Miescher-Institut
Basel, Switzerland
www.fmi.ch/html/research/
research_groups/epigenetics/
Dirk_Schuebeler/Dirk_Schuebeler.html

Manel Esteller
CNIO
Madrid, Spain
www.cnio.es/ing/grupos/plantillas/
presentacion.asp?grupo=50004270

Tony Kouzarides
Gurdon Institute
Cambridge, United Kingdom
www.gurdon.cam.ac.uk/~kouzarideslab/
tony.html

155
ACRONYM Contract number: LSHB-CT-2007-037703
Starting date: 1 June 2007
STEMDIAGNOSTICS
www.stemdiagnostics.com
SUMMARY
The StemDiagnostics project aims at the
development of next-generation of med-
ical tests and tools for significantly
improving the survival rate of patients
undergoing haematopoietic stem cell
transplant also known as HSCT – a med-
ical treatment for life threatening condi-
tions such as leukaemia and lymphoma.
| EC contribution: € 2 500 000
The development of new diagnostic tests, new
tools and non-invasive methods for the prevention,
early diagnosis and monitoring for haematopoietic
stem cell transplantation (HSCT)
Background
Over 7 000 allogeneic haematopoietic stem cell
transplants (HSCT) are carried out each year in
Europe alone, as a treatment for leukaemia and
lymphoma. Techniques and cure rates are improv-
ing but the overall survival rate remains between
40-60 %.
Aim
This project will develop new proteomic, biologi-
cal and genomic tests and tools for early diagno-
sis and monitoring of patient response to novel
therapeutics for the most severe complication of
HSCT; graft versus host disease (GvHD) and will
bring to the clinic a new generation of diagnostics
that will significantly improve HSCT therapy and
patient outcome.
The Consortium unites 5 European SMEs with
expertise and markets in genomic and proteomic
testing, diagnostic assay development and
biochips, with clinical partners selected for their
world leading research in HSCT and access to clin-
ical samples and patient groups.
The project will focus on the role of relevant genes
and biomarkers associated with acute and chronic
GvHD, using retrospective samples from estab-
lished biobanks and prospective clinical trials to:
• identify novel bio and genomic markers for
diagnostics;
• develop novel diagnostic tools using genomics,
proteomics, in vitro bioassays and biochips;
• test the new diagnostics in animal models & on
clinical samples;
• exploit the new tools for commercial use.
Expected results
The above will be realised by:
• development of diagnostic tests using single
nucleotide polymorphism (SNP) analyses (SME
IMGM), based on results from previous EC
funded research (EUROBANK, TRANSEUROPE);
• using proteomics via mass spectrometry evalua-
tion/development of diagnostic patterns (SME
156
| Duration: 36 months
MOSAIQUES), ELISA kits (SME APOTECH) and
protein biochip prototypes (SME ORLA), for the
development of fast high throughput technologies;
• development of novel reagents for monitoring
graft versus leukaemia, GvHD and targeted ther-
apy (SME MULTIMUNE; SME NASCACELL);
• comparative studies in an autoimmune disease
model of inflammation, rheumatoid arthritis.
The SMEs primary specific Aims include:
• development of new tools for novel diagnostics,
novel drug targets and therapeutics for use both
in the transplant and autoimmune setting;
• access to important clinical and biological sam-
ples and data for use in accurate assessment of
results and confirmatory studies for the devel-
opment of novel diagnostics;
• testing and evaluation of new diagnostics on
independent cohorts and correlation of data
across HSCT centres;
• testing of new prototypes against current
assays via collaboration between SMEs;
• use of new target molecules in monitoring of
response to therapy and during the post trans-
plant period to assess acute and chronic GvHD.
Potential applications
• Identification of new diagnostics in the form of
novel proteins associated with graft versus host
disease (GvHD) compared to viral disease.
• Development of early diagnostic tools for GvHD
and rheumatoid arthritis using gene profiling.
• The fast throughput development of novel mono-
clonal antibodies and ELISA kits for research,
diagnostics, and potentially therapeutic use.
• Development of novel peptides for use in moni-
toring GvHD and graft versus leukaemia effects
in transplant patients.
• Development of prototype biochips (Fig. 1).
• Identification of new single nucleotide polymor-
phisms (SNPs) for analysis in prognostic/diag-
nostic indices.
Key words: haematopoeitic stem cell transplantation, graft versus host disease, graft versus leukaemia, proteomics,
genomics, pharmacogenomics, clinical trials, early diagnostics

ROLE OF SMEs Scientific coordinator

Anne Dickinson
University of Newcastle upon Tyne,
The STEMDIAGNOSTICS Consortium comprises SME’s that are already key players in the School of Clinical and Laboratory Sciences,
European diagnostics market and already have the infrastructure and established market cred- Haematological Sciences, The Medical School
Framlington Place, Newcastle upon Tyne
ibility to turn research outputs from the STEMDIAGNOSTICS Project into marketable diagnos- NE2 4HH, United Kingdom
tic products. The SMEs will target not only the European market, but also international health a.m.dickinson@ncl.ac.uk
markets including opportunities in the USA, Japan and Asia. The Consortium consists of 5 SMEs
with expertise in state of the art technologies (IMGM, MOSAIQUES, mi, APOTECH, ORLA). Partners
APOTECH is a life science reagents company discovering, developing and producing new prod- Ernst Holler
ucts in the field of apoptosis and inflammation for laboratory based diagnostic tests. Klinikum der Universität Regensburg
ORLA has already developed a platform technology, which may form the basis of a clinic based Dept. Hamatology und Internistiche Onkologie
Regensburg, Germany
or bedside assay. Orla Protein Technologies is a leader in the emerging European nanotechnol-
ogy sector. The company has developed a ‘surface biology platform’ which is finding application Harald Mischak
in many areas including nanoscale diagnostics. Mosaiques Diagnostics GmbH
Multimmune GmbH is a biopharmaceutical company dedicated to the discovery and develop- Hannover, Germany
mosaiques-diagnostics.de
ment of novel products, including antibodies and peptides, for the treatment of cancer through
its innovative manipulation of the immune system. Gabriele Multhoff
IMGM Laboratories GmbH is one of the leading SMEs for functional genomics and biomedical multimmune GmbH
Munich, Germany
research in Germany and has extensive experience in molecular diagnostics. IMGM is among www.multimmune.de
the top 5 laboratories in Europe that are experienced in the ABI microarray technology.
Microarrays, real-time PCR low-density arrays and SNP-detection technologies will be used Ralph Oehlmann
throughout the project. IMGM Laboratories
Martinstried, Germany
MOSAIQUES’ established protein discovery systems will contribute to discovery of new bio- www.gene-expression-center.de
markers. Mosaiques Diagnostics will define and identifiy peptides and proteins in body fluids, www.imgm.com
which will enable diagnosis, of graft versus host disease as well as and response to therapy
Lars French
based on patterns of polypeptides in patients urine samples. To this end, Mosaiques Department of Dermatology
Diagnostics has developed proprietary technology and software which enable the diagnosis of Zurich University Hospital
diseases based on polypeptides. Zürich, Switzerland
CENAMPS is a not-for-profit technology commercialisation company, established in 2003. Olivier Donzé
Cenamps is dedicated to the development and exploitation of emerging small-scale tech- CSO and Operating Manager
nologies for applications in healthcare, ambient intelligence and consumer products. The com- Apotech Corporation (Headquarters)
pany will play a major role in management and exploitation of the project using state of the art Epalinges, Switzerland
www.apotech.com
management software and aid in bringing new developments to market and protecting IP.
Hans-Jochem Kolb
Klinical Cooperation Group Hematopoietic Cell
Transplantation, Institute of Molecular
The cytokine storm and involvement of the inflammasome/non HLA genetics
| Fig. 1 Immunology, Forschungszentrum fuer
Phase 1: Patient conditioning leads Umwelt und Gesundheit
to tissue damage in host tissues Phase 1: Patient conditioning- activation of inflammasome and early events Muenchen, Germany
producing pro- and anti- inflammatory
cytokines influenced by the patient Host tissues:
Pro-inflammatory cytokines Dale Athey
TNF-alpha, IL-1, IL6-
non-HLA genotype.
Host antigen presenting cells (APC) skin Heat shock protein activation Orla Protein Technologies Ltd., Nanotechnology
Irradiation/chemotherapy
Phase 2: In coming donor T cells and
Liver
GI tract
Anti-inflammatory cytokines IL-1Ra, IL-10 Centre, University of Newcastle upon Tyne
Newcastle upon Tyne, United Kingdom
their activation is influenced by donor
Phase 2: Donor T cell activation- further activation of inflammasome www.orlaproteins.com
non- HLA genotype with further release
of cytokines and upregulation of Host APC, fibroblasts,
epithelial/endothelial cells Gérard Socié
surface HLA Class II and adhesion Association de Recherche sur la Greffe
TCR-
molecules on target tissues. MHC IL-1 TNF-α, chemokines; IL-8 de CSP, Aplasies et HPN
Phase 3: Patient and donor non- HLA Donor T cell Paris, France
TNF-α IL-2 IFNγ
genotype may influence the
exacerbation or reduction of severity Phase 3: Inflammatory effectors Hildegard Greinix
of GvHD. Molecules involved in early Bone Marrow Transplantation Unit
events in phases 1 and 2 of cell (IL-1Ra IL-10) University Hospital of Vienna
activation via activation of the T
Nitric oxide Target cell Vienna, Austria
inflammasome. TNF-α APOPTOSIS
NK and tissue
(Reprinted from Dickinson A.M., and Ilona Hromadníková
damage
Charron, D. 2005. Non-HLA Differential cytokine IL-1, IFNγ / chemokine release
3rd Medical Faculty, Charles University
immunogenetics in hematopoietic stem Prague, Czech Republic
IL-10 IL-1Ra TGFβ
cell transplantation. Curr. Opin. Immune Modulation
Immunol., 17, 517. with Th1 IL-2, IFNγ Th2 IL-4, IL-6,IL-10 Shak Gohir
CENAMPS
permission from Elsevier.) aGvHD cGvHD
The Fabriam Centre, Middle Engine Lane
Newcastle upon Tyne, United Kingdom
www.cenamps.com
157
ACRONYM Contract number: LSHG-CT-2006-037586
Starting date: 1 January 2007
STREPTOMICS
www.streptomics.org
SUMMARY
The Gram-positive soil bacterium Strep-
tomyces is an invaluable host for the
secretory production of biopharmaceu-
ticals and other heterologous proteins.
STREPTOMICS aims to further evaluate
this host as a cell factory for the industrial
production of proteins of diverse origin
including from mammalians, bacteria and
archeae of interest for human health and
environment.
| EC contribution: € 2 850 851
Systems biology strategies and metabolome
engineering for the enhanced production of
recombinant proteins in Streptomyces
Background
The biotechnology industry is constantly search-
ing for better hosts for the production of biophar-
maceuticals and enzymes of diverse origin. The
Gram-positive soil bacterium Streptomyces has
already proved an invaluable host for this pur-
pose, since it can secrete several heterologous
proteins in satisfactory amounts. However, in
order to optimise strain selection, knowledge is
required concerning the following points:
• how protein secretion processes are integrated
within the metabolome, and how they interact;
• how heterologous protein secretion stresses
the metabolome and induces negative cellular
cascades.
Systems biology, the science of analysing and
modelling genetic, macromolecular and meta-
bolic networks, provides the means to address
these questions. By combining biochemical infor-
mation with genetic and molecular data, the
Streptomics consortium hopes to gain novel
insights into the functions of genes related to pro-
tein secretion, as well as how that protein secre-
tion mechanism responds to external and internal
stimuli. With a better understanding of this mech-
anism at the cellular level, it should be possible to
optimise protein secretion.
Aim
Streptomics aims to enhance the production of
heterologous proteins, using Streptomyces as a
host. More specifically, it has the following goals:
• to evaluate Streptomyces lividans as a cell fac-
tory for the production of heterologous proteins
of interest;
• to investigate the transcriptome and proteome
of the host strain under different growth condi-
tions, with different expression/secretion vectors,
and using different fermentation strategies, in
order to identify the genes important for optimal
cell performance, with respect to heterologous
protein secretion;
158
| Duration: 36 months
• to analyse metabolic flux control and flux bal-
ance with a view to engineering metabolic path-
ways found in a Streptomyces background, and
hence to exploit cellular pathways which pro-
vide improved energy transduction, balanced
growth and supramolecular assembly;
• to engineer better production/secretion strains
of Streptomyces based on the above, and based
on information about secretion bottlenecks that
will be identified through the production of
muteins, either via direct mutation of specific
amino acids, or by directed evolution;
• to optimise the protein production process.
Expected results
Based on a better understanding of metabolome-
secretome interplay, strategies for improved
protein secretion will be designed. These will
combine better energy generation and directed
energy consumption for either cell mass pro-
duction or heterologous protein secretion. Ulti-
mately, a ‘toolbox’ of Streptomyces strains will
be engineered and refined, which optimally over-
secrete proteins of interest during fermentation.
Consequently, Streptomics will generate knowl-
edge which will assist SMEs in the biotechnol-
ogy and other industries to develop new and
more efficient systems for the industrial produc-
tion of heterologous proteins, using S. lividans
as a cell factory. These systems will be useful in
both red (medical) and white (industrial) areas
of biotechnology.
Potential applications
This project aims to increase the number of effi-
cient cell factory platforms for the production of
heterologous proteins important in health, bio-
catalysis and the environment, using Streptomyces
as a host. It will therefore contribute to a competi-
tive, knowledge-based economy and sustainable
development in Europe, by serving the needs of
a research-intensive industrial sector in which
many SMEs have traditionally been involved.
Key words: systems biology, streptomyces, protein secretion, enzymes, biopharmaceuticals, directed evolution,
metabolomics, transcriptomics, proteomics

ROLE OF SMEs Scientific coordinator

Jozef Anné
Rega Institute
The four SMEs involved in the project, Prokaria (Matis) (Reykjavik, Iceland), Direvo, (Köln, Catholic University of Leuven
Germany), Eurogentec (Liège, Belgium) and BioXPr (Namur, Belgium) each have their specific Laboratory of Bacteriology
Minderbroedersstraat 10
task, from assessing the Streptomyces protein production platform for the production of pro- 3000 Leuven, Belgium
teins of their interest (Prokaria and Direvo) to helping to strain improvement of proteins which jozef.anne@rega.kuleuven.be
play a role in protein secretion via directed evolution (Direvo). Prokaria will take responsibility www.kuleuven.be/rega
for cloning, expressing and secretion of various enzymes from extremophiles, primarily from Partners
bacterial and archeal thermophiles into Streptomyces. These thermostable enzymes have pre-
viously been proven to be difficult expressed or produced in other hosts like E. coli or Thermus Michael Hecker
thermophilus. Direvo, a leading company in protein engineering by screening-based directed Ernst-Moritz-Arndt-University
Institute for Microbiology
evolution and its application to biomolecules, specifically to biocatalysts for chemical, techni- Greifswald, Germany
cal, industrial, scientific and pharmaceutical purposes, will test Streptomyces lividans and www.uni-greifswald.de/indexuk.html
evaluate expression/secretion levels and product characteristics for the production of engi-
neered proteins/enzymes with market potential in Pharma and Industrial Biotechnology, and Wayne M. Coco
Direvo Biotech AG
evaluate whether SecA mutants could improve secretion characterization. As such, Direvo com- Cologne, Germany
plements the expertise of the other partners with its broad and advanced technological www.direvo.com
portfolio in Directed Evolution and high-throughput protein screening. Eurogentec will take
Anastassios Economou
responsibility for the transcriptomic analysis of S. lividans. This SME developed previously in Foundation of Research
collaboration with different members of this project a complete DNA micro array based on long and Technology FORTH
oligo’s representing the entire set of ORFs specific to Streptomyces coelicolor. The use of the Institute of Molecular Biology
S. coelicolor DNA array for S. lividans transcriptomic analysis will be validated and the array and Biotechnology,
Iraklio, Crete, Greece
modified if necessary. Eurogentec will act as service provider for transcriptomic analysis for all www.forth.gr
partners of this project. Data will be generated in collaboration with different partners for analy-
sis of up and down regulated genes in different experimental conditions. BioXpr will organise Marc Daukandt
Eurogentec S.A.
and set-up a data repository system that will allow all the member of the consortium to store DNA MicroArray Dept.
the results of their work packages on a centralized system. The central database used to store Seraing, Belgium
the data will also be the source of information for analysis and visualisation system that will www.eurogentec.com/eu-home.html
combine proteomics, transcriptomics and metabolomics information to define the best condi- Jakob Kristjánsson
tions for protein secretion. BioXpr will therefore collect information to combine the sources Prokaria Ltd.
of data into one picture. Reykjavik, Iceland
The successful integration of the various aspects of this project STREPTOMICS will provide www.prokaria.is
in-depth knowledge about interactions that may occur at the genetic or proteomic level dur- Benjamin Damien
ing the heterologous protein secretion process in S. lividans of heterologous proteins. BioXpr S.A.
Partners will work together to apply a step-by-step approach to analyze the physiological Namur, Belgium
www.bioxpr.be
state and performance of the cell, and based on these results, to engineer strains that may
overcome or suppress negative effects. Roy Goodacre
University of Manchester
School of Chemistry
Manchester, United Kingdom
www.chemistry.manchester.ac.uk

Anna Eliasson Lantz

Technical University of Denmark
Centre for Microbial Biotechnology
Lyngby, Denmark
www.cmb.dtu.dk/English.aspx

Daniel Badcock
GlaxoSmithKline
Harlow, United Kingdom
www.gsk.com

| Automated protein engineering: A precision robot arm retrieves

a custom manufactured 1536-well plate in one corner of a room full
of robotics-compatible equipment including nano-liter volume liquid
handlers, single cell sorters, humidified incubators, heating and
cooling blocks, centrifuges, confocal laser-based plate readers and
other equipment integrated for fully automated high throughput
protein engineering at Direvo Biotech AG in Cologne, Germany.

