Table of Contents
ISRN Nutrition
Volume 2013 (2013), Article ID 403792, 19 pages
http://dx.doi.org/10.5402/2013/403792
Review Article

The Use of Transcriptomics to Unveil the Role of Nutrients in Mammalian Liver

1Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, 50013 Zaragoza, Spain
2CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain

Received 14 July 2013; Accepted 4 August 2013

Academic Editors: P. Crenn and R. Moore-Carrasco

Copyright © 2013 Jesús Osada. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. Z. G. Han, “Functional genomic studies: insights into the pathogenesis of liver cancer,” Annual Review of Genomics and Human Genetics, vol. 13, pp. 171–205, 2012. View at Publisher · View at Google Scholar
  2. J. Kaput, “Developing the promise of nutrigenomics through complete science and international collaborations,” Forum of Nutrition, vol. 60, pp. 209–223, 2007. View at Publisher · View at Google Scholar · View at Scopus
  3. A. Mustafa, C. Cenayko, R. R. Mitry, and A. Quaglia, “Laser microdissection microscopy: application to cell culture,” Methods in Molecular Biology, vol. 806, pp. 385–392, 2012. View at Publisher · View at Google Scholar · View at Scopus
  4. D. Moher, A. Liberati, J. Tetzlaff, and D. G. Altman, “Reprint-Preferred Reporting items for systematic reviews and meta-analyses: the PRISMA statement,” Physical Therapy, vol. 89, no. 9, pp. 873–880, 2009. View at Google Scholar · View at Scopus
  5. S. E. Wildsmith, G. E. Archer, A. J. Winkley, P. W. Lane, and P. J. Bugelski, “Maximization of signal derived from cDNA microarrays,” BioTechniques, vol. 30, no. 1, pp. 202–208, 2001. View at Google Scholar · View at Scopus
  6. D. R. Dorris, R. Ramakrishnan, D. Trakas et al., “A highly reproducible, linear, and automated sample preparation method for DNA microarrays,” Genome Research, vol. 12, no. 6, pp. 976–984, 2002. View at Publisher · View at Google Scholar · View at Scopus
  7. S. E. Spruill, J. Lu, S. Hardy, and B. Weir, “Assessing sources of variability in microarray gene expression data,” BioTechniques, vol. 33, no. 4, pp. 916–923, 2002. View at Google Scholar · View at Scopus
  8. L.-L. Hsiao, R. V. Jensen, T. Yoshida, K. E. Clark, J. E. Blumenstock, and S. R. Gullans, “Correcting for signal saturation errors in the analysis of microarray data,” BioTechniques, vol. 32, no. 2, pp. 330–336, 2002. View at Google Scholar · View at Scopus
  9. M. Arcellana-Panlilio and S. M. Robbins, “Cutting-edge technology I. Global gene expression profiling using DNA microarrays,” American Journal of Physiology, vol. 282, no. 3, pp. G397–G402, 2002. View at Google Scholar · View at Scopus
  10. R. A. Irizarry, B. M. Bolstad, F. Collin, L. M. Cope, B. Hobbs, and T. P. Speed, “Summaries of Affymetrix GeneChip probe level data,” Nucleic Acids Research, vol. 31, no. 4, article e15, 2003. View at Google Scholar · View at Scopus
  11. A. Reiner, D. Yekutieli, and Y. Benjamini, “Identifying differentially expressed genes using false discovery rate controlling procedures,” Bioinformatics, vol. 19, no. 3, pp. 368–375, 2003. View at Publisher · View at Google Scholar · View at Scopus
  12. I. Dozmorov and M. Centola, “An associative analysis of gene expression array data,” Bioinformatics, vol. 19, no. 2, pp. 204–211, 2003. View at Publisher · View at Google Scholar · View at Scopus
  13. H. H. Thygesen and A. H. Zwinderman, “Comparing transformation methods for DNA microarray data,” BMC Bioinformatics, vol. 5, article 77, 2004. View at Publisher · View at Google Scholar · View at Scopus
  14. R. Jörnsten, H.-Y. Wang, W. J. Welsh, and M. Ouyang, “DNA microarray data imputation and significance analysis of differential expression,” Bioinformatics, vol. 21, no. 22, pp. 4155–4161, 2005. View at Publisher · View at Google Scholar · View at Scopus
  15. M. A. Ovacik, S. Sukumaran, R. R. Almon, D. C. DuBois, W. J. Jusko, and I. P. Androulakis, “Circadian signatures in rat liver: from gene expression to pathways,” BMC Bioinformatics, vol. 11, article 540, 2010. View at Publisher · View at Google Scholar · View at Scopus
  16. M. J. Nueda, A. Ferrer, and A. Conesa, “ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments,” Biostatistics, vol. 13, no. 3, pp. 553–566, 2012. View at Google Scholar
  17. S. Vlaic, W. Schmidt-Heck, M. Matz-Soja et al., “The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes,” BMC Systems Biology, vol. 6, p. 147, 2012. View at Google Scholar
  18. Y. Woo, J. Affourtit, S. Daigle et al., “A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms,” Journal of Biomolecular Techniques, vol. 15, no. 4, pp. 276–284, 2004. View at Google Scholar · View at Scopus
  19. R. Kakuhata, M. Watanabe, T. Yamamoto et al., “Possible utilization of in vitro synthesized mRNAs specifically expressed in certain tissues as standards for quantitative evaluation of the results of microarray analysis,” Journal of Biochemical and Biophysical Methods, vol. 70, no. 5, pp. 755–760, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. O. Gotoh, Y. Murakami, and A. Suyama, “Multiplex cDNA quantification method that facilitates the standardization of gene expression data,” Nucleic Acids Research, vol. 39, no. 10, article e70, 2011. View at Publisher · View at Google Scholar · View at Scopus
  21. J. Russ and M. E. Futschik, “Comparison and consolidation of microarray data sets of human tissue expression,” BMC Genomics, vol. 11, no. 1, article 305, 2010. View at Publisher · View at Google Scholar · View at Scopus
  22. P. T. Vedell, K. L. Svenson, and G. A. Churchill, “Stochastic variation of transcript abundance in C57BL/6J mice,” BMC Genomics, vol. 12, article 167, 2011. View at Publisher · View at Google Scholar · View at Scopus
  23. C. C. Pritchard, L. Hsu, J. Delrow, and P. S. Nelson, “Project normal: defining normal variance in mouse gene expression,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 23, pp. 13266–13271, 2001. View at Publisher · View at Google Scholar · View at Scopus
  24. C. Pritchard, D. Coil, S. Hawley, L. Hsu, and P. S. Nelson, “The contributions of normal variation and genetic background to mammalian gene expression,” Genome Biology, vol. 7, no. 3, article R26, 2006. View at Publisher · View at Google Scholar · View at Scopus
