Nutritional Genomics Discovering the Path to Personalized Nutrition

by Kaput, Jim; Rodriguez, Raymond L.

• ISBN13: 9780471683193
• ISBN10: 0471683191
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-05-05
• Publisher: Wiley-Interscience

Summary

The definitive guide to the basic principles and latest advances in Nutritional Genomics Though still in its infancy, nutritional genomics, or "nutrigenomics," has revealed much about the complex interactions between diet and genes. But it is in its potential applications that nutrigenomics promises to revolutionize the ways we manage human health and combat disease in the years ahead. Great progress already has been made in modeling "personalized" nutrition for optimal health and longevity as well as in genotype-based dietary interventions for the prevention, mitigation, or possible cure of a variety of chronic diseases and some types of cancer. Topics covered include: * Nutrients and gene expression * The role of metabolomics in individualized health * Molecular mechanisms of longevity regulation and calorie restriction * Green tea polyphenols and soy peptides in cancer prevention * Maternal nutrition and fetal gene expression * Genetic susceptibility to heterocyclic amines from cooked foods * Bioinformatics and biocomputation in nutrigenomics * The pursuit of optimal diets Written by an all-star team of experts from around the globe, this volume provides an integrated overview of the cutting-edge field of nutritional genomics. The authors and editors lead an in-depth discussion of the fundamental principles and scientific methodologies that serve as the foundation for nutritional genomics and explore important recent advances in an array of related disciplines. Each self-contained chapter builds upon its predecessor, leading the reader seamlessly from basic principles to more complex scientific findings and experimental designs. Scientific chapters are carefully balanced with those addressing the social, ethical, regulatory, and commercial implications of nutrigenomics.

Author Biography

Jim Kaput, PhD, is the founder, President, and Chief Scientific Officer of NutraGenomics, Inc.

Raymond L. Rodriguez, PhD, is Professor of Molecular and Cellular Biology and Director of the Centerof Excellence in Nutritional Genomics at the University of California, Davis.