159
ACRONYM Contract number: LSHG-CT-2006-037231
Starting date: 1 September 2007
SYSCO
www.biobase-international.com/pages/index.php?id=438
SUMMARY
The overall objective of the SYSCO project
is to decipher the intracellular biological
pathways and basic cellular processes
that act in physiological conditions as
well as in the context of intracellular par-
asitism, in order to highlight the alter-
ation in gene expression that stems from
the conflict between the host and
pathogen genomes. More specifically,
the project will use human and mouse
macrophages as cellular targets, and the
Leishmania parasite as a prototype for
intracellular pathogens. Leishmania is
one of the most intensively studied bio-
logical models in terms of parasite, host
immune response and genetics.
| EC contribution: € 1 840 719
Systematic Functional analysis of Intracellular
Parasitism as a model of genomes conflict
Background
A study conducted by an international expert
panel for the University of Toronto, ranked the
computational examination of host-pathogen
interactions among the top 10 biotechnologies
most likely to improve global health in the next
10 years (1). However, information about funda-
mental aspects of the cellular machinery involved
in the interactions between macrophages and
intracellular pathogens has not yet been suffi-
ciently categorised, particularly with regard to
macrophage function, and there is a need for
a systematic and integrative approach to the
identification of interconnected functional mod-
ules and salient modifications triggered by
intracellular parasitism.
Aim
SYSCO will decipher and modularise the cascade
of intracellular events generated by parasite-cell
interactions, and also how they result in either par-
asite elimination or infection in humans. A com-
parative analysis with mouse strains expressing
differing susceptibilities will help identify key
determinants of natural resistance or susceptibil-
ity to parasites acting at the macrophage level.
In a combined strategy of experimental and theo-
retical work, the SYSCO consortium will systemat-
ically capture data at different levels of cellular
information, using state-of-the-art, multi-para-
metric molecular technologies (both in human
and in mouse). These data will be used to identify
regulatory motifs through systematic promoter
analysis, and to populate computer models with
the relevant motifs and associated signalling
pathways. The computer models will be designed
as independent modules covering gene regula-
tion, gene expression, protein interactions and
signalling. This modular approach will be used to
mimic different types of innate macrophage
responses, and to map theoretical predictions to
experimental data.
160
| Duration: 36 months
Expected results
After 36 months, SYSCO will have achieved the
following aims:
• development of a hybrid, in silico model for the
innate response of macrophages to an intra-
cellular pathogen, based on the composition of
interconnected modules that mimic different
cellular events;
• development of a comprehensive systems
ontology;
• experimental investigation and categorisation
of four different modules, namely gene regula-
tion, gene and protein expression and signal
transduction;
• complementary high throughput analysis of
the macrophage transcriptome by Affymetrix
oligonucleotide arrays and serial analysis of
gene expression, both in parasite-infected and
in non-infected cells;
• prediction and validation of the regulatory net-
works in macrophages;
• experimental determination of cell regulation by
quantitative transcription factor assays and by
RNA interference.
Potential applications
Leishmaniasis is one of the world’s major para-
sitic diseases, but there is no vaccine for it as
yet, and the drugs currently prescribed to treat it
are fairly toxic. Millions of people living in devel-
oping countries, mainly in southern and east -
ern Mediterranean regions and in central and
South America, are exposed to leishmaniasis. The
Leishmania parasite is also a major co-pathogen
in the context of HIV infection in southern Europe.
The results of this project will be significant,
not only in the context of leishmaniasis, but
also for the understanding and treatment of
infection by other intracellular pathogens, such
as Mycobacterium tuberculosis, the bacterium
which causes tuberculosis.
References
(1) Daar et al, 2002.
Key words: intracellular parasitism, host-pathogen interaction, functional genomics

ROLE OF SMEs Scientific coordinator

Alexander Kel
BIOBASE GmbH
BIOBASE is the leading content provider of biological databases, knowledge tools and Department of Research and Development
software for the life science industry. They offer well-structured data, assembled by highly Halchtersche strasse 33
38304 Wolfenbüttel, Germany
qualified subject-matter experts, organized in an accessible and easily searchable manner Alexander.kel@biobase-international.com
that enables researchers to identify connections between disparate pieces of information www.biobase-international.com/pages
and to apply that knowledge to their specific topic of interest.
Partners
The tasks of BIOBASE are high quality manual literature annotation of project relevant David Piquemal
data into the proprietary databases TRANSFAC(R), TRANSPATH(R) TRANSCompel(R) and Skuld-Tech SARL
Proteome™. They collect data on mechanisms of gene regulation, transcription factors and Montpellier, France
www.skuldtech.com
their binding sites and on signal transduction pathways in the human cells in response to
Leshmania. The collected data along with the full content of the databases will be provided Ralf Herwig
to the consortia. BIOBASE will also do DNA sequence analysis: search for putative binding Max Planck Institute
sites for TFs in promoters of genes regulated during cellular response to the parasite attack. for Molecular Genetics
Berlin, Germany
Biobase will be involved in development of software for the reconstruction of a gene regu- www.molgen.mpg.de
latory network (transcription network) and in designing artificial promoters which can be
used to study mechanisms of gene regulation in various immune responses. Béatrice Regnault
Institut Pasteur
Paris, France
Furthermore, BIOBASE will manage the project. Management activities include communi- www.pasteur.fr/english.html
cation with the commission, organisation of regular financial audits, dissemination and
exploitation of project results, and regular project meetings. Patricia Renard
Facultés Universitaires Notre-Dame de la Paix
Unité de recherche en biologie cellulaire
Skuld-Teck (SKT) set up one bioinformatics platform, and two gene profiling technical Namur, Belgium
platforms one based on the SAGE™ and one based on real-time quantitative PCR (qPCR). www.fundp.ac.be
The SAGE platform has two advantages: the exhaustiveness of the results and the network Koussay Dellagi
of its users (who share their gene profiles data). Through its two gene profiling platforms Institut Pasteur de Tunis,
SKT has developed a first thematic dedicated to Leukaemia (end of 2002). This has permit- Laboratoire d’immunopathologie,
vaccinologie et génétique moleculaire (LIVGM)
ted to identify a set of genes allowing for the design of a Leukaemia diagnosis/prognosis Tunis, Tunisia
tool. This tool is being validated within clinical trials to draw up the gene profiles of patients www.pasteur-international.org
suffering from Leukaemia and to monitor them during the treatment.
Winston Hide
University of the Western Cape
SKT will provide a relational database integrating all public and private SAGE data. SKT will South African National
develop another relational database integrating the data generated along the project i.e.: Bioinformatics Institute
the gene profiles data that is being generated using SAGE and those that will be generated Bellville, South Africa
www.sanbi.ac.za
using Affymetrix. This platform will include two interfaces: a working interface that allows
introducing annotations and integrating new data (under PostgreSQL/Linux) and an Pierre-Andre Cazenave
exploitation interface, regularly updated that will be easy to query for non-specialists. Université Pierre et Marie Curie-Paris VI
Considering the increasing volume of data in public databases, the working interface will be Laboratoire d’immunophysiopathologie
infectieuse – URA 1961
implemented under Oracle. SKT will also validate the expression of target genes obtained Paris, France
in WP2 through its Real-Time PCR (qPCR) platform. english.upmc.fr/UK/info/00

161
ACRONYM Contract number: LSHG-CT-2006-037457
Starting date: 1 January 2007
SysProt
www.sysprot.eu
SUMMARY
SysProt aims at the development of a new
paradigm for the integration of pro-
teomics data into systems biology. The
goal is to gain relevant knowledge on
biological processes that are important
for human health and to use this
knowledge for the purpose of disease
modelling. The strategy to achieve this
objective is an innovative, explorative
systems biology approach both on the
molecular and physiological level with
a strong focus on protein function and
modification.
The consortium aims at demonstrating
the newly developed technologies in
a proof-of-principle study in an obesity-
induced type-2 diabetes mouse model.
| EC contribution: € 2 097 268
System-wide analysis and modelling of
protein modification
Background
Bioinformatics methods for diagnostic screening
are a bottleneck in current biomedical research.
While exploratory methods – such as statistical
hypotheses testing, clustering of gene expression
profiles and classification methods – have been
successful in the detection of molecular markers
for interesting diseases, these techniques fail to
validate these markers in their gene regulatory
context and to integrate other data sources rele-
vant for diagnostic purposes. For these tasks,
novel modelling techniques, network analyses,
and data integration methods are indispensable.
The analysis of processes involved in the course
of complex polygenic diseases, such as obesity
and type-2 diabetes, is in fact a multi-step proce-
dure that has to cope with data from diverse
experimental functional genomics platforms
(gene and protein expression), physiological
data, environmental factors, and others.
Aim
The project SysProt aims to develop a new para-
digm for the integration of proteomics data into
systems biology. The goal is to gain relevant
knowledge on the biological processes that are
important for human health and to use this knowl-
edge for the purpose of disease modelling.
In order to achieve this objective, an innovative,
explorative biological systems approach (on both
the molecular and the physiological level) will be
adopted, with a strong focus on protein function
and modification. SysProt will produce pro-
teomics data, indispensable for the identification
of novel circulating protein factors, and post-
translational protein modifications that are impor-
tant for the onset, dynamics, and progression of
complex diseases.
Data generation will be complemented by the
development of computational analysis methods
for these novel data types and the creation of ade-
quate modelling technology. The project will ben-
efit from the utilisation of established mouse
disease models, existing benchmarking modules
for computational analysis, and the functional
162
| Duration: 36 months
genomics platforms developed by and accessible
to the partners. In particular, the consortium aims
to demonstrate newly developed technologies in
a proof-of-principle study within an obesity-
induced type-2 diabetes mouse model.
The project consortium is headed by an SME and
includes four academic partners from three
European countries. This composition of commer-
cial and academic interests guarantees high-level
scientific research, as well as a strong focus on
the commercial relevance and exploitation of the
project’s results. As a consequence, the proposed
project will strengthen Europe’s scientific and
commercial competitiveness in the field of sys-
tems biology, one of the key technologies in
future medical and pharmacogenetics research.
Expected results
An important feature of the project’s approach
will be the integration of phenotypic and physio-
logical parameters with proteomics data and
expression profiles from time course series repre-
senting the onset and progression of insulin
resistance of type-2 diabetes. Ultimately, the plat-
form will enable medical researchers to combine
heterogeneous biomolecular data with physiolog-
ical and clinically relevant parameters to predict
individual predispositions to obesity-induced
type-2-diabetes.
The objectives of this project are:
• model the knowledge about biological objects
(genes, proteins and protein complexes) in
the context of nutrition and type-2 diabetes in
equivalent computer objects;
• integrate heterogeneous data types from pro-
teomics and functional genomics approaches;
• develop and use a prototype framework for the
automatic detection and localisation of protein
modifications on high-accuracy mass spectrom-
etry data;
• generate specific proteomics and functional
genomics data providing the necessary infor-
mation for disease model generation with an
appropriate animal model;
Key words: systems biology, fundamental biological processes, proteomics, bioinformatics

Project coordinator
ROLE OF SMEs Arif Malik
MicroDiscovery GmbH
NutriSystemics
MicroDiscovery is coordinator of SysProt having as a bioinformatics company a strong focus Marienburger Str. 1
on systems biology. The company sees a high potential for modelling and simulation tech- 10405 Berlin, Germany
nologies in the life science arena. However, currently available methods are far from commer- arif.malik@microdiscovery.de
www.microdiscovery.de
cial applications and need massive additional scientific and developmental efforts. The
SysProt consortium offers the possibility of an efficient technology transfer from key players Partners
in the nutrigenomics, proteomics and systems biology field into a commercial application.
MicroDiscovery intends to develop the resulting knowledgebase into a product ready for the Hadi Al-Hasani
Deutsches Institut fuer
Life Science market. There will be a rising demand for solutions in the area of systems biology. Ernaehrungsforschung (DIFE)
Systems biology will have a tremendous impact on the development of new drugs, diagnos- Department of Pharmacology-German
tics of complex diseases and personal medicine. Pharmaceutical companies, and also to Institute of Human Nutrition
a large extent biotech companies, design and market products which affect, inhibit or excite, Potsdam-Rehbruecke
Nuthetal (OT Bergholz-Rehbruecke), Germany
biological systems, often via highly specific intervention points. Nevertheless these products www.dife.de/en/index.php
typically change systemic aspects of cells, tissues, entire organs, or organisms. There is no
doubt that new knowledge extending the ability to control biological systems via combined Ralph Schlapbach
Eidgenössische Technische
computational and experimental approaches will be key in health care and in particular in the Hochschuleule, Zürich
drug development process in the next 5-10 years. This will for example be highly relevant in Functional Genomics Center Zurich
the area of complex diseases, such as obesity induced type-2 diabetes, where many genes are Zurich, Switzerland
www.fgcz.ethz.ch
responsible for a particular, pathogenic phenotype.
The commitment of MicroDiscovery to the project guarantees the midterm conversion of the Rainer Cramer
consortium results into an applicable product. The long-term goal is the establishment of sys- The University of Reading
tems biology technologies in the life science arena. There are currently various companies out- The Biocentre
Reading, United Kingdom
side the EU (e.g. Entelos (US), Gene Network Sciences (CAN), BioSeek (US), Genstruct (US), www.biocentre.reading.ac.uk
GeneGO (US)) with large financial backing positioning themselves competing into this emerg-
ing future market. There is still a large potential in the European academic community in sys- Ralf Herwig
Max Planck Institute for Molecular Genetics
tems biology field with has to be mobilised in order to cope with the efforts outside the EU. Department Vertebrate Genomics
Berlin, Germany
www.molgen.mpg.de
• gain new knowledge on the pathways and the expanding body of gene and protein data to
marker genes relevant for obesity-induced gain the knowledge necessary to discover better
type-2 diabetes disease progression that will and safer drugs. In-silico disease modelling will
lead to the discovery of novel diagnostic bio- not only cut the costs of future drug development
markers for disease susceptibility; by reducing the number of false drug targets but
• stimulate perturbations of the disease-relevant will also save development time. Additionally the
pathways; in-silico systems will reduce the necessary number
• develop tools and methods for the correlation of of animal trails in drug development explicitly.
phenotype and genotype; Thus, the proposed platform has a high commer-
• accelerate the identification and positional cialisation potential in future diagnostics applica-
cloning of disease candidate genes by combin- tions as well as in drug development.
ing gene expression, proteomics, genotype, and Systems biology approaches will increasingly
clinical data; have an impact on Life Science and Health pro-
• set up a knowledge base that integrates all avail- grammes in general and on drug development in
able data and methodology as an exploitable particular. They provide a huge potential for
product for disease modelling. improving the quality of life through the creation
of highly skilled jobs, improved competitiveness,
Potential applications and economic growth in Europe, as well as better
| C57BL/6J mouse (black), Swiss Jim Lambert (SJL)
healthcare and new tools to address different and mouse (white) and New Zealand Obese (NZO) mouse
The main result of the project will be an exploitable important challenges of the EC. Through the appli- are used as animal model for diabetes and obesity in
prototype that allows medical researchers to draw cation and broadening of systems biology the SysProt project. The NZO mouse is an established
predictions on disease-relevant pathways. These approaches, the SysProt project is likely to impact disease model in diabetes research and characterised
by heredity in obesity and by Typ2-diabetes with
predictions will be valuable for diagnosis and drug on the scientific understanding of biological Insulin resistance. The SJL mouse never develops
development purposes. The platform will enable processes, with particular relevance to improving obesity and therefore serves as counterpart to the
the validation of potential drug targets in-silico human health and wellbeing. NZO mouse. C57BL/6J mice serve as control strain.
and thus give support in explorative data mining of

