Nutrigenomics: Goals and strategies

Nature Reviews Genetics

Volumn 4, Issue 4, 2003, Pages 315-322

  Müller, Michael ^a   Kersten, Sander ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; ALPHA TOCOPHEROL; AMINO ACID; APOLIPOPROTEIN E; BILE SALT; CALCIUM; CARBOHYDRATE; CHOLESTEROL; FAT; FATTY ACID; FLAVONOID; GLUCOSE; HORMONE RECEPTOR; IRON; MINERAL; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA; PHOSPHOLIPID TRANSFER PROTEIN; PROTEIN; RETINOID X RECEPTOR; RETINOL; TRACE ELEMENT; TRANSCRIPTION FACTOR; VITAMIN; VITAMIN D; VITAMIN D RECEPTOR; XENOBIOTIC AGENT; ZINC;

DIET; DIET RESTRICTION; DNA MICROARRAY; FEEDING; GENE EXPRESSION; GENETIC PREDISPOSITION; GENOMICS; GENOTYPE; HOMEOSTASIS; HUMAN; INFLAMMATION; MACRONUTRIENT; METABOLISM; NUTRIENT; NUTRIGENOMICS; NUTRITION; PRIORITY JOURNAL; REVIEW; STRESS;

ANIMALS; DIET; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; INFLAMMATION; MICE; MICE, KNOCKOUT; NUTRITION PHYSIOLOGY; OXIDATIVE STRESS; RESEARCH DESIGN;

EID: 0037380812     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrg1047     Document Type: Review

References (100)