  25. X. Peng, C. L. Wood, E. M. Blalock, K. C. Chen, P. W. Landfield, and A. J. Stromberg, “Statistical implications of pooling RNA samples for microarray experiments,” BMC Bioinformatics, vol. 4, article 26, 2003. View at Publisher · View at Google Scholar · View at Scopus
  26. G.-M. Do, E.-Y. Kwon, E. Kim, H.-S. Kim, and M.-S. Choi, “Hepatic transcription response to high-fat treatment in mice: microarray comparison of individual vs. pooled RNA samples,” Biotechnology Journal, vol. 5, no. 9, pp. 970–973, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. G. Marquet, A. Burgun, F. Moussouni, E. Guérin, F. Le Duff, and O. Loréal, “BioMeKe: an ontology-based biomedical knowledge extraction system devoted to transcriptome analysis,” Studies in Health Technology and Informatics, vol. 95, pp. 80–85, 2003. View at Google Scholar
  28. Y. Wang, C. Barbacioru, F. Hyland et al., “Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays,” BMC Genomics, vol. 7, article 59, 2006. View at Publisher · View at Google Scholar · View at Scopus
  29. A. Dahl, M. Sultan, A. Jung et al., “Quantitative PCR based expression analysis on a nanoliter scale using polymer nano-well chips,” Biomedical Microdevices, vol. 9, no. 3, pp. 307–314, 2007. View at Publisher · View at Google Scholar · View at Scopus
  30. X. Wang and B. Seed, “A PCR primer bank for quantitative gene expression analysis,” Nucleic Acids Research, vol. 31, no. 24, article e154, 2003. View at Google Scholar
  31. R. Martínez-Beamonte, M. A. Navarro, A. Larraga et al., “Selection of reference genes for gene expression studies in rats,” Journal of Biotechnology, vol. 151, no. 4, pp. 325–334, 2011. View at Publisher · View at Google Scholar · View at Scopus
  32. A. Le Béchec, P. Zindy, T. Sierocinski et al., “M@IA: a modular open-source application for microarray workflow and integrative datamining,” In Silico Biology, vol. 8, no. 1, pp. 63–69, 2008. View at Google Scholar · View at Scopus
  33. F. Battke and K. Nieselt, “Mayday SeaSight: combined analysis of deep sequencing and microarray data,” PLoS ONE, vol. 6, no. 1, Article ID e16345, 2011. View at Publisher · View at Google Scholar · View at Scopus
  34. M. Sokolović, A. Sokolović, C. P. A. A. van Roomen et al., “Unexpected effects of fasting on murine lipid homeostasis—transcriptomic and lipid profiling,” Journal of Hepatology, vol. 52, no. 5, pp. 737–744, 2010. View at Publisher · View at Google Scholar · View at Scopus
  35. M. Sokolović, A. Sokolović, D. Wehkamp et al., “The transcriptomic signature of fasting murine liver,” BMC Genomics, vol. 9, p. 528, 2008. View at Google Scholar
  36. H.-J. Jun, S. Kim, K. Dawson et al., “Effects of acute oral administration of vitamin C on the mouse liver transcriptome,” Journal of Medicinal Food, vol. 14, no. 3, pp. 181–194, 2011. View at Publisher · View at Google Scholar · View at Scopus
  37. S.-I. Oka, E. Yoshihara, A. Bizen-Abe et al., “Thioredoxin binding protein-2/thioredoxin-interacting protein is a critical regulator of insulin secretion and peroxisome proliferator-activated receptor function,” Endocrinology, vol. 150, no. 3, pp. 1225–1234, 2009. View at Publisher · View at Google Scholar · View at Scopus
  38. S. Ushiama, T. Nakamura, T. Ishijima, T. Misaka, K. Abe, and Y. Nakai, “The hepatic genes for immunoproteasome are upregulated by refeeding after fasting in the rat,” Bioscience, Biotechnology and Biochemistry, vol. 74, no. 6, pp. 1320–1323, 2010. View at Publisher · View at Google Scholar · View at Scopus
  39. H. Oike, K. Nagai, T. Fukushima, N. Ishida, and M. Kobori, “Feeding cues and injected nutrients induce acute expression of multiple clock genes in the mouse liver,” PLoS ONE, vol. 6, no. 8, Article ID e23709, 2011. View at Publisher · View at Google Scholar · View at Scopus
  40. A. K. Reiter, S. J. Crozier, S. R. Kimball, and L. S. Jefferson, “Meal feeding alters translational control of gene expression in rat liver,” Journal of Nutrition, vol. 135, no. 3, pp. 367–375, 2005. View at Google Scholar · View at Scopus
  41. Y. Higami, T. Tsuchiya, T. Chiba et al., “Hepatic gene expression profile of lipid metabolism in rats: impact of caloric restriction and growth hormone/insulin-like growth factor-1 suppression,” The Journals of Gerontology. Series A, vol. 61, no. 11, pp. 1099–1110, 2006. View at Google Scholar · View at Scopus
  42. R. C. Oita, D. J. Mazzatti, F. L. Lim, J. R. Powell, and B. J. Merry, “Whole-genome microarray analysis identifies up-regulation of Nr4a nuclear receptors in muscle and liver from diet-restricted rats,” Mechanisms of Ageing and Development, vol. 130, no. 4, pp. 240–247, 2009. View at Publisher · View at Google Scholar · View at Scopus
  43. K. Saito, Y. Ohta, M. Sami, T. Kanda, and H. Kato, “Effect of mild restriction of food intake on gene expression profile in the liver of young rats: reference data for in vivo nutrigenomics study,” British Journal of Nutrition, vol. 104, no. 7, pp. 941–950, 2010. View at Publisher · View at Google Scholar · View at Scopus
  44. S. X. Cao, J. M. Dhahbi, P. L. Mote, and S. R. Spindler, “Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 19, pp. 10630–10635, 2001. View at Publisher · View at Google Scholar · View at Scopus
  45. R. Pohjanvirta, P. C. Boutros, I. D. Moffat, J. Lindén, D. Wendelin, and A. B. Okey, “Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue,” Toxicology and Applied Pharmacology, vol. 230, no. 1, pp. 41–56, 2008. View at Publisher · View at Google Scholar · View at Scopus
  46. J. C. Corton, U. Apte, S. P. Anderson et al., “Mimetics of caloric restriction include agonists of lipid-activated nuclear receptors,” Journal of Biological Chemistry, vol. 279, no. 44, pp. 46204–46212, 2004. View at Publisher · View at Google Scholar · View at Scopus
  47. T. Chiba, T. Tsuchiya, T. Komatsu et al., “Development of a bioassay to screen for chemicals mimicking the anti-aging effects of calorie restriction,” Biochemical and Biophysical Research Communications, vol. 401, no. 2, pp. 213–218, 2010. View at Publisher · View at Google Scholar · View at Scopus
