1. 9/11/20151 http://creativecommons.org/licens es/by-sa/2.0/

2. Nutrigenomics Prof:Rui Alves ralves@cmb.udl.es 973702406 Dept Ciencies Mediques Basiques, 1st Floor, Room 1.08 Website of the Course:http://web.udl.es/usuaris/pg193845/Courses/Bioinformatics_2007/ Course: http://10.100.14.36/Student_Server/

3. 9/11/20153 What is Nutrigenomics? Nutrigenomics is the science that examines the response of individuals to food compounds using post-genomic and related technologies. The long-term aim of nutrigenomics is to understand how the whole body responds to real foods using an integrated approach. Studies using this approach can examine people (i.e. populations, sub-populations - based on genes or disease - and individuals), food, life- stage and life-style without preconceived ideas.

4. 9/11/20154 Problem 1: Nutrition – tasty + complex

5. 9/11/20155 Genes – Lifestyle – Calories

6. 100 50 0 % Energy Low-fat meat Chicken Eggs Fish Fruit Vegetables (carrots) Nuts Honey 100 50 0 % Energy Fruit Vegetables Beans Meat Chicken Fish Grain Milk/-products Isolated Carbohydrates Isolated Fat/Oil Alcohol 1.200.000 Generations between feast en famine Paleolithic era 2-3 Generations in energy abundance Modern Times The same genes – The changed diet

7. 9/11/20157 Molecular nutrition

8. 9/11/20158 Optimal Nutrition Lifestyle Individual genotype Functional phenotype Problem 2: Our “gene passports” and nutrition AA AB BB Improvement Maintenance of Health “Eat right for your genotype??”

9. 9/11/20159 Personalized diets?

10. 9/11/201510 Nutrigenomics Target Genes Mechanisms Pathways Signatures Profiles Biomarkers Foods Nutrition Molecular Nutrition & Genomics Nutritional Systems Biology Identification of dietary signals Identification of dietary sensors Identification of target genes Reconstruction of signaling pathways Measurement of stress signatures Identification of early biomarkers Small research groups Small budgets Large research consortia Big money Complexity

11. 9/11/201511 Energy homeostasis Nutrient absorption Cell proliferation Nutritional factors Transcription factors Gene transcription Nutrients acts as dietary signals

12. 9/11/201512 “Molecular Nutrition & Genomics” The strategy of Nutrigenomics 80-100000 proteins 20-25000 genes 100000 transcripts 50000 (?) metabolites

13. 9/11/201513 Transcription-factor pathways mediating nutrient-gene interaction

14. 9/11/201514 A key instrument in Nutrigenomics research: The GeneChip® System

15. 9/11/201515 Predisposition Genotype Prognostic markers Diagnostic markers Changes in pathway dynamics to maintain homeostasis Surrogate Biomarkers Late biomarkers of disease Early biomarkers of disease Onset of disease Nutritional Systems Biology

16. 9/11/201516 Intestine Liver, Muscle Blood Adipose tissue Nutrients Signaling Cells Animal Humans Organs Functions Proteins Genes Healthy Food Lipids Fatty acids Sugars Calcium Lipids Fatty acids Sugars Calcium Transporters Transcription factors Transporters Transcription factors Enterocytes Hepatocytes Adipocytes Lymphocytes Enterocytes Hepatocytes Adipocytes Lymphocytes Target genes of nutrients Mouse Models Intervention Studies Proteins Post- translational Regulation Proteins Post- translational Regulation Metabolic Implications Metabolites Metabolic Implications Metabolites Signaling Cells Animal Humans Organs Functions Proteins Genes Nutrient-related cellular sensing + Metabolic stress Diet-related organ sensing, Sensitivity genes + Molecular Phenotype Gene expression Signatures Gene regulation by nutrients Prevention of Metabolic Syndrome Dietary Programming Metabolomics Systems Biology Molecular Biology Tools Early Molecular Biomarkers Transcriptome Proteome

17. 9/11/201517 LIPGEN Lipids & genes (EU, 14M€) DIOGENES obesity (EU, 12M€) Innovative Cluster Nutrigenomics Chronic metabolic stress (Dutch, 21M€) EARNEST early life nutrition (EU, 14M€) Linking to other EU programs NuGO

18. 9/11/201518 Two Strategies (1)The traditional hypothesis-driven approach: specific genes and proteins, the expression of which is influenced by nutrients, are identified using genomics tools — such as transcriptomics, proteomics and metabolomics — which subsequently allows the regulatory pathways through which diet influences homeostasis to be identified. Transgenic mouse models and cellular models are essential tools. provide us with detailed molecular data on the interaction between nutrition and the genome. (2) The SYSTEMS BIOLOGY approach: gene, protein and metabolite signatures that are associated with specific nutrients, or nutritional regimes, are catalogued, and might provide ‘early warning’molecular biomarkers for nutrient-induced changes to homeostasis. Be more important for human nutrition, given the difficulty of collecting tissue samples from ‘healthy’ individuals.