Table of Contents

Contributors	xv
Foreword	xix
Preface	xxi
Acknowledgments	xxv
1 AN INTRODUCTION AND OVERVIEW OF NUTRITIONAL GENOMICS: APPLICATION TO TYPE 2 DIABETES AND INTERNATIONAL NUTRIGENOMICS	1	(36)
Jim Kaput
1.1 Introduction	2	(1)
1.2 Understanding T2DM: The Current View of T2DM and Treatment Options	3	(2)
1.3 Understanding T2DM: Begin Before Conception	5	(2)
1.4 Understanding T2DM: Genetic Complexity	7	(2)
1.5 Understanding T2DM: QTLs in Humans	9	(4)
1.6 Understanding T2DM: From Birth Onward	13	(1)
1.7 Understanding T2DM: Metabolomics	14	(2)
1.8 Understanding T2DM: Environmental Influences	16	(2)
1.9 Understanding T2DM: Environment Is More Than Diet	18	(2)
1.10 Understanding T2DM: Data Acquisition and Analyses	20	(1)
1.11 Bioinformatics and Biocomputation	20	(1)
1.12 Converting Science into Practice	21	(3)
1.13 Research Ethics and Genetic Privacy	24	(1)
1.14 Health Disparities	24	(1)
1.15 Public and International Policies	25	(2)
1.16 Conclusion	27	(1)
Acknowledgment	27	(1)
References	27	(10)
2 THE PURSUIT OF OPTIMAL DIETS: A PROGRESS REPORT	37	(20)
Walter C. Willett
2.1 Introduction	37	(1)
2.2 Considerations in Defining an Optimal Diet	37	(2)
2.3 Dietary Fat and Specific Fatty Acids	39	(2)
2.4 Carbohydrates	41	(1)
2.5 Protein	42	(1)
2.6 Vegetables and Fruits	43	(1)
2.7 Calcium and Dairy Products	44	(1)
2.8 Salt and Processed Meats	44	(1)
2.9 Alcohol	45	(1)
2.10 Vitamin and Mineral Supplements	45	(2)
2.11 Potential Impact of Optimal Diet and Life-Style Changes	47	(1)
2.12 Conclusion	48	(1)
Acknowledgment	49	(1)
References	49	(8)
3 GENE–ENVIRONMENT INTERACTIONS: DEFINING THE PLAYFIELD	57	(28)
Jose M. Ordovas and Dolores Corella
3.1 Introduction	57	(3)
3.2 Genetic Variability	60	(2)
3.3 How to Detect Genetic Variability	62	(1)
3.4 What to Analyze	63	(1)
3.5 Environmental Factors	64	(2)
3.6 Gene–Environment Interactions: Focus on Diet	66	(3)
3.7 Common Genetic Variants and Gene–Diet Interactions Modulating Plasma Lipoprotein Concentrations	69	(2)
3.8 Gene–Microorganisms Interactions	71	(4)
3.9 The Microbiome (Microbiota)	75	(1)
3.10 Conclusion	75	(1)
Acknowledgments	76	(1)
References	76	(9)
4 METABOLOMICS: BRINGING NUTRIGENOMICS TO PRACTICE IN INDIVIDUALIZED HEALTH ASSESSMENT	85	(20)
J. Bruce German, Cora J. Dillard, S. Luke Hillyard, Matthew C. Lange, Jennifer T. Smilowitz, Robert E. Ward, and Angela M. Zivkovic
4.1 Introduction	85	(1)
4.2 Opportunities for Foods and Health	86	(1)
4.3 Nutrigenomics	87	(1)
4.4 Metabolomics	88	(3)
4.5 Genomics	91	(4)
4.6 Metabolome Assembly and Annotation	95	(6)
4.7 Bioinformatics: Knowledge Management from Genomics and Metabolomics to Health Assessment	101	(1)
4.8 Conclusion	102	(1)
References	103	(2)
5 GENETIC AND MOLECULAR BUFFERING OF PHENOTYPES	105	(30)
John L. Hartman IV
5.1 Introduction	105	(4)
5.2 Examples of Buffering	109	(8)
5.3 Experimental Concepts for Genetic Buffering Analysis	117	(5)
5.4 Experimental Platforms for Global Genetic Interaction Analysis	122	(7)
5.5 Conclusion	129	(1)
Acknowledgments	129	(1)
References	130	(5)
6 GENE—GENE EPISTASIS AND GENE—ENVIRONMENT INTERACTIONS INFLUENCE DIABETES AND OBESITY	135	(18)
