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Lydia A Afman
Michael Muller
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Keywords:
Nutrigenomics
Fatty acids
Transcriptomics
Gene expression
Peripheral blood mononuclear cells (PBMCs)
a b s t r a c t
Nutrigenomics employs high-throughput genomics technologies to unravel how nutrients modulate gene
and protein expression and ultimately inuence cellular and organism metabolism. The most oftenapplied genomics technique so far is transcriptomics, which allows quantifying genome-wide changes
in gene expression of thousands of genes at the same time in one sample. The performance of gene
expression quantication requires sufcient high-quality homogenous cellular material, therefore
research in healthy volunteers is restricted to biopsies from easy accessible tissues such as subcutaneous
adipose tissue, skeletal muscle and intestinal biopsies or even more easily accessible cells such as peripheral blood mononuclear cells from blood. There is now signicant evidence that fatty acids, in particular
unsaturated fatty acids, exert many of their effects through modulation of gene transcription by regulating the activity of numerous transcription factors, including nuclear receptors such as peroxisome proliferator activated receptors, liver X receptor and sterol regulatory binding proteins. This review evaluates
the human nutrigenomics studies performed on dietary fat since the initiation of nutrigenomics research
around 10 years ago. Although the number of studies is still limited, all studies clearly suggest that
changes in dietary fatty acids intake and composition can have a signicant impact on cellular adaptive
response capacity by gene transcription changes in humans. This adds important knowledge to our
understanding of the strong effects that various fatty acids can have on numerous metabolic and inammatory pathways, signaling routes and homeostatic control in the cell and ultimately on whole body
health. It is important to use and integrate nutrigenomics in all future nutrition studies to build up the
necessary framework for evidence-based nutrition in near future.
2011 Elsevier Ltd. All rights reserved.
Contents
1.
2.
3.
4.
5.
6.
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Challenges in human nutrigenomics studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Transcriptional gene regulation by (dietary) fatty acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Application of transcriptomics in human intervention studies with dietary fatty acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.
Postprandial intervention studies with dietary fatty acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2.
Longer-term intervention studies with dietary fatty acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.3.
Overlap between long term and postprandial effects of n 3 PUFA on PBMC transcriptome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Future challenges in nutrigenomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Conclusions and perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1. Introduction
Human nutrition research is still largely focused on issues related
to nutrient deciencies and impairment of health and disease due to
Corresponding author. Address: Nutrition, Metabolism and Genomics Group,
Division of Human Nutrition, Wageningen University, Bomenweg 2, 6703 HD
Wageningen, The Netherlands. Tel.: +31 (0)317 485789; fax: +31 (0)317 483342.
E-mail addresses: lydia.afman@wur.nl (L.A. Afman), michael.muller@wur.nl
(M. Mller).
0163-7827/$ - see front matter 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.plipres.2011.11.005
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Three different highly conserved PPAR isotypes have been identied: PPARa (NR1C1), PPARb/r (NR1C2) and PPARc (NR1C3).
They act as nutrient sensors for fatty acids, but bind also numerous
fatty acid derivatives and compounds showing structural resemblance to fatty acids and inuence the expression of specic genes
[23,24] The PPARa isotype has been shown to govern expression of
numerous genes involved in fatty acid oxidation, ketogenesis,
gluconeogenesis, cholesterol catabolism and lipoprotein metabolism as mainly studied using mouse models. More recent evidence
indicates that hepatic PPARa is not largely activated by plasma free
fatty acids as high during fasting, whereas it can be activated by
dietary fatty acids and fatty acids generated via de novo lipogenesis [25]. Recently, it was also shown that the effects of dietary
unsaturated fatty acids on hepatic gene expression are almost
exclusively mediated by PPARa and mimic the effect of synthetic
PPARa agonists [26]. Much less is known about the relevance of
these mainly mouse-based ndings for human physiology. A recent
analysis provided new insights into the mechanisms and impact of
transcriptional regulation by PPARa in human liver by performing
chromatin immunoprecipitation (ChIP)-chip in combination with
transcriptional proling on HepG2 human hepatoma cells treated
with the specic PPARa agonist GW7647. Several genes known
to be regulated by PPARa showed GW7647-induced PPARa binding to their promoter. Interestingly also certain SREBP-target genes
exhibited PPARa binding, suggesting cross-talk between PPARa
and SREBP signaling [27]. Another study compared the function
of PPARa in mouse and human hepatocytes via analysis of target
gene regulation. Minor overlap was observed between the
PPARa-regulated genes from mouse and human by a gene-by-gene
comparison, although more substantial overlap was observed at
the pathway level. This study clearly suggest that PPARa activation
has a major impact on gene regulation in human hepatocytes and
that the role of PPARa as master regulator of hepatic lipid metabolism is generally well-conserved between mouse and human [28].
