Effect of Synthetic Dietary Triglycerides: A Novel Research Paradigm for Nutrigenomics

Background The effect of dietary fats on human health and disease are likely mediated by changes in gene expression. Several transcription factors have been shown to respond to fatty acids, including SREBP-1c, NF-κB, RXRs, LXRs, FXR, HNF4α, and PPARs. However, it is unclear to what extent these transcription factors play a role in gene regulation by dietary fatty acids in vivo. Methodology/Principal Findings Here, we take advantage of a unique experimental design using synthetic triglycerides composed of one single fatty acid in combination with gene expression profiling to examine the effects of various individual dietary fatty acids on hepatic gene expression in mice. We observed that the number of significantly changed genes and the fold-induction of genes increased with increasing fatty acid chain length and degree of unsaturation. Importantly, almost every single gene regulated by dietary unsaturated fatty acids remained unaltered in mice lacking PPARα. In addition, the majority of genes regulated by unsaturated fatty acids, especially docosahexaenoic acid, were also regulated by the specific PPARα agonist WY14643. Excellent agreement was found between the effects of unsaturated fatty acids on mouse liver versus cultured rat hepatoma cells. Interestingly, using Nuclear Receptor PamChip® Arrays, fatty acid- and WY14643-induced interactions between PPARα and coregulators were found to be highly similar, although several PPARα-coactivator interactions specific for WY14643 were identified. Conclusions/Significance We conclude that the effects of dietary unsaturated fatty acids on hepatic gene expression are almost entirely mediated by PPARα and mimic those of synthetic PPARα agonists in terms of regulation of target genes and molecular mechanism. Use of synthetic dietary triglycerides may provide a novel paradigm for nutrigenomics research.

[1]  Y. Benjamini,et al.  More powerful procedures for multiple significance testing. , 1990, Statistics in medicine.

[2]  J. Gustafsson,et al.  Fatty acids activate a chimera of the clofibric acid-activated receptor and the glucocorticoid receptor. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[3]  I. Issemann,et al.  The peroxisome proliferator-activated receptor:retinoid X receptor heterodimer is activated by fatty acids and fibrate hypolipidaemic drugs. , 1993, Journal of molecular endocrinology.

[4]  A. Mahfoudi,et al.  Fatty acids and retinoids control lipid metabolism through activation of peroxisome proliferator-activated receptor-retinoid X receptor heterodimers. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[5]  R. Mensink,et al.  Effects of fats and fatty acids on blood lipids in humans: an overview. , 1994, The American journal of clinical nutrition.

[6]  R. Mensink,et al.  Dietary trans fatty acids and their impact on plasma lipoproteins. , 1995, The Canadian journal of cardiology.

[7]  H. Gronemeyer,et al.  Transcription factors 3: nuclear receptors. , 1995, Protein profile.

[8]  Jasmine Chen,et al.  Hypolipidemic drugs, polyunsaturated fatty acids, and eicosanoids are ligands for peroxisome proliferator-activated receptors alpha and delta. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[9]  J. Lehmann,et al.  Fatty acids and eicosanoids regulate gene expression through direct interactions with peroxisome proliferator-activated receptors alpha and gamma. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[10]  J. Peters,et al.  Polyunsaturated Fatty Acid Suppression of Hepatic Fatty Acid Synthase and S14 Gene Expression Does Not Require Peroxisome Proliferator-activated Receptor α* , 1997, The Journal of Biological Chemistry.

[11]  Peter J. Brown,et al.  Fatty acids and eicosanoids regulate gene expression through direct interactions with peroxisome proliferator-activated receptors α and γ , 1997 .

[12]  K. Stuhlmeier,et al.  Arachidonic Acid Influences Proinflammatory Gene Induction by Stabilizing the Inhibitor-κBα/Nuclear Factor-κB (NF-κB) Complex, thus Suppressing the Nuclear Translocation of NF-κB* , 1997, The Journal of Biological Chemistry.

[13]  W. Wahli,et al.  Fatty acids, eicosanoids, and hypolipidemic agents identified as ligands of peroxisome proliferator-activated receptors by coactivator-dependent receptor ligand assay. , 1997, Molecular endocrinology.

[14]  Barry M. Forman,et al.  Hypolipidemic drugs, polyunsaturated fatty acids, and eicosanoids are ligands for peroxisome proliferator-activated receptors α and δ , 1997 .

[15]  J. Bar-Tana,et al.  Fatty acyl-CoA thioesters are ligands of hepatic nuclear factor-4α , 1998, Nature.

[16]  P. Mayes,et al.  Comparison of short- and long-term effects of different dietary fats on the hepatic uptake and metabolism of chylomicron remnants in rats , 1998, British Journal of Nutrition.