1. International Human Genome Sequencing Consortium. Inital sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
2. Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
3. Venter J. C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
4. Francis, G. A., Fayard, E., Picard, F. & Auwerx, J. Nuclear receptors and the control of metabolism. Annu. Rev. Physiol. 65, 261-311 (2002).
5. Willett, W. C. Balancing life-style and genomics research for disease prevention. Science 296, 695-698 (2002).
6. Chuaqui, R. F. et al. Post-analysis follow-up and validation of microarray experiments. Nature Genet. 32 (Suppl.), 509-514 (2002).
7. Slonim, D. K. From patterns to pathways: gene expression data analysis comes of age. Nature Genet. 32 (Suppl.), 502-508 (2002).
8. Quackenbush, J. Microarray data normalization and transformation Nature Genet. 32 (Suppl.), 496-501 (2002).
9. Churchill, G. A. Fundamentals of experimental design for cDNA microarrays, Nature Genet. 32 (Suppl.), 490-495 (2002).
10. Stoeckert, C. J., Causton, H. C. & Ball, C. A Microarray databases: standards and ontologies. Nature Genet. 32 (Suppl), 469-473 (2002).
11. Roberts, M. A., Mutch, D. M. & German, J. B. Genomics: food and nutrition. Curr. Opin. Biotechnol. 12, 516-522 (2001).
12. Peregrin, T. The new frontier of nutrition science: nutrigenomics. J. Am. Diet Assoc 101, 1306 (2001).
13. Elliott, R. & Ong, T. J. Nutritional genomics. BMJ 324, 1438-1442 (2002).
14. Daniel, H, Genomics and proteomics: importance for the future of nutrition research, Br. J. Nutr. 87 (Suppl.), 305-311 (2002).
15. van Ommen, B & Stierum, R. Nutrigenomics: exploiting systems biology in the nutrition and health arena. Curr. Opin. Biotechnol, 13, 517-521 (2002).
16. Watkins, S. M., Reifsnyder, P. R. Pan, H. J., German, J. B. & Leiter, E. H. Lipid metabolome-wide effects of the PPAR-γ-agonist rosiglitazone. J. Lipid Res. 43, 1809-1817 (2002).
17. MacBeath, G. Protein microarrays and proteomics, Nature Genet. 32 (Suppl.), 526-532 (2002).
18. Evans, W. E. & McLeod, H. L. Pharmacogenomics - Drug disposition, drug targets, and side effects, N. Engl. J. Med. 348, 538-549 (2003).
19. Evans, W. E. & Johnson, J. A. Pharmacogenomics: the inherited basis for interindividual differences in drug response. Annu. Rev. Genomics Hum. Genet. 2, 9-39 (2001).
20. Brouwer, I. A. Zock, P. L., van Amelsvoort, L. G., Katan, M. B. & Schouten, E. G. Association between n-3 fatty acid status in blood and electrocardiographic predictors of arrhythmia risk in healthy volunteers. Am J. Cardiol. 89, 629-631 (2002).
21. Sacks, F. M. & Katan, M. Randomized clinical trials on the effects of dietary fat and carbohydrate on plasma lipoprofeins and cardiovascular disease Am. J. Med. 113 (Suppl.), S13-S24 (2002).
22. Lu, T. T., Repa, J. J. & Mangelsdorf, D. J. Orphan nuclear receptors as eLiXiRs and FiXeRs of sterol metabolism, J, Biol. Chem. 276, 37735-37738 (2001).
23. Mangelsdorf, D. J. et al. The nuclear receptor superfamily: the second decade. Cell 83, 835-839 (1995).
24. Chawla, A., Repa, J. J., Evans, R. M. & Mangelsdorf, D. J. Nuclear receptors and lipid physiology: opening the X-files. Science 294, 1866-1870 (2001).
25. Jansen, P. L., Müller, M. & Sturm, E. Genes and cholestasis. Hepatology 34, 1067-1074, (2001).
26. Chiang, J. Y. Bile acid regulation of gene expression: roles of nuclear hormone receptors. Endocr. Rev. 23, 443-463 (2002).
27. Plass, J. R. et al. Farnesoid X receptor and bile salts are involved in transcriptional regulation of the gene encoding the human bile salt export pump. Hepatology 35, 889-596 (2002).
28. Pineda Torra, I. et al. Bile acids induce the expression of the human peroxisome proliferator-activated receptor-α gene via activation of the farnesoid X receptor. Mol. Endocrinol, 17, 259-272 (2003).
29. Ananthanarayanan, M., Balasubramanian, N., Makishima, M., Mangelsdorf, D. J. & Suchy, F. J. Human bile salt export pump promoter is transactivated by the farnesoid X receptor/bile acid receptor. J. Biol. Chem. 276, 28857-28865 (2001).
30. Hwang, S. T., Urizar, N. L., Moore, D. D. & Henning, S. J. Bile acids regulate the ontogenic expression of ileal bile acid binding protein in the rat via the farnesoid X receptor. Gastroenterology 122, 1483-1492 (2002).
31. Lu, T. T. et al. Molecular basis for feedback regulation of bile acid synthesis by nuclear receptors. Mol. Cell 6. 507-515 (2000).
32. He, K. et al. Fish consumption and risk of stroke in men. JAMA 288, 3130-3136 (2002)
33. Albert, C. M. et al. Blood levels of long-chain n-3 fatty acids and the risk of sudden death N. Engl. J. Med. 346, 1113-1118 (2002).
34. Jump, D. B. & Clarke, S. D. Regulation of gene expression by dietary fat. Annu. Rev. Nutr. 19, 63-90 (1999).
35. Jump, D. B. Dietary polyunsaturated fatty acids and regulation of gene transcription, Curr. Opin. Lipidol. 13, 155-164 (2002).
36. Kersten, S., Desvergne, B. & Wahli, W. Roles of PPARs in health and disease. Nature 405, 421-424 (2000).