  48. Y. Chen, C. Gondro, K. Quinn, R. M. Herd, P. F. Parnell, and B. Vanselow, “Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake,” Animal Genetics, vol. 42, no. 5, pp. 475–490, 2011. View at Publisher · View at Google Scholar · View at Scopus
  49. D. Du, Y.-H. Shi, and G.-W. Le, “Oxidative stress induced by high-glucose diet in liver of C57BL/6J mice and its underlying mechanism,” Molecular Biology Reports, vol. 37, no. 8, pp. 3833–3839, 2010. View at Publisher · View at Google Scholar · View at Scopus
  50. K. Nojima, K. Sugimoto, H. Ueda, N. Babaya, H. Ikegami, and H. Rakugi, “Analysis of hepatic gene expression profile in a spontaneous mouse model of type 2 diabetes under a high sucrose diet,” Endocrine Journal, vol. 60, no. 3, pp. 261–274, 2013. View at Google Scholar
  51. Y. Tokuji, K. Akiyama, K. Yunoki et al., “Screening for beneficial effects of oral intake of sweet corn by DNA microarray analysis,” Journal of Food Science, vol. 74, no. 7, pp. H197–H203, 2009. View at Publisher · View at Google Scholar · View at Scopus
  52. Y. Watanabe, A. Kamei, F. Shinozaki et al., “Ingested maple syrup evokes a possible liver-protecting effect-physiologic and genomic investigations with rats,” Bioscience, Biotechnology and Biochemistry, vol. 75, no. 12, pp. 2408–2410, 2011. View at Publisher · View at Google Scholar · View at Scopus
  53. T. Fukasawa, A. Kamei, Y. Watanabe, J. Koga, and K. Abe, “Short-chain fructooligosaccharide regulates hepatic peroxisome proliferator-activated receptor α and farnesoid X receptor target gene expression in Rats,” Journal of Agricultural and Food Chemistry, vol. 58, no. 11, pp. 7007–7012, 2010. View at Publisher · View at Google Scholar · View at Scopus
  54. T. Fukasawa, K. Murashima, T. Nemoto et al., “Identification of marker genes for lipid-lowering effect of a short-chain fructooligosaccharide by DNA microarray analysis,” Journal of Dietary Supplements, vol. 6, no. 3, pp. 254–262, 2009. View at Publisher · View at Google Scholar · View at Scopus
  55. S. Narasaka, Y. Endo, Z. Fu et al., “Safety evaluation of hypoallergenic wheat flour by using a DNA microarray,” Bioscience, Biotechnology and Biochemistry, vol. 70, no. 6, pp. 1464–1470, 2006. View at Publisher · View at Google Scholar · View at Scopus
  56. R. Martinez-Beamonte, M. A. Navarro, N. Guillen et al., “Postprandial transcriptome associated with virgin olive oil intake in rat liver,” Frontiers in Bioscience, vol. 3, pp. 11–21, 2011. View at Google Scholar · View at Scopus
  57. K. Yoshinari, S. Takagi, T. Yoshimasa, J. Sugatani, and M. Miwa, “Hepatic CYP3A expression is attenuated in obese mice fed a high-fat diet,” Pharmaceutical Research, vol. 23, no. 6, pp. 1188–1200, 2006. View at Publisher · View at Google Scholar · View at Scopus
  58. A. A. Toye, M. E. Dumas, C. Blancher et al., “Subtle metabolic and liver gene transcriptional changes underlie diet-induced fatty liver susceptibility in insulin-resistant mice,” Diabetologia, vol. 50, no. 9, pp. 1867–1879, 2007. View at Publisher · View at Google Scholar · View at Scopus
  59. W. R. Swindell, A. Johnston, and J. E. Gudjonsson, “Transcriptional profiles of leukocyte populations provide a tool for interpreting gene expression patterns associated with high fat diet in mice,” PLoS ONE, vol. 5, no. 7, Article ID e11861, 2010. View at Publisher · View at Google Scholar · View at Scopus
  60. Z. Xie, H. Li, K. Wang et al., “Analysis of transcriptome and metabolome profiles alterations in fatty liver induced by high-fat diet in rat,” Metabolism: Clinical and Experimental, vol. 59, no. 4, pp. 554–560, 2010. View at Publisher · View at Google Scholar · View at Scopus
  61. X. Deng, M. B. Elam, H. G. Wilcox et al., “Dietary olive oil and menhaden oil mitigate induction of lipogenesis in hyperinsulinemic corpulent JCR:LA-cp rats: microarray analysis of lipid-related gene expression,” Endocrinology, vol. 145, no. 12, pp. 5847–5861, 2004. View at Publisher · View at Google Scholar · View at Scopus
  62. D. Eletto, A. Leone, M. Bifulco, and M. F. Tecce, “Effect of unsaturated fat intake from Mediterranean diet on rat liver mRNA expression profile: selective modulation of genes involved in lipid metabolism,” Nutrition, Metabolism and Cardiovascular Diseases, vol. 15, no. 1, pp. 13–23, 2005. View at Publisher · View at Google Scholar · View at Scopus
  63. A. Lapillonne, S. D. Clarke, and W. C. Heird, “Polyunsaturated fatty acids and gene expression,” Current Opinion in Clinical Nutrition and Metabolic Care, vol. 7, no. 2, pp. 151–156, 2004. View at Publisher · View at Google Scholar · View at Scopus
  64. A. Berger, M. A. Roberts, and B. Hoff, “How dietary arachidonic- and docosahexaenoic- acid rich oils differentially affect the murine hepatic transcriptome,” Lipids in Health and Disease, vol. 5, article 10, 2006. View at Publisher · View at Google Scholar · View at Scopus
  65. N. Guillén, M. A. Navarro, C. Arnal et al., “Microarray analysis of hepatic gene expression identifies new genes involved in steatotic liver,” Physiological Genomics, vol. 37, no. 3, pp. 187–198, 2009. View at Publisher · View at Google Scholar · View at Scopus
  66. J. Miranda, A. Fernández-Quintela, I. Churruca, V. M. Rodríguez, E. Simón, and M. P. Portillo, “Hepatomegaly induced by trans-10,cis-12 conjugated linoleic acid in adult hamsters fed an atherogenic diet is not associated with steatosis,” Journal of the American College of Nutrition, vol. 28, no. 1, pp. 43–49, 2009. View at Google Scholar · View at Scopus
  67. C. M. Reynolds, S. Toomey, R. McBride et al., “Divergent effects of a CLA-enriched beef diet on metabolic health in ApoE-/- and ob/ob mice,” The Journal of Nutritional Biochemistry, vol. 24, no. 2, pp. 401–411, 2013. View at Google Scholar
  68. M. Inoue, T. Ohtake, W. Motomura et al., “Increased expression of PPARγ in high fat diet-induced liver steatosis in mice,” Biochemical and Biophysical Research Communications, vol. 336, no. 1, pp. 215–222, 2005. View at Publisher · View at Google Scholar · View at Scopus
  69. K. N. Maxwell, R. E. Soccio, E. M. Duncan, E. Sehayek, and J. L. Breslow, “Novel putative SREBP and LXR target genes identified by microarray analysis in liver of cholesterol-fed mice,” Journal of Lipid Research, vol. 44, no. 11, pp. 2109–2119, 2003. View at Publisher · View at Google Scholar · View at Scopus