163
ACRONYM Contract number: LSHM-CT-2007-037472 | EC contribution: € 3 000 000 | Duration: 42 months
Starting date: 1 January 2007

TAMAHUD
www.tamahud.eu/home.jsp

SUMMARY
Huntington’s Disease (HD) is a devas-
Identification of early disease markers,
tating neurodegenerative disease with novel pharmacologically tractable targets
many unmet patient needs. There are no
known ways of slowing or preventing the
and small molecule phenotypic modulators
neurodegeneration associated with the in Huntington’s Disease
disease, and clinical trials in humans are
hampered by the slow disease progres-
sion and the absence of suitable bio-
markers of short-term progression. The
Background possible relationships (proteins, genes, regulation,
genetics of HD is characterised, and
and pathology). Therefore, TAMAHUD aims at
involves the expansion of a polygluta-
No curative therapy is currently available for delivering novel targets causally associated with
mine tract at the amino-terminus of the
patients with HD and the pathophysiology of HD is aspects of the HD pathology in model systems,
Huntingtin gene (HTT). However, the
still not well understood. Generally, the current where biological target validation is accompanied
translation of this knowledge into thera-
treatment of HD combines non-pharmacological by demonstration of target relevance through
peutic and diagnostic approaches is ham-
therapy with management of the symptoms of small-molecule pharmacological modulation. In
pered by the scarce knowledge of HTT
the disease. Pharmacological treatment of the parallel, the biomaterial repository made available
biology, the paucity of information on
disease must be tailored to the specific needs of to the consortium from a disease-specialist aca-
how cellular signalling pathways interact
the patient. Physicians may prescribe a number of demic partner will be investigated through state-
with the HD mutation, and the lack of sys-
medications to help control emotional and move- of-the-art metabonomics approaches to identify
tematic and modern approaches aimed at
ment problems associated with HD, although biomarkers predictive of disease onset.
identifying useful biopredictors of dis-
no drug is yet available to stop or reverse the pro-
ease progression in individuals diag-
nosed with HD. The TAMAHUD project
gression of the disease. Expected results
The significant unmet medical need for HD
addresses key areas of HD patient needs,
includes the following: The expected results can be summarised into:
namely the discovery and development
• better understanding of pathophysiology to • the identification of novel, tractable targets
of therapeutically meaningful novel tar-
yield more relevant targets; causally associated with the pathology, along
gets and biomarkers. More precisely,
• improved symptomatic treatments; with small molecules capable of modifying
TAMAHUD project aims to deliver solidly
• drugs that slow, halt or reverse disease progres- aspects of the pathology in cellular disease
validated, druggable targets accompa-
sion; models via modulation of target activity; and
nied by developable small molecule mod-
• diagnostics of disease onset/progression. • biomarkers of disease onset/progression.
ulators and candidate diagnostics for
monitoring of disease progression. To
achieve these aims, a consortium of spe-
Aim Potential applications
cialist partners has been assembled, rep-
This project addresses the challenge of identifying If met with success, the scope of the project goes
resenting complementary and specific
novel tractable targets causally associated with beyond the 3.5 year granting period and the
know-how and expertise which will be
the pathology, to support the development of dis- research outcomes are relevant to:
integrated and further developed in the
ease-modifying therapeutics for the cure of HD • further development of therapeutic compounds
course of the project.
and of discovering novel early biomarkers leading through preclinical and clinical studies;
to the development of new diagnostic tools. • reduction of costs in clinical development: the
High throughput-RNAi, focusing on genes encod- lack of reliable and predictive biomarkers of dis-
ing pharmacologically tractable proteins rather ease onset requires clinical trials of higher com-
than on a whole-genome approach, will be plexity in order to reach statistical significance;
employed on a novel and robust HD cellular dis- • creation and development of a network of com-
ease model to identify genes whose inhibition of petencies aimed at progressing drug discovery in
expression is protective against the HD mutation. such a specialist field as the neuroscience area.
Following a stringent target validation approach, TAMAHUD aims to terminate its activities in the
selected validated targets will be progressed to constitution of a solid base for the later comple-
assay development and primary screening activi- tion of pre-clinical development of potential
ties, to identify druggable compounds active on the drugs, comprising the demonstration of in vivo
target and efficacious against the HD mutation in efficacy of TAMAHUD-derived chemical series also
cellular disease models. The complete process will through the use of TAMAHUD-derived biomark-
be accompanied by an extensive data and text min- ers. At even later times, clinical studies on candi-
ing workflow providing background information for date drugs originating from TAMAHUD activities
the HD knowledge network. This network will guide will again benefit from the inclusion of TAMAHUD
the experts in the generation of hypotheses about biomarkers to determine clinical efficacy.

164
Key words: Huntington’s disease, HT-RNAi, functional genomics, validated target, chemical hit, metabonomics,
biomarker, text-mining, data-mining, data visualization

ROLE OF SMEs Scientific coordinator

Andrea Caricasole
Siena Biotech SpA
TAMAHUD’s aims are designed to meet two unmet needs in Huntington’s Disease (HD): first, via Fiorentina 1
the identification of novel small molecule modulators of therapeutically relevant targets and 53100 Siena, Italy
info.tamahud@sienabiotech.it
secondly, the identification of novel biomarkers. The coordinating SME, Siena Biotech, is www.sienabiotech.it/index/index.jsp
pivotal to TAMAHUD as it will provide novel potential pharmacological targets of therapeutic
relevance in HD, contribute to their validation and exploit its pervasive drug discovery plat- Partners
form to discover small molecule modulators of such targets. A second SME, TCP Innovations
David Rubinsztein
Ltd., participates to identify novel biomarkers of HD onset and progression. Once achieved, University of Cambridge
these aims will form the basis for the development of novel pharmacological therapies and Cambridge, United Kingdom
provide the means to monitor their efficacy in pre-clinical and clinical studies. www.cimr.cam.ac.uk/index.html

David Grainger
TCP Innovations Ltd.
Cambridge, United Kingdom
www.tcpinnovations.com

Christian Blaschke
Alma Bioinformatics S.L.
Madrid, Spain
www.bioalma.com/index.php

Reinhard Schneider
EMBL
Heidelberg, Germany
www.embl.de

165
ACRONYM Contract number: LSHG-CT-2006-037517
Starting date: 1 January 2007
TargetHerpes
www.targetherpes.org
SUMMARY
Herpesviruses are important human
pathogens. As of today, their infections
can only be controlled by acyclovir or
derivates. The TargetHerpes project will
apply novel technologies provided by
three SMEs to design and develop novel
classes of antiviral treatments. Key to
the project is the SMEs connection with
fundamental advances being made in
Europe’s leading herpesvirus research
laboratories. The technologies to be
applied to the search of novel, effective
treatments against a broad spectrum of
herpesvirus diseases include the rational
design of peptide-based and siRNA-
based herpesviral inhibitors. The steps of
the viral life cycle to be targeted are virus
entry, evasion of host defences, persist-
ence in infected individuals, reactivation
from latency.
| EC contribution: € 2 351 818
Molecular intervention strategies targeting
latent and lytic herpesvirus infections
Background
Herpes viruses cause many serious and life-threat-
ening diseases, especially in immunocompro-
mised patients, such as transplant recipients and
HIV-infected individuals. Even in healthy ones,
herpesviruses can result in serious diseases. For
example, the herpes simplex virus (HSV) remains
one of the most common sexually transmitted dis-
eases, while human cytomegalovirus (HCMV) is
a leading cause of birth defects, and human her-
pes virus 8 (HHV-8) causes a number of cancers.
At present, the options for antiviral therapy are
limited and, owing to toxicity, the current anti-
herpesvirus drugs cannot be administered to
pregnant women. There is a continuing need to
develop new treatments, as drug-resistant viruses
are constantly evolving.
A principal characteristic of herpesvirus infec-
tions, is that after primary infection (usually in
childhood), the viruses establish a latent state
that remains for life. Up to 90 % of the population
may be latently infected with one or more herpes
viruses. The social and psychological conse-
quences of the herpesvirus infections are severe.
Aim
TargetHerpes will translate basic knowledge of
viral replication strategies and evasion from host
attack into the concept of a multi-pronged attack,
using combinatorial sets of antiviral compounds
with proven antiviral efficacy in cells and a small
animal model. Specifically, TargetHerpes will per-
form the following actions:
• develop peptide inhibitors that interfere with
virus entry;
166
| Duration: 36 months
• generate synthetic peptides that enable anti-
body dependent cellular cytolysis against her-
pesviruses;
• define, investigate and apply RNA silencing
reagents that block the expression of viral genes
that enhance herpesvirus replication;
• define, investigate and apply RNA silencing
reagents that interfere with proviral host genes;
• identify viral and cellular genes involved in her-
pesvirus-mediated oncogenesis, and define RNA
silencing reagents and peptide inhibitors; and
• develop approaches to inhibit the reactivation
of HSV from latency. This programme of work
will provide innovative technologies for the
identification and development of future prod-
ucts targeted at preventive and therapeutic
interventions for human herpesvirus diseases.
Moreover, these strategies will be transferable
to many other persistent infections.
Expected results
The TargetHerpes project is divided into six exper-
imental work packages (WPs). The aim of WP1 is
the development of peptide molecules that will
inhibit the functions of herpesvirus glycoproteins
and their roles in entry of the virus particles into
cells. Preliminary work has provided proof-of-
principle that mimetic peptides to HSV gH inhibit
infection. However, the first-generation peptides
were active only at very high concentrations, and
as such they could only be applied to cultured
cells. TargetHerpes expects to generate highly
bioactive and specific peptides that do not exhibit
toxicity to uninfected cells. Such peptides target-
ing HSV glycoproteins, will be suitable for future
animal experimentation and translational research
by partners PRIMM and IBA. WP2 will generate
Key words: herpes virus, chemiotherapeutics, herpes simplex virus, human cytomegalovirus, human herpesvirus 8,
fusion, glycoproteins, siRNA, innate immunity, host response, IFN

ROLE OF SMEs Scientific coordinator

Gabriella Campadelli-Fiume
University of Bologna
Four SMEs are involved in the project. Their respective roles are as follows. BioDec, Centro Interdipartimentale Galvani (CIG)
a young Italian spin-off company born out of University of Bologna, will perform bio- via S. Giacomo 12
40126 Bologna, Italy
informatics searches, develop algorithms and software for the design of siRNAs or gabriella.campadelli@unibo.it
shRNAs and for prediction of protein structures involved in protein:protein interactions; www.microbiology-virology.unibo.it/
IBA, a small German-based biotec industry will provide tools for si-RNA production as persone_en.html
well as for protein purification and studies of protein:protein interactions. PRIMM, an Partners
Italian small biotec company will provide tools for design and synthesis of antagonist and
mimetic peptides as well as immunological reagents; ARTTIC, a transnational European Roger Everett
company specializing in the management of large projects will take care of the management Medical Research Council
MRC Virology Unit
of the project, dissemination of results to public, intellectual property issues. Glasgow, United Kingdom
www.mrc.co.uk

synthetic peptides that enable IgG antibodies to Potential applications Hartmut Hengel
University of Duesseldorf
execute cell-mediated cytolysis against HSV and Institute for Virology
HCMV. Such peptides will be evaluated for their TargetHerpes will identify novel strategies, lead- Dusseldorf, Germany
individual potency in vitro, then bioactive peptides ing to the development of new approaches to www.uni-duesseldorf.de
will be evaluated with regard to safety and harm- inhibit the replication of, or pathogenesis caused Joachim Bertram
lessness to cells, as well as optimal stability in cul- by, HSV, HCMV and HHV-8. Due to the conserva- IBA GmbH
tured cell systems. WP3, WP4, WP5 and WP6 will tion of genes and replication strategies within her- Goettingen, Germany
identify suitable molecular targets for antiviral pesviruses, the approaches discovered will be www.iba-go.com
intervention by RNAi. These targets will include applicable to other human herpesviruses as well. Frank Neipel
important herpes virus gene products that have For example, treatments that target HSV-1 are University of Erlangen
known or suspected roles in promoting viral repli- highly likely to be effective against HSV-2 and may Institut fuer Klinische
und Molekulare Virologie
cation directly or indirectly. In case of WP5, siRNAs be adapted to counteract VZV. Similarly, treat- Erlangen, Germany
targeted at viral genes will be selected based on ments that are effective against HHV-8 may also www.viro-med.uni-erlangen.de
their capacity to interfere with HHV-8 mediated be applicable to EBV. Given the figures on the
Michael Nevels
cell transformation and immortalisation. WP6 health burden and costs of herpesvirus infections, University of Regensburg
expects to identify the cellular interaction partners the potential impact of a successful outcome of Institute for Medical
of ICP0 (the viral protein that is necessary for HSV the TargetHerpes project, is considerable. Microbiology and Hygiene
to reactivate from latency), and to define those Faculty of Medicine
Molecular Virology Unit
elements that are required for its activity. Regensburg, Germany
www.uni-regensburg.de

Angela Pontillo
PRIMM Srl
Milan, Italy
www.primm.it

Ivan Rossi
BioDec Srl
Bologna, Italy
www.biodec.com

Wolfgang Laepple-Boettiger
ARTTIC S.A.
Office Mannheim
Schifferstadt, Germany
www.arttic.com

167
ACRONYM Contract number: LSHB-CT-2007-037365 | EC contribution: € 3 389 184 | Duration: 48 months
Starting date: 1 March 2007

TargetScreen2

SUMMARY
Elucidation of protein function is the next
Novel post-genomic cell-based screens for
post-genomic challenge towards the drug targeting in membrane protein disorders
understanding of biological processes in
health and disease. Transcriptomics and
proteomics approaches usually deliver
long lists of “candidate” genes that are
supposedly associated with the respec-
tive diseases. However, neither functional
information nor a direct relationship with
Background Expected results
the pathology is established.
Membrane proteins include antibodies, receptors, The major scientific and technological milestones
Strategies and tools are thus critically
channels, carriers, transporters, etc. and constitute to be achieved within TargetScreen2 are:
needed to distinguish genes and pro-
some of the largest families encoded in the human • development and establishment of robust
teins with mere pathologic association
genome, including the ATP-binding cassette (ABC) immunofluorescence-based microscopy high-
from those primarily responsible for the
transporters superfamily, the G protein-coupled throughput assays to study traffic and/or func-
basic cellular defect(s) in such patholo-
receptors (GPCRs) as well as a large number of tion of membrane proteins;
gies. Membrane proteins, including
channels. Given their major roles in cells and organ- • development and establishment of a novel pro-
receptors, channels, antibodies, trans-
isms (e.g., communication, signalling, response to tein complementation platform (PCP) and a split-
porters, etc. play major roles in cells and
environmental stimuli, immunity, heart rhythm, ubiquitin assay to screen for proteins interacting
organisms as they are involved in impor-
multiple nervous system functions, etc.), mem- with a membrane protein of choice;
tant cellular mechanisms, such as com-
brane proteins are extremely relevant to a high • identification and validation of novel therapeu-
munication, immunity, signalling and
number of human disorders, including common tic targets following the application of the two
response to environmental stimuli.
ones (like cardiovascular diseases, obesity, cancer above innovative approaches to the three dis-
or diabetes) and rare genetic diseases. GPCRs and ease-associated model membrane proteins;
By bringing together experienced aca-
ion channels currently represent the most attrac- • target-tailored design and pre-clinical validation
demic and industrial (SMEs) partners in
tive target classes for the drug discovery industry. of novel therapeutic small-molecules.
a close and balanced collaboration,
utilising a multidisciplinary approach,
TargetScreen2 proposes to develop cut-
Aim Potential applications
ting-edge post-genomics functional cell-
The objective of the TargetScreen2 proposal is to Potential applications include identification of
based assays aimed at identifying novel
demonstrate the identification of novel therapeutic novel target-tailored lead compounds to three
gene targets to correct for traffic and/or
targets for disorders associated with membrane model membrane proteins associated with human
function of three model membrane pro-
proteins, using as examples three model proteins, diseases (obesity, hyperinsulinemia, hypertension
teins (MC4R, ENaC and CFTR) involved in
namely: one ABC transporter (the cystic fibrosis and cystic fibrosis) and possibly other protein
human disorders. TargetScreen2 will also
transmembrane conductance regulator, CFTR), one trafficking disorders. As additional potential appli-
validate such targets in the most appro-
oligomeric channel (the epithelial sodium channel, cations, novel assays for the identification of
priate cellular systems and, through
ENaC) and one GPCR (melanocortin receptor 4, protein-protein functional/physical interactions
structural modelling of targets, novel
MC4R). To achieve this, TargetScreen2 will develop involving membrane proteins will result from
small molecule compounds will be tai-
tools and standardise protocols for new post- this project.
lored-designed, optimised and tested to
genomic approaches addressing the functional
the pre-clinical stage.
study of membrane proteins. TargetScreen2 thus
proposes to develop and establish several new
The expected results will consist of novel
high performance techniques which will be used
cell-based assays to identify relevant
and fully exploited so as to demonstrate their appli-
therapeutic targets in a wide number of
cability. Hence, the project’s ultimate aim is to facil-
diseases related to membrane proteins.
itate the generation of new knowledge in functional
As a proof-of-concept, TargetScreen2 will
genomics.
apply these innovative ‘from the bench to
the bedside’ approaches to ultimately
deliver novel therapeutic small mole-
cules, tested to preclinical stage and
applicable to common diseases such as
obesity, hyperinsulinemia, hypertension
and cystic fibrosis.

