Nutritional systems biology of type 2 diabetes

Genes and Nutrition

Volumn 10, Issue 5, 2015, Pages

  Zhao, Yuqi ^a   Barrere Cain, Rio Elizabeth ^a   Yang, Xia ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Diet; Nutrition; Omics; Systems biology; Type 2 diabetes

Indexed keywords

HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE KINASE; INSULIN; IRON; LONG UNTRANSLATED RNA; MESSENGER RNA; MICRORNA; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA COACTIVATOR 1ALPHA; PROTEOME; SIRTUIN 1; SMALL INTERFERING RNA; TRANSCRIPTOME; VITAMIN D;

ARTICLE; BIOMICS; DIET; DIETARY INTAKE; DNA METHYLATION; EPIGENETICS; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GLUCOSE METABOLISM; HIGH FRUCTOSE DIET; HIGH SUCROSE DIET; HIGH THROUGHPUT SEQUENCING; HUMAN; INSULIN RELEASE; INSULIN RESISTANCE; INTESTINE FLORA; LIPID DIET; METABOLOMICS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NON INSULIN DEPENDENT DIABETES MELLITUS; NONHUMAN; NUTRIEPIGENOMICS; NUTRIMETABOLOMICS; NUTRIMICROBIOMICS; NUTRIPROTEOMICS; NUTRITIONAL DISORDER; NUTRITIONAL IMBALANCE; NUTRITIONAL SYSTEMS BIOLOGY; NUTRITRANSCRIPTOMICS; PANCREAS ISLET BETA CELL; PANCREAS ISLET CELL FUNCTION; PATHOGENESIS; PROTEIN PROCESSING; PROTEIN RESTRICTION; PROTEOMICS; RISK FACTOR; RNA SEQUENCE; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS;

EID: 84938086595     PISSN: 15558932     EISSN: 18653499     Source Type: Journal    
DOI: 10.1007/s12263-015-0481-3     Document Type: Article

References (138)