Sally Chiu, Adam L. Diament, Janis S. Fisler, and Craig H. Warden
6.1 Gene—Gene and Gene—Environment Interactions	135	(2)
6.2 Epistasis and Gene—Environment Interactions in Obesity and Diabetes	137	(1)
6.3 Animal Models for Detecting Gene Interactions	138	(2)
6.4 Gene—Gene Interaction in Obesity and Diabetes	140	(1)
6.5 Dietary Fat in Obesity and Diabetes	141	(4)
6.6 Maternal Effects	145	(1)
6.7 Future Directions and Conclusion	146	(1)
References	147	(6)
7 NUTRIENTS AND GENE EXPRESSION	153	(24)
Gertrud U. Schuster
7.1 Introduction	153	(1)
7.2 SREBPs and ChREBP: Transcription Factors Influenced by Dietary Lipids and Glucose	153	(3)
7.3 Superfamily of Nuclear Receptors	156	(1)
7.4 Nuclear Receptors: Structure and Function	157	(2)
7.5 Nuclear Receptors as Metabolic Sensor	159	(5)
7.6 Vitamins	164	(2)
7.7 Phytoestrogens: Nutrients Mimicking Estrogens	166	(1)
7.8 Polymorphisms	167	(3)
7.9 Conclusion	170	(1)
Acknowledgments	170	(1)
References	170	(7)
8 GREEN TEA POLYPHENOLS AND CANCER PREVENTION	177	(30)
Shangqin Guo and Gail Sonenshein
8.1 Introduction	177	(2)
8.2 Green Tea and Cancer Epidemiology	179	(2)
8.3 Animal Models	181	(3)
8.4 Mechanisms of Green Tea Action: Molecular Signaling Pathways and Gene Targets	184	(9)
8.5 Clinical Studies and the Promise of Tea in Combinatorial Therapy	193	(1)
8.6 Future Directions and Conclusion	194	(1)
Acknowledgments	194	(1)
References	194	(13)
9 MOLECULAR MECHANISMS OF LONGEVITY REGULATION AND CALORIE RESTRICTION	207	(12)
Su-Ju Lin
9.1 Introduction	207	(1)
9.2 A Conserved Longevity Factor, Sir2	207	(1)
9.3 Molecular Mechanisms of Calorie Restriction	208	(3)
9.4 Role of NAD/NADH Ratio in Aging and Human Diseases	211	(1)
9.5 Possible CR Mimetics—Small Molecules That Regulate Sir2 Activity	211	(1)
9.6 Molecular Targets of Sir2 Proteins in Mammals	212	(1)
9.7 A Possibly Conserved Longevity Pathway	213	(1)
9.8 Applications to Nutritional Genomics	214	(1)
References	214	(5)
10 MATERNAL NUTRITION: NUTRIENTS AND CONTROL OF EXPRESSION	219	(36)
Craig A. Cooney
10.1 Introduction	219	(1)
10.2 Methyl Metabolism	220	(2)
10.3 DNA Methylation, Epigenetics, and Imprinting	222	(2)
10.4 Endogenous Retroviruses and Genome Integrity	224	(1)
10.5 Epigenetics and Nutrition Can Greatly Modulate Genetic Predispositions	225	(2)
10.6 Yellow Mouse Models of Epigenetic Regulation	227	(7)
10.7 A Variety of Maternal Effects Seen in Mice	234	(1)
10.8 Rat Models of Maternal Effects Leading to Diabetes	234	(2)
10.9 Maternal Effects on Memory and Aging	236	(1)
10.10 Epigenctic Effects in Foxes	237	(2)
10.11 Epigenetic Effects Related to Reproduction in Humans	239	(1)
10.12 Nutrients and Compounds That May Affect Early Development and Epigenetics	240	(3)
10.13 Conclusion	243	(1)
Acknowledgments	244	(1)
References	244	(11)
11 NUTRIENT—GENE INTERACTIONS INVOLVING SOY PEPTIDE AND CHEMOPREVENTIVE GENES IN PROSTATE EPITHELIAL CELLS	255	(22)
Mark Jesus M. Magbanua, Kevin Dawson, Liping Huang, Wasyl Malyj, Jeff Gregg, Alfredo Galvez, and Raymond L. Rodriguez
11.1 Introduction	255	(1)