19. 9/11/201519 Caenorhaboditis elegans (completed genome segence) Zebrafish (Danio rerino) Mouse Role of nutrients in Alzhelmer and Parkinson diseases. Use model organisms in nutrition research Role of nutrients in development and organ functions. Role of nutrition in development and organ functions.

20. 9/11/201520 Nutrigenomics and nutritional systems biology apply the same set of technologies Nutrition (2004), 20: 4-8

21. 9/11/201521 Integration of enabling technologies in nutrigenomics Microarray & SAGE

22. 9/11/201522 Aging-related changes in gene expression in gastrocnemius muscle Science (1999) 285:1390-1393

23. 9/11/201523 Science (1999) 285:1390-1393 Caloric restriction–induced alterations in gene expression

24. 9/11/201524 Conclusion of gene expression profile of aging and its retardation by caloric restriction Science (1999) 285:1390-1393

25. 9/11/201525 (1) Nutrigenomics researchers must know the challenge of understanding polygenic diet related diseases. (2) Short-term goals: 1. to identify the dietary signals. 2. to elucidate the dietary sensor mechanisms. 3. to characterize the target genes of these sensors. 4. to understand the interaction between these signalling pathways and pro-inflammatory signalling to search for sensitizing genotypes. 5. to find ‘signatures’ (gene/protein expression and metabolite profiles). Conclusion and future perspective

26. 9/11/201526 (3) Long-term goals: Nutrigenomics is to help to understand how we can use nutrition to prevent many of the same diseases for which pharmacogenomics is attempting to identify cures. SNP database will be effect on disease risk. Future personalized diets

27. 9/11/201527 To Do Find examples in the literature of nutrigenomic studies. Review their finding Prepare a presentation about it.

28. 9/11/201528 -Nutrient metabolism (lipid, glucose, AAs) - Proliferation - Inflammation - Lipid and glucose metabolism - Cell cycle control - Inflammation - Lipid metabolism - Keratinocyte differentiation - Inflammation PPAR  PPAR  PPAR  Functions of PPARs

29. 9/11/201529 PPARs are ligand activated transcription factors PPAR 9 cis retinoic acid fatty acids DNA transcription PPAR RXR AGGTCAaAGGTCA + Gene Response element - Protein synthesis Function

30. 9/11/201530 Why are PUFAs healthy?  -Oxidation FA synthesis Triglyceride synthesis PPAR PPRE Fatty acid oxidation genes + SREBP1 SP1/NF-Y Lipogenic genes - VLDL-TG

31. 9/11/201531 Pharmacological activation Physiological activation Nutritional activation WY14643 Fasting High fat diet PPAR  +/+ PPAR  -/- PPAR  +/+ PPAR  -/- PPAR  +/+ PPAR  -/-

32. 9/11/201532 Pharmacological activation Physiological activation Nutritional activation WY14643 Fasting High fat diet - WY + WY low fat fasted fed high fat  PPAR  -/-  PPAR  +/+  PPAR  -/-  PPAR  +/+  PPAR  -/-  PPAR  +/+ Kersten et al. 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4

33. 9/11/201533 Role of PPAR  in the hepatic response to fasting Liver FFA Elucidation by employing: 1)k.o.-mice 2)specific ligands 3)transcriptome analysis 4)In vitro studies (Promoter studies, ChIP, etc) Elucidation by employing: 1)k.o.-mice 2)specific ligands 3)transcriptome analysis 4)In vitro studies (Promoter studies, ChIP, etc) CMLS, Cell. Mol. Life Sci. 61 (2004) 393–416

34. 9/11/201534 Decreased glucose tolerance Decreased glucose tolerance Muscle insulin resistence  Cell compensation Increased gluconeogenesis in liver Increased lipolysis in visceral fat  Cell decompensation Genes Ageing Obesity hyperinsulemia Increased fatty acids levels Increased glucose output Decreased insulin secretion Diabetes Metabolic Syndrome and Diabetes

35. 9/11/201535 FFA Mdr2 Portal blood Hepatocyte Bile WAT TG PC + + + Acute phase response Fatty acid oxidation Fatty acid hydroxylation Hydrolysis of Acyl-CoA Fatty acid transport Hepatobiliary lipid transport Gluconeogenesis - + Fxr/Lxr Gene regulation by fatty acids ABCG5/G8 Ppar 

36. 9/11/201536 What happens during fasting? TG glucose FFA WAT G3P DHAP Blood FFA Glycerol Liver

37. 9/11/201537 Mouse liver gene expression signatures during fasting Metabolic reprogramming during fasting