1. Abdelmalek MF et al (2012) Higher dietary fructose is associated with impaired hepatic adenosine triphosphate homeostasis in obese individuals with type 2 diabetes. Hepatology 56:952–960
2. Ahmad S et al (2013) PPAR signaling pathway is a key modulator of liver proteome in pups born to vitamin B-12 deficient rats. J Proteomics 91:297–308. doi:10.1016/j.jprot.2013.07.027
3. Akude E, Zherebitskaya E, Chowdhury SK, Smith DR, Dobrowsky RT, Fernyhough P (2011) Diminished superoxide generation is associated with respiratory chain dysfunction and changes in the mitochondrial proteome of sensory neurons from diabetic rats. Diabetes 60:288–297. doi:10.2337/db10-0818
4. Albenberg LG, Wu GD (2014) Diet and the intestinal microbiome: associations, functions, and implications for health and disease. Gastroenterology 146:1564–1572. doi:10.1053/j.gastro.2014.01.058
5. Alberti KGM, Zimmet P (2013) Epidemiology: global burden of disease—Where does diabetes mellitus fit in? Nat Rev Endocrinol 9:258–260
6. Ardisson Korat AV, Willett WC, Hu FB (2014) Diet, lifestyle, and genetic risk factors for type 2 diabetes: a review from the nurses’ health study, nurses’ health study 2, and health professionals’ follow-up study. Curr Nutr Rep 3:345–354. doi:10.1007/s13668-014-0103-5
7. Asif M (2014) The prevention and control the type-2 diabetes by changing lifestyle and dietary pattern. J Educ Health Promot 3:1. doi:10.4103/2277-9531.127541
8. Atkins RC, Zimmet P, St I-IWKD (2010) DIABETES diabetic kidney disease: act now or pay later. Nat Rev Nephrol 6:134–136. doi:10.1038/nrneph.2010.10
9. Barbosa-Sampaio HC et al (2013) Nupr1 deletion protects against glucose intolerance by increasing beta cell mass. Diabetologia 56:2477–2486. doi:10.1007/s00125-013-3006-x
10. Bennett BJ et al (2010) A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res 20:281–290. doi:10.1101/gr.099234.109
11. Bordbar A, Palsson BO (2012) Using the reconstructed genome-scale human metabolic network to study physiology and pathology. J Intern Med 271:131–141. doi:10.1111/j.1365-2796.2011.02494.x
12. Breker M, Schuldiner M (2014) The emergence of proteome-wide technologies: systematic analysis of proteins comes of age. Nat Rev Mol Cell Biol 15:453–464. doi:10.1038/Nrm3821
13. Capozzi F, Bordoni A (2013) Foodomics: a new comprehensive approach to food and nutrition. Genes Nutr 8:1–4. doi:10.1007/s12263-012-0310-x
14. Cech TR, Steitz JA (2014) The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157:77–94. doi:10.1016/j.cell.2014.03.008
15. Chang W-C, Jia H, Aw W, Saito K, Hasegawa S, Kato H (2014) Beneficial effects of soluble dietary Jerusalem artichoke (Helianthus tuberosus) in the prevention of the onset of type 2 diabetes and non-alcoholic fatty liver disease in high-fructose diet-fed rats. Br J Nutr 112:709–717. doi:10.1017/s0007114514001421
16. Chassaing B, Koren O, Goodrich JK, Poole AC, Srinivasan S, Ley RE, Gewirtz AT (2015) Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature 519:92–96. doi:10.1038/nature14232
17. Chen L, Magliano DJ, Zimmet PZ (2012a) The worldwide epidemiology of type 2 diabetes mellitus-present and future perspectives. Nat Rev Endocrinol 8:228–236. doi:10.1038/nrendo.2011.183
18. Chen R et al (2012b) Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148:1293–1307. doi:10.1016/j.cell.2012.02.009
19. Choi SW, Claycombe KJ, Martinez JA, Friso S, Schalinske KL (2013) Nutritional epigenomics: a portal to disease prevention advances. Nutrition 4:530–532. doi:10.3945/an.113.004168
20. Chowdhury SKR, Dobrowsky RT, Femyhough P (2011) Nutrient excess and altered mitochondrial proteome and function contribute to neurodegeneration in diabetes. Mitochondrion 11:845–854. doi:10.1016/j.mito.2011.06.007
21. Cirillo P et al (2009) Ketohexokinase-dependent metabolism of fructose induces proinflammatory mediators in proximal tubular cells. J Am Soc Nephrol 20:545–553. doi:10.1681/Asn.2008060576
22. Coffey R, Nam H, Knutson MD (2014) Microarray analysis of rat pancreas reveals altered expression of Alox15 and regenerating islet-derived genes in response to iron deficiency and overload. PLoS ONE. doi:10.1371/journal.pone.0086019
23. Cui J, Le G, Yang R, Shi Y (2009) Lipoic acid attenuates high fat diet-induced chronic oxidative stress and immunosuppression in mice jejunum: a microarray analysis. Cell Immunol 260:44–50. doi:10.1016/j.cellimm.2009.08.001
