Introduction to Nutrigenomics Lecture 26 April 27, 2015 Dr. Quadro

Improper diets are risk factors for diseases Epidemiological studies associate specific foods with incidence and severity of obesity, diabetes, cardiovascular, cancer and/or other chronic diseases.

Nutrigenomics The study of the effects of diet on the activity of individual’s genes and health

From Dawson KAS, 2007

From Dawson KAS, 2007

From Dawson KAS, 2007

CH3-DNA DNA mRNA Proteins Genomic Transcription and translation Epigenomic CH3-DNA Genomic Transcription and translation DNA mRNA Proteins Enzymes, structural, transport, signaling caused by phosphorylation, glycosylation, etc. Bioactive Food Components

Effects on: -Transcription -DNA structure Dietary constituents can affect gene expression and/or genome structure Effects on: -Transcription -DNA structure

Structure of Cells Plasma membrane Cytoplasm Nucleus (compartment where DNA is stored)

Functions of Nucleus Keeps the DNA molecules of eukaryotic cells separate from metabolic machinery of cytoplasm Makes it easier to organize DNA and to copy it before parent cells divide into two daughter cells

Deoxyribonucleic Acid (DNA) Is the molecule of life It contains all the information needed to build an organism The genetic material (http://siggy.chem.ucla.edu/~tim/chemistry/DNA.jpg)

Role of the genetic material “A genetic material must carry out two jobs: duplicate itself and control the development of the rest of the cell in a specific way.” -Francis Crick

DNA is a chain of nucleotides Nucleotides are composed of: -Sugar-deoxyribose -Phosphate group -Base-one of four types: adenine (A), thymine (T) guanine (G), cytosine (C)

Structure of DNA C T G A Two nucleic acid chains running in opposite directions The two nucleic acid chains are coiled around a central axis to form a double helix For each chain – the backbone comes from linking the pentose sugar bases between nucleotides The bases face inward and pair in a highly specific fashion with bases in the other chain A only with T, G only with C Because of this pairing, each strand is complementary to the other 5’ ACGTC 3’ 3’ TGCAG 5’ 

RNA is a chain of nucleotides -Single chain of nucleotides -Nucleotides are composed of: Sugar-ribose Phosphate group Base-one of four types: adenine (A), uracile (U) guanine (G), cytosine (C)

Gene expression: the flow of genetic information from DNA to protein via RNA

Gene: molecular definition A gene is a segment of DNA which codes the formation of RNA which in turn directs the formation of a protein. Genotype= the genetic information Phenotype= the “external” features

The protein creates the phenotype The genetic information is coded by the sequence of the nucleotides DNA RNA Protein The protein creates the phenotype

The genetic information is coded by the sequence of the nucleotides expression Transcription DNA RNA Protein Translation

Nutrigenomics Diet Genotype Health or Disease Phenotype

Molecular nutrition

Genes → Metabolism → Function Key Points: Everyone has the same genes in slightly different versions, called “gene variants” It’s these variations that distinguish one person from another Different variations (gene variants) lead to different metabolism and function between individuals due to different nutrient requirements that result from the specific gene variants one has

Many genes are regulated by diet through the interaction of a given food component with a specific receptor or set of receptors Diet plays a crucial role in chronic diseases

…..Again Transcription Genes are flanked by untranscribed regions called Promoters. These are DNA sequences near the beginning of genes that signal RNA polymerase where to begin transcription. Gene of interest PROMOTER Beginning of transcription RNA Polymerase

Transcriptional regulation by vitamin A CoA HAT RA NCoR Sin3A HDAC RAR RXR Gene of interest RARE PROMOTER

Transcription-factor pathways mediating nutrient-gene interaction

Functions of PPARs PPARa PPARg PPARb Nutrient metabolism (lipid, glucose, AAs) - Proliferation - Inflammation - Lipid and glucose metabolism - Cell cycle control - Inflammation - Lipid metabolism - Keratinocyte differentiation - Inflammation

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

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

Estrogen Receptors Two Different Estrogen Receptors Recent studies have revealed the existence of two distinct estrogen receptors in our bodies: ERa and ERb. While they both bind estrogen as well as other agonists and antagonists, the two receptors have distinctly different localizations and concentrations within our body. Structural differences also exist between the two. allowing for a wide range of diverse and complex processes to take place. The following diagram, adapted from the Gustafsson review (1999), shows the distribution of ERa and ERb http://www.bio.cmu.edu/Courses/BiochemMols/ER/#ERchime