More in depth studies are required to elucidate the specic role of
nutrient-sensing transcription factors in mediating the effects of
dietary fatty acids in other human cells including small intestinal
epithelial cells, macrophages or adipocytes.
LXRs, closely PPAR-related members of the nuclear receptor family, are important regulators of cholesterol, fatty acid, glucose
homeostasis and play an essential role at the interface between
metabolism and inammation [29]. Their endogenous activators
are oxysterols and other derivatives of cholesterol metabolism
(22(R)-hydroxycholesterol, 24(S)-hydroxycholesterol, 24(S), 25epoxycholesterol). LXRa is highly expressed in the liver but is also
found in kidney, intestine, adipose tissue, and macrophages. LXRb
is expressed ubiquitously[30]. Nutritional or pharmacological modulation of the activity of these ligand-activated transcription factors
have been shown to inuence the development of metabolic disorders such as hyperlipidemia and atherosclerosis [30]. Mice without
functional LXRa e.g. are healthy when fed with a low-cholesterol
diet but when fed a high-cholesterol diet these LXRa knockout mice
develop enlarged fatty livers, less functional hepatocytes, high cholesterol levels in liver, and impaired liver function [31]. LXR is a major regulator of fatty acid synthesis and the expression of other
lipogenic genes through direct interaction with their promoters as
well as inducing sterol regulatory element binding protein-1c
(SREBP-1c) gene transcription. Activation of LXR by oxysterols (related to high dietary cholesterol) or other agonists elevates nuclear
content of SREBP-1 and increases expression of the enzymes involved in de novo lipogenesis [32].
SREBPs are transcription factors of the helix-loop-helix family
and important regulators of cholesterol and fatty acid metabolism.
SREBPs are encoded by two genes, SREBP-1 and SREBP-2 resulting
in 3 proteins SREBP-1a, SREBP-1c and SREBP-2 (for more information in particular on the complex mode of activation of these
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what the systemic implications are. In the study of Gorjao [46] besides pooled macroarrays, stimulation assays were performed on
the lymphocytes showing an increased production of IL-10, IFNgamma and TNFa and a decreased production of IL2. However, most
other studies observed a decrease in production of cytokines after
sh oil supplementation, which is more in line with the observed effect on transcriptional regulation [4851]. In addition, Meydani observed a higher reduction in cytokine response upon stimulation in
older compared to young women [50] after n 3 PUFA supplementation, underlining the potential age-dependency of responses.
Overall, long-term sh oil supplementation reduces expression
of leukocyte inammatory genes and decreases cytokine production upon leukocyte stimulation. The relevance for health outcome
of this reduced immune response has been postulated to be benecial in progression and treatment of inammatory diseases such
as rheumatoid arthritis [52,53].
Besides effects of consumption of fatty acids on transcriptional
activity in blood cells dietary fatty acid effects have also been determined on whole genome gene expression of adipose tissue. Within a
completely controlled randomized dietary intervention trial of
8 weeks the effects of different types of fatty acids was studied on
adipose tissue transcriptome. Participants either consumed a butter-derived saturated fatty acids (SFA)-rich diet or a rened olive
oilderived monounsaturated fatty acids (MUFA)-rich diet and adipose tissue biopsies were taken before and after intervention. Whole
genome microarray analyses of these samples revealed that the SFAdiet resulted in the most distinct changes in gene expression. Where
SFA-diet effected expression of around 1500 genes, MUFA consumption effected expression of 600 genes. The most remarkable observation was the increased transcription of genes involved in immune
function after consumption of the SFA-rich diet, which was
distinctly different from the effects on the MUFA diet, after which
a much smaller and more or less opposite effect was observed on
expression of immune-related genes. Interestingly, the SFA-induced
changes in gene expression were similar to differences observed in
gene expression in adipose tissue of obese versus lean subject
[54,55] and opposite to the changes observed after weight loss in obese subjects [56]. Keeping in mind that no weight changes were
present in the participants, consumption of the more healthy type
of dietary fat (unsaturated) may be of great relevance for healthy
functional adipose tissue in obesity. Although no changes in macrophage inltration were observed, prolonged consumption of a SFArich diet may result in inltration of macrophages as frequently perceived in obesity [57,58]. Some studies have shown that SFA may
activate immune related genes by binding and activation of Toll-like
receptor 4 [59,60]. In addition, saturated FA are poor ligands for
PPARy [61], and as PPARy activation result in a reduced inammation, a decreased activation of PPARy by SFA might lead to increased
inammation. PPARy gene expression in adipose tissue and expression of some target genes was reduced upon SFA consumption.