24. da Silva VR et al (2013) Metabolite profile analysis reveals functional effects of 28-day vitamin B-6 restriction on one-carbon metabolism and tryptophan catabolic pathways in healthy men and women. J Nutr 143:1719–1727
25. Dangwal S et al (2015) Impairment of wound healing in patients with type 2 diabetes mellitus influences circulating MicroRNA patterns via inflammatory cytokines. Arterioscl Throm Vas 35:1480–1488. doi:10.1161/Atvbaha.114.305048
26. David LA et al (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559. doi:10.1038/Nature12820
27. De Filippo C et al (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci 107:14691–14696
28. de Fourmestraux V et al (2004) Transcript profiling suggests that differential metabolic adaptation of mice to a high fat diet is associated with changes in liver to muscle lipid fluxes. J Biol Chem 279:50743–50753. doi:10.1074/jbc.M408014200
29. de Graaf AA et al (2009) Nutritional systems biology modeling: from molecular mechanisms to physiology. PLoS Comput Biol. doi:10.1371/journal.pcbi.1000554
30. de Wilde J et al (2009) An 8-week high-fat diet induces obesity and insulin resistance with small changes in the muscle transcriptome of C57BL/6J mice. J Nutrigenetics Nutrigenomics 2:280–291. doi:10.1159/000308466
31. Dearden L, Balthasar N (2014) Sexual dimorphism in offspring glucose-sensitive hypothalamic gene expression and physiological responses to maternal high-fat diet feeding. Endocrinology 155:2144–2154
32. Deng WJ, Nie S, Dai J, Wu JR, Zeng R (2010) Proteome, phosphoproteome, and hydroxyproteome of liver mitochondria in diabetic rats at early pathogenic stages. Mol Cell Proteomics 9:100–116. doi:10.1074/mcp.M900020-MCP200
33. Devkota S et al (2012) Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/-mice. Nature 487:104–108
34. Di Bella JM, Bao YG, Gloor GB, Burton JP, Reid G (2013) High throughput sequencing methods and analysis for microbiome research. J Microbiol Meth 95:401–414. doi:10.1016/j.mimet.2013.08.011
35. Ding Y et al (2013) DNA hypomethylation of inflammation-associated genes in adipose tissue of female mice after multigenerational high fat diet feeding. Int J Obes (Lond). doi:10.1038/ijo.2013.98
36. Donath MY, Shoelson SE (2011) Type 2 diabetes as an inflammatory disease. Nat Rev Immunol 11:98–107. doi:10.1038/Nri2925
37. Eckel-Mahan KL et al (2013) Reprogramming of the circadian clock by nutritional challenge. Cell 155:1464–1478. doi:10.1016/j.cell.2013.11.034
38. Eid J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138. doi:10.1126/science.1162986
39. Finkelstein JL, Pressman EK, Cooper EM, Kent TR, Bar HY, O’Brien KO (2014) Vitamin D status affects serum metabolomic profiles in pregnant adolescents. Reprod Sci. doi:10.1177/1933719114556477
40. Gao Z et al (2009) Butyrate improves insulin sensitivity and increases energy expenditure in mice. Diabetes 58:1509–1517. doi:10.2337/db08-1637
41. Ghazalpour A et al (2012) Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits. Mamm Genome 23:680–692. doi:10.1007/s00335-012-9411-5
42. Gibbons H, O’Gorman A, Brennan L (2015) Metabolomics as a tool in nutritional research. Curr Opin Lipidol 26:30–34. doi:10.1097/Mol.0000000000000140
43. Gika HG, Theodoridis GA, Plumb RS, Wilson ID (2014) Current practice of liquid chromatography–mass spectrometry in metabolomics and metabonomics. J Pharm Biomed Anal 87:12–25. doi:10.1016/j.jpba.2013.06.032
44. Ginter E, Simko V (2013) Type 2 diabetes mellitus, pandemic in 21st century. Adv Exp Med Biol 771:42–50
45. Gluckman PD, Hanson MA, Buklijas T, Low FM, Beedle AS (2009) Epigenetic mechanisms that underpin metabolic and cardiovascular diseases. Nat Rev Endocrinol 5:401–408. doi:10.1038/nrendo.2009.102
46. Goran MI, Ulijaszek SJ, Ventura EE (2013) High fructose corn syrup and diabetes prevalence: a global perspective. Glob Pub Health 8:55–64. doi:10.1080/17441692.2012.736257
47. Guo YR et al (2013) Quantitative proteomic and functional analysis of liver mitochondria from high fat diet (HFD) diabetic mice. Mol Cell Proteomics 12:3744–3758
48. Hartstra AV, Bouter KEC, Backhed F, Nieuwdorp M (2015) Insights into the role of the microbiome in obesity and type 2 diabetes. Diabetes Care 38:159–165. doi:10.2337/Dc14-0769
