Nutrition in the post-genome era: ‘omic’ tools basics and applications
Keywords:
Nutrition public health, Nutrigenomics, Transcriptomics, ProteomicsAbstract
After sequencing the human genome, genomic studies have been focusing on elucidating the function of all genes, as well as characterizing their interactions with environmental factors. Nutrigenomics emerged in the pos-genome era and is considered a key-area for nutrition in the present decade. Its research focus is nutrientgene interaction. The main objective of this recent science is to establish personalized genotype-based diets that promote health and reduce the risk of non-communicable chronic diseases such as cardiovascular diseases, cancer, diabetes and others. In this context, it is essential to use functional genomic tools to analyze the transcriptome (transcriptomics), proteome (proteomics) and metabolome (metabolomics) in the field of nutrition. The applicabilities of such methodologies in nutritional studies seem unlimited since they can be conducted in cell cultures, animal models and pre-clinical and clinical studies. Such techniques may allow one to identify biomarkers that respond specifically to a certain dietary nutrient or bioactive compound and to establish the best individual dietary advice to reduce the risk of non-communicable chronic diseases and promote health.
References
Lieble DC. Introduction to proteomics. Tools for the new biology. Totowa: Humana Press; 2002.
Simpson RJ. Proteins and proteomics. A laboratory manual. New York: Cold Spring Harbor Laboratories Press; 2003.
Fairweather-Tait SJ. Human nutrition and food research: opportunities and challenges in the post-genomic era. Phil Trans S Royal Lond B. 2003; 358(1438):1709-27.
Kaput J, Rodriguez RL. Nutritional genomics: the next frontier in the postgenomic era. Physiol Genomics. 2004;16(2):166-77.
Kussmann M, Raymond F, Affolter M. OMICSdriven biomarker discovery in nutrition and health. J Biotechnol. 2006; 124(4):758-87.
DeBusk RM, Fogarty CP, Ordovas JM, Kornman KS. Nutritional genomics in practice: where do we begin? JADA. 2005;105(4):589-98.
Zhang X, Yap Y, Wei D, Chen G, Chen F. Novel omics technologies in nutrition research. Biotechnol Adv. 2008; 26(2):169-76.
Hirsch JB, Evans D. Beyond the impact of food on genes. Food Technol. 2005; 59(7):24-33.
Rist MJ, Wenzel U, Daniel H. Nutrition and food science go genomic.Trends Biotechnol. 2006; 24(4):172-8.
Moreno FS, Rossiello MR, Manjeshwar S, Nath R, Rao PM, Rajalakshmi S, et al. Effect of betacarotene on the expression of 3-hydroxymethylglutaryl coenzyme A reductase in rat liver. Cancer Lett. 1995; 96(2):201-8.
Naves MM, Silveira ER, Dagli ML, Moreno FS. Effects of beta-carotene and vitamin A on oval cell proliferation and connexin 43 expression during hepatic differentiation in the rat. Nutr Biochem. 2001;12(12):685-92.
Espíndola RM, Mazzantini RP, Ong TP, Conti A, Heidor R, Moreno FS. Geranylgeraniol and betaionone inhibit hepatic preneoplastic lesions, cell proliferation, total plasma cholesterol and DNA damage during the initial phases of hepatocarcinogenesis, but only the former inhibits NF-kappaB activation. Carcinogenesis. 2005; 26(6):1091-9.
Ong TP, Heidor R, Conti A, Dagli ML, Moreno FS. Farnesol and geraniol chemopreventive activities during the initial phases of hepatocarcinogenesis involve similar actions on cell proliferation and DNA damage, but distinct actions on apoptosis, plasma cholesterol and HMGCoA reductase. Carcinogenesis. 2006; 27(6):1194-203.
Ghosh D, Skinner MA, Laing WA. Pharmacogenomics and nutrigenomics: synergies and differences. Eur J Clin Nutr. 2007; 61(5):567-74.
Kussmann M, Affolter M. Proteomic methods in nutrition. Curr Opin Clin Nutr Metab Care. 2006; 9(5):575-83.
Spielbauer B, Stahl F. Impact of microarray technology in nutrition and food research. Mol Nutr Food Res. 2005; 49(10):908-17.
Mutch DM, Wahli W, Williamson G. Nutrigenomics and nutrigenetics: the emerging faces of nutrition. FASEB J. 2005; 19(12):1602-16.
Pozhitkov AE, Tautz D, Noble PA. Oligonucleotide microarrays: widely applied-poorly understood. Brief Funct Genomic Proteomic. 2007; 6(2):141-8.
Traka M, Gasper AV, Smith JA, Hawkey CJ, Bao Y, Mithen RF. Transcriptome analysis of human colon Caco-2 cells exposed to sulforaphane. J Nutr. 2005; 135(8):1865-72.
Hoekstra M, Stitzinger M, van Wanrooij EJ, Michon IN, Kruijt JK, Kamphorst J, et al. Microarray analysis indicates an important role for FABP5 and putative novel FABPs on a Western-type diet. Lipid Res. 2006; 47(10):2198-207.
Kallio P, Kolehmainen M, Laaksonen DE, Kekäläinen J, Salopuro T, Sivenius K, et al. Dietary carbohydrate modification induces alterations in gene expression in abdominal subcutaneous adipose tissue in persons with the metabolic syndrome: the FUNGENUT Study. Am J Clin Nutr. 2007; 85(5): 1417-27.