PPARc also plays an important role in alternative M2 macrophage
activation that is of key importance for adipose tissue remodeling,
inammatory status and health [62] as shown in numerous mouse
studies [63] and increasingly also in human studies [62]. Interestingly, in a recently performed mouse study we found that adipose
tissue function is essential for the prevention of non-alcoholic fatty
liver disease [12]. This again highlights the importance of the comprehensive understanding of nutrition-relevant inter-organ dependency and crosstalk as essential basis for a healthy body function.
Future nutrigenomics research should be leading in this effort.
4.3. Overlap between long term and postprandial effects of n
on PBMC transcriptome
3 PUFA
The above described studies show that fatty acids can not only
affect gene transcription directly after consumption but will also
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Fig. 1. Average gene expression changes of genes signicantly changed upon long term and acute consumption of omega3-FA. Each row represents a single gene; the rst
column represents the long-term study, the second column represents the acute study. The expression scale is log2-based and ranges from 6 0.3 (green) to P0.3 (red).
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of responder-genes which is still complicated in the small populations studied, so far. This variance in response also emphasizes the
need for within person measurements and the relevance of crossover interventions or large intervention groups when using parallel
designs. The underlying reason for this response variance can be several and may vary from genetic and epigenetic variation to nutritional and life style factors. For example, imprinting during
pregnancy or during early years in life may affect phenotypic
responses at older age with the consequence of increased risk to develop nutrition-related diseases [71]. Nutritional habits may also be
a reason why persons will or will not respond to a change in a diet.
Nutrigenomics can be used to asses this. For instance, people that
regularly consume sh rich in n 3 PUFA will likely exhibit a less
pronounced transcriptional response upon a sh oil challenge than
subjects that do not eat sh at all. This also may be the scientic basis
for the nutritional advice to enjoy a healthy diet consisting of a varied food pattern as this will keep the homeostatic balance of our
organs most exible.
Many diseases are a result of disturbance of homeostasis or
homeostatic imbalance. As a hallmark of ageing every organism
will lose its efciency in its sensing and regulatory systems.
Diseases with a strong link to nutrition result from a homeostatic
imbalance such as obesity, metabolic syndrome or diabetes type
2. We increasingly understand the complex regulation of homeostatic control mechanisms on cellular, organ and system level that
should prevent this imbalance from occurring. However, in some
people, these mechanisms do not work efciently enough because
of signicant genetic susceptibility [1] and or epigenetic mechanism [71]. These people are much more vulnerable to develop a
disease in particular if the homeostatic control mechanisms are
chronically challenged by surplus of calories, non-ideal dietary patterns and lifestyles [72]. Because we are still not able to detect the
early warning signals of such homeostatic imbalance efciently
most often medical intervention is necessary at a very late stage
of the disease development that is often unable however to restore
the homeostatic balance to regain normal health with irreversible
damage of organs as a consequence.
To change this inefcient concept in treatment of lifestyle
diseases we have to use interventions that allow the quantication
of the homeostatic balance or resilience by assessing it after challenging or perturbing a homeostatic situation. A well known example for such as challenge is the oral glucose tolerance test (OGTT). A
standard 2 h OGTT is sufcient to diagnose or exclude forms of
diabetes mellitus at the various stages of development. Recently,
plasma metabolic proling combined with a glucose challenge
was used to differentiate between healthy individuals and individuals with an impaired glucose tolerance [73]. Application of metabolic perturbation with comprehensive nutrigenomics-based
metabolic proling may improve the diagnostic sensitivity to help
discriminating between healthy, less-healthy and unhealthy people.
Furthermore, it may allow to predict differences in the responses between treatments [74]. In addition, combination of dietary interventions with metabolic challenges magnies the difcult measurable
and relatively mild effects of nutritional alterations by testing the
cellular adaptive response capacity (for a more in depth discussion
[75,76]). This rather new concept of applying various challenges
on homeostatic control mechanisms in nutritional interventions is
still in its infancies and it is therefore necessary to carefully study
its value and limitations. One may expect important sex-dependent
differences in applying various homeostatic challenge-test as demonstrated recently for OGTT [77]. But ultimately it will be the most
promising strategy to combine nutrigenomics-based comprehensive phenotyping with systems perturbation interventions to allow
the precise assessment of individual health and nutritional needs.
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