My recent lecture at COSBI June 2011

1. From Nutrigenomics to nutritional systems biology of fatty acid sensing Michael MüllerNetherlands Nutrigenomics Centre & Nutrition, Metabolism and Genomics GroupDivision of Human Nutrition, Wageningen University

2. The Nutrigenomics challenge: What's healthy?

3. What do we know about the health network?

4. We eat different foods

5. We are different

6. How many human genes do we have?Not so many but….

7. Duality of biological information:Epigenetic & Genetic

8. Nutrigenomics Quantification of the nutritional genotype-phenotype Lifestyle Nutrition Environment

9. Phenotype plasticity Phenotypic plasticity is the ability of an organism to change its phenotype in response to changes in the environment (e.g. nutrition).

10. Objectives of our mechanistic nutrigenomics research Comprehensively understand the cellular specific responses to dietary lipids. Characterize the role of fatty acid sensing transcription factors such as PPARs. Identify target genes of dietary fatty acids& reconstruct related pathways. Demonstrate organ-specific difference of fatty acid-specific transcriptomes. Characterize the molecular basis for interaction between lipid and inflammatory signaling (related to “two hits” in initiation of organ dysfunction).

11. Metabolic organs & energy homeostasis

12. Lipids FFA Remnant LPL VLDL Chylomicrons Organ and systemic responses to dietary lipids

13. We build databases forevidence-basednutrition Evidence-basedNutrition Genes regulated by fatty acidsGenes regulated by high fat Genes also regulated by inflammation Query DIET GenomeEpigenomeTranscriptomeProteomeMetabolome “DIETome”database Query Nutrigenomics Potential BiomarkersOrgan-specific secreted proteins

14. How nutrients regulate our genes: via sensing molecular switches Improved organcapacity by PUFAs Am J ClinNutr. 2009; 90:415-24Am J ClinNutr. 2009;90:1656-64Mol CellBiology2009;29:6257-67 Am J ClinNutr. 2010;91:208-17BMC Genomics2009 Physiol. Genomics2009Circulation 2010Diabetes 2010 Cell Metabolism 2010Nature 2011 Am J Clin Nutr. 2007;86(5):1515-23 PLOS ONE 2008;3(2):e1681 BMC Genomics 2008; 9:231BMC Genomics 2008; 9:262J Biol Chem. 2008;283:22620-7Arterioscler Thromb Vasc Biol. 2009;29:969-74. Plos One 2009;4(8):e6796HEPATOLOGY 2010;51:511-522 J Clin Invest. 2004;114:94-103 J Biol Chem. 2006;28:934-44 Endocrinology. 2006;147:1508-16 Physiol Genomics. 2007;30:192-204Endocrinology. 2007;148:2753-63 BMC Genomics 2007; 8:267 Arterioscler Thromb Vasc Biol. 2007;27:2420-7

15. We have to improve existing “biased” pathways

16. Function of hepatic mouse & human PPARa Studies in mice have shown that PPARa is an important regulator of hepatic lipid metabolism and the acute phase response. However, little information is available on the role of PPARain human liver. Here we set out to compare the function of PPARain mouse and human hepatocytes via analysis of target gene regulation. Primary hepatocytes from 6 human and 6 mouse donors were treated with PPARa agonist Wy14643 and gene expression profiling was performed using Affymetrix GeneChips followed by a systems biology analysis. Rakhshandehroo M, Hooiveld G, Müller M, Kersten S (2009) Comparative Analysis of Gene Regulation by the Transcription Factor PPARa between Mouse and Human. PLoS ONE 4(8): e6796

17. Partial conservation of PPARa-regulated genes in hepatocytes between human and mouse between mouse and human PLoS ONE 4(8): e6796.

18. Species-specific regulation of two gene sets originating from gene set enrichment analysis (GSEA) Glycolysis-gluconeogenesis as a mouse-specific upregulated gene set Xenobiotic metabolism as a human-specific upregulated gene set PLoS ONE 4(8): e6796.

19. PPARa controls lipid metabolism & is the hepatic sensor for dietary fatty acids in mice & men

20. Conclusion I Species-specific differences in PPARa signaling (underlying mechanisms?) Common part in PPARa-dependent biology between human & mouse.

