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METABOLOMICS
Toral Joshi
M.Phil (Bioinformatics)
Disha Life Sciences
INTRODUCTION
Metabolism:- It is the set of chemical reactions that happen in
living organisms to maintain life.
Catabolism :- Breaks down organic matter.
Anabolism :- Uses energy to construct components of cells
such as proteins and mucliec acid
Metabolite :- Metabolites are the intermediates and products of metabolism.
Usually metabolites refers to small molecules.
Metabolic Pathway :- Series of Chemical reaction occuring within the
cell.
Metabolic Network :- Collection of Metabolic pathways is called a
metabolic Network.
INTRODUCTION
• Metabolome :- Metabolome refers to the complete set of small-
molecule metabolites
• Metabolomics:-Investigation of metabolic regulation and fluxes in
individual cells or cell types.Metabolomics is the "systematic study of
the unique chemical fingerprints that specific cellular processes leave
behind" - specifically, the study of their small-molecule metabolite
profiles.
• Metabonomics:- the determination of systemic biochemical profiles
and regulation of function in whole organisms by analysing biofluids
and tissues
The History of Metabolomics
Linus Pauling hypothesised on the predictive capacity of
chromatographic profiling of bodily fluids for detection and
diagnosis of human disease.
In January 2007 the Human Metabolome Project, completed the first draft of the
human metabolome, consisting of 2,500 metabolites, 1,200 drugs and 3,500 food
components.
WHAT IS A METABOLITE?
• Serum Creatinine
• Late stage organ stress and tissue breakdown
• TMAO
• Early stage buffering response
• Creatine, methyl-histidine, taurine, glycine
• Tissue damage, muscle breakdown, remodelling
• Citrate, lactate, acetate, acetone
• Oxidative stress, apoptosis, anoxia, ischemia
• Histamine, chlorotyrosine, thromoxane, NO3
• Immune response, inflammation
THE PYRAMID OF LIFE
Metabolomics
1400
Chemicals
Proteomics
2500 Enzymes
Genomics
25,000 Genes
Metabolomics
Primary Molecules
Secondary Molecules
Chemical Fingerprint
METABONOMICS
Biochemical Profile
20
ANALYTICAL TECHNOLOGIES
GC
Separation
HPLC
Methods
Capillary
Metabolomics Electrophoresis
MS
Detection
Methods
NMR
ANALYTICAL TECHNOLOGIES: SEPARATION
Gas chromatography
It offers high resolution, but requires chemical derivatization for many
biomolecules and only volatile chemicals can be analysed without derivatization.
Gas-liquid chromatography - involves
a sample being vapourised and
injected onto the head of the
chromatographic column. The sample
is transported through the column by
the flow of inert, gaseous mobile
phase. The column itself contains a
liquid stationary phase which is
adsorbed onto the surface of an inert
solid.
ANALYTICAL TECHNOLOGIES: SEPARATION
Capillary electrophoresis
It has a higher theoretical separation efficiency than HPLC and is suitable for use
with a wider range of metabolite classes than is GC. As for all electrophoretic
techniques, it is most appropriate for charged analytes.
ANALYTICAL TECHNOLOGIES: DETECTION
Mass spectrometry
Used to identify and to quantify metabolites after separation by GC, HPLC, or
CE. In addition, mass spectral fingerprint libraries exist that allow
identification of a metabolite according to its fragmentation pattern.
Genome
Gene expression
(mRNA)
Metabolism
Proteins
POST-GENOMIC ERA OF BIOLOGY
Genome
Transcriptomics (Microarrays)
Metabolomics
Gene expression
Genomics
(mRNA)
Metabolism
Proteins
Proteomics
POST-GENOMIC ERA OF BIOLOGY
Genotype
Genome
Transcriptomics (Microarrays)
Metabolomics
Gene expression
Genomics
(mRNA)
Metabolism
Proteins
FunctionalM
olecular
Proteomics Phenotype
POST-GENOMIC ERA OF BIOLOGY
Genotype
Genome
Transcriptomics (Microarrays)
Metabolomics
Gene expression
Genomics
(mRNA)
Metabolism
Environmental Proteins
stressors FunctionalM
olecular
Proteomics Phenotype
"METABOLOMICS: HOW AND WHAT FOR ? "
6 steps:
1- sampling (storage)
2- metabolite extraction (standardisation, reproducibility)
3- biochemical analysis (GC-MS, LC-MS, NMR)
4- data pre-processing (base line correction….)
