9/11/ es/by-sa/2.0/

Nutrigenomics Prof:Rui Alves Dept Ciencies Mediques Basiques, 1st Floor, Room 1.08 Website of the Course: Course:

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.

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

9/11/20155 Genes – Lifestyle – Calories

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

9/11/20157 Molecular nutrition

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??”

9/11/20159 Personalized diets?

9/11/ 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

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

9/11/ “Molecular Nutrition & Genomics” The strategy of Nutrigenomics proteins genes transcripts (?) metabolites

9/11/ Transcription-factor pathways mediating nutrient-gene interaction

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

9/11/ 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

9/11/ 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

9/11/ 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

9/11/ 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.

9/11/ 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.

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

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

9/11/ Aging-related changes in gene expression in gastrocnemius muscle Science (1999) 285:

9/11/ Science (1999) 285: Caloric restriction–induced alterations in gene expression

9/11/ Conclusion of gene expression profile of aging and its retardation by caloric restriction Science (1999) 285:

9/11/ (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

9/11/ (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

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

9/11/ 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

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

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

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

9/11/ 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

9/11/ 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

9/11/ 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

9/11/ 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 

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

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

9/11/ cluster Avg Diff Fold- Change Acc. No. down cluster Avg Diff Fold- Change Acc. No. up transcription factors SREBP D1X61800 C/EBP  3.373U1 SREBP D1X62600 C/EBP  U1 SREBP D1AA106163CAR U1 retinoid O receptor RORgamma D1U09416FXR U1 retinoid O receptor RORalpha D2U09419 LXR  U2 AA AA AA U39071 Y08640 U44752hepatic nuclear factor HNF3alpha3.572D2X57638 PPAR  U5 M34476 RAR  U3 receptors and binding proteins X70533corticosteroid binding globulin D1X81579insulin-like growth factor binding protein U4 M33324high molecular weight growth hormone receptor D2L05439insulin-like growth factor binding protein U1 AA038239plasma retinol binding protein RBP D3L38613glucagon receptor U2 X14961heart fatty acid binding protein H-FABP D1X57796tumor necrosis factor receptor 55 kD U4 U40189pancreatic polypeptide/neuropeptide Y receptor U3 J03398Abcb4 (Mdr2) U1 M65034intestinal fatty acid binding protein I-FABP U3 amino acid metabolism Z14986adenosylmethionine decarboxylase D1 M17030*ornithine transcarbamylase D2 X51942phenylalanine hydroxylase D2 J02623aspartate aminotransferase D4 U38940asparagine synthetase D4 U24493tryptophan 2,3-dioxygenase D5 X16314glutamine synthetase2925D5 nucleotide metabolism X75129xanthine dehydrogenase D1 M urate oxidase D5 X56548purine nucleoside phosphorylase D2 other enzymes W54790ATP synthase A chain D4X80899SIG81 (cytochrome c oxidase VIIa homologue)2762.5U2 W91222cytochrome c oxidase subunit VIIa D5U14390aldehyde dehydrogenase (Ahd3) U3 X01756cytochrome c D5Z37107epoxide hydrolase U3 U39200epidermal 12(S)-lipoxygenase2.3142D2U33557folylpolyglutamate synthetase U5 W41963acetyl-CoA synthetase D2D49744farnesyltransferase alpha U3 M27796carbonic anhydrase III D3U12922CD1 geranylgeranyl transferase beta subunit U3 X51971carbonic anhydrase V D1J03733ornithine decarboxylase U3 AA cis-retinol/3-alpha-hydroxysterol short chain dehydr D5D16333coproporphyrinogen oxidase U3 U00445glucose-6-phosphatase D4J02652malate NADP oxidoreductase1.7249U3 U27014sorbitol dehydrogenase D2 M63245amino levulinate synthase (ALAS-H) D4 M74570aldehyde dehydrogenase II D4 Metabolic reprogramming during fasting

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

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

9/11/ 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

9/11/ 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

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

9/11/ Nature reviews/genetics (2003), 4: 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 ！

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

9/11/ Strategies we need in gene-nutrient interactions