11.2 Lunasin Structure and Function	256	(2)
11.3 Lunasin Treatment of Prostate Cancer and Gene Expression Profiling	258	(1)
11.4 Lunasin-Induced Gene Expression Profiles	259	(1)
11.5 Genes for Apoptosis	260	(6)
11.6 Genes Involved in Suppression of Cell Proliferation	266	(1)
11.7 Mitotic Checkpoint Genes	267	(1)
11.8 Genes Involved in Protein Degradation	268	(1)
11.9 Connexin 43 Gene for the Gap Junction Protein	268	(1)
11.10 Target Verification Using RT—PCR	269	(1)
11.11 Conclusion	269	(3)
Acknowledgments	272	(1)
References	272	(5)
12 ENZYMES LOSE BINDING AFFINITY (INCREASED KM) FOR COENZYMES AND SUBSTRATES WITH AGE: A STRATEGY FOR REMEDIATION	277	(18)
Bruce N. Ames, Jung H. Suh, and Jiankang Liu
12.1 Introduction	277	(1)
12.2 Remediation by High B Vitamin Intake of Variant Enzymes with Poor Binding Affinity (Km) for Coenzymes	277	(1)
12.3 Deformation of Proteins in Mitochondria with Aging	278	(7)
12.4 Nonmitochondrial Enzymes that Are Deformed with Age	285	(3)
12.5 Conclusion	288	(1)
Acknowledgments	288	(1)
References	288	(7)
13 DIETARY AND GENETIC EFFECTS ON ATHEROGENIC DYSLIPIDEMIA	295	(10)
Ronald M. Krauss and Patty W. Siri
13.1 Introduction	295	(1)
13.2 LDL Represents a Heterogeneous Population of Particles	296	(2)
13.3 LDL Subclasses Influenced by Genes and the Environment	298	(3)
13.4 Conclusion	301	(1)
References	301	(4)
14 GENISTEIN AND POLYPHENOLS IN THE STUDY OF CANCER PREVENTION: CHEMISTRY, BIOLOGY, STATISTICS, AND EXPERIMENTAL DESIGN	305	(26)
Stephen Barnes, David B. Allison, Grier P. Page, Mark Carpenter, Gary L. Gadbury, Sreelatha Meleth, Pamela Horn-Ross, Helen Kim, and Coral A. Lamartinere
14.1 Introduction	306	(1)
14.2 Diet and Cancer	306	(1)
14.3 Chemistry of the Polyphenols	306	(1)
14.4 Uptake, Distribution, Metabolism, and Excretion of Polyphenols	307	(2)
14.5 Polyphenols and Cancer Prevention	309	(1)
14.6 Mechanisms of Action of Polyphenols	310	(1)
14.7 Importance of Timing of Exposure to Polyphenols	310	(2)
14.8 Assessing Events Leading to Cancer: Low-Dimensional Approaches	312	(1)
14.9 Statistical Consequences of High-Dimensional Approaches	312	(1)
14.10 High-Dimensional Systems and the Importance of the False Discovery Rate	313	(1)
14.11 DNA Microarray Analysis: High-Dimensional Research into Gene Expression	314	(1)
14.12 Proteomics Analysis: An Even Bigger Challenge	314	(3)
14.13 Statistical Problems with Fold-Change in DNA Microarray and Proteomics Analyses	317	(1)
14.14 Design in Experiments Involving DNA Microarray and Proteomics Analysis	317	(1)
14.15 The Design	318	(4)
14.16 Role of the Computer in High-Dimensional Analysis	322	(1)
Acknowledgments	323	(1)
References	324	(7)
15 SUSCEPTIBILITY TO EXPOSURE TO HETEROCYCLIC AMINES FROM COOKED FOOD: ROLE OF UDP-GLUCURONOSYLTRANSFERASES	331	(22)
Michael A. Malfatti and James S. Felton
15.1 Introduction	331	(1)
15.2 Genetic Susceptibility	331	(1)
15.3 UDP-Glucuronosyltransferase	332	(1)
15.4 UDP-Glucuronosyltransferase Biochemistry	332	(1)
15.5 UDP-Glucuronosyltransferase Gene Structure	333	(1)
15.6 Substrate Specificity and Selectivity	334	(1)
15.7 Tissue Distribution of UPD-Glucuronosyltransferase	335	(1)