  70. L. Vergnes, J. Phan, M. Strauss, S. Tafuri, and K. Reue, “Cholesterol and cholate components of an atherogenic diet induce distinct stages of hepatic inflammatory gene expression,” Journal of Biological Chemistry, vol. 278, no. 44, pp. 42774–42784, 2003. View at Publisher · View at Google Scholar · View at Scopus
  71. T. Režen, P. Juvan, K. Fon Tacer et al., “The sterolgene v0 cDNA microarray: a systemic approach to studies of cholesterol homeostasis and drug metabolism,” BMC Genomics, vol. 9, article 76, 2008. View at Publisher · View at Google Scholar · View at Scopus
  72. T. Obama, S. Nagaoka, K. Akagi et al., “Dietary cholesterol reduces plasma triacylglycerol in apolipoprotein E-null mice: suppression of lipin-1 and -2 in the glycerol-3-phosphate pathway,” PLoS ONE, vol. 6, no. 8, Article ID e22917, 2011. View at Publisher · View at Google Scholar · View at Scopus
  73. K. Takamatsu, N. Tachibana, I. Matsumoto, and K. Abe, “Soy protein functionality and nutrigenomic analysis,” BioFactors, vol. 21, no. 1–4, pp. 49–53, 2004. View at Google Scholar · View at Scopus
  74. N. Tachibana, I. Matsumoto, K. Fukui et al., “Intake of soy protein isolate alters hepatic gene expression in rats,” Journal of Agricultural and Food Chemistry, vol. 53, no. 10, pp. 4253–4257, 2005. View at Publisher · View at Google Scholar · View at Scopus
  75. H. Jia, S. Takahashi, K. Saito, and H. Kato, “DNA microarray analysis identified molecular pathways mediating the effects of supplementation of branched-chain amino acids on CCl4-induced cirrhosis in rats,” Molecular Nutrition & Food Research, vol. 57, no. 2, pp. 291–306, 2013. View at Google Scholar
  76. W. Zhou, S. Alonso, D. Takai et al., “Requirement of RIZ1 for cancer prevention by methyl-balanced diet,” PLoS ONE, vol. 3, no. 10, Article ID e3390, 2008. View at Publisher · View at Google Scholar · View at Scopus
  77. K. Ghoshal, X. Li, J. Datta et al., “A folate- and methyl-deficient diet alters the expression of DNA methyltransferases and methyl CpG binding proteins involved in epigenetic gene silencing in livers of F344 rats,” Journal of Nutrition, vol. 136, no. 6, pp. 1522–1527, 2006. View at Google Scholar · View at Scopus
  78. H. Mziaut, G. Korza, A. G. Elkahloun, and J. Ozols, “Induction of stearoyl CoA desaturase is associated with high-level induction of emerin RNA,” Biochemical and Biophysical Research Communications, vol. 282, no. 4, pp. 910–915, 2001. View at Publisher · View at Google Scholar · View at Scopus
  79. A. A. Toye, J. D. Lippiat, P. Proks et al., “A genetic and physiological study of impaired glucose homeostasis control in C57BL/6J mice,” Diabetologia, vol. 48, no. 4, pp. 675–686, 2005. View at Publisher · View at Google Scholar · View at Scopus
  80. G. Musso, R. Gambino, G. Pacini, F. De Michieli, and M. Cassader, “Prolonged saturated fat-induced, glucose-dependent insulinotropic polypeptide elevation is associated with adipokine imbalance and liver injury in nonalcoholic steatohepatitis: dysregulated enteroadipocyte axis as a novel feature of fatty liver,” American Journal of Clinical Nutrition, vol. 89, no. 2, pp. 558–567, 2009. View at Publisher · View at Google Scholar · View at Scopus
  81. M. Hoekstra, Z. Li, J. K. Kruijt, M. V. Eck, T. J. C. V. Berkel, and J. Kuiper, “The expression level of non-alcoholic fatty liver disease-related gene PNPLA3 in hepatocytes is highly influenced by hepatic lipid status,” Journal of Hepatology, vol. 52, no. 2, pp. 244–251, 2010. View at Publisher · View at Google Scholar · View at Scopus
  82. Y. Kim and T. Park, “DNA microarrays to define and search for genes associated with obesity,” Biotechnology Journal, vol. 5, no. 1, pp. 99–112, 2010. View at Publisher · View at Google Scholar · View at Scopus
  83. I. A. Kirpich, L. N. Gobejishvili, M. B. Homme et al., “Integrated hepatic transcriptome and proteome analysis of mice with high-fat diet-induced nonalcoholic fatty liver disease,” Journal of Nutritional Biochemistry, vol. 22, no. 1, pp. 38–45, 2011. View at Publisher · View at Google Scholar · View at Scopus
  84. A. J. Kreeft, C. J. A. Moen, G. Porter et al., “Genomic analysis of the response of mouse models to high-fat feeding shows a major role of nuclear receptors in the simultaneous regulation of lipid and inflammatory genes,” Atherosclerosis, vol. 182, no. 2, pp. 249–257, 2005. View at Publisher · View at Google Scholar · View at Scopus
  85. H. J. Jun, J. Kim, M. H. Hoang, and S. J. Lee, “Hepatic lipid accumulation alters global histone h3 lysine 9 and 4 trimethylation in the peroxisome proliferator-activated receptor alpha network,” PLoS ONE, vol. 7, no. 9, Article ID e44345, 2012. View at Google Scholar
  86. F. Capel, M. H. Delmotte, M. Brun et al., “Aging and obesity induce distinct gene expression adaptation in the liver of C57BL/6J mice,” Journal of Nutrigenetics and Nutrigenomics, vol. 4, no. 3, pp. 154–164, 2011. View at Publisher · View at Google Scholar · View at Scopus
  87. I. Alevizos, J. Misra, J. Bullen et al., “Linking hepatic transcriptional changes to high-fat diet induced physiology for diabetes-prone and obese-resistant mice,” Cell Cycle, vol. 6, no. 13, pp. 1631–1638, 2007. View at Google Scholar · View at Scopus
  88. J. Misra, I. Alevizos, D. Hwang, G. Stephanopoulos, and G. Stephanopoulos, “Linking physiology and transcriptional profiles by quantitative predictive models,” Biotechnology and Bioengineering, vol. 98, no. 1, pp. 252–260, 2007. View at Publisher · View at Google Scholar · View at Scopus
  89. D. Hall, C. Poussin, V. R. Velagapudi et al., “Peroxisomal and microsomal lipid pathways associated with resistance to hepatic steatosis and reduced pro-inflammatory state,” Journal of Biological Chemistry, vol. 285, no. 40, pp. 31011–31023, 2010. View at Publisher · View at Google Scholar · View at Scopus
  90. C. Poussin, M. Ibberson, D. Hall et al., “Oxidative phosphorylation flexibility in the liver of mice resistant to high-fat diet-induced hepatic steatosis,” Diabetes, vol. 60, no. 9, pp. 2216–2224, 2011. View at Publisher · View at Google Scholar · View at Scopus