Estrogen Receptors ER-a ER-b (Kuiper et al. 1996) Uterus, testis, pituitary, ovary, epididymis, and adrenal gland. ER-b (Kuiper et al. 1996) brain, kidney, prostrate, ovary, lung, bladder, intestine, and epididymis. Membrane localized ER (Pietras and Szego, 1997) ER-a and b differ in C-terminal ligand binding domains and N-terminal transactivation domains. Highest homology in DNA binding domain.

ER effects on different cell types

Phytoestrogens Aherne and O’Brien, 2002. Nutrition 18:75-81.

Dietary Sources of Phytoestrogens

Soy Phytoestrogens Genistein, daidzein, coumesterol, and equol bind to and transactivate both ER-and ER- (0.1-10mM) Genistetin has a higher affinity for ER. Soy PEs effect cell cycle progression, growth, and differentiation. Have antioxidant and antiangiogenic activities.

Phytoestrogens in Human Health Cancer prevention Post-menopausal supplement Prevention of osteoporosis Cardiovascular health Fertility Breast enhancement

Other examples Omega-3 downregulation of cytokine genes Glucosinolate upregulation of Phase II enzymes Cruciferous vegetables are relatively unique in our diet as a source of glucosinolates, a series of plant secondary metabolites derived from amino acids with a thioglucose and an N-sulfate moiety.

Diet May Influence Epigenetics Epigenetics: the study of heritable changes in gene expression that occur without a change in DNA sequence. DNA methylation- CpG islands Histone posttranslational modifications: Acetylation of lysines Methylation of lysines and arginines Phosphorylations of serines and threonines ADP-ribosylation of glutamic acids Ubiquitination of lysine residues Sumolyation of lysine residues Biotinylation of lysines Recently, in human cells small-interfering RNAs (siRNAs) have been shown to mediate transcriptional gene silencing (Morris KV, Cell Mol. Life Sci. 62:3057-3066, 2005).

Maternal supplementation with LTR Hypomethylated LTR Hypermethylated Maternal supplementation with zinc methionine betaine choline, folate B12 Yellow Mouse Agouti Mouse High risk cancer, diabetes, obesity & reduced lifespan Lower risk of cancer, diabetes, obesity and prolonged life Cooney et al. J Nutr 132:2393S (2002)

From Dawson KAS, 2007

From Dawson KAS, 2007

From Dawson KAS, 2007

Transcriptomic Studies Are Providing Clues About Molecular Targets for Specific Food Components Corn Oil Fish Oil Olive Oil Davidson et al., Cancer Res. 64: 6797-6804, 2004

Nutrigenomics Nutrigenomics attempts to study the genome-wide influences of nutrition. From a nutrigenomics perspective, nutrients are dietary signals that are detected by the cellular sensor systems that influence gene and protein expression and, subsequently, metabolite production. Patterns of gene expression, protein expression and metabolite production in response to particular nutrients or nutritional regimes can be viewed as 'dietary signatures'. Müller M,  Kersten S. Nutrigenomics: Goals and Perspectives. Nature Reviews Genetics 4, 315 -322 (2003)

Nutrigenomics Nutrigenomics seeks to examine these dietary signatures in specific cells, tissues and organisms, and to understand how nutrition influences homeostasis. Nutrigenomics aims to identify the genes that influence the risk of diet-related diseases on a genome-wide scale, and to understand the mechanisms that underlie these genetic predispositions. Müller M,  Kersten S. Nutrigenomics: Goals and Perspectives. Nature Reviews Genetics 4, 315 -322 (2003)

Nutrigenomics Foods Nutrition Target Genes Mechanisms Pathways Signatures Profiles Biomarkers 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

From Dawson KAS, 2007

Influence of diet on health depends upon an individual’s genetic makeup “Personalized nutrition”- diets based upon genotype, nutritional requirements and status It prevents and mitigates chronic diseases

Personalized diets?

Diet and genes Changing the environment can change outcomes by influencing the goodness-of-fit of a genotype for that particular environment

Climate change=Diet change Diet and genes Jurassic Climate change Extinction Climate change=Diet change