37. Barbier, O. et al. Pleiotropic actions of peroxisome proliferator-activeted receptors in lipid metabolism and atherosclerosis. Arterioscler. Thromb. Vasc. Biol. 22, 717-726 (2002).
38. Walczak, R. & Tontonoz, P. PPARadigms and PPARadoxes: expanding roles for PPAR-γ in the control of lipid metabolism, J. Lipid. Res. 43, 177-186 (2002).
39. Xu, J. et al. Peroxisome proliferator-activated receptor-α (PPAR-α) influences substrate utilization for hepatic glucose production. J. Biol. Chem. 277, 50237-50244 (2002).
40. Kersten, S. et al. Peroxisome proliferator-activated receptor-α mediates the adaptive response to fasting. J. Clin. Invest. 103, 1489-1498 (1999).
41. Jump, D. B., Thelen, A. & Mater, M. Dietary polyunsaturated fatty acids and hepatic gene expression. Lipids 34 (Suppl.), S209-S212 (1999).
42. Desvergne, B. & Wahli, W. Peroxisome proliferator- activated receptors: nuclear control of metabolism. Endocr. Rev. 20, 649-688 (1999).
43. Hooper, L. V. & Gordon, J. I. Commensal host-bacterial relationships in the gut. Science 292, 1115-1118 (2001).
44. Stappenbeck, T. S., Hooper, L. V., Manchester, J. K., Wong, M. H. & Gordon, J. L. Laser capture microdissection of mouse Intestine: characterizing mRNA and protein expression, and profiling intermediary metabolism in specified cell populations. Methods Enzymol. 356, 167-196 (2002).
45. Shimomura, I., Shimano, H., Horton, J. D., Goldstein, J. L. & Brown, M. S. Differential expression of exons 1a and 1c in mRNAs for sterol regulatory element binding protein-1 in human and mouse organs and cultured cells. J Clin. Invest 99, 838-845 (1997).
46. Whitney, A. R. et al. individuality and variation in gene expression patterns in human blood. Proc. Natl Acad. Sci. USA 100, 1896-1901 (2003).
47. Staudt, L. M. Gene expression profiling of lymphoid malignancies. Annu. Rev. Med. 53, 303-318 (2002).
48. Rosenwald, A. et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N. Engl. J. Med. 346, 1937-1947 (2002).
49. Davis, R. E. & Staudt, L. M. Molecular diagnosis of lymphoid malignancies by gene expression profiling, Curr Opin. Hematol. 9, 333-338 (2002).
50. Tang, Y., Lu, A., Aronow, B. J. & Sharp, F. R. Blood genomic responses differ after stroke, seizures, hypoglycemia, and hypoxia: blood genomic fingerprints of disease, Ann Neurol. 50, 699-707 (2001).
51. Boldrick, J. C. et al. Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc. Natl Acad. Sci. USA 99, 972-977 (2002).
52. Staudt, L. M. Gene expression physiology and pathophysiology of the immune system. Trends Immunol. 22, 35-40 (2001).
53. Shaffer, A. L. et al. Signatures of the immune response. Immunity 15, 375-385 (2001).
54. Grody, W. W. Molecular genetic risk screening. Annu. Rev. Med. 54, 473-490 (2003).
55. Bailey, L. B. & Gregory, J. Polymorphisms of methylenetetrahydrofolate reductase and other enzymes metabolic significance, risks and impact on folate requirement. J. Nutr. 129, 919-922 (1999).
56. Omer, R. E. et al. Peanut butter intake, GSTM1 genotype and hepatocellular carcinoma: a case-control study in Sudan. Cancer Causes Control 12, 23-32 (2001).
57. Sachidanandam, R. et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms Nature 409, 928-933 (2001).
58. Potter, J. D. At the interfaces of epidemiology, genetics and genomics, Nature Rev. Genet. 2, 142-147 (2001)
59. Kong, A. et al. A high-resolution recombination map of the human genome. Nature Genet. 31, 241-247 (2002).
60. Boomsma, D., Busjahn, A. & Peltonen, L. Classical twin studies and beyond, Nature Rev. Genet. 3, 872-882 (2002).
61. Cascante, M et al. Metabolic control analysis in drug discovery and disease. Nature Biotechnol. 20, 243-249 (2002).
62. Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
63. Ideker, T., Galitski, T. & Hood, L. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343-372 (2001).
64. Jansen, R. C Studying complex biological systems using multifactoral perturbation. Nature Rev. Genet. 4, 145-151 (2003).
65. Kitano, H. Systems biology: a brief overview. Science 295, 1662-1664 (2002).
66. Watkins, S. M. & German, J. B. Toward the implementation of metabolomic assessments of human health and nutrition, Curr. Opin. Brotechnol. 13, 512-516 (2002).
67. Ideker, T., Ozier, O., Schwikowski, B. & Siegel, A. F. Discovering regulatory and signalling circuits in molecular interaction networks Bionformatics, 18 (Suppl.) 233-240 (2002)
68. Bradham, C. A., Plumpe, J., Manes, M. P., Brenner, D. A. & Trautwein, C. Mechanisms of hepatic toxicity. I. TNF-induced liver injury. Am. J. Physiol. 275, 387-392 (1998).
69. Streetz, K. L., Wustefeld, T, Klein, C., Manns, M. P. & Trautwein, C. Mediators of inflammation and acute phase response in the liver. Cel. Mel. Biol. 47, 661-673 (2001).
70. Diehl, A. M. Cytokine regulation of liver injury and repair. Immunol. Rev. 174, 160-171 (2000).
71. Ruminy, P. et al. Gene transcription in hepatocytes during the acute phase of a systemic inflammation: from transcription factors to target genes. Inflamm. Res. 50, 383-390 (2001).