168
Key words: functional genomics, membrane proteins, target-tailored drugs, protein trafficking disorders,
protein-protein interactions, robotised confocal microscopy

ROLE OF SMEs Scientific coordinator

Margarida D. Amaral
Department of Chemistry and Biochemistry
Three SMEs (ECBio, SygnatureChem and Dualsystems) and one additional company participate Faculty of Sciences, University of Lisboa
in TargetScreen2. Their profiles and roles are, respectively: Campo Grande-C8
1749-016 Lisboa, Portugal
www.fc.ul.pt
ECBio, is a biotech SME that established its own animal and human cell R&D laboratory in
2002 and carries out its research and development activities towards the development of Coordinator Cystic Fibrosis Research Unit
Centre of Human Genetics
various cell isolation and culture processes, including media development, cryopreservation National Institute of Health
and development of cytotoxicity and drug testing using innovative target cells. ECBio has also Av. Padre Cruz,
made a strategic alliance with a recently established Portuguese cell therapy GMP company, 1649-016 Lisboa, Portugal
being responsible for human stem cell isolation, culture, cryopreservation and differentiation.
mdamaral@fc.ul.pt
Within TargetScreen2, ECBio will be mostly involved in the establishment/immortalisation www.dqb.fc.ul.pt/docentes/mdbotelho/
of primary cultures for the production of novel cell lines in order to both validate the protein
targets resulting from the screens in more appropriate cellular systems and also test the Partners
therapeutic effects of small molecules in such systems.
Rainer Pepperkok
European Molecular Biology
SygnatureChem is a young computational-based drug discovery company with capacities in LaboratoryHeidelberg, Germany
computational compound design and synthetic medicinal chemistry, with particular experi- www.embl-heidelberg.de
ence and focus on GPCRs and kinases. It has in-house experience in automated and semi- Karl Kunzelmann
automated library preparation of small- and medium-scale compound libraries resulting from University of Regensburg
synthetic work. It also possesses state-of-the-art analytical and purification technology. Regensburg, Germany
The role of SygnatureChem within TargetScreen2 is to design and optimise novel small mole- www.uni-regensburg.de/Universitaet/
welcome2.html
cules of potential therapeutic interest by specifically modulating the action of the targets
identified in the screens and to be subsequently tested up to the pre-clinical phase. John BC Findlay
University of Leeds
Leeds, United Kingdom
Dualsystems major focus is to provide tools and services in the field of interactive proteomics www.leeds.ac.uk
to the life sciences community. Currently, Dualsystems uses two platform technologies to
identify and characterise novel protein-protein interactions. DUALhybrid is an improved yeast Constança Coelho
Investigação e Desenvolvimento
two-hybrid platform developed in-house, which allows screening for novel interactors of a pro- em Biotecnologia, S.A.
tein of interest. This technology is aimed mainly at soluble proteins, domains or protein frag- Oeiras, Portugal
ments. The DUALmembrane system is a unique screening platform aimed at identifying www.ecbio.com
interactions involving integral membrane proteins and membrane-associated proteins.
Simon Hirts
Within TargetScreen2, Dualsystems will further develop this technology as novel genetic Sygnature Chemical Services Limited
assays for protein-protein interactions, based on the split-ubiqutin system and other protein Nottingham, United Kingdom
complementation assays. www.sygnaturechem.com

Daniel Auerbach
OSIS (until recently, OBS – Olympus BioSystem GmbH) develops integrated digital imaging Dualsystems Biotech AG
systems for life-science applications serving biological, pharmaceutical and medical research Zurich, Switzerland
institutions worldwide. With the launch of the real-time fluorescence imaging station cell in www.dualsystems.com
June 2003 OSIS was setting a new standard for leading edge research imaging systems with Konstantin Joanidopoulos
highest precision and optimum synchronisation. Meanwhile a whole family of cell Imaging Olympus Soft Imaging Solutions GmbH
Stations are available. Based on the real-time technology of the cell Imaging Station a fully Planegg, Germany
www.soft-imaging.net
automated high speed image acquisition and image analysis system for screening applica-
tions was developed: the Screening Station scan (responsibility of K Joanidopoulos) that will
be launched in February 2006. OSIS is focused on innovative technology development and has
more than 10 patents pending or granted. OSIS excels in system integration and has the fol-
lowing development expertise: optics, mechanics, electronics, firmware development, soft-
ware development, image analysis, data analysis. A well equipped workshop allows for fast
prototyping and specific adaptations. OSIS can draw on the competence and experience of
a young team of physicists, biologists, chemists that still have close contacts to research lab-
oratories, as well as highly qualified mechanical and electronics engineers and technicians.
The role of OSIS in TargetScreen2 will be during the development of confocal microscope-
based software to monitor the robotised screening assays, aimed at identifying protein tar-
gets involved in the traffic and function of three model membrane proteins, which prove
suitable for high-throughput screening (HTS) analyses.

169
ACRONYM Contract number: LSHP-CT-2006-037217 | EC contribution: € 1 945 000 | Duration: 36 months
Starting date: 1 December 2006

TB-DRUG
www.tbdrug.eu

SUMMARY
The primary objective of this project is to
A SME-STREP for Tuberculosis Drug Development
identify suitable drug targets and to dis-
cover lead compounds suitable for devel-
opment into new drugs active against
tuberculosis. The plan of action is to:
• express and purify each protein being
targeted using available expression
systems;
• determine the structure of each protein
Background • screening for and identification of inhibitors for
by X-ray crystallography;
each protein for which a suitable assay has been
• develop biochemical assays suitable for
Tuberculosis (TB) causes more deaths worldwide developed;
adaptation to high-throughput screening
than almost any other infectious disease, with • assessment of the effectiveness of the best
(HTS);
nearly two million deaths per year and has a dev- inhibitors identified against live M. tuberculosis
• screen for and identify inhibitors for each
astating impact on developing countries. More in vitro;
protein where a suitable assay has been
effective means of medical intervention are • optimisation of lead compounds by medicinal
developed;
required, both to reduce the number of deaths chemistry.
• assess the effectiveness of the best
from tuberculosis and to allow for more effective
inhibitors identified against Mycobac-
terium tuberculosis in vitro, and;
treatment of drug-resistant infections. Potential applications
• optimise lead compounds by medicinal
chemistry.
Aim TB patients in parts of Eastern Europe and Central
Asia have a significant risk of acquiring multidrug-
The TB-DRUG project aims to discover novel com- resistant TB (MDR-TB). TB incidence rates also
pounds against Mycobacterium tuberculosis continue to rise at an alarming rate in African
which can be developed into products that can countries with high HIV prevalence. This rise of
alleviate the global burden of TB, by carefully MDR-TB and increased susceptibility to TB caused
selecting proteins to be taken into the drug dis- by co-infection with HIV is driving the worldwide
covery process as novel targets. In anticipation of TB epidemic and is likely to worsen in the years to
the significant attrition rate of the drug discovery come. The discovery of novel antitubercular drugs
process, it is suggested that the different targets not only promises to benefit people in the eastern
are included at the earliest stages of drug devel- European, Asian and African countries who suffer
opment, followed by a more focused approach on most from TB, but also to fight the spread of MDR-
the most promising candidates in the later stages. TB that could fuel a TB epidemic in all of Europe.
The project will be carefully managed by taking
advantage of industrial knowledge in planning By bringing together scientists from many differ-
and management. As a minimal outcome of this ent disciplines and by connecting academics with
consortium, the aim is to identify 2-3 attractive industry research, TB-DRUG establishes an inte-
leads to be taken forward into a preclinical drug grated drug discovery and development process.
development phase. The range of complementary expertise available
within the proposed Project, together with a state-
Expected results of-the-art discovery technology, facilitates the
entire process of preclinical drug discovery. The
It is expected that the proposed work will result in: TB-DRUG Consortium strives to have a significant
• expression and purification of each protein impact in the area of TB drug development and
being targeted; to contribute to the education of young scien-
• structure determination of each protein purified tists by offering exceptional teaching and train-
by X-ray crystallography; ing opportunities for post-doctoral fellows and
• development of biochemical assays suitable for PhD students.
adaptation to HTS for each target purified;

170
Key words: microbiology, infections, pharmaceutical chemistry, drug targets, biochemistry, structural biology, tuberculosis

ROLE OF SMEs Scientific coordinator

György Keri
Vichem Chemie Research Ltd.
Within this Consortium, there are two SMEs: Herman Ottó utca 15
1022 Budapest, Hungary
keri@vichem.hu
Vichem is the coordinator and contributes with hit finding and lead optimization against the www.vichem.hu
target molecules chosen. Following initial development of biochemical and cellular assays
from the different partners within this Project, Vichem will proceed to the development of Partners
high-through put screenings assays.
Mamadou Daffé
Institut de Pharmacologie
R&D Management GmbH organises and chair consortia meetings and gives general et Biologie Structurale
administrative support to the management of the project. Université Paul Sabatier
CNRS UMR 5089
Toulouse, France
www.ipbs.fr

Menico Rizzi
Dipartimento di Scienze Chimiche,
Alimentari, Farmaceutiche
e Farmacologiche (DiSCAFF)
University of Piemonte Orientale
‘Amedeo Avogadro’
Novara, Italy
www.discaff.unipmn.it

Peter Sander
Institut für Medizinische Mikrobiologie
University of Zurich
Zurich, Switzerland
www.imm.unizh.ch

Andrea F. Degen Iseli

R&D Management GmbH
Zurich, Switzerland
www.researchmanagement.ch

© Shutterstock

171
ACRONYM Contract number: LSHP-CT-2006-037785 | EC contribution: € 2 000 000 | Duration: 36 months
Starting date: 1 January 2007

TB-trDNA

SUMMARY
Tuberculosis (TB) continues to be a global
Evaluation of transrenal-DNA
threat to public health of important social detection to diagnose tuberculosis
and financial concern to the expanding
European Union and a cause of enormous
morbidity and mortality in much of the
developing world. Timely and accurate
diagnosis is a critical obstacle to TB con-
trol and the currently available diagnostic
methods are marked by being insensitive,
Background Expected results
slow, and/or cumbersome to use. Nucleic
acid amplification is the only rapid detec-
Tuberculosis remains among the most prevalent TB-trDNA is designed to develop a rapid diagnos-
tion method with proven sensitivity and
causes of death from an infectious disease in the tic procedure for utilising transrenal DNA as a tar-
specificity, but is difficult to implement in
world. While global targets for rates of cure have get sample for the identification of Tuberculosis
its current format. A method that avoided
been reached in many areas, case detection patients. The findings of TB-trDNA will also con-
complex sputum processing and cell lysis
remains a significant bottleneck to effective dis- tribute to policy development through knowledge
steps that was applicable across multiple
eases control. Microscopy, the only widely avail- and awareness of the importance of TB diagnosis,
amplification formats (e.g. in addition to
able laboratory diagnostic test for tuberculosis, with close association with the respective min-
PCR) would be a tremendous advantage.
is both difficult to implement and insensitive. istries of health and international organisations
Consequently, the availability of new diagnostic such as the World Health Organisation.
There is growing evidence that short DNA
tools that are more accurate and accessible may
fragments, arising from human or bacter-
ial cells dying throughout the body, pass
greatly benefit individual patients and signifi- Potential applications
cantly contribute to the control of the disease.
through the renal barrier and appear in
Given the significant challenges of Mtb detection
urine as transrenal DNA (Tr-DNA). In
a preliminary study conducted at the
Aim and monitoring in developing countries, the
application of the Tr-DNA test could provide
National Institute of Infectious Diseases
TB tr-DNA aims to develop a new and highly inno- a very useful new diagnostic tool. By simplifying
in Rome, it has been shown that Tr-DNA
vative platform for the detection of poverty- the sampling procedure and combining this with
from M. tuberculosis was detectable in
related diseases (TB followed by HIV, malaria). improved molecular detection methods (which
the urine by polymerase chain reaction
This platform is based on the principle that dying could eventually lead to simple dip-stick methods)
(PCR) in 100 % of patients with pulmonary
cells release cell-free DNA into the blood stream the findings of TB tr-DNA could ensure that simple,
tuberculosis and that these DNA frag-
that then passes through the renal barrier and can cheap, efficacious TB diagnosis is made available
ments disappeared following anti-TB
subsequently detected in urine. to the developing world to ensure targeted use of
drug therapy. TB tr-DNA aims to validate
the available therapy.
the diagnostic potential of Tr-DNA detec-
tion for TB, to optimise and simplify the
sample preparation methods, and to
explore the feasibility of using a diagnos-
tic approach based on this method in
a developing world setting.