  91. N. M. Morton, Y. B. Nelson, Z. Michailidou et al., “A stratified transcriptomics analysis of polygenic Fat and Lean mouse adipose tissues identifies novel candidate obesity genes,” PLoS ONE, vol. 6, no. 9, Article ID e23944, 2011. View at Publisher · View at Google Scholar · View at Scopus
  92. V. de Fourmestraux, H. Neubauer, C. Poussin et al., “Transcript profiling suggests that differential metabolic adaptation of mice to a high fat diet is associated with changes in liver to muscle lipid fluxes,” Journal of Biological Chemistry, vol. 279, no. 49, pp. 50743–50753, 2004. View at Publisher · View at Google Scholar · View at Scopus
  93. H. Li, Z. Xie, J. Lin et al., “Transcriptomic and metabonomic profiling of obesity-prone and obesity-resistant rats under high fat diet,” Journal of Proteome Research, vol. 7, no. 11, pp. 4775–4783, 2008. View at Publisher · View at Google Scholar · View at Scopus
  94. A. Vigé, C. Gallou-Kabani, M. S. Gross, A. Fabre, C. Junien, and J. P. Jais, “An oligonucleotide microarray for mouse imprinted genes profiling,” Cytogenetic and Genome Research, vol. 113, no. 1–4, pp. 253–261, 2006. View at Publisher · View at Google Scholar · View at Scopus
  95. K. M. Aagaard-Tillery, K. Grove, J. Bishop et al., “Developmental origins of disease and determinants of chromatin structure: maternal diet modifies the primate fetal epigenome,” Journal of Molecular Endocrinology, vol. 41, no. 1-2, pp. 91–102, 2008. View at Publisher · View at Google Scholar · View at Scopus
  96. J.-C. Chuang, H. Cui, B. L. Mason et al., “Chronic social defeat stress disrupts regulation of lipid synthesis,” Journal of Lipid Research, vol. 51, no. 6, pp. 1344–1353, 2010. View at Publisher · View at Google Scholar · View at Scopus
  97. A. M. Bérard, M.-F. Dumon, and M. Darmon, “Dietary fish oil up-regulates cholesterol 7α-hydroxylase mRNA in mouse liver leading to an increase in bile acid and cholesterol excretion,” FEBS Letters, vol. 559, no. 1–3, pp. 125–128, 2004. View at Publisher · View at Google Scholar · View at Scopus
  98. R. Rasooly, D. S. Kelley, J. Greg, and B. E. Mackey, “Dietary trans 10, cis 12-conjugated linoleic acid reduces the expression of fatty acid oxidation and drug detoxification enzymes in mouse liver,” British Journal of Nutrition, vol. 97, no. 1, pp. 58–66, 2007. View at Publisher · View at Google Scholar · View at Scopus
  99. A. Brolinson, S. Fourcade, A. Jakobsson, A. Pujol, and A. Jacobsson, “Steroid hormones control circadian Elovl3 expression in mouse liver,” Endocrinology, vol. 149, no. 6, pp. 3158–3166, 2008. View at Publisher · View at Google Scholar · View at Scopus
  100. K. Yunoki, G. Sasaki, Y. Tokuji et al., “Effect of dietary wine pomace extract and oleanolic acid on plasma lipids in rats fed high-fat diet and its DNA microarray analysis,” Journal of Agricultural and Food Chemistry, vol. 56, no. 24, pp. 12052–12058, 2008. View at Publisher · View at Google Scholar · View at Scopus
  101. Y. Kobayashi, M. Miyazawa, A. Kamei, K. Abe, and T. Kojima, “Ameliorative effects of mulberry (Morus alba L.) leaves on hyperlipidemia in rats fed a high-fat diet: induction of fatty acid oxidation, inhibition of lipogenesis, and suppression of oxidative stress,” Bioscience, Biotechnology and Biochemistry, vol. 74, no. 12, pp. 2385–2395, 2010. View at Publisher · View at Google Scholar · View at Scopus
  102. F. Aoki, S. Honda, H. Kishida et al., “Suppression by licorice flavonoids of abdominal fat accumulation and body weight gain in high-fat diet-induced obese C57BL/6J mice,” Bioscience, Biotechnology and Biochemistry, vol. 71, no. 1, pp. 206–214, 2007. View at Publisher · View at Google Scholar · View at Scopus
  103. R.-L. Yang, W. Li, Y.-H. Shi, and G.-W. Le, “Lipoic acid prevents high-fat diet-induced dyslipidemia and oxidative stress: a microarray analysis,” Nutrition, vol. 24, no. 6, pp. 582–588, 2008. View at Publisher · View at Google Scholar · View at Scopus
  104. Y. Kobayashi, T. Hiroi, M. Araki et al., “Facilitative effects of Eucommia ulmoides on fatty acid oxidation in hypertriglyceridaemic rats,” Journal of the Science of Food and Agriculture, vol. 92, no. 2, pp. 358–365, 2012. View at Publisher · View at Google Scholar · View at Scopus
  105. M. Zhou, S. Wang, A. Zhao et al., “Transcriptomic and metabonomic profiling reveal synergistic effects of quercetin and resveratrol supplementation in high fat diet fed mice,” Journal of Proteome Research, vol. 11, no. 10, pp. 4961–4971, 2012. View at Google Scholar
  106. Y. Kim, Y. Choi, and T. Park, “Hepatoprotective effect of oleuropein in mice: mechanisms uncovered by gene expression profiling,” Biotechnology Journal, vol. 5, no. 9, pp. 950–960, 2010. View at Publisher · View at Google Scholar · View at Scopus
  107. N. Togawa, R. Takahashi, S. Hirai, T. Fukushima, and Y. Egashira, “Gene expression analysis of the liver and skeletal muscle of psyllium-treated mice,” British Journal of Nutrition, pp. 1–11, 2012. View at Google Scholar
  108. J. Phan, T. Pesaran, R. C. Davis, and K. Reue, “The Diet1 locus confers protection against hypercholesterolemia through enhanced bile acid metabolism,” Journal of Biological Chemistry, vol. 277, no. 1, pp. 469–477, 2002. View at Publisher · View at Google Scholar · View at Scopus
  109. M. Asahina, W. Haruyama, Y. Ichida, M. Sakamoto, M. Sato, and K. Imaizumi, “Identification of SMEK2 as a candidate gene for regulation of responsiveness to dietary cholesterol in rats,” Journal of Lipid Research, vol. 50, no. 1, pp. 41–46, 2009. View at Publisher · View at Google Scholar · View at Scopus
  110. S. Watanabe, T. Katsube, H. Hattori et al., “Effect of Lactobacillus brevis 119-2 isolated from Tsuda kabu red turnips on cholesterol levels in cholesterol-administered rats,” Journal of Bioscience and Bioengineering, vol. 116, no. 1, pp. 45–51, 2013. View at Publisher · View at Google Scholar
  111. A. Sirvent, T. Claudel, G. Martin et al., “The farnesoid X receptor induces very low density lipoprotein receptor gene expression,” FEBS Letters, vol. 566, no. 1–3, pp. 173–177, 2004. View at Publisher · View at Google Scholar · View at Scopus