21. Collection of livers Oral gavage PPARα knock-out Removal of food 5 am 3 pm 9 am wild-type 78 Affymetrix Mouse Genome 430 2.0 microarrays QPCR Is there a significant role of PPARa in gene regulation by dietary fatty acids in vivo ? Sanderson, PlosONE 2008

22. Experimental design 4 or 5 mice per group, in total 78 arrays

23. Fatty acids regulate gene expression via PPARa Sanderson, PlosONE 2008

24. Gene regulation by dietary fat requires PPARa Sanderson, PlosONE 2008

25. Conclusions II Dietary fatty acids are able to ligand-activate Ppara in mouse liver. The effects of dietary fatty acids on hepatic gene expression are almost entirely mediated by Ppara.

26. Liver http://pathways.embl.de/

27. PPARβ/δ but not PPARα serves as plasma free fatty acid sensor in liver Sanderson Mol CellBiology2009 Dec;29(23):6257-67 PPARβ/δ but not PPARα serves as plasma free fatty acid sensor in liver

28. The intestine as a gatekeeper Food intake Satiety FGF21ANGPTL4 SFAGlucoseFructose LPL Adipokines: Adiponectin Leptin ResistinANGPTL4 TNFa etc LPL LPL GI hormones:Insulin GIP GLP1 PYY Ghrelin ANGPTL4 FGF15/19

29. The small intestine as primary organ is response to nutrients & food components

30. A major role for PPARa in intestinal fatty acid sensing Physiol Genomics. 2007 ;30(2):192-204

31. Intestinal fatty acid sensing by PPARa Physiol Genomics. 2007 ;30(2):192-204

32. Intestinal PPAR target genes are largely regulated by dietary PUFAS/MUFAs

33. Intestine

34. Comparison intestine / liver

35. Dose-dependent effects of dietary fat on development of obesity in relation to intestinal differential gene expression in C57BL/6J mice PLOS one 2011

36. Robust & concentration dependent effects in small intestineDifferentially regulated intestinal genes by high fat diet C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 PLOS one 2011

37. Heat map diagrams of fat-dose dependently regulated genes, categorized according to their biological function PLOS one 2011

38. Cellular localization and specific lipid metabolism-related function of fat-dose dependently regulated genes PLOS one 2011

39. The intestinal tube model for lipid absorption 40 cm 4 cm C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 Microbiota 10% FAT 45% FAT

40. The PPAR tube model C1 C2 C3 C4 C5 C6 C7 C8 C9 C10

41. Conclusions III Transcriptomics is powerful to comprehensively screen for PPAR target genes in various organs. Challenge is get organ & cell specific information on role of PPARs, target genes and (dietary) ligands. Future goal is to construct quantitative models for PPAR function related to organ health / metabolic plasticity.

42. Controllability of complex networks Naturally occurring networks, such as those involving gene regulation, are surprisingly hard to control. To fully control a gene regulatory network, roughly 80% of the nodes should be driver nodes. (in contrast to social networks) To a certain extent this is reassuring, because it means that such networks are fairly immune to hostile takeovers: a large fraction of the network's nodes must be directly controlled for the whole of it to change. By contrast, engineered networks are generally much easier to control, which may or may not be a good thing, depending on who is trying to control the network. This may explain also the big difference between “food & pharma”. Yang-Yu Liu, Jean-Jacques Slotine& Albert-LászlóBarabási Nature 473, 167–173

43. Difference between Food & Pharma Drugs A B C PPARg PPARb PPARa Receptor C3 C2 C1 Fatty acids F C6 C5 C4 Multiple targets

44. Chylomicron CE/TG Angptl4 LPL CE/TG FFA Chylomicron remnant

45. Angptl4- mice on HFD become very ill Lichtenstein et al. Cell Metabolism 2010

46. Massive enlargement of mesenteric lymph nodes in Angptl4-/- mice fed HFD Lichtenstein et al. Cell Metabolism 2010

47. No effect of medium chain or PUFA TGs Lichtenstein et al. Cell Metabolism 2010

48. Angptl4 protects against lipolysis and subsequent foam cell formation

49. Angptl4 protects against lipolysis and subsequent foam cell formation

50. Sander KerstenLinda SandersonNatasha Georgiadi Mark BouwensLydia Afman Guido Hooiveld Meike Bunger Philip de Groot Mark Boekschoten Nicole de Wit Mohammad Ohid Ullah Christian Trautwein Folkert Kuipers Ben van Ommen + many more