172
Key words: transrenal DNA, tuberculosis, diagnosis

ROLE OF SMEs Scientific coordinator

Jim Huggett
Centre for Infectious
The SME of the project, FIND, is an independent, not-for-profit, foundation wholly dedicated Diseases and International Health
to the development, evaluation, and demonstration of diagnostics for infectious diseases Windeyer Institute
University College London
relevant for the developing world. FIND has a minor role in most of the WPs of the project, 46 Cleveland St.
but they will coordinate the interface between test development and product evaluation London, W1T 4JF, United Kingdom
and conduct a project workshop in 2007 and project public health advisory meeting in j.huggett@ucl.ac.uk
www.ucl.ac.uk/medicalschool/
2009. FIND will provide documentation and technical expertise related to the customer infection-immunity/
requirements and design of the product version(s) to be tested and will ensure that clinical
protocols will yield data that will have the greatest utility to determining the future of the Partners
technology for the public health sector.
Peter Mwaba
Department of Medicine
UNZA-UCLMS project
University Teaching Hospital D Block
Lusaka, Zambia

Michael Hoelscher
Department of Infectious Diseases
& Tropical Medicine
University of Munich
Munich, Germany

Leonard Maboko
Mbeya Medical Research Programme
Mbeya, Tanzania

Enrico Girardi
Dipartimento di Epidemiologia
Istituto Nazionale per le Malattie
Infettive L. Spallanzani – IRCCS
Rome, Italy

Giorgio Roscigno
FIND, Foundation for Innovative
New Diagnostics
Cointrin, Switzerland
www.finddiagnostics.org

173
ACRONYM Contract number: LSHG-CT-2006-037543
Starting date: 1 October 2006
TEMPO
SUMMARY
TEMPO will combine functional genomics,
proteomics, cell signalling, systems biol-
ogy and pharmacokinetics to optimise
therapeutic efficacy. In vivo, in vitro, in sil-
ico approaches are integrated through the
multidisciplinary excellence in the consor-
tium. TEMPO will offer a proof of principle
of tailored chronotherapeutics in mouse
models for irinotecan, an active drug
against colorectal cancers, and for selici-
clib, currently in clinical testing. TEMPO
will gather the corresponding human pre-
requisites and technology for subsequent
application to patients.
| EC contribution: € 2 086 720
Temporal Genomics for Tailored
Chronotherapeutics
Background
Non-communicable, chronic diseases represent
the bulk of morbidity, disability and premature
deaths in Europe, and account for 75 % of disabil-
ity-adjusted life years. Among those diseases,
cancer is the second most important cause of
morbidity and mortality. Differences in the molec-
ular characteristics of tumour cells, as well as dif-
ferences in patients’ genetic make-up, gender,
age, lifestyle and circadian rhythms, account for
large variability in the time-course of cancer and
in patients’ responses to treatment.
Aim
The general objective of TEMPO is to design mouse
and in silico models that reflect this variability and
allow the prediction of optimal chronotherapeutic
delivery patterns for anti-cancer drugs.
174
| Duration: 36 months
Expected results
TEMPO combines functional genomics, pro-
teomics, cell signalling, systems biology and
pharmacokinetics to optimise the therapeutic
index in patients. This index in turn determines the
chronotherapeutics schedules, according to which
temporal delivery patterns of the same anticancer
drug vary. Each schedule is adjusted to a different
dynamic class of temporal genomics and phe-
nomics parameters, relating to interwoven circa-
dian and cell division cycles as well as drug
metabolism. The multidisciplinary nature of the
consortium means that in vivo, in vitro and in silico
approaches will be integrated to achieve this end.
Potential applications
TEMPO epitomises the translation of basic
research findings into useful clinical applications.
Through the identification of nodes in the interplay
between the circadian timing system, the cell divi-
sion cycle and drug pharmacology parameters, it
will provide critically important information for the
targeted development of new anti-cancer drugs.
Key words: cell cycle, circadian clock, chronotherapeutics, anti-cancer drugs

ROLE OF SMEs Scientific coordinator

Francis Lévi
Institut National de La Santé
Three SMEs play a pivotal role for the impact of TEMPO on European health, economics and et de la Recherche Médicale
society. Novel and complementary in silico dynamic models of coordinated clock, cell cycle INSERM U776 – Rythmes
biologiques et cancers
and pharmacology pathways will identify new therapeutic targets and delivery schedules of Hôpital Paul Brousse
active molecules, thus improving drug development processes. Avenue Paul-Vaillant Couturier 14
Villejuif, France
levi-m@vjf.inserm.fr

Partners
Franck Delaunay
Centre National de la
Recherche Scientifique (CNRS)
Université de Nice – CNRS UMR 6348 –
Bâtiment de Sciences Naturelles
Physiologie cellulaire et moléculaire
des systèmes intégrés
Nice, France

Laurent Meijer
Centre National de la
Recherche Scientifique (CNRS)
Laboratoire Mer et santé UMR7150
Station Biologique –
Amyloïds and Cell Division Cycle
Roscoff Cedex, France
Metabolism
Jean Clairambault
Institut national de recherche
en informatique et automatique
INRIA Rocquencourt Research Unit –
Teams Bang and Contraintes
Le Chesnay, France
Proliferation
Stefano Iacobelli
Consorzio Interuniversitario
Nazionale per la Bio-oncologia (CINBO)
Laboratori of molecular oncology
center of excellence on aging Ce. S.I.
Chieti, Italy

| Schematic representation of cellular circadian rhythms Marco Pirovano

The expression of many genes, proteins and enzymatic activities responsible H.S. Hospital Services S.p.A
for cellular metabolism and proliferation display marked 24-hour rhythms in Therapeutic delivery
healthy mammalian tissues. These rhythms are generated by a molecular clock Aprilia (Latina), Italy
constituted of 12 specific genes.
Todor Vujasinovic
Helios Biosciences SARL
Créteil, France

Christophe Chassagnole
Physiomics PLC
The Magdalen Centre
The Oxford Science Park
Oxford, United Kingdom

Isabelle Geahel
Inserm Transfert
European Project Management
Department
Paris, France

175
ACRONYM Contract number: LSHB-CT-2006-037560
Starting date: 1 November 2006
USDEP
www.usdep.eu
SUMMARY
The threat of emerging or re-emerging
infectious diseases, as well as the risk of
bioterrorism, has enhanced the current
requirements for novel, highly sensitive
and specific diagnostics technologies. The
USDEP project will focus on improving the
detection of emerging pathogens, devel-
oping novel techniques for pathogen
isolation and detection from clinical and
environmental samples, including those
that could be used in bioterrorism, and
increasing the sensitivity and specificity of
the currently available detection methods
used for pathogenic bacteria and viruses.
| EC contribution: € 2 004 952
Capture and enrichment of emerging pathogens
for multiple and ultra-sensitive diagnostic
Background
In the 1970’s WHO proclaimed that eradication of
smallpox should be attempted. This goal was suc-
cessfully achieved in 1979. Nonetheless, presently
there is a general consensus that the list of newly
emerging or re-emerging pathogens is continu-
ously growing. Indeed, during the last decades
pathogens such as Marburg, Ebola, Hepatitis-C,
Hantavirus, HIV and more recently, SARS corona-
virus have emerged. Furthermore, the apparent
risk of a new influenza pandemic again highlights
the global threat of infectious diseases. In addi-
tion, the possibility of bioterrorist attacks using
highly pathogenic viruses and bacteria can not be
ignored. In consequence, the current require-
ments for novel, highly sensitive and specific diag-
nostics technologies have increased.
A major obstacle for the detection of pathogens in
clinical or environmental samples are false nega-
tive results, e.g. for HCV ‘occult infections’. This is
mainly due to the lack of a rapid and reliable
pathogen concentration methodology, and the
inability of most of the currently used tech-
nologies to eliminate or neutralize interfering
molecules, ‘natural inhibitors’, present in most
complex samples.
176
| Duration: 36 months
Aim
The aim of this research programme is to exploit
the ‘non-self’ recognition and binding proper-
ties of human apolipoprotein H (ApoH) for the
development of novel tools to isolate pathogens
from complex biological mixtures. ApoH binds
pathogens enabling their capture and concentra-
tion from different biological samples. Magnetic
beads coated with ApoH protein can be efficiently
used as a pre-treatment step to greatly improve
the detection threshold and thereby increasing the
sensitivity for diagnosis of emerging pathogens,
regardless of the molecular or immunological
techniques used in the final diagnostic step.
Expected results
The project will focus on:
• increasing the sensitivity and specificity of the
currently available detection methods used for
pathogenic bacteria and viruses;
• on the development of novel techniques for
pathogen detection from clinical and environ-
mental samples including those that could be
used in bioterrorism.
Potential applications
The industrial partners will develop and standard-
ise novel technologies for rapid, multiple and ultra-
sensitive pathogen diagnosis such as mini-array
systems with the objective of commercialisation.
Key words: virus diagnostics, ultra sensitive detection, magnetic beads, Apolipoprotein H, emerging pathogens

ROLE OF SMEs Scientific coordinator

Heinz Ellerbrok
Robert Koch-Institut
The USDEP project has a very complementary consortium, where the publicly funded part- Centre for Biological Safety
ners, the Robert Koch Institut (RKI), the Institut de Recherches pour le Développement Nordufer 20
133353 Berlin, Germany
(IRD), the privately funded Pontifica Universidad Catolica de Chile, working in virology and EllerbrokH@rki.de
public health will incorporate ApoH technology into their panel of regular techniques for www.rki.de
pathogen detection. It will be the task of the industrial partners to develop and standardise
the new diagnostic technologies. Namely, ApoH-Technologies develop ApoH coated supports Partners
for diagnostic purposes, GenExpress is specialized in the development and optimisation of Dorothy Bray
molecular biology assays, the Institut für Siliziumtechnologie (ISIT) is specialised in the ImmunoClin Ltd.
development and production of microelectronic components and will supply the electronic London, United Kingdom
www.immunoclin.com
biochips, eBiochip Systems is focussed on manufacturing of technology for electronic
biochip applications, SKULD-TECH develops a mini array system for virus detection and Elias Stefas
IMMUNOCLIN provides strategic direction as well as management and laboratory services ApoH-Technologies
for clinical development and pre-clinical contract research. Montpellier, France

Francisco Veas
Viral Immuno-Physiopathology Lab
U178/IRD Viral Emerging Diseases
EA 3755 (Bacteriology-Virology)
University of Montpellier 1
Montpellier, France

Marcelo Lopez Lastra

Pontificia Universidad Católica de Chile
Santiago, Chile
www.puc.cl

Roland Lauster
GenExpress Gesellschaft
für Proteindesign mbH
Berlin, Germany
www.genexpress.de

Rainer Hintsche
Fraunhofer Institut
für Silizium Technologie
Itzehoe, Germany
www.isit.fhg.de

Ralf Wörl
eBiochip Systems GmbH
Itzehoe, Germany
www.ebiochipsystems.com

Didier Ritter
Stamatis Varsamos
Skuld-Tech
Montpellier, France
www.skuldtech.com

177
ACRONYM Contract number: LSHG-CT-2006-037277
Starting date: 1 October 2006
VALAPODYN
www.valapodyn.eu
SUMMARY
The VALAPODYN project seeks to further
the development of multidisciplinary func-
tional genomics relating to complex bio-
logical processes and cellular networks.
The project is concerned with both DNA
and protein applications, to be followed by
innovative dynamic modelling of patho-
logical disease states, such as epilepsy
and cancer, in order to validate the model.
The overall aim is to develop an innovative
systems biology approach, in order to
model the dynamics of Molecular Inter-
action Networks (MINs) related to cell
death and survival in the organism.
| EC contribution: € 1 488 560
Validated Predictive Dynamic Model of
Complex Intracellular PaCell Death and Survival
Background
Selecting the best therapeutic target(s) is one of
the major challenges in developing new and effi-
cient drugs. In addition to its scientific relevance,
it has a profound impact on the health/quality of
life of the European population, as well as the
pharmaceutical industry, by decreasing the cost
of drug development.
Nowadays, although our understanding of individ-
ual gene and protein function becomes important,
it is not sufficient for unravelling the complexity of
biological and pathological processes! Indeed,
modern high throughput technologies in biologi-
cal science, such as genomics, transcriptomics
and proteomics, often generate lists of molecules
of interest. However, they do not always increase
our knowledge of the biological processes or the
subsequent identification of therapeutic targets.
It therefore becomes critical to develop our under-
standing of biological system’s structure and
dynamics.
A biological system is more than an assembly of
genes and proteins. Its properties cannot be fully
unravelled through static diagrammatic representa-
tions of their interconnections. Although such dia-
grams represent an important step, we now need
information on the dynamics of these interconnec-
tions and how we can control them. The challenge is
therefore, to construct a descriptive model from
these lists of molecules that could reflect the
underlying biological mechanisms as accurately as
possible and, ultimately, allow the identification
and selection of the best therapeutic targets to
treat human disease.
The aim of Systems Biology is to decipher the intri-
cacies of complex biological systems/organisms
through the integration of biological, clinical
chemical, physical, mathematical, and computer
knowledge.
Their approach uses theorical concepts, compu-
tational modelling and experiment data to allow
178
| Duration: 36 months
the development of mathematical models of the
complex molecular interaction networks (MINs).
Moreover, this approach is emerging also in Life
Sciences, with systems pathology guiding an under-
standing of the multidimensional aspects of disease
system fingerprints and systems pharmacology.
This provides important insights into dynamic sys-
tem responses upon multiple drug perturbations.
Knowledge of the changes of system characteristics
during the progression of a disease is mandatory
to create a conceptual framework for the design of
new therapeutic strategies.
Aim
The aim of the VALAPODYN project is to set up the
scientific and technological basis, for tasks within
the following areas:
• Pathway analysis: functional annotation of genes
and proteins, investigation of structure and
dynamics of signal transduction and transcription
regulatory networks.
• Predictive bioinformatics platform for dynamic
modelling: use of innovative biomathematics/
bioinformatics to integrate experimental MIN
data with biological tissue and pathological
states data obtained through the use of tran-
scriptomic and proteomic approaches.
• Bioinformatics: establishment of a highly spe-
cialised database on the genomics and proteomics
of MIN modelling.
• Pathological tissue & animal models: analysis of
validated animal models of brain pathologies to
evaluate gene/protein expression during initial
cell death.
• Microarrays: extensive multi-level global gene
expression profiling using the Affimetrix platform.
• Proteomics: application of advanced quantitative
proteomics technologies (MALDI, ICAT, 2-DPAGE,
Heavy Peptides isotopic dilution) for large-scale
proteome screening.
• Neuroprotective molecules: characterization of
molecules in the MIN of cell death the modulation
of which should improve or cure neurodegenerative
brain disease.
Key words: functional genomics, predictive dynamic models Molecular Interaction Networks,
cell death and survival, neurodegeneration

ROLE OF SMEs Scientific coordinator

Antoine Depaulis
Grenoble – Institut des Neurosciences
There are two SMEs in this consortium Biobase GmbH and Helios Biosciences SARL. Centre de recherche Inserm U 836
Université Joseph Fourier
BP170, 38042 Grenoble Cedex, France
The role of Biobase GmbH in the Valapodyn project is to provide high quality manually anno- Antoine.depaulis@ujf-grenoble.fr
tated databases to the consortium and applying them to the particular biological field in http://neurosciences.ujf-grenoble.fr/
order to systematically produce experimentally testable hypotheses. As Valapodyn is
devoted to study mechanisms of neurodegeneration, Biobase focuses on collecting relevant Partners
data including regulation of cell cycle, apoptosis and mechanisms of neurodegeneration. Olga Kel-Margoulis
BIOBASE, in collaboration with the other partners, plans to integrate data coming from Edgar Wingender
partners, and, provide this information to all partners. This activity is in the frame of WP3. Biobase Wolfenbuettel GmbH
Germany
www.biobase-international.com/pages
Instead, Helios BioSciences will select and classify the therapeutic targets or combina-
tion of therapeutic to cure neuro-degenerescence. Helios activity is at the cross-road of Todor Vujasinovic
the different work-packages of the project as Helios has to integrate (with the help of HELIOS Biosciences SARL
Créteil, France
Biobase) Molecular Interaction Network and Biological data to build Dynamic Models of www.helios-bioscience.com
Molecular Interaction Networks and select therapeutic targets which will be then validated
in vivo. In addition to that Helios will commercialize the validated therapeutic targets. Despina Sanoudou
Foundation of Biomedical Research
of the Academy of Athens FBRAA
Molecular Biology Division
Center for basic research
Athens, Greece

Expected results
The VALAPODYN network is composed of leading
authorities in the fields of genomics, proteomics,
bioinformatics and neuroscience in Europe. They
have decided to join their efforts to develop a new
innovative System Biology approach to model the
dynamics of Molecular Interaction Networks (MIN)
related to cell death and survival in the brain. This
model will be dedicated to the selection of drug
targets for human brain.
The project will first validate dynamic models for
cell death through the characterisation of new
potential drug targets in an animal model for
epilepsy where neurodegeneration is the initial
step of the development of epileptic seizures.
Edwin De Pauw
basis for the next generation of biological valida- University of Liege ULG
tions for novel therapeutic targets, instead of the Department of chemistry
Mass Spectrometry Laboratory
methods currently in use, namely those involving Liège, Belgium
animal models for drugs acting symptomatically at
end receptors and effectors. Hermona Soreq
Hebrew University of Jerusalem
Department of Biological Chemistry
VALAPODYN will also have a significant impact on Institute of Life Sciences
the ERA, by creating a new foundation for the Jerusalem, Israel
exchange of fundamental research and know -
Raffaella Catena
ledge. The development of the international Alma Consulting Group
R&D network of SMEs in the biotechnology sec- France
tor (HELIOS, BIOBASE and SynapCell through www.almacg.com
INSERM during the project) will accelerate the
emergence of the EU as a powerful contender in
the global technological market. The VALAPODYN
consortium will also allow for optimal use of the
available EU resources and human potential.