Garosi P, De Filippo C, van Erk M, Rocca-Serra P, Sansone SA, Elliott R. Defining best practice for microarray analyses in nutrigenomic studies. Br J Nutr. 2005; 93(4):425-32.
Liu-Stratton Y, Roy S, Sen CK. DNA microarray technology in nutraceutical and food safety. Toxicol Lett. 2004;150(1):29-42.
Lovmar L, Syvänen AC. Genotyping singlenucleotide polymorphisms by minisequencing using tag arrays. Methods Mol Med. 2005;114: 79-92.
Pandey A, Mann M. Proteomics to study genes and genome. Nature. 2000; 405(6788), 837-46.
Fields, S. Proteomics: proteomics in genomeland. Science. 2001; 291(5507):1221-4.
Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 1999; 19(3): 1720-30.
Kvasnicka V. Proteomics: general strategies and application to nutritionally relevant proteins. J Chromatogr B Analyt Technol Biomed Life Sci. 2003; 787(1):77-89.
Bodzon-Kulakowska A, Bierczynska-Krzysik A, Dylag T, Drabik A, Suder P, Noga M, et al. Methods for samples preparation in proteomic research. J Chromatogr B Analyt Technol Biomed Life Sci. 2007; 849(1):1-31.
Matsudaira PT. Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J Biol Chem. 1987; 262(21): 10035-8.
Cañas B, Lopez-Ferrer D, Ramos-Fernandez A, Camafeita E, Calvo E. Mass spectrometry technologies for proteomics. Brief Funct Genomic Proteomic. 2006; 4(4):295-320.
Buchanan MV, Hettich RL. Fourier transform mass spectrometry of high-mass biomolecules. Anal Chem. 1993; 65(3):245A-59A.
Carbonaro, M. Proteomics: present and future in food quality evaluation. Trends in Food Sci & Technol. 2004; 15(3-4):209-16.
Ge Y, Lawhorn BG, ElNaggar M, Strauss E, Park JH, Begley TP, et al. Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J Am Chem Soc. 2002; 124(4): 672-8.
Jonscher KR, Yates JR. The quadrupole ion trap mass spectrometer: a small solution to a big challenge. Anal Biochem. 1997; 244(1):1-15.
Yates JR. Mass spectrometry and the age of the proteome. J Mass Spectrom. 1998; 33(1): 1-19.
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science. 2001; 291(5507):1304-51.
Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science. 2002; 298(5600): 1912-34.
Raggiaschi R, Gotta S, Terstappen GC. Phosphoproteome analysis. Biosci Rep. 2005; 25(1/2):33-34.
McLoughlin P, Roengvoraphoj M, Gissel C, Hescheler J, Certa U, Sachinidis A. Transcriptional responses to epigallocatechin-3 gallate in HT 29 colon carcinoma spheroids. Genes Cells. 2004; 9(7):661-9.
Deshane, J, Chaves L, Sarikonda KV, Isbell S, Wilson L, Kirk M, et al. Proteomics analysis of rat brain protein modulations by grape seed extract. J Agric Food Chem. 2004; 52(26):7872-83.
Fuchs D, Erhard P, Rimbach G, Daniel H, Wenzel U. Genistein blocks homocysteine-induced alterations in the proteome of human endothelial cells. Proteomics. 2005; 5(11):2808-18.
Solanky KS, Bailey N-J; Beckwith-Hall BM, Bingham S, Davis A, Holmes E, et al. Biofluid 1H NMR-based metabonomic techniques in nutrition research - metabolic effects of dietary isoflavones in humans. J Nutr Biochem. 2005; 16(4):236-44.
Dieck H, Döring F, Fuchs D, Roth H-P, Daniel H. Transcriptome and proteome analysis identifies the pathways that increase hepatic lipid accumulation in zinc-deficient rats. J. Nutr. 2005; 135(2): 199-205.
Roncada P, Gaviraghi A, Greppi GF, Gigli S. A proteomic approach to compare meat from different species. Proceedings of the 48th International Congress of Meat Science Anal Tecnology; 2002 Ago 25-30; Roma; 2002. v.2, p. 640-41.
Lametsch R, Bendixen E. Proteome analysis applied to meat science: characterizing post mortem changes in porcine muscle. J Agric Food Chem. 2001; 49(10):4531-7.
Gottlieb D M, Schultz J, Petersen M, Nesic L, Jacobsen S, Sondergaard I. Determination of wheat quality by mass spectrometry and multivariate data analysis. Rapid Commun Mass Spectrom. 2002;16(21):2034-9.
Astle J, Ferguson JT, German JB, Harrigan GG, Kelleher NL, Kodadek T, et al. Characterization of proteomic and metabolomic responses to dietary factors and supplements. J Nutr. 2007; 137(12): 2787-93.
Trujillo E, Davis C, Milner J. Nutrigenomics, proteomics, metabolomics, and the practice of dietetics. JADA. 2006; 106(3):403-13.
Wishart DS. Metabolomics: applications to food science and nutrition research. Trends in Food Sci Technol. 2008. Article in press.
Whitfield PD, German AJ, Noble PJ. Metabolomics: an emerging post-genomic tool for nutrition. Br J Nutr. 2004; 92(4):549-55.
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2023 Eliane FIALHO, Fernando Salvador MORENO, Thomas Prates ONG
This work is licensed under a Creative Commons Attribution 4.0 International License.