38. 9/11/201538 cluster Avg Diff Fold- Change Acc. No. down cluster Avg Diff Fold- Change Acc. No. up transcription factors SREBP-13104.3D1X61800 C/EBP  3.373U1 SREBP-110.4580.3D1X62600 C/EBP  2.3261.3U1 SREBP-18.5172.4D1AA106163CAR2.9134.8U1 retinoid O receptor RORgamma4.5267.3D1U09416FXR2.3 531.7 U1 retinoid O receptor RORalpha11.8266.6D2U09419 LXR  2110.3U2 AA061461 AA068578 AA067092 U39071 Y08640 U44752hepatic nuclear factor HNF3alpha3.572D2X57638 PPAR  2.6217.8U5 M34476 RAR  3.8100.2U3 receptors and binding proteins X70533corticosteroid binding globulin4.32351.5D1X81579insulin-like growth factor binding protein 15.9300.7U4 M33324high molecular weight growth hormone receptor3.8168.5D2L05439insulin-like growth factor binding protein 23.41993.4U1 AA038239plasma retinol binding protein RBP3.13248.1D3L38613glucagon receptor2.3462.8U2 X14961heart fatty acid binding protein H-FABP2.7143.4D1X57796tumor necrosis factor receptor 55 kD3.2166.2U4 U40189pancreatic polypeptide/neuropeptide Y receptor3.234.4U3 J03398Abcb4 (Mdr2)4.4504.1U1 M65034intestinal fatty acid binding protein I-FABP2.4486.5U3 amino acid metabolism Z14986adenosylmethionine decarboxylase3.3335.2D1 M17030*ornithine transcarbamylase2.33615.5D2 X51942phenylalanine hydroxylase2.24171.4D2 J02623aspartate aminotransferase1.6783.6D4 U38940asparagine synthetase2.2177.9D4 U24493tryptophan 2,3-dioxygenase1.74116.4D5 X16314glutamine synthetase2925D5 nucleotide metabolism X75129xanthine dehydrogenase1.8395.9D1 M27695.0urate oxidase2.22848.7D5 X56548purine nucleoside phosphorylase21149.7D2 other enzymes W54790ATP synthase A chain4.4456.7D4X80899SIG81 (cytochrome c oxidase VIIa homologue)2762.5U2 W91222cytochrome c oxidase subunit VIIa2.9913.2D5U14390aldehyde dehydrogenase (Ahd3)3.6660.9U3 X01756cytochrome c1.71678.7D5Z37107epoxide hydrolase1.83012.6U3 U39200epidermal 12(S)-lipoxygenase2.3142D2U33557folylpolyglutamate synthetase2.1648.8U5 W41963acetyl-CoA synthetase3.3106.6D2D49744farnesyltransferase alpha1.9475.8U3 M27796carbonic anhydrase III8.74283.8D3U12922CD1 geranylgeranyl transferase beta subunit2.1260.1U3 X51971carbonic anhydrase V1.7787.4D1J03733ornithine decarboxylase1.6257.8U3 AA106634 cis-retinol/3-alpha-hydroxysterol short chain dehydr. 4.53997.4D5D16333coproporphyrinogen oxidase2.5216.9U3 U00445glucose-6-phosphatase1.81587.7D4J02652malate NADP oxidoreductase1.7249U3 U27014sorbitol dehydrogenase2.23607.4D2 M63245amino levulinate synthase (ALAS-H)2.51842.4D4 M74570aldehyde dehydrogenase II2.64177.9D4 Metabolic reprogramming during fasting

39. 9/11/201539 How to crack the code? Rosetta Resolver 5/Base 2 Bioconductor et al. (WWW) Spotfire MS Excel Pathway assist GeneGo Ingenuity Thinking!!

40. 9/11/201540 The common diseases are complex: Factors influencing the development of metabolic syndrome MSX 1 3 Diabetes Obesity Hypertension Inflammation Hyperlipidemia 2

41. 9/11/201541 Pharma Nutrition Prevention versus Therapy – Nutrition versus Pharma TIME (months/years) DISEASE STATE (arbitrary units) Homeostasis Health Complex Disease Different targets Metabolic stress Metabolic syndrome

42. 9/11/201542 Interplay between diet, organs and metabolic stress Signals gut mucosa: satiety hormones cytokines  barrier Unabsorbed nutrients Systemic effects: Glucose intolerance Insulin resistance Lipid disorders Absorbed nutrients Diet Entero- Hepatic Cycle Homeostasis by liver Adipose tissue Muscle  Gut contents Digestion and absorption Lipids

43. 9/11/201543 Signatures of health & stress -The “two hits”: Metabolic and pro-inflammatory stress

44. 9/11/201544 Nature reviews/genetics (2003), 4:315-322 HNF, hepatocyte nuclear factor; LXR, liver X receptor; MTF1, metal-responsive transcription factor; PPAR,peroxisome proliferator-activated receptor; TGF, transforming growth factor. Use model organisms in nutrition research Knockout mice is useful ！

45. 9/11/201545 The ‘smart’ combination of molecular nutrition and nutrigenomics. Nature reviews/genetics (2003), 4:315-322

46. 9/11/201546 Strategies we need in gene-nutrient interactions