Potential applications To disseminate the project results as widely as

The development of new and unique dynamic mod-
elling tools will allow the consortium to participate
in the process of applying integrative biology to
pathology research. This should significantly
improve the quality of life for EU citizens, by
advancing the identification of new generations of
more efficient drug targets; these drugs will be
used to treat numerous diseases accounting for
mortality and several serious illnesses in the EU,
such as cancer, cardiovascular diseases, neurolog-
ical diseases, etc. Dynamic models will form the
possible, several different levels of information
distribution are proposed. This will involve pre-
sentations and forums for discussion, both in
a scientific context (doctors, researchers, neuro-
science students and collaborators in the field of
neurodegenerative disease research), and also
directed towards pharmaceutical industrials and
European citizens.

179
ACRONYM Contract number: LSHM-CT-2006-037254 | EC contribution: € 1 955 856 | Duration: 24 months
Starting date: 1 January 2007

VASOPLUS
www.vasoplus.eu

SUMMARY
The Vasoplus project evaluates the poten-
Placental Growth Factor (PlGF): new diagnostic
tial of PlGF as a pharmaceutical for major and therapeutic applications in cardiovascular disease
chronic progressive ischemic cardiovas-
cular disorders (ischemic heart disease,
heart failure) and arterial insufficiency
(intermittent claudication and critical limb
ischemia) and as a biomarker for cardio-
vascular disease. The project is based on
basic research on the VEGF-signaling
Background attributed to refractoriness of such disease
pathway (via PlGF) performed over the
groups to angiogenic growth factors. These
last five years (CTG, VIB-3), prototype
Ischemic heart disease (IHD) and peripheral arte- models and strategies will not only be of value
research performed with recombinant
rial occlusive disease (PAOD) are the major cause for the present project but also for the devel-
PlGF for pro-angiogenesis (GT and TG/TX),
of severe morbidity and mortality in Western soci- opment of pro-/anti-angiogenic medicines in
basic research on the association of
eties. Patients who presently survive acute coro- general.
plasma PlGF and VEGF levels and human
nary events as a result of coronary intervention • Once the pro-angiogenic effect of PlGF will be
diseases (IGB) and the development of
(angioplasty, stenting or coronary bypass surgery) established in rodent models, these effects need
a diagnostic test to evaluate PlGF as
or pharmacological coronary artery reperfusion to be confirmed and validated in large animal
a biomarker for cardiovascular disease.
often develop congestive heart failure that is resist- models that are physiologically more closely
ant to intervention or pharmacological treatment. related to the situation in patients. Therefore
The comprehensive strategy encom-
Thus, the progress in the treatment of cardiovascu- newly established models of cardiac ischemia in
passes the validation of the ‘proof of
lar disease has converted acute lethal syndromes pigs and in baboons will be used. Demonstration
concept’ observations made by the aca-
into a chronic debilitating disease. Therapeutic that PlGF stimulates vessel growth in diseases
demic partners of the consortium into
angiogenesis is a novel treatment paradigm but conditions closely related to the situation in
therapeutic concepts in new relevant
ongoing clinical trials with the angiogenic proteins patients will markedly increase the likelihood of
small animal models, development of
VEGF and bFGF have not achieved convincing pri- success in humans.
industrial scale GLP/GMP quality materi-
mary endpoints of improved tissue perfusion and
als and confirmation of their safety and
functional recovery. Therefore, current strategies 2. Further development of the production process.
efficacy in new, relevant large animal
must be reconsidered and alternative angiogenic • The production process has been transferred from
models. The strategy will be applied to
targets validated. its original site of development to an industrial
the development of pro-angiogenic
The pro-angiogenic drug candidate PlGF, unlike manufacturer for further development so as to fit
recombinant PlGF in ischemic heart dis-
VEGF, has in proof of concept studies been demon- with final production scale and GMP constraints.
ease models and in peripheral arterial
strated to target pathological angiogenesis and not • State of the art application of ‘in process’ and
insufficiency models. In parallel, the
physiological angiogenesis and to be devoid of ‘final’ quality and stability control will require
value of PlGF as a predictive biomarker
most of the systemic side effects associated with additional validation of new assays.
and as a diagnostic test for cardiovas-
administration of VEGF. In initial proof of concept • Discovery research will be performed on compound
cular disease will be explored in a collab-
studies, PlGF levels in blood have been shown to be improvements, involving Cys-to-Gly substitution
orative effort with a large diagnostic
a distinct biomarker for cardiovascular disease. for improved stability and alternative isoforms
company.
(glycosylated PlGF-1 and PlGF-2 produced in
The principal aim of the project is to
Aim Chinese hamster ovary (CHO) cells).
develop a new, safe and efficacious med-
The aim is threefold and summarised below. 3. Determine the potential of PlGF as biomarker for
icine to enhance the formation of blood
cardiovascular disease.
vessels and in doing so, to develop new
1. Determine the potential of PLGF as therapeutic • Population study: A database, recently developed
treatment paradigms for heart failure
for major chronic progressive ischemic cardio- by IGB, holds the description of the health status,
and critical limb ischemia.
vascular disorders. the genealogy and the genome-wide microsatellite
• Determine the pro-angiogenic effects of PlGF on: marker scan of approximately 4 000 individuals
– Revascularisation of ischemic limbs. This will from genetically isolated villages in Italy. This
be studied in mice, rats and in rabbits. database will be studied to determine the con-
– Revascularisation of ischemic cardiac tissue. tribution of PlGF and VEGF to specific human
This will be investigated in mice. These models cardiovascular diseases and cancer.
will be of critical importance as these diseases • Development of a reliable diagnostic test for
are prevalent in patients eligible for therapeu- measurement of PlGF concentrations in human
tic angiogenesis, and the limited success of blood samples based on compounds from
clinical trials with VEGF and basic fibroblast Geymonat and ThromboGencics/Thromb-X. It is
growth factor (bFGF) has indeed been in part intended to evaluate the degree of angiogenesis

180
Key words: placental growth factor, PlGF, ischemia, cardiovascular disease

ROLE OF SMEs Scientific coordinator

J.M. Stassen
ThromboGenics Ltd.
Three European SMEs based in Ireland, Belgium and Italy are involved. The project is led by 14 Bridgecourt Office Park
Thrombogenics/Thromb-X, an Irish biopharmaceutical company focused on the clinical Walkinstown Avenue
Dublin 12, Ireland
development of cardiovascular drugs in-licensed from academic institutions via its R&D jmstassen@thrombogenics.com
affiliate Thromb-X. Their research focuses on the preclinical development of biopharmaceu- www.thrombogenics.com
ticals for innovative treatments of severe diseases as well as on the development of improved
technologies for transgenesis in mammalian species and for regenerative medicine. An Italian Partners
pharmaceutical SME, Geymonat SpA, has experience in translational biopharmaceutical Mauro Battisti
research and development. A Belgian biotech SME, Eurogentec S.A., will provide valuable Geymonat SpA
expertise in industrial development of recombinant PlGF compounds. Anagni, Italy
www.geymonat.com/profilo.htm
These SMEs will receive 58 % of the project budget. There is a well-balanced integration of
the industrial partners (three SMEs plusl a large company) and academic groups, orientated Florence Xhonneux
towards industrial exploitation of expected results. Eurogentec S.A.
Liege Science Park
Seraing, Belgium
www.eurogentec.com/eu-home.html
based on PlGF blood levels, together with other 2. Further development of the production process.
biomarkers of cardiovascular disorders, in a well- • GLP qualified and GMP qualified rhPlGF-1. Stefan Janssens
KULeuven
characterised Italian cohort with the intent to • High yield production of the mutein. Leuven, Belgium
stratify patients who might benefit from proan- • Stability of the mutein in solution and gel analysed.
giogenic treatment. • Biological activity of the mutein verified by in vitro Maria G. Persico
assays. Institute of Genetics and Biophysics A.B.T.
Naples, Italy
Expected results • Small scale preparations available of CHO-pro-
duced rhPlGF-1, rhPlGF-2 and rhPlGF-1CG. Philip Badenhorst
Expected results for the different objectives are as • Validation for each assay development. University of the Free State
Bloemfontein, South Africa
follows. • GLP compliant certification/recognition of the www.uovs.ac.za
Belgian Monitoring authorities based on a fictive
1. Determine the potential of PLGF as therapeutic GLP stability study with the aim to determine the Georg Hess
Roche Diagnostics GmbH
for major chronic progressive ischemic cardiovas- shelf life and stability on rhPlGF-1. Mannheim, Germany
cular disorders. www.roche.de/diagnostics/index.htm
• Efficacy analysis of rhPlGF-1 for revascularisation 3. Determine the potential of PlGF as biomarker for
of ischemic myocardium and limb muscle. cardiovascular disease.
• Comparative analysis of rhPlGF-1 efficacy for • Correlation of the plasma levels of VEGF and PlGF
revascularisation of ischemic tissue in rat and (-1 and -2) and health status of 2 800 samples by
rabbit ischemia models. analysis of the project database.
• Comparative analysis of rhPlGF-1 efficacy for • Definition of the VEGF and PlGF haplotypes in
revascularisation of ischemic tissue in a mouse 2 800 individuals.
model of ischemic cardiac failure. • Association analysis of VEGF and PlGF variants and
• Data on the percentage of animals that develop a haplotypes with a trait or disease.
dysfunctional and ischemic myocardium versus • Status of PlGF assay development including pre-
those that develop significant transmural necrosis analytical conditions.
caused by acute occlusion of the stented seg- • Completion of sample measurements using PlGF Placebo
ment. This will allow the project to determine the prototype assay, sCD40L and NT-pro-BNP diag-
number of animals required to enter the study. nostic assays.
• An evaluation of the size of dysfunctional but viable • Correlation of plasma levels of PlGF, sCD40L, NT-
myocardium by magnetic resonance imaging with pro-BNP and health status of the study individuals.
delayed enhancement as well as dobutamine • Multi-variate analysis of the study completed.
stress echo and quantitation of global LV function
allowing power calculations for the NNT in order to Potential applications
observe a significant increase in global LV function
(increase in Ejection Fraction by 4-6%). Two possible applications are being pursued with
• Perfusion studies to quantify the degree of this programme: a new, safe and effective medi- PIGF treatment
myocardial perfusion both in the endo- and epi- cine to enhance the formation of new blood vessels
cardial myocardium. The effect of intervention on in ischemic tissues and a new diagnostic tool for | More visible collateral vessels after 7 days of
LV function will be expected within 1.5 years. cardiovascular disease. PIGF treatment in rabbit hindlimb ischemia.

181
ACRONYM Contract number: LSHC-CT-2006-037874 | EC contribution: € 2 050 000 | Duration: 36 months
Starting date: 1 January 2007

VITAL
www.cro.sanita.fvg.it/progetti/vital/index.htm

SUMMARY
Therapeutic vaccines targeting B cell
Development of optimized recombinant idiotypic
non-Hodgkin lymphoma (NHL) idiotype vaccines for subset-specific immunotherapy
(Id) represent a promising approach
against these malignancies. A broad use
of B cell lymphomas
of Id-based vaccination, however, is
hampered by the complexity and costs
due to the individualized production of
these vaccines. Recent evidence indi-
cates that these limitations may be over-
Background Aim
come. In fact, distinct sets of stereotyped
immunoglobulins have been identified in
Non-Hodgkin’s lymphomas (NHL) constitute The objective of VITAL is the development and
various B-NHL, suggesting that patients
a heterogeneous group of malignancies whose production of optimized recombinant idiotypic
share Id with a higher frequency than
incidence has significantly increased in recent vaccines for the treatment of subgroups of lym-
appreciated previously. Through the
decades. In the year 2000, more than 145 000 phoproliferative disorders expressing molecularly
complementary and synergistic work of
cases of NHL were diagnosed in developed coun- correlated idiotypes. These vaccines will be
academic partners and three SMEs, we
tries, representing thus the sixth most common included in new formulations for innovative trials
plan to exploit the molecular features
cancer occurring among men and the eighth of immunotherapy potentially targeting a large
of Id proteins of distinct B cell lym-
among women. Low-grade B-cell NHLs, in par- fraction of lymphoma/leukemia patients.
phomas/leukemias, particularly those
ticular, are incurable diseases characterized by
pathogenically associated with antigen
stimulation and/or selection, to develop
relatively slow growth and excellent initial respon- Expected results
siveness to chemotherapy but also by continuous
pre-made, recombinant Id proteins to
relapses. In particular, for patients with follicular • Establishment of a large database including
vaccinate subgroups of lympho-prolifer-
lymphoma, median overall survival (7-10 years) sequences of idiotypic VH and VL genes
ative disorders expressing molecularly
has not improved over the past 30 years. expressed by a variety of lympho-proliferative
correlated idiotypes. A database of Id
Although in the vast majority of patients complete disorders, including low grade B-NHL, autoim-
sequences expressed by different B-NHL
or partial remissions can be obtained with either munity-associated lympho-proliferations, and
will be constructed to identify subgroups
single agents or combination chemotherapy, the chronic lymphocytic leukemia. This will allow
of tumors expressing molecularly corre-
clinical course is characterized by a high relapse the identification of candidate Id proteins for
lated Id proteins. Selected Id proteins will
rate. After relapse, both the response rate and ‘cross-reactive’ immunotherapy.
be characterized for their immunogenic-
relapse-free survival after subsequent salvage
ity and, particularly, for the ability to
treatment regimens steadily decrease, resulting • Pre-clinical characterization of the immuno-
induce cross-reactive immune responses
in a median survival of only 4-5 years after the first genicity of selected natural Id proteins, with par-
against related Id proteins. B and T cell
relapse. These clinical findings, coupled with the ticular regard to their ability to induce immune
epitopes will be identified using innova-
substantial toxicities of standard treatments, responses against lymphoma cells expressing
tive approaches and dedicated assays
have stimulated the search for novel and more molecularly correlated Id proteins. The charac-
for immunomonitoring will be devel-
tumor-selective therapies. Therapeutic vaccines terization will include the identification of B cell
oped. Optimized versions of selected Id
targeting B cell lymphoma idiotype (Id) represent epitopes and HLA Class I-restricted cytotoxic T
vaccines will be produced using new
a promising immunotherapeutic approach for cell epitopes using innovative approaches and
strategies and validated in animal mod-
a better clinical control of these malignancies. will allow the development of dedicated assays
els. New adjuvants and delivery systems
This strategy is based on the observation that for immunomonitoring.
for improved Id vaccine formulations and
immunoglobulins (Ig) expressed by neoplastic B
administration will be also evaluated and
lymphocytes carry unique determinants in their • Design and validation of optimized Id vaccines.
validated. The most promising Id proteins
variable regions (idiotypes), which can be recog-
will be produced and purified according
nized as tumor specific-antigens. Indeed, both • Evaluation and validation of new adjuvants and
to GMP standards and included in new
protein- and dendritic cell-based vaccines that innovative delivery systems for improved Id
vaccine formulations for innovative trials
use the patient-specific Id have resulted in clini- vaccine formulations and administration.
of ‘cross-reactive’ immunotherapy.
cally significant tumor-specific cellular responses
with very little toxicity. A broad use of Id-based • ‘Clinical-grade’ production and purification of
vaccination for B cell lymphomas, however, is optimized Id proteins for patient vaccination.
hampered by the fact that these approaches are
patient-specific so that the vaccine must be indi- The SMEs are an integral part in the project in
vidually produced for each patient. On these making the new diagnostic and therapeutic tools
grounds, new strategies obviating the need to available, not only for Europe but also for the
produce customized vaccines would further sim- world market. The close integration between clin-
plify clinical applications of idiotypic vaccines. ical and research activities at several university

182
Key words: lymphoma, leukaemia, vaccine, idiotype, immunotherapy

ROLE OF SMEs Scientific coordinator

Riccardo Dolcetti
Centro di Riferimento Oncologico – IRCCS
Three SMES, out of seven participants, play a key role in the research activities of the project. National Cancer Institute
Via Franco Gallini, 2
33081 Aviano, Italy
In particular, PEPSCAN will be responsible for design, preparation and screening of syn- rdolcetti@cro.it
thetic peptide libraries and for the reconstruction of interaction sites in the complexes
included in VITAL. It will coordinate the mapping of B cell epitopes and test the efficacy of Partners
new adjuvants.
Bjarne Bogen
University of Oslo and
ProImmune Ltd. will be involved in the identification of HLA Class I-restricted CTL epitopes. Rikshospitalet University Hospital
It will do so by using its Pro5® MHC Pentamers and ProVE™ MHC Pentamer Libraries. In close Oslo, Norway
collaboration with PEPSCAN, optimised versions of selected Id vaccines will be produced Maria Masucci
using different new strategies to enhance both humoral and cellular immune responses. Karolinska Institutet
Stockholm, Sweden
Areta International will, through process development and manufacturing of tailored-made
Antonio Rosato
batches, produce the most promising Id proteins according to GMP standards. If necessary, it Department of Oncology
will define innovative technological approaches for GMP scale-up production and purification and Surgical Sciences
of selected recombinant Id proteins. University of Padova
Padova, Italy

Hans Petrus
Maria Langedijk
Pepscan Therapeutics B.V.
Lelystad, The Netherlands
www.pepscan.nl

Nikolai Schwabe
ProImmune Limited
Oxford, United Kingdom
hospitals and Cancer Centers with the SMEs will www.proimmune.com/ecommerce
form new centres of excellence where European
Maria Luisa Nolli
SMEs will benefit from close collaboration at the Areta International S.r.l.
same time as new diagnostic and therapeutic Gerenzano (VA), Italy
products will be developed to the benefit of www.aretaint.com
patients with lymphoid malignancies.