  112. Y. Endo, Z. Fu, K. Abe, S. Arai, and H. Kato, “Dietary protein quantity and quality affect rat hepatic gene expression,” Journal of Nutrition, vol. 132, no. 12, pp. 3632–3637, 2002. View at Google Scholar · View at Scopus
  113. H. Kato and T. Kimura, “Evaluation of the effects of the dietary intake of proteins and amino acids by DNA microarray technology,” Journal of Nutrition, vol. 133, no. 6, 2003. View at Google Scholar · View at Scopus
  114. H. Kato, S. Narasaka, Y. Endo, K. Abe, and S. Arai, “DNA microarray analyses of the effects of dietary proteins,” BioFactors, vol. 21, no. 1–4, pp. 11–13, 2004. View at Google Scholar · View at Scopus
  115. W. Imamura, R. Yoshimura, M. Takai, J. Yamamura, R. Kanamoto, and H. Kato, “Adverse effects of excessive leucine intake depend on dietary protein intake: a transcriptomic analysis to identify useful biomarkers,” Journal of Nutritional Science and Vitaminology, vol. 59, no. 1, pp. 45–55, 2013. View at Google Scholar
  116. A. Gornicka, G. Morris-Stiff, S. Thapaliya, B. G. Papouchado, M. Berk, and A. E. Feldstein, “Transcriptional profile of genes involved in oxidative stress and antioxidant defense in a dietary murine model of steatohepatitis,” Antioxidants and Redox Signaling, vol. 15, no. 2, pp. 437–445, 2011. View at Publisher · View at Google Scholar · View at Scopus
  117. M. Oster, E. Murani, C. C. Metges, S. Ponsuksili, and K. Wimmers, “A low protein diet during pregnancy provokes a lasting shift of hepatic expression of genes related to cell cycle throughout ontogenesis in a porcine model,” BMC Genomics, vol. 13, no. 1, article 93, 2012. View at Publisher · View at Google Scholar · View at Scopus
  118. H. Oike, K. Nagai, T. Fukushima, N. Ishida, and M. Kobori, “High-salt diet advances molecular circadian rhythms in mouse peripheral tissues,” Biochemical and Biophysical Research Communications, vol. 402, no. 1, pp. 7–13, 2010. View at Publisher · View at Google Scholar · View at Scopus
  119. O. Yoshinari, A. Takenake, and K. Igarashi, “Trigonelline ameliorates oxidative stress in type 2 diabetic Goto-Kakizaki rats,” Journal of Medicinal Food, vol. 16, no. 1, pp. 34–41, 2013. View at Google Scholar
  120. J. Champier, F. Claustrat, N. Nazaret, M. F. Montange, and B. Claustrat, “Folate depletion changes gene expression of fatty acid metabolism, DNA synthesis, and circadian cycle in male mice,” Nutrition Research, vol. 32, no. 2, pp. 124–132, 2012. View at Publisher · View at Google Scholar · View at Scopus
  121. L. Massip, C. Garand, E. R. Paquet et al., “Vitamin C restores healthy aging in a mouse model for Werner syndrome,” FASEB Journal, vol. 24, no. 1, pp. 158–172, 2010. View at Publisher · View at Google Scholar · View at Scopus
  122. L. Barella, P. Y. Muller, M. Schlachter et al., “Identification of hepatic molecular mechanisms of action of alpha-tocopherol using global gene expression profile analysis in rats,” Biochimica et Biophysica Acta, vol. 1689, no. 1, pp. 66–74, 2004. View at Publisher · View at Google Scholar · View at Scopus
  123. S. Nell, R. Bahtz, A. Boßecker et al., “PCR-verified microarray analysis and functional in vitro studies indicate a role of α-tocopherol in vesicular transport,” Free Radical Research, vol. 41, no. 8, pp. 930–942, 2007. View at Publisher · View at Google Scholar · View at Scopus
  124. Y. Ohsaki, H. Shirakawa, K. Hiwatashi, Y. Furukawa, T. Mizutani, and M. Komai, “Vitamin K suppresses lipopolysaccharide-induced inflammation in the rat,” Bioscience, Biotechnology and Biochemistry, vol. 70, no. 4, pp. 926–932, 2006. View at Publisher · View at Google Scholar · View at Scopus
  125. H. tom Dieck, F. Döring, D. Fuchs, H.-P. Roth, and H. Daniel, “Transcriptome and proteome analysis identifies the pathways that increase hepatic lipid accumulation in zinc-deficient rats,” Journal of Nutrition, vol. 135, no. 2, pp. 199–205, 2005. View at Google Scholar · View at Scopus
  126. A. Kamei, Y. Watanabe, T. Ishijima et al., “Dietary iron-deficient anemia induces a variety of metabolic changes and even apoptosis in rat liver: a DNA microarray study,” Physiological Genomics, vol. 42, no. 2, pp. 149–156, 2010. View at Publisher · View at Google Scholar · View at Scopus
  127. H. Zeng, C. D. Davis, and J. W. Finley, “Effect of selenium-enriched broccoli diet on differential gene expression in min mouse liver,” Journal of Nutritional Biochemistry, vol. 14, no. 4, pp. 227–231, 2003. View at Publisher · View at Google Scholar · View at Scopus
  128. J. M. Lou-Bonafonte, C. Arnal, M. A. Navarro, and J. Osada, “Efficacy of bioactive compounds from extra virgin olive oil to modulate atherosclerosis development,” Molecular Nutrition & Food Research, vol. 56, no. 7, pp. 1043–1057, 2012. View at Google Scholar
  129. S. Acín, M. A. Navarro, J. S. Perona et al., “Microarray analysis of hepatic genes differentially expressed in the presence of the unsaponifiable fraction of olive oil in apolipoprotein E-deficient mice,” British Journal of Nutrition, vol. 97, no. 4, pp. 628–638, 2007. View at Publisher · View at Google Scholar · View at Scopus
  130. N. Guillen, S. Acín, J. C. Surra et al., “Apolipoprotein E determines the hepatic transcriptional profile of dietary maslinic acid in mice,” Journal of Nutritional Biochemistry, vol. 20, no. 11, pp. 882–893, 2009. View at Publisher · View at Google Scholar · View at Scopus
  131. J. A. Menendez, J. Joven, G. Aragonès et al., “Xenohormetic and anti-aging activity of secoiridoid polyphenols present in extra virgin olive oil: a new family of gerosuppressant agents,” Cell Cycle, vol. 12, no. 4, pp. 555–578, 2013. View at Google Scholar
  132. M.-L. Ricketts, M. V. Boekschoten, A. J. Kreeft et al., “The cholesterol-raising factor from coffee beans, cafestol, as an agonist ligand for the farnesoid and pregnane X receptors,” Molecular Endocrinology, vol. 21, no. 7, pp. 1603–1616, 2007. View at Publisher · View at Google Scholar · View at Scopus
  133. C. Luceri, L. Giovannelli, V. Pitozzi et al., “Liver and colon DNA oxidative damage and gene expression profiles of rats fed Arabidopsis thaliana mutant seeds containing contrasted flavonoids,” Food and Chemical Toxicology, vol. 46, no. 4, pp. 1213–1220, 2008. View at Publisher · View at Google Scholar · View at Scopus