15.8 Gene Regulation	335	(1)
15.9 Genetic Variation	336	(2)
15.10 UDP-Glucuronosyltransferase and Cancer Susceptibility	338	(1)
15.11 Heteroyclic Amine Carcinogens in Food	338	(1)
15.12 Carcinogenicity of PhIP	339	(2)
15.13 Metabolism of PhIP	341	(2)
15.14 UDP-Glucuronosyltransferase and PhIP Risk Susceptibility	343	(1)
15.15 Conclusion	343	(2)
Acknowledgments	345	(1)
References	345	(8)
16 THE INFORMATICS AND BIOINFORMATICS INFRASTRUCTURE OF A NUTRIGENOMICS BIOBANK	353	(22)
Warren A. Kibbe
16.1 Introduction	353	(3)
16.2 Next Generation Biobanks	356	(1)
16.3 Intended Audience for This Chapter	357	(1)
16.4 Assumptions, Use Cases, and Design Criteria	358	(2)
16.5 Regulatory and Policy Environment	360	(1)
16.6 HIPAA Health Insurance Portability and Accountability Act of 1996	360	(2)
16.7 GMPs, GLPs, and GCPs	362	(1)
16.8 Funding of Biobanks	362	(1)
16.9 Biobanking in Clinical Trials	362	(1)
16.10 Data Standards/Semantic Interoperability	363	(2)
16.11 Other Standards Bodies: CDISC	365	(1)
16.12 Informatics Infrastructure	366	(1)
16.13 System Architecture	366	(1)
16.14 Separation of the Clinical Trial/Patient Identity Management from the Genotype/Phenotype Repository	367	(1)
16.15 Database Architecture/Data Modeling	368	(2)
16.16 Design Practices	370	(3)
16.17 Conclusion	373	(1)
References	373	(2)
17 BIOCOMPUTATION AND THE ANALYSIS OF COMPLEX DATA SETS IN NUTRITIONAL GENOMICS	375	(28)
Kevin Dawson, Raymond L. Rodriguez, Wayne Chris Hawkes, and Wasyl Malyj
17.1 Introduction	375	(1)
17.2 Nutritional Genomics: Part of High-Throughput Biology	376	(2)
17.3 Gene Expression Arrays	378	(1)
17.4 Proteomics and Metabolomics Data	379	(1)
17.5 Sources of Complexity in Nutritional Genomics	380	(2)
17.6 Data Sets in Nutritional Genomics	382	(1)
17.7 Level of Complexity in Gene Expression Experiments	383	(2)
17.8 Dimensionality Reduction Methods	385	(7)
17.9 Case Study (Microarray Experiment of a Dietary Intervention)	392	(5)
17.10 Conclusion	397	(1)
Acknowledgments	397	(2)
References	399	(4)
18 CULTURAL HUMILITY: A CONTRIBUTION TO HEALTH PROFESSIONAL EDUCATION IN NUTRIGENOMICS	403	(16)
Melanie Tervalon and Erik Fernandez
18.1 Introduction	403	(1)
18.2 Cultural Humility	404	(3)
18.3 Summary	407	(2)
18.4 Goals and Objectives: Curriculum Content	409	(1)
18.5 Goals and Objectives: Curriculum Design	410	(1)
18.6 Curriculum Structure and Content: Didactics, Small Groups, and Videotaping	411	(2)
18.7 The Teaching Staff	413	(1)
18.8 Evaluation	413	(1)
18.9 Conclusion	414	(1)
Acknowledgment	415	(1)
References	415	(4)
19 NUTRIENTS AND NORMS: ETHICAL ISSUES IN NUTRITIONAL GENOMICS	419	(16)
David Castle, Cheryl Cline, Abdallah S. Daar, Charoula Tsamis, and Peter A. Singer
19.1 Proactive Ethics and Nutritional Genomics	419	(3)
19.2 Claims of Health Benefits Arising from Nutrigenomics	422	(1)
19.3 Managing Nutrigenomics Information	423	(4)
19.4 Methods for Delivering Nutrigenomics Services	427	(2)
19.5 Nutrigenomics Products	429	(2)
19.6 Access to Nutrigenomics	431	(2)
19.7 Conclusion	433	(1)
References	434	(1)
Glossary	435	(12)
Index	447