Potential applications

The results obtained in the present project will

allow the design and activation of phase I/II clin-
ical trials aimed at validating the use of opti-
mized, pre-made vaccines for the treatment of
a relatively broad spectrum of lymphoid malig-
nancies. The proposed Id vaccination may be ben-
eficial also for patients with pre-neoplastic B-cell
lymphoproliferations, such as mixed cryoglobu-
linaemia. These vaccines, in fact, may be used
with the purpose to alleviate the symptoms and,
ultimately, to prevent the possible evolution
towards an overt B cell malignancy. Once vali-
dated as drugs, the vaccines will have the advan-
tage to be easily distributed to all Hematology
and Oncology Departments, including those of
peripheral Hospitals/Universities. Thus, results | Flow chart, outlining the main expected
results, leading from identification
obtained in the present project will have an
of shared idiotypes to the development
important strategic impact in solving, at least in of optimized vaccines for the treatment
part, the dramatic social and health problem of B-cell lymphoproliferations.
represented by NHL.

183
ACRONYM Contract number: LSHG-CT-2006-037220
Starting date: 1 January 2007
ZF-TOOLS
biology.leidenuniv.nl/ibl/S1/research/ZF-TOOLS
SUMMARY
The ZF-TOOLS project comprises the coor-
dinated efforts of three research laborato-
ries and three SMEs aimed to achieve
the following two main objectives: First,
a genomic-based marker discovery for
biomedical screens in zebrafish and, sec-
ondly, the use of high-throughput marker
analysis and tumour cell implants for
the identification of tumour growth and
metastasis factors and organismal
defence factors.
| EC contribution: € 1 739 000
High-throughput Tools for Biomedical
Screens in Zebrafish
Background
Human disease research and drug development
rely heavily on the use of animal models. Among
these, the mouse model is the most intensively
studied. However, over the last decade the
zebrafish has emerged as an attractive alternative
model and has progressively gained importance.
This is due to the fact that the zebrafish offers
exciting novel research opportunities because of
the optical transparency of its embryos and its
amenability to genetics. To date, the value of
zebrafish in pharmacological studies has not yet
been extensively explored and exploited. However,
findings emphasise the potential of using zebrafish
in several phases of drug discovery processes and
in toxicological screens.
The ZF-TOOLS project is focused on the incorpora-
tion of zebrafish into the preclinical drug screening
pipelines. The small size of zebrafish embryos and
the large numbers in which they can be obtained
make them particularly suitable for high-through-
put drug screens. Furthermore, drugs can be easily
applied to zebrafish embryos through dilution in
the embryo medium and absorption through skin
and gills.
Aim
The project aims to develop a case study for an anti-
tumour drug screening system, based on the
implantation of fluorescently labelled tumour cells
into zebrafish embryos. This innovative tumour cell
implantation system is currently being developed
by one of the SME partners and has the major
advantage that it does not involve the use of trans-
genic animals. Growth and metastasis properties of
implanted tumour cells can be efficiently monitored
by fluorescence microscopy during the develop-
ment of the transparent zebrafish embryos. This
system resembles the natural situation of tumour
growth, as the tumour cells are derived from
zebrafish cell cultures of embryonic origin and
implanted back into zebrafish embryos. It is envis-
aged that a powerful screening system can arise by
combining high-throughput marker analysis with
the possibility to visualise tumour growth and
184
| Duration: 36 months
metastasis in an optically transparent vertebrate
model organism.
However, for the realisation of this complex screen-
ing system, the identification of relevant disease
marker genes in zebrafish represents a crucial step.
In ZF-TOOLS, different genomics approaches will be
used to discover novel markers, which will be suit-
able for application in the ZF-TOOLS tumour screen-
ing system and will also have a broader utility for
disease research in the zebrafish model. The exper-
imental design of this genomics approach is
expected to result in the identification of two
classes of markers, namely markers correlating
with growth and metastasis of tumour cells and
markers correlating with the immune or other
defence responses of the organism towards tumour
cells. The project will concentrate on both classes
of markers because the interactions between
developing tumours and the tumour microenviron-
ment are decisive for tumour survival or rejection.
Expected results
The strategic aim of ZF-TOOLS is the development
of a zebrafish embryo screening system as an
innovative genomics tool. This system will be
employed for high-throughput effectiveness test-
ing of pharmaceutical compounds that have the
potential to influence disease processes, including
tumour growth, metastasis and immune defence
responses. This zebrafish screening tool offers
some unique features that make it very attractive in
comparison with existing tools. First, it combines
the power of genomic analysis of disease marker
genes with the power of in vivo monitoring of dis-
ease processes in a transparent vertebrate model
organism. Secondly, it has the potential for high-
throughput application due to the small size of
zebrafish embryos, to the high numbers with which
embryos can be obtained, and to the choice of
high-throughput molecular screening tools that
will be developed within the project.
In order to establish the zebrafish screening tools,
the project will undertake a multidisciplinary
functional genomics approach which integrates
different global expression profiling techniques
and bioinformatics. Based on this approach, the
Key words: zebrafish embryo model, oncogenic cell implants, anti-tumor drug discovery, reporter cell lines, tumor markers,
immune response markers, expression profiling

ROLE OF SMEs Scientific coordinator

Annemarie H. Meijer
Leiden University
Three research intensive SMEs, ZF-screens B.V, BaseClear B.V and ZenonBio Ltd., play a crucial Institute of Biology
role in the ZF-TOOLS project. Clusius Laboratory
Wassenaarseweg 64
2333 AL Leiden, The Netherlands
The activities of ZF-Screens B.V. are focused on the development and application of the tumour a.h.meijer@biology.leidenuniv.nl
implantation system, including drug screens and the identification and exploitation of novel www.biology.leidenuniv.nl/ibl/about.shtml
tumour factors. Zebrafish embryo-based screens, integrated at an early phase in the drug dis- Partners
covery pipeline, can likely increase efficiency of further tests in a rodent system. It is expected
that a proof-of-principle of the tumour implant screening system would open up a fast market, Herman P. Spaink
not only for contract research in screens for new therapeutics but also for licensing of the novel ZF-screens B.V.
The Netherlands
technology that ZF-Screens has developed and will further strengthen during this project. www.zf-screens.com

The main role of BaseClear B.V. in the project is the development of high-throughput expression Nicholas Simon Foulkes
analysis tests, based on the use of MLPA (Multiplex Ligation-dependent Probe Amplification) Forschungszentrum Karlsruhe
Karlsruhe, Germany
technology. MLPA has been an important breakthrough in DNA diagnostics and is also extremely www.fzk.de
valuable to increase efficiency of mRNA expression profiling (RT-MLPA). BaseClear has been
active in custom molecular services and contract research projects since 1993. Currently, the Bas Reichert
BaseClear B.V.
company serves more than 2 400 customers from 450 national and international companies and The Netherlands
university research departments. BaseClear intends to exploit the experience gained from www.baseclear.com
the ZF-TOOLS project to add MLPA and RT-MLPA custom services to their portfolio. In addition,
RT-MLPA probe sets developed in the project will be sold for research purposes. Tamás Forrai
Zenon Bio Ltd.
Hungary
ZenonBio Ltd. is the main bioinformatics partner in the project, responsible for analysis and inte- www.zenonbio.hu
gration of genomic data sets. The company markets state-of-the-art diagnostic systems in
Mátyás Mink
Hungary and previously developed software for signal and image processing. Their bioinfor- Szeged University
matics expertise, further strengthened by the project, will be directed towards development of Department of Genetics
services. A potentially good market for new entrepreneurial activities of ZenonBio Ltd. lies in the and Molecular Biology
Hungary
South-Eastern European region, including Hungary, Serbia-Montenegro, Romania and Bulgaria. www.u-szeged.hu/indexe.html

ZF-TOOLS project expects to achieve the following
results:
• knowledge of tumour growth and metastasis
factors and organismal defence factors;
• high-throughput tools for quantitative analysis
of disease marker sets;
• a collection of constitutive and inducible, onco-
genic and non-oncogenic reporter cell lines use-
ful for basic disease research and for application
in screening systems;
• case study results of a novel anti-tumour drug
screening system, based on the implantation of
fluorescently labelled tumour cells into zebrafish
embryos.
Potential applications
The ZF-TOOLS project aims to reinforce European
competitiveness by generating strategic know-
ledge, thanks to its multidisciplinary research
approach. The developed tools and technology
will be exploited for basic research on vertebrate
disease and for strategic research and service
activities on behalf of three high-tech SMEs.
The ZF-TOOLS objectives are focused on the incor-
poration of the zebrafish embryo model into the
preclinical drug screening pipelines. The use of
mice for in vivo monitoring of disease processes
such as tumourigenesis, metastasis and immune
response to tumours is limited by costs and
throughput level. Introducing a high-throughput
zebrafish embryo model could potentially con-
tribute to cost-effective and more efficient methods
in the anti-tumour drug discovery process.
Moreover, acceleration of drug lead time benefits
economy as well as quality of life of cancer patients.
The lack of basic knowledge of disease marker
genes is the current bottleneck for biomedical
research in zebrafish and for genomics-based com-
pound screens in this model organism. The ZF-
| Transparent zebrafish embryo.
TOOLS project uses multidisciplinary functional
genomics approaches to discover novel disease
markers. The expected identification of factors
important for tumour growth and metastasis and
organismal defence responses will generate funda-
mental knowledge relevant to human health and
will open the door to the establishment of zebrafish-
based biomedical research and screening tools.

185
ACRONYM Contract number: LSHB-CT-2006-037244 | EC contribution: € 2 326 567 | Duration: 36 months
Starting date: 1 December 2006

PREGENESYS
www.pregenesys.net/main

SUMMARY
Preeclampsia is a multi-system disorder
Development of Early Non-Invasive Biomarkers
that complicates 5-7% of all pregnancies, and Means for the Diagnosis and Progression
is responsible for 18% (the second largest
cause) of maternal deaths during preg-
Monitoring of Preeclampsia and Tailoring
nancy, and for a third of premature births. Putative Therapies
This complex disorder is expressed as
a newly onset hypertension and protein
loss in urine (proteinuria) that develops in
the mother after the 20th week of gesta- ROLE OF SMEs
tion, in association with varying degrees
of end-organ damage. It may be coupled Diagnostic Technologies Ltd. (DTL) is the project coordinator. It is a medical diagnostic and
to potentially life-threatening complica- biotechnology company at the forefront of placental protein molecular biology and bio-
tions of the kidney, liver, blood system chemistry incubated at the Technion-Israel Institute of Technology (Haifa, Israel) in 1994
and brain, and can result in convul- and emerged as an independent company in 2001.
sions/seizures (eclampsia).
ImunoSTAR – Research and Commercialisation of Bio-diagnostic Products S.A. – aims at
Concerning the baby, preeclampsia is promoting and commercialising innovative immunology tests and diagnostic services
responsible for approximately 7-9 % of for application in biomedical and health market. It specialises in the Obstetrics and
neonatal morbidity and mortality. Major Gynaecology field.
motor and cognitive disabilities, blind-
ness and life-long complications can take
their toll.
Scientific coordinator
While clinically diagnosed in the second
half of pregnancy, the underlying patho- Hamutal Meiri
physiology is associated with deleterious Diagnostic Technologies Ltd.
2 Ha’Carmel St.,
alterations of implantation and placen- Building B, 4th floor
tation, which already begin in the first Yokneam 20692, Israel
trimester. hamutal.meiri@pregenesys.com
hamutalmeiri@hotmail.com
There is no ‘gold standard’ for an effec-
tive preventive therapy and the only cur-
rently accepted treatment of established
preeclampsia is (premature) delivery. This
is often done at the expense of foetal well-
being (excess neonatal morbidity and
mortality).

The Pregenesys research project is co- | Confocal microscopy of normal term placental villi.
financed by and carried out within Priority 1 Placental villi from a normal term placenta stained for PP13
of FP6. It aims to develop early (1st trimester (red) and actin (green) are shown. Nuclei were counter
of pregnancy) non-invasive biomarkers stained with DAPI. Shown is an overlay of a stack of 20
single images. (Courtesy of B. Huppertz, Graz.)
and means for the diagnosis and monitor-
ing of preeclampsia and its progression,
that would help to tailor appropriate puta-
tive therapies, thus optimising them for
the prevention of preeclampsia or the
reduction of its severity.

The project is undertaken by a consortium

consisting of 10 members from 9 different
countries, including universities, hospitals,
private research organisations, SMEs and
a large industrial company.