  134. M. Kobori, S. Masumoto, Y. Akimoto, and Y. Takahashi, “Dietary quercetin alleviates diabetic symptoms and reduces streptozotocin-induced disturbance of hepatic gene expression in mice,” Molecular Nutrition & Food Research, vol. 53, no. 7, pp. 859–868, 2009. View at Publisher · View at Google Scholar · View at Scopus
  135. Y. Takahashi, T.-O. Odbayar, and T. Ide, “A comparative analysis of genistein and daidzein in affecting lipid metabolism in rat liver,” Journal of Clinical Biochemistry and Nutrition, vol. 44, no. 3, pp. 223–230, 2009. View at Publisher · View at Google Scholar · View at Scopus
  136. R. Kitawaki, Y. Nishimura, N. Takagi, M. Iwasaki, K. Tsuzuki, and M. Fukuda, “Effects of lactobacillus fermented soymilk and soy yogurt on hepatic lipid accumulation in rats fed a cholesterol-free diet,” Bioscience, Biotechnology and Biochemistry, vol. 73, no. 7, pp. 1484–1488, 2009. View at Publisher · View at Google Scholar · View at Scopus
  137. T. Ide, J. S. Lim, T.-O. Odbayar, and Y. Nakashima, “Comparative study of sesame lignans (Sesamin, Episesamin and Sesamolin) affecting gene expression profile and fatty acidoxidation in rat liver,” Journal of Nutritional Science and Vitaminology, vol. 55, no. 1, pp. 31–43, 2009. View at Publisher · View at Google Scholar · View at Scopus
  138. T. Ide, Y. Nakashima, H. Iida, S. Yasumoto, and M. Katsuta, “Lipid metabolism and nutrigenomics—impact of sesame lignans on gene expression profiles and fatty acid oxidation in rat liver,” Forum of Nutrition, vol. 61, pp. 10–24, 2009. View at Publisher · View at Google Scholar · View at Scopus
  139. N. Tsuruoka, A. Kidokoro, I. Matsumoto, K. Abe, and Y. Kiso, “Modulating effect of sesamin, a functional lignan in sesame seeds, on the transcription levels of lipid- and alcohol-metabolizing enzymes in rat liver: a DNA microarray study,” Bioscience, Biotechnology and Biochemistry, vol. 69, no. 1, pp. 179–188, 2005. View at Publisher · View at Google Scholar · View at Scopus
  140. Y. Kiso, “Antioxidative roles of sesamin, a functional lignan in sesame seed, and it's effect on lipid- and alcohol-metabolism in the liver: a DNA microarray study,” BioFactors, vol. 21, no. 1–4, pp. 191–196, 2004. View at Google Scholar · View at Scopus
  141. Y. Kiso, N. Tsuruoka, A. Kidokoro, I. Matsumoto, and K. Abe, “Sesamin ingestion regulates the transcription levels of hepatic metabolizing enzymes for alcohol and lipids in rats,” Alcoholism: Clinical and Experimental Research, vol. 29, no. 11, pp. 116S–120S, 2005. View at Publisher · View at Google Scholar · View at Scopus
  142. K. Motojima and T. Hirai, “Peroxisome proliferator-activated receptor α plays a vital role in inducing a detoxification system against plant compounds with crosstalk with other xenobiotic nuclear receptors,” FEBS Journal, vol. 273, no. 2, pp. 292–300, 2006. View at Publisher · View at Google Scholar · View at Scopus
  143. Y. M. Choi, I. S. Choi, S. M. Lee, D. Y. Hwang, Y. W. Choi, and Y. H. Park, “Transcriptome analysis of the effects of gomisin a on the recovery of carbon tetrachloride-induced damage in rat liver,” Laboratory Animal Research, vol. 27, no. 2, pp. 161–169, 2011. View at Google Scholar
  144. M. Kamakura, T. Moriyama, and T. Sakaki, “Changes in hepatic gene expression associated with the hypocholesterolaemic activity of royal jelly,” Journal of Pharmacy and Pharmacology, vol. 58, no. 12, pp. 1683–1689, 2006. View at Publisher · View at Google Scholar · View at Scopus
  145. M. Kamakura, M. Maebuchi, S. Ozasa et al., “Influence of royal jelly on mouse hepatic gene expression and safety assessment with a DNA microarray,” Journal of Nutritional Science and Vitaminology, vol. 51, no. 3, pp. 148–155, 2005. View at Google Scholar · View at Scopus
  146. R. Im, H. Mano, S. Nakatani, J. Shimizu, and M. Wada, “Safety evaluation of the aqueous extract Kothala himbutu (Salacia reticulata) stem in the hepatic gene expression profile of normal mice using DNA microarrays,” Bioscience, Biotechnology and Biochemistry, vol. 72, no. 12, pp. 3075–3083, 2008. View at Publisher · View at Google Scholar · View at Scopus
  147. W.-Y. Cheng, S.-L. Wu, C.-Y. Hsiang et al., “Relationship between San-Huang-Xie-Xin-Tang and its herbal components on the gene expression profiles in HepG2 cells,” American Journal of Chinese Medicine, vol. 36, no. 4, pp. 783–797, 2008. View at Publisher · View at Google Scholar · View at Scopus
  148. F. M. Han, X. M. Zhang, Q. S. Xia, J. J. Wang, and Y. Chen, “Gene expression profiling of mice liver tissue after intragastric administration of Chinese nutgall extract,” Fen Zi Xi Bao Sheng Wu Xue Bao, vol. 42, no. 2, pp. 101–108, 2009. View at Google Scholar · View at Scopus
  149. C.-C. Li, C.-Y. Hsiang, S.-L. Wu, and T.-Y. Ho, “Identification of novel mechanisms of silymarin on the carbon tetrachloride-induced liver fibrosis in mice by nuclear factor-κB bioluminescent imaging-guided transcriptomic analysis,” Food and Chemical Toxicology, vol. 50, no. 5, pp. 1568–1575, 2012. View at Publisher · View at Google Scholar · View at Scopus
  150. K. Abe, N. Okada, H. Tanabe et al., “Effects of chronic ingestion of catechin-rich green tea on hepatic gene expression of gluconeogenic enzymes in rats,” Biomedical Research, vol. 30, no. 1, pp. 25–29, 2009. View at Google Scholar · View at Scopus
  151. Q. Meng, C. N. Velalar, and R. Ruan, “Regulating the age-related oxidative damage, mitochondrial integrity, and antioxidative enzyme activity in Fischer 344 rats by supplementation of the antioxidant epigallocatechin-3-gallate,” Rejuvenation Research, vol. 11, no. 3, pp. 649–660, 2008. View at Publisher · View at Google Scholar · View at Scopus
  152. K. Aizawa, T. Matsumoto, T. Inakuma et al., “Administration of tomato and paprika beverages modifies hepatic glucose and lipid metabolism in mice: a DNA microarray analysis,” Journal of Agricultural and Food Chemistry, vol. 57, no. 22, pp. 10964–10971, 2009. View at Publisher · View at Google Scholar · View at Scopus