[17]  T. Osborne,et al.  Polyunsaturated Fatty Acids Decrease Expression of Promoters with Sterol Regulatory Elements by Decreasing Levels of Mature Sterol Regulatory Element-binding Protein* , 1998, The Journal of Biological Chemistry.

[18]  J. Lehmann,et al.  Molecular recognition of fatty acids by peroxisome proliferator-activated receptors. , 2000, Molecular cell.

[19]  Manabu T. Nakamura,et al.  Sterol Regulatory Element Binding Protein-1 Expression Is Suppressed by Dietary Polyunsaturated Fatty Acids , 1999, The Journal of Biological Chemistry.

[20]  H. Shimano,et al.  A Crucial Role of Sterol Regulatory Element-binding Protein-1 in the Regulation of Lipogenic Gene Expression by Polyunsaturated Fatty Acids* , 1999, The Journal of Biological Chemistry.

[21]  P. Chambon,et al.  Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains. , 2000, Molecular cell.

[22]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[23]  T. Perlmann,et al.  Docosahexaenoic acid, a ligand for the retinoid X receptor in mouse brain. , 2000, Science.

[24]  J. Goldstein,et al.  Unsaturated Fatty Acids Down-regulate SREBP Isoforms 1a and 1c by Two Mechanisms in HEK-293 Cells* , 2001, The Journal of Biological Chemistry.

[25]  B. Shan,et al.  Unsaturated fatty acids inhibit transcription of the sterol regulatory element-binding protein-1c (SREBP-1c) gene by antagonizing ligand-dependent activation of the LXR , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[26]  R. Evans,et al.  Nuclear receptors and lipid physiology: opening the X-files. , 2001, Science.

[27]  Guangping Chen,et al.  Photoaffinity labeling of human retinoid X receptor beta (RXRbeta) with 9-cis-retinoic acid: identification of phytanic acid, docosahexaenoic acid, and lithocholic acid as ligands for RXRbeta. , 2002, Biochemistry.

[28]  Timothy M Willson,et al.  Hepatocyte nuclear factor 4 is a transcription factor that constitutively binds fatty acids. , 2002, Structure.

[29]  S. Shoelson,et al.  Crystal Structure of the HNF4α Ligand Binding Domain in Complex with Endogenous Fatty Acid Ligand* , 2002, The Journal of Biological Chemistry.

[30]  D. Moras,et al.  Molecular recognition of agonist ligands by RXRs. , 2002, Molecular endocrinology.

[31]  H. Sone,et al.  Polyunsaturated Fatty Acids Suppress Sterol Regulatory Element-binding Protein 1c Promoter Activity by Inhibition of Liver X Receptor (LXR) Binding to LXR Response Elements* , 2002, The Journal of Biological Chemistry.

[32]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[33]  Naisyin Wang,et al.  Chemopreventive n-3 fatty acids activate RXRalpha in colonocytes. , 2003, Carcinogenesis.

[34]  H. DeLuca,et al.  Isolation and characterization of unsaturated fatty acids as natural ligands for the retinoid-X receptor. , 2003, Archives of biochemistry and biophysics.

[35]  T. Pineau,et al.  RXR activators molecular signalling: involvement of a PPARα‐dependent pathway in the liver and kidney, evidence for an alternative pathway in the heart , 2003, British journal of pharmacology.

[36]  John D. Storey.  The positive false discovery rate: a Bayesian interpretation and the q-value , 2003 .

[37]  Bruce A. Johnson,et al.  Distinct properties and advantages of a novel peroxisome proliferator-activated protein [gamma] selective modulator. , 2003, Molecular endocrinology.

[38]  Naisyin Wang,et al.  Chemopreventive n-3 fatty acids activate RXRα in colonocytes , 2003 .

[39]  B. Seed,et al.  A PCR primer bank for quantitative gene expression analysis. , 2003, Nucleic acids research.

[40]  S. Wright,et al.  Polyunsaturated fatty acids are FXR ligands and differentially regulate expression of FXR targets. , 2004, DNA and cell biology.

[41]  Robert Gentleman,et al.  Expression with the Bioconductor Project , 2004 .

[42]  Rafael A. Irizarry,et al.  A Model-Based Background Adjustment for Oligonucleotide Expression Arrays , 2004 .

[43]  T. Willson,et al.  Polyunsaturated fatty acids including docosahexaenoic and arachidonic acid bind to the retinoid X receptor alpha ligand-binding domain. , 2004, Molecular & cellular proteomics : MCP.

[44]  C. Ruxton,et al.  The health benefits of omega-3 polyunsaturated fatty acids: a review of the evidence. , 2004, Journal of human nutrition and dietetics : the official journal of the British Dietetic Association.