186
SME CALL

Index
by project
number
• LSHP-CT-2005-037912 • LSHG-CT-2006-037277
FASTEST-TB . . . . . . . . . . . . . . . . . 66 VALAPODYN . . . . . . . . . . . . . . . 178

• LSHP-CT-2006-036871 • LSHB-CT-2006-037293
INNOVAC . . . . . . . . . . . . . . . . . . 88 QuAGSIC . . . . . . . . . . . . . . . . . . 144

• LSHM-CT-2006-036534 • LSHB-CT-2006-037319
NEOBRAIN . . . . . . . . . . . . . . . . . 120 IBDchip . . . . . . . . . . . . . . . . . . . 80

• LSHB-CT-2006-036813 • LSHB-CT-2006-037325
PROLIGEN . . . . . . . . . . . . . . . . . 142 BacAbs . . . . . . . . . . . . . . . . . . . . 18

• LSHM-CT-2006-037050 • LSHB-CT-2006-037386
INDABIP. . . . . . . . . . . . . . . . . . . . 86 ANGIOSTOP . . . . . . . . . . . . . . . . . 12

• LHSB-CT-2006-037168 • LSHM-CT-2006-037400
EXERA . . . . . . . . . . . . . . . . . . . . 62 IMMUNATH . . . . . . . . . . . . . . . . . 82

• LSHP-CT-2006-037200 • LSHG-CT-2006-037415
MUNANOVAC . . . . . . . . . . . . . . . . 112 SMARTER . . . . . . . . . . . . . . . . . . 154

• LSHB-CT-2006-037212 • LSHG-CT-2006-037457
Diagnosis . . . . . . . . . . . . . . . . . . 44 SysProt . . . . . . . . . . . . . . . . . . . 162

• LSHP-CT-2006-037217 • LSHG-CT-2006-037462
TB-DRUG . . . . . . . . . . . . . . . . . . 170 ChILL . . . . . . . . . . . . . . . . . . . . . 28

• LSHG-CT-2006-037220 • LSHB-CT-2006-037479
ZF-TOOLS . . . . . . . . . . . . . . . . . . 184 MYOAMP . . . . . . . . . . . . . . . . . . 116

• LSHG-CT-2006-037226 • LSHC-CT-2006-037489
MEGATOOLS . . . . . . . . . . . . . . . . 104 Immuno-PDT . . . . . . . . . . . . . . . . 84

• LSHM-CT-2006-037227 • LSHP-CT-2006-037494
CVDIMMUNE . . . . . . . . . . . . . . . . 38 PRIBOMAL . . . . . . . . . . . . . . . . . 138

• LSHG-CT-2006-037231 • LSHB-CT-2006-037499
SYSCO . . . . . . . . . . . . . . . . . . . . 160 liintop . . . . . . . . . . . . . . . . . . . . 96

• LSHB-CT-2006-037244 • LSHG-CT-2006-037517
PREGENESYS . . . . . . . . . . . . . . . 186 TargetHerpes . . . . . . . . . . . . . . . 166

• LSHB-CT-2006-037245 • LSHG-CT-2006-037543
NanoSense . . . . . . . . . . . . . . . . . 118 TEMPO. . . . . . . . . . . . . . . . . . . . 174

• LSHC-CT-2006-037251 • LSHB-CT-2006-037545
CAPPELLA . . . . . . . . . . . . . . . . . . 26 ENLIGHT . . . . . . . . . . . . . . . . . . . 56

• LSHM-CT-2006-037254 • LSHM-CT-2006-037554
VASOPLUS . . . . . . . . . . . . . . . . . 180 AGLAEA . . . . . . . . . . . . . . . . . . . . 10

• LSHP-CT-2006-037276 • LSHC-CT-2006-037555
RespViruses . . . . . . . . . . . . . . . . 148 MAMMI . . . . . . . . . . . . . . . . . . . 100

188
• LSHC-CT-2006-037559 • LSHM-CT-2006-037846 • LSHM-CT-2007-037472
CancerGrid . . . . . . . . . . . . . . . . . . 22 RATstream™. . . . . . . . . . . . . . . . 146 TAMAHUD . . . . . . . . . . . . . . . . . . 164

• LSHB-CT-2006-037560 • LSHC-CT-2006-037852 • LSHB-CT-2007-037590

USDEP . . . . . . . . . . . . . . . . . . . . 176 LIGHTS . . . . . . . . . . . . . . . . . . . . 94 Net2Drug . . . . . . . . . . . . . . . . . . . 122

• LSHB-CT-2006-037575 • LSHM-CT-2006-037870 • LSHB-CT-2007-037636

COMICS . . . . . . . . . . . . . . . . . . . . 36 EACCAD . . . . . . . . . . . . . . . . . . . 54 InVitroHeart . . . . . . . . . . . . . . . . . . 92

• LSHG-CT-2006-037586 • LSHC-CT-2006-037874 • LSHC-CT-2007-037642

STREPTOMICS . . . . . . . . . . . . . . 158 VITAL . . . . . . . . . . . . . . . . . . . . . 182 HighReX . . . . . . . . . . . . . . . . . . . . 74

• LSHP-CT-2006-037587 • LSHG-CT-2006-037897 • LSHM-CT-2007-037669

PlasmodiumdUTPase . . . . . . . . . . 134 AUTOSCREEN . . . . . . . . . . . . . . . . 16 PHECOMP . . . . . . . . . . . . . . . . . . 130

• LSHP-CT-2006-037651 • LSHE-CT-2006-037899 • LSHB-CT-2007-037703

EPIVAC . . . . . . . . . . . . . . . . . . . . 58 MANASP . . . . . . . . . . . . . . . . . . 102 STEMDIAGNOSTICS. . . . . . . . . . . . . 156

• LSHB-CT-2006-037653 • LSHG-CT-2006-037939 • LSHB-CT-2007-037730

OMVac . . . . . . . . . . . . . . . . . . . . 126 BioBridge . . . . . . . . . . . . . . . . . . 20 COBRED . . . . . . . . . . . . . . . . . . . . 34

• LSHB-CT-2006-037661 • LSHM-CT-2006-037950 • LSHB-CT-2007-037740

GLYFDIS . . . . . . . . . . . . . . . . . . . 70 cNEUPRO . . . . . . . . . . . . . . . . . . 32 PRISM . . . . . . . . . . . . . . . . . . . . . 140

• LSHB-CT-2006-037681 • LSHM-CT-2006-037957 • LSHP-CT-2007-037760

DiaNa . . . . . . . . . . . . . . . . . . . . . 48 MagRSA . . . . . . . . . . . . . . . . . . . 98 HIVResInh. . . . . . . . . . . . . . . . . . . . 76

• LSHG-CT-2006-037683 • LSHM-CT-2006-037965 • LSHM-CT-2007-037765

FGENTCARD . . . . . . . . . . . . . . . . 68 INTELLIMAZE . . . . . . . . . . . . . . . . 90 PHOTOLYSIS . . . . . . . . . . . . . . . . . 132

• LSHM-CT-2006-037692 • LSHB-CT-2007-036644 • LSHM-CT-2007-037831

NPARI . . . . . . . . . . . . . . . . . . . . 124 DIALOK . . . . . . . . . . . . . . . . . . . . 46 MEMORIES . . . . . . . . . . . . . . . . . . 106

• LSHB-CT-2006-037702 • LSHB-CT-2007-037241 • LSHC-CT-2007-037834

Mimovax . . . . . . . . . . . . . . . . . . 108 SAGE . . . . . . . . . . . . . . . . . . . . . 150 DEPPICT . . . . . . . . . . . . . . . . . . . . 40

• LSHC-CT-2006-037737 • LSHB-CT-2007-037283 • LSHM-CT-2007-037862

HI-CAM . . . . . . . . . . . . . . . . . . . . 72 EURO-PHARMACO-GENE . . . . . . . . 60 ARTEMIS . . . . . . . . . . . . . . . . . . . . . 14

• LSHB-CT-2006-037739 • LSHG-CT-2007-037291 • LSHB-CT-2007-037933

Drop-Top . . . . . . . . . . . . . . . . . . 50 MODEST . . . . . . . . . . . . . . . . . . 110 POC4life . . . . . . . . . . . . . . . . . . . . 136

• LSHP-CT-2006-037785 • LSHP-CT-2007-037301
TB-trDNA . . . . . . . . . . . . . . . . . . 172 HIVSTOP . . . . . . . . . . . . . . . . . . . 78

• LSHG-CT-2006-037793 • LSHB-CT-2007-037303
OptiCryst . . . . . . . . . . . . . . . . . . 128 DeZnIT . . . . . . . . . . . . . . . . . . . . 42

• LSHP-CT-2006-037796 • LSHP-CT-2007-037304
SERO-TB. . . . . . . . . . . . . . . . . . . 152 CILMALVAC . . . . . . . . . . . . . . . . . 30

• LSHM-CT-2006-037833 • LSHB-CT-2007-037365
MYASTAID . . . . . . . . . . . . . . . . . 114 TargetScreen2 . . . . . . . . . . . . . . 168

189
SME CALL

Index
by coordinator
• Allaer Didier . . . . . . . . . . . . . . . . . . . . . . 28 • Daura Xavier . . . . . . . . . . . . . . . . . . . . . . . 18
Diagenode S.A. Universitat Autònoma de Barcelona

• Amaral Margarida D. . . . . . . . . . . . 168 • Depaulis Antoine . . . . . . . . . . . . . . . . . 178

University of Lisboa UMR 704 Inserm-Université
Joseph Fourier
• Anné Jozef . . . . . . . . . . . . . . . . . . . . . . . . . 158
Catholic University of Leuven • Di Lorenzo Diego . . . . . . . . . . . . . . . . . 64
Ospedale Civile di Brescia
• Bágyi István . . . . . . . . . . . . . . . . . . . . . . . 22
AMRI Hungary • Dickinson Anne . . . . . . . . . . . . . . . . . . . 156
University of Newcastle upon Tyne
• Benlloch Jose Ma . . . . . . . . . . . . . . . . 100
Consejo Superior de • Dolcetti Riccardo . . . . . . . . . . . . . . . . . 182
Investigaciones científicas National Cancer Institute

• Berrih-Aknin Sonia . . . . . . . . . . . . . . 114 • Einsele Hermann . . . . . . . . . . . . . . . . 102

Université Paris Sud (UPS) University of Wuerzburg

• Bill Roslyn . . . . . . . . . . . . . . . . . . . . . . . . 128 • Ekström Björn . . . . . . . . . . . . . . . 56

Aston University Olink AB

• Birch Mike . . . . . . . . . . . . . . . . . . . . . . . . 124 • Ellerbrok Heinz . . . . . . . . . . . . . . . . . . 176

F2G Ltd. Robert Koch-Institut

• Bois Emmanuel . . . . . . . . . . . . . . . . . . 136 • Falciani Chiara . . . . . . . . . . . . . . . . . . . . . 66

Cezanne SAS Philogen

• Brandt Remco . . . . . . . . . . . . . . . . . . . . . 30 • Finn Paul . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Cilian AG InhibOx Ltd.

• Campadelli-Fiume Gabriella . . . 166 • Fiorini Carlo . . . . . . . . . . . . . . . . . . . . . . . 20

University of Bologna Politecnico di Milano

• Caricasole Andrea . . . . . . . . . . . . . . . . 164 • Frostegård Johan . . . . . . . . . . . . . . . . . 38

Siena Biotech SpA Karolinska University Hospital

• Cattaneo Antonino . . . . . . . . . . . . . . . 106 • Gauguier Dominique . . . . . . . . . . . . . 68

European Brain Research Institute University of Oxford

• Collins Andrew . . . . . . . . . . . . . . . . . . . . 36 • Gilbert Ian. . . . . . . . . . . . . . . . . . . . . . . . . 134

University of Oslo University of Dundee

• Costi Maria Paola . . . . . . . . . . . . . . . . . 94 • Goudsmit Jaap . . . . . . . . . . . . . . . . . . . . 138

University of Modena
and Reggio Emilia
• Cutting Simon M.
Royal Holloway University of London
• Dammann Olaf
Hannover Medical School
• Danielsson Mats
Sectra Mamea AB
. . . . . . . . . . . . . . . . . 88
. . . . . . . . . . . . . . . . . . . 120
. . . . . . . . . . . . . . . . . . 74
Crucell Holland B.V.
• Hartmann Marcus . . . . . . . . . . . . . . . . . 30
Cilian AG
• Holthofer Harry. . . . . . . . . . . . . . . . . . . . 48
Haartman Institute
• Hotter Georgina . . . . . . . . . . . . . . . . . 142
Instituto de Investigaciones
Biomédicas de Barcelona

190
• Huet Jacqueline . . . . . . . . . . . . . . . . . . 112 • Martinsson-Niskanen Titti. . . . . . . . 12 • Schildgen Oliver . . . . . . . . . . . . . . . . . . 148
PHUSIS BioInvent International AB Institute for Medical Microbiology,
Immunology, and Parasitology
• Huggett Jim . . . . . . . . . . . . . . . . . . . . . . . 172 • Meijer Annemarie H. . . . . . . . . . . . . 184
University College London Leiden University • Schillberg Stefan . . . . . . . . . . . . . . . . . . . 150
Fraunhofer-Institut für Molekularbiologie und
• Imhof Axel . . . . . . . . . . . . . . . . . . . . . . . 154 • Meinke Andreas . . . . . . . . . . . . . . . . . . 126 Angewandte Oekologie IME
Ludwig Maximilians University Intercell AG
of Munich • Schrenzel Jacques . . . . . . . . . . . . . . . . . . 98
• Meiri Hamutal . . . . . . . . . . . . . . . . . . . 186 Geneva University Hospitals
• Jensen Sanne . . . . . . . . . . . . . . . . . . . . . 26 Diagnostic Technologies Ltd.
Evolva S.A. • Singh Mahavir . . . . . . . . . . . . . . . . . . . . . . . 66
• Mouly Vincent . . . . . . . . . . . . . . . . . . . . 116 LIONEX Diagnostics
• Kel Alexander . . . . . . . . . . . . . . . 122/160 INSERM & Therapeutics GmbH
BIOBASE GmbH
• Müller-Hartmann Herbert . . . . . . . 110 • Skjeltorp Guri . . . . . . . . . . . . . . . . . . . . . . . 118
• Keri György . . . . . . . . . . . . . . . . . . . . . . . 170 AMAXA GmbH Dalen Diagnostics AS
Vichem Chemie Research Ltd.
• Ochoa Gorka . . . . . . . . . . . . . . . . . . . . . . . 50 • Smith C. I. Edvard . . . . . . . . . . . . . . . . . . . 60
• Kuijper Ed J. . . . . . . . . . . . . . . . . . . . . . . . 54 Progenika Biopharma Clinical Research Center
Leiden University Medical Center
• Ogden David . . . . . . . . . . . . . . . . . . . . . . 132 • Stanescu Ioana . . . . . . . . . . . . . . . . . . . . . 58
• Kulikowski Tadeusz . . . . . . . . . . . . . . . 76 CNRS UMR 8118 FIT Biotech Plc
Instytut Biochemii iBiofizyki PAN
• Overduin Michael . . . . . . . . . . . . . . . 140 • Stassen J.M. . . . . . . . . . . . . . . . . . . . . . . . . 180
• Leiser Robert-Matthias . . . . . . . . . . 44 University of Birmingham ThromboGenics Ltd.
Agrobiogen GmbH
• Palme Klaus . . . . . . . . . . . . . . . . . . . . . . . 16 • Takacs Laszlo . . . . . . . . . . . . . . . . . . . . . . . . 34
• Lenas Petros . . . . . . . . . . . . . . . . . . . . . . . 14 University of Freiburg BioSystems International
Complutense University
of Madrid (UCM) • Pâques Frédéric . . . . . . . . . . . . . . . . . 104 • van Holst Gerrit-Jan . . . . . . . . . . . . . . . . . 78
CELLECTIS S A Viruvation B.V.
• Lévi Francis . . . . . . . . . . . . . . . . . . . . . . . . 174
INSERM U776 • Pasterkamp Gerard . . . . . . . . . . . . . . 82 • Veuskens Jack . . . . . . . . . . . . . . . . . . . . . . . 46
University Medical Center Utrecht KREATECH Biotechnology B.V.
• Lipp Hans-Peter . . . . . . . . . . . . . . . . . . . 90
NewBehavior AG • Porgador Angel . . . . . . . . . . . . . . . . . . . . 70 • Weisbuch Claude . . . . . . . . . . . . . . . . . . . 144
Ben-Gurion University of the Negev Genewave SAS
• Ludwig Bernard . . . . . . . . . . . . . . . . . . . 10
ADDEX Pharmaceuticals France SAS • Reinerio Gonzalez . . . . . . . . . . . . . . . . . 84 • Weldingh Karin . . . . . . . . . . . . . . . . . . . . . 152
Philogen Statens Serum Institut
• Maes Tamara . . . . . . . . . . . . . . . . . . . . . 86
C. S. O. Oryzon genomics • Riess Olaf . . . . . . . . . . . . . . . . . . . . . . . . 146 • Wiltfang Jens . . . . . . . . . . . . . . . . . . . . . . . . . 32
Eberhard-Karls-Universität Tübingen University of Erlangen-Nuremberg
• Maldonado Rafael . . . . . . . . . . . . . . 130
Universitat Pompeu Fabra (UPF) • Robertson Graeme . . . . . . . . . . . . . . . . 40 • Zucco Flavia . . . . . . . . . . . . . . . . . . . . . . . . . 96
Siena Biotech SpA Istituto di Neurobiologia e Medicina
• Malik Arif . . . . . . . . . . . . . . . . . . . . . . . . . 162 Molecolare
MicroDiscovery GmbH • Roca Josep . . . . . . . . . . . . . . . . . . . . . . . . . 20
Institut d’Investigacions
• Mandenius Carl-Fredrik . . . . . . . . . . 92 Biomèdiques August Pi i Sunyer
Linköping University
• Sans Miquel . . . . . . . . . . . . . . . . . . . . . . 80
• Mandler Markus . . . . . . . . . . . . . . . . . 108 Hospital Clínic/IDIBAPS
Affiris GmbH

191
European Commission

EUR 23457 — Synopses of projects funded through the SME call for “Life sciences,
genomics and biotechnology for health”

Luxembourg: Office for Official Publications of the European Communities

2008 — 191 pp. — 21.0 x 29.7 cm

ISBN 978-92-79-08803-2
DOI 10.2777/13756