5- data visualisation and mining (PCA, data bases)
6- integration of data (metabolic pathways, genome..)
Identify metabolites and pathways that influence drug response
Nature Reviews Genetics 5; 669-676 (2004);
To monitor in parallel hundreds or even
thousands of metabolites, high-
throughput techniques are required that
enable screening for relative changes
rather than absolute concentrations of
compounds
METABOLOME ANALYSIS
Glutamate
Citrate
Alanine
Absent
Normal
Below Normal
Above Norrmal
Patient 9
Patient 8
Patient 7
Patient 6
Patient 5
Patient 4
Patient 3
Patient 2
Patient 1
Patient 11
Patient 15
Patient 14
Patient 13
Patient 12
Patient 10
Acetic Acid
Betaine
Carnitine
Citric Acid
Creatinine
Dimethylglycine
Dimethylamine
Hippulric Acid
Lactic Acid
METABOLIC MICROARRAYS
Succinic Acid
Trimethylamine
Trimn-N-Oxide
Urea
Lactose
Suberic Acid
Sebacic Acid
Homovanillic Acid
Threonine
Alanine
Glycine
Glucose
The “Omics” of Nutrition
N
u DNA
t Nutrigenetics
r
i Nutritional
g
Epigenetics
e
n RNA
o
Nutritional
Bioactive Food m
Transcriptomics Phenotype
Component i
c
s
Protein
Proteomics
Metabolomics
Metabolite
Nutritional Metabolomics
N
u DNA
t Nutrigenetics
r
i Nutritional
g
Epigenetics Metabolomics
e
n RNA
o
Nutritional
Bioactive Food m Metabolite
Transcriptomics
Component i
c
s
Protein
Proteomics
Phenotype
Can Metabolomics Shed Light
on these 3 Nutrition Related Biomarkers
Inactive Metabolite
Absorbed
Dose Biologically
Effective
Dose
Early
Detection
Genetic Biomarkers
Risk
METABOLOMICS: APPLICATIONS
• Identification of metabolic biomarkers that change
as an indicator of the presence of disease or in
response to drug-based intervention.
• Bacterial characterizations
• Metabolic engineering
Metabolomics Applications
Diagnosis
Functional genomics
Systems biology
msalign from Matlab Bioinformatics Toolbox - for MS data (example using msalign)
pairseqsim - (Bioconductor - Witold Wolski) - for mass spectra [DOI]
Randolph Yasui code - [DOI] download Matlab code and WMTSA wavelet toolbox
RTAlign algorithm of MSFACTs (noble.org) - GC-MS and LC-MS data
Genedata Expressionist (genedata.com) - for LC-MS and infusion MS data.
MS Align (David Grant - Uconn.edu) - for high resolution mass spectral data [DOI]
LCMSWARP (PNNL) - for proteomics and metabolomics LC-MS data (http://ncrr.pnl.gov/software)
ChromAlign (Thermo) - included in Sieve and Biosieve package for LC-MS and LC-MS-MS data
PETAL - Peptide Element Alignment for LC-MS data (http://peiwang.fhcrc.org/research-project.html)
MarkerView (ABI/Sciex) - for LC-MS and MALDI data peak picking and alignment and statistics
SOFTWARES
• MathDAMP (Keio University) - for GC-MS, LC-MS, CE-MS data with Mathematica source code [DOI]
• NameLess - for MALDI MS and FT-MS data with JAVA source code [DOI]
• CPM MatLab toolbox (J Listgarten) - for LC-MS, proteomics, metabolomics and time series data + source
code.
• GASP (genedrift.org) - for GC-MS alignment
• AnalyzerPro (SpectralWorks) - for alignment of GC-MS data
• meta-b (Vladimir Likic) - for alignment of LC-MS data with python source code (go SVN)
• spectconnect (MIT) - for alignment of GC-MS data using AMDIS for deconvolution
• ChenomX Profiler (Chenomx) - for binning and alignment of NMR signals (+ DB search)
• KnowItAll Metabolomics Editions (BioRad) - with IntelliBucket bucketing and binning of NMR data (+ DB
search)
• MS-Xelerator (MSMETRIX) - Advanced Algorithms for LC/MS Data Processing (Marco Ruijken)
• OBI-Warp (U Texas) - Ordered Bijective Interpolated Warping for LC-MS data [PDF]
THANK YOU FOR YOUR PATIENCE