  153. N. Matsui, R. Ito, E. Nishimura et al., “Ingested cocoa can prevent high-fat diet-induced obesity by regulating the expression of genes for fatty acid metabolism,” Nutrition, vol. 21, no. 5, pp. 594–601, 2005. View at Publisher · View at Google Scholar · View at Scopus
  154. D. L. Croteau, N. C. de Souza-Pinto, C. Harboe et al., “DNA repair and the accumulation of oxidatively damaged DNA are affected by fruit intake in mice,” The Journals of Gerontology. Series A, vol. 65, no. 12, pp. 1300–1311, 2010. View at Google Scholar
  155. M. Sato, Y. Tokuji, S. Yoneyama, K. Fujii-Akiyama, M. Kinoshita, and M. Ohnishi, “Profiling of hepatic gene expression of mice fed with edible Japanese mushrooms by DNA microarray analysis: comparison among pleurotus ostreatus, Grifola frondosa, and Hypsizigus marmoreus,” Journal of Agricultural and Food Chemistry, vol. 59, no. 19, pp. 10723–10731, 2011. View at Publisher · View at Google Scholar · View at Scopus
  156. R. Izuchi, Y. Nakai, H. Takahashi et al., “Hepatic gene expression of the insulin signaling pathway is altered by administration of persimmon peel extract: a DNA microarray study using type 2 diabetic Goto-Kakizaki rats,” Journal of Agricultural and Food Chemistry, vol. 59, no. 7, pp. 3320–3329, 2011. View at Publisher · View at Google Scholar · View at Scopus
  157. G. C. Han, S. K. Ko, J. H. Sung, and S. H. Chung, “Compound K enhances insulin secretion with beneficial metabolic effects in db/db mice,” Journal of Agricultural and Food Chemistry, vol. 55, no. 26, pp. 10641–10648, 2007. View at Publisher · View at Google Scholar · View at Scopus
  158. A. Labbé, C. Garand, V. C. Cogger et al., “Resveratrol improves insulin resistance hyperglycemia and hepatosteatosis but not hypertriglyceridemia, inflammation, and life span in a mouse model for werner syndrome,” The Journals of Gerontology. Series A, vol. 66, no. 3, pp. 264–278, 2011. View at Publisher · View at Google Scholar · View at Scopus
  159. R. Im, H. Mano, T. Matsuura, S. Nakatani, J. Shimizu, and M. Wada, “Mechanisms of blood glucose-lowering effect of aqueous extract from stems of Kothala himbutu (Salacia reticulata) in the mouse,” Journal of Ethnopharmacology, vol. 121, no. 2, pp. 234–240, 2009. View at Publisher · View at Google Scholar · View at Scopus
  160. S. Honda, F. Aoki, H. Tanaka et al., “Effects of ingested turmeric oleoresin on glucose and lipid metabolisms in obese diabetic mice: a DNA microarray study,” Journal of Agricultural and Food Chemistry, vol. 54, no. 24, pp. 9055–9062, 2006. View at Publisher · View at Google Scholar · View at Scopus
  161. Y. Jiang, Z.-S. Li, F.-S. Jiang, X. Deng, C.-S. Yao, and G. Nie, “Effects of different ingredients of zedoary on gene expression of HSC-T6 cells,” World Journal of Gastroenterology, vol. 11, no. 43, pp. 6780–6786, 2005. View at Google Scholar · View at Scopus
  162. R. C. Prasad, B. Herzog, B. Boone, L. Sims, and M. Waltner-Law, “An extract of Syzygium aromaticum represses genes encoding hepatic gluconeogenic enzymes,” Journal of Ethnopharmacology, vol. 96, no. 1-2, pp. 295–301, 2005. View at Publisher · View at Google Scholar · View at Scopus
  163. S. Yoshiko and N. Hoyoko, “Fucoxanthin, a natural carotenoid, induces G1 arrest and GADD45 gene expression in human cancer cells,” In Vivo, vol. 21, no. 2, pp. 305–309, 2007. View at Google Scholar · View at Scopus
  164. Y. Masuo, T. Imai, J. Shibato et al., “Omic analyses unravels global molecular changes in the brain and liver of a rat model for chronic Sake (Japanese alcoholic beverage) intake,” Electrophoresis, vol. 30, no. 8, pp. 1259–1275, 2009. View at Publisher · View at Google Scholar · View at Scopus
  165. I. V. Deaciuc, X. Peng, N. B. D'Souza et al., “Microarray gene analysis of the liver in a rat model of chronic, voluntary alcohol intake,” Alcohol, vol. 32, no. 2, pp. 113–127, 2004. View at Publisher · View at Google Scholar · View at Scopus
  166. R. Stierum, A. Conesa, W. Heijne et al., “Transcriptome analysis provides new insights into liver changes induced in the rat upon dietary administration of the food additives butylated hydroxytoluene, curcumin, propyl gallate and thiabendazole,” Food and Chemical Toxicology, vol. 46, no. 8, pp. 2616–2628, 2008. View at Publisher · View at Google Scholar · View at Scopus
  167. S. Nair, C. Xu, G. Shen et al., “Pharmacogenomics of phenolic antioxidant butylated hydroxyanisole (BHA) in the small intestine and liver of Nrf2 knockout and C57BL/6J mice,” Pharmaceutical Research, vol. 23, no. 11, pp. 2621–2637, 2006. View at Publisher · View at Google Scholar · View at Scopus
  168. G. M. Karere, J. P. Glenn, J. L. VandeBerg, and L. A. Cox, “Differential microRNA response to a high-cholesterol, high-fat diet in livers of low and high LDL-C baboons,” BMC Genomics, vol. 13, p. 320, 2012. View at Publisher · View at Google Scholar
  169. K. C. Vickers, B. M. Shoucri, M. G. Levin et al., “MicroRNA-27b is a regulatory hub in lipid metabolism and is altered in dyslipidemia,” Hepatology, vol. 57, no. 2, pp. 533–542, 2013. View at Publisher · View at Google Scholar
  170. A. Dolganiuc, J. Petrasek, K. Kodys et al., “MicroRNA expression profile in lieber-decarli diet-induced alcoholic and methionine choline deficient diet-induced nonalcoholic steatohepatitis models in mice,” Alcoholism: Clinical and Experimental Research, vol. 33, no. 10, pp. 1704–1710, 2009. View at Publisher · View at Google Scholar · View at Scopus
  171. B. Wang, S. Majumder, G. Nuovo et al., “Role of microRNA-155 at early stages of hepatocarcinogenesis induced by choline-deficient and amino acid-defined diet in C57BL/6 mice,” Hepatology, vol. 50, no. 4, pp. 1152–1161, 2009. View at Publisher · View at Google Scholar · View at Scopus
  172. W. P. Tsang and T. T. Kwok, “Epigallocatechin gallate up-regulation of miR-16 and induction of apoptosis in human cancer cells,” Journal of Nutritional Biochemistry, vol. 21, no. 2, pp. 140–146, 2010. View at Publisher · View at Google Scholar · View at Scopus
  173. T. Chen, T. D. Williams, A. Mally et al., “Gene expression and epigenetic changes by furan in rat liver,” Toxicology, vol. 292, no. 2-3, pp. 63–70, 2012. View at Publisher · View at Google Scholar · View at Scopus