72. Pineda Torra, I., Gervois, P. & Staets, B. Peroxisome proliferator-activated receptor-α in metabolic disease, inflammation, atherosclerosis and aging. Curr Opin. Lipidol. 10, 151-159 (1999).
73. Streetz, K. et al. Tumor necrosis factor-α in the pathogenesis of human and munne fulminant hepatic failure. Gastroenterology 119, 446-460 (2000).
74. Clark, J. M., Brancati, F. L. & Diehl, A M. Nonalcoholic fatty liver disease, Gastroenterology 122, 1649-1657 (2002).
75. Bas, U. N. Is metabolic syndrome X an inflammatory condition? Exp. Biol. Med. 227, 989-997 (2002).
76. Evans, J. L., Goldfine, I. D., Maddux, B. A. & Grodsky, G. M. Oxidative stress and stress-activated signaling pathways: a unifying hypothesis of type 2 diabetes. Endocr. Rev. 23, 599-622 (2002).
77. Libby, P. Inflammation in atherosclerosis. Nature 420, 868-874 (2002).
78. Tilg, H. & Diehl, A. M, Cytokines in alcoholic and nonalcoholic steatohepatitis. N. Engl J. Med. 343, 1467-1476 (2000).
79. Ren, B., Thelen, A. P., Peters, J. M., Gonzalez, F. J. & Jump, D. B, Polyunsaturated fatty acid suppression of hepatic fatty acid synthase and S14 gene expression does not require peroxisome proliferator-activated receptor-α. J. Biol. Chem. 272, 26827-26832 (1997).
80. Dallongeville, J. et al. Peroxisome proliferator-activated receptor-α is not rate-limiting for the lipoprotein-lowering action of fish oil. J. Biol. Chem. 276, 4634-4639 (2001).
81. Clagett-Dame, M. & DeLuca, H. F. The role of vitamin A in mammalian reproduction and embryonic development, Annu. Rev. Nutr. 22, 347-381 (2002).
82. Stanford, W. L., Cohn, J. B. & Cordes, S. P. Gene-trap mutagenesis: past, present and beyond. Nature Rev. Genet. 2, 756-768 (2001).
83. Copeland, N, G., Jenkins, N. A. & Court, D. L. recombineering: a powerful new tool for mouse functional genomics. Nature Rev. Genet. 2, 769-779 (2001).
84. Lewandoski, M. Conditional control of gene expression in the mouse. Nature Rev. Genet. 2, 743-755 (2001)
85. Weindruch, R., Kayo, T., Lee, C. K. & Prolla, T. A. Gene expression profiling of aging using DNA microarrays. Mech. Ageing Dev. 123, 177-193 (2002).
86. Cao, S. X., Dhahbi, J, M., Mote, P. L. & Spindler, S. R. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc. Natl Acad. Sci. USA 98, 10630-10635 (2001).
87. Lee, C. K. Allison, D. B., Brand, J., Weindruch, R. & Prolla, T. A. Transcriptional profiles associated with aging and middle age-onset caloric restriction in mouse hearts. Proc. Natl Acad. Sci. USA 99, 14988-14993 (2002).
88. Prolla, T. A. DNA microarray analysis of the aging brain. Chem. Senses 27, 299-306 (2002).
89. Sreekumar, R., Halvatsiotis, P. Schimke, J. C., & Nair, K. S. Gene expression profile in skeletal muscle of type 2 diabetes and the effect of insulin treatment Diabetes 51. 1913-1920 (2002).
90. Maier, S. & Olek. A. Diabetes: a candidate disease for efficient DNA methylation profiling. J. Nutr. 132, 2440-2443 (2002).
91. Shalev, A. et al. Oligonucleotide microarray analysis of intact human pancreatic islets: identification of glucose-responsive genes and a highly regulated TGFβ signaling pathway. Endocrinology 143, 3695-3698 (2002).
92. Shih, D. Q. et al. Hepatocyte nuclear factor-1α is an essential regulator of bile acid and plasma cholesterol metabolism. Nature Genet. 27, 375-382 (2001).
93. Naiki, T. et al. Analysis of gene expression profile induced by hepatocyte nuclear factor 4α in hepatoma cells using an oligonucleotide microarray. J. Biol. Chem. 277, 14011-14019 (2002).
94. Ross, S. E. et al. Microarray analyses during adipogenesis: understanding the effects of Wnt signaling on adipogenesis and the roles of liver X receptor-α in adipocyte metabolism. Mol. Cell. Biol. 22, 5989-5999 (2002).
95. Kersten, S. et al. The peroxisome proliferator-activated receptor-α regulates amino acid metabolism. FASEB J. 15, 1971-1978 (2001).
96. Lichtlen, P. et al. Target gene search for the metal- responsive transcription factor MTF-1. Nucleic Acids Res. 29, 1514-1523 (2001).
97. Blanchard, R. K., Moore, J. B., Green, C. L. & Cousins, R. J. Modulation of intestinal gene expression by dietary zinc status: effectiveness of cDNA arrays for expression profiling of a single nutrient deficiency. Proc Natl Acad. Sci. USA 98, 13507-13513 (2001).
98. Xiao, J. et al. The effect of chronic exposure to fatty acids on gene expression in clonal insulin-producing cells: studies using high density oligonucleotide microarray. Endocrinology 142, 4777-4784 (2001).
99. Endo, Y., Fu, Z., Abe, K., Arai, S. & Kato, H. Dietary protein quantity and quality affect rat hepatic gene expression J. Nutr. 132, 3632-3637 (2002).
100. Mariadason, J. M., Corner, G. A. & Augenlicht, L. H. Genetic reprogramming in pathways of colonic cell maturation induced by short chain fatty acids: comparison with trichostatin A, sulindac, and curcumin and implications for chemoprevention of colon cancer. Cancer Res. 60, 4561-4572 (2000).