[45]  B. Teusink,et al.  Intestinal lipid absorption is not affected in CD36 deficient mice , 2002, Molecular and Cellular Biochemistry.

[46]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[47]  Cheng Cheng,et al.  Improving false discovery rate estimation , 2004, Bioinform..

[48]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[49]  Robert Gentleman,et al.  Differential expression with the Bioconductor Project , 2005 .

[50]  G. Luc,et al.  Regulation of Human ApoA-I by Gemfibrozil and Fenofibrate Through Selective Peroxisome Proliferator–Activated Receptor &agr; Modulation , 2005, Arteriosclerosis, thrombosis, and vascular biology.

[51]  H. Sampath,et al.  Polyunsaturated fatty acid regulation of genes of lipid metabolism. , 2005, Annual review of nutrition.

[52]  Paul Pavlidis,et al.  ErmineJ: Tool for functional analysis of gene expression data sets , 2005, BMC Bioinformatics.

[53]  S. Kersten,et al.  Peroxisome proliferator-activated receptor alpha mediates the effects of high-fat diet on hepatic gene expression. , 2006, Endocrinology.

[54]  Carol L Cheatham,et al.  N-3 fatty acids and cognitive and visual acuity development: methodologic and conceptual considerations. , 2006, The American journal of clinical nutrition.

[55]  John P. Vanden Heuvel,et al.  Differential Activation of Nuclear Receptors by Perfluorinated Fatty Acid Analogs and Natural Fatty Acids: A Comparison of Human, Mouse, and Rat Peroxisome Proliferator-Activated Receptor-α, -β, and -γ, Liver X Receptor-β, and Retinoid X Receptor-α , 2006 .

[56]  Nuclear Receptors and the Control of Gene Expression by Fatty Acids , 2006 .

[57]  J. V. Vanden Heuvel,et al.  Differential activation of nuclear receptors by perfluorinated fatty acid analogs and natural fatty acids: a comparison of human, mouse, and rat peroxisome proliferator-activated receptor-alpha, -beta, and -gamma, liver X receptor-beta, and retinoid X receptor-alpha. , 2006, Toxicological sciences : an official journal of the Society of Toxicology.

[58]  W. Harris,et al.  Why do omega-3 fatty acids lower serum triglycerides? , 2006, Current opinion in lipidology.

[59]  D. Mozaffarian,et al.  Trans fatty acids and cardiovascular disease. , 2006, The New England journal of medicine.

[60]  S. Kersten,et al.  PPARα and dyslipidemia , 2007 .

[61]  C. Ruxton.  Commentary on Ruxton, C. H. S., Reed, S. C., Simpson, M. J. A. & Millington, K. J. (2004) The health benefits of omega-3 polyunsaturated fatty acids: a review of the evidence. Journal of Human Nutrition and Dietetics; 17, 449-459. , 2007, Journal of human nutrition and dietetics : the official journal of the British Dietetic Association.

[62]  Pascal G. P. Martin,et al.  Novel aspects of PPARα‐mediated regulation of lipid and xenobiotic metabolism revealed through a nutrigenomic study , 2007, Hepatology.

[63]  Aurélien Grosdidier,et al.  The Endocrine Disruptor Monoethyl-hexyl-phthalate Is a Selective Peroxisome Proliferator-activated Receptor γ Modulator That Promotes Adipogenesis* , 2007, Journal of Biological Chemistry.

[64]  S. Kersten,et al.  PPARalpha and dyslipidemia. , 2007, Biochimica et biophysica acta.

[65]  F. Gregoire,et al.  Selective Modulators of PPAR-γ Activity: Molecular Aspects Related to Obesity and Side-Effects , 2007, PPAR research.

[66]  K. V. van Dijk,et al.  Angptl4 Upregulates Cholesterol Synthesis in Liver via Inhibition of LPL- and HL-Dependent Hepatic Cholesterol Uptake , 2007, Arteriosclerosis, thrombosis, and vascular biology.

[67]  S. Kersten,et al.  PPARα‐dependent induction of the energy homeostasis‐regulating nuclear receptor NR1i3 (CAR) in rat hepatocytes: Potential role in starvation adaptation , 2007, FEBS letters.

[68]  A. Leaf.  Omega-3 fatty acids and prevention of arrhythmias , 2007, Current opinion in lipidology.

[69]  M. S. Ozers,et al.  Analysis of ligand-dependent recruitment of coactivator peptides to RXRβ in a time-resolved fluorescence resonance energy transfer assay , 2007, Molecular and Cellular Endocrinology.

[70]  Marjoke Heneweer,et al.  Estrogenic effects in the immature rat uterus after dietary exposure to ethinylestradiol and zearalenone using a systems biology approach. , 2007, Toxicological sciences : an official journal of the Society of Toxicology.