49. Heyn H, Esteller M (2012) DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet 13:679–692. doi:10.1038/Nrg3270
50. Holoch D, Moazed D (2015) RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet 16:71–84. doi:10.1038/Nrg3863
51. Hu FB (2011) Globalization of diabetes: the role of diet, lifestyle, and genes. Diabetes Care 34:1249–1257. doi:10.2337/dc11-0442
52. Inoue M et al (2005) Increased expression of PPAR gamma in high fat diet-induced liver steatosis in mice. Biochem Biophys Res Commun 336:215–222. doi:10.1016/j.bbrc.2005.08.070
53. Ioannidis JPA, Tarone R, McLaughlin JK (2011) The false-positive to false-negative ratio in epidemiologic studies. Epidemiology 22:450–456. doi:10.1097/Ede.0b013e31821b506e
54. Kaidar-Person O, Person B, Szomstein S, Rosenthal RJ (2008a) Nutritional deficiencies in morbidly obese patients: a new form of malnutrition? Part A: vitamins. Obes Surg 18:870–876. doi:10.1007/s11695-007-9349-y
55. Kaidar-Person O, Person B, Szomstein S, Rosenthal RJ (2008b) Nutritional deficiencies in morbidly obese patients: a new form of malnutrition? Part B: minerals. Obes Surg 18:1028–1034. doi:10.1007/s11695-007-9350-5
56. Kalsbeek A, la Fleur S, Fliers E (2014) Circadian control of glucose metabolism. Mol Metab 3:372–383
57. Kastorini CM, Panagiotakos DB (2009) Dietary patterns and prevention of type 2 diabetes: from research to clinical practice; a systematic review. Curr Diabetes Rev 5:221–227
58. Kawashima Y, Singh A, Kodera Y, Matsumoto H (2013) Nutritional proteomics: investigating molecular mechanisms underlying the health beneficial effect of functional foods. Funct Foods Health Dis 3:300–309
59. Kim S, Sohn I, Ahn JI, Lee KH, Lee YS (2004) Hepatic gene expression profiles in a long-term high-fat diet-induced obesity mouse model. Gene 340:99–109. doi:10.1016/j.gene.2004.06.015
60. Kim HJ et al (2011) Metabolomic analysis of livers and serum from high-fat diet induced obese mice. J Proteome Res 10:722–731. doi:10.1021/Pr100892r
61. Kim KA, Gu W, Lee IA, Joh EH, Kim DH (2012) High fat diet-induced gut microbiota exacerbates inflammation and obesity in mice via the TLR4 signaling pathway. PLoS ONE. doi:10.1371/journal.pone.0047713
62. Kim MS et al (2014) A draft map of the human proteome. Nature 509:575. doi:10.1038/Nature13302
63. Knoll M, Lodish HF, Sun L (2015) Long non-coding RNAs as regulators of the endocrine system. Nat Rev Endocrinol 11:151–160. doi:10.1038/nrendo.2014.229
64. Kornfeld JW, Bruning JC (2014) Regulation of metabolism by long, non-coding RNAs. Front Genet 5:57. doi:10.3389/fgene.2014.00057
65. Koza RA et al (2006) Changes in gene expression foreshadow diet-induced obesity in genetically identical mice. PLoS Genet 2:e81. doi:10.1371/journal.pgen.0020081
66. Laird PW (2010) Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11:191–203. doi:10.1038/nrg2732
67. Lambrot R et al (2013) Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes. Nat Commun 4:2889. doi:10.1038/ncomms3889
68. Larsen N et al (2010) Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS ONE 5:e9085. doi:10.1371/journal.pone.0009085
69. Latouche C et al (2014) Maternal overnutrition programs changes in the expression of skeletal muscle genes that are associated with insulin resistance and defects of oxidative phosphorylation in adult male rat offspring. J Nutr 144:237–244. doi:10.3945/jn.113.186775
70. Lee AK et al (2010) Effect of high-fat feeding on expression of genes controlling availability of dopamine in mouse hypothalamus. Nutrition 26:411–422. doi:10.1016/j.nut.2009.05.007
71. Lee RK, Hittel DS, Nyamandi VZ, Kang L, Soh J, Sensen CW, Shearer J (2012) Unconventional microarray design reveals the response to obesity is largely tissue specific: analysis of common and divergent responses to diet-induced obesity in insulin-sensitive tissues. Appl Physiol Nutr Metab 37:257–268. doi:10.1139/h11-159
72. Leung A et al (2014) Open chromatin profiling in mice livers reveals unique chromatin variations induced by high fat diet. J Biol Chem 289:23557–23567. doi:10.1074/jbc.M114.581439
73. Levian C, Ruiz E, Yang X (2014) The pathogenesis of obesity from a genomic and systems biology perspective. Yale J Biol Med 87:113–126
74. Li CC et al (2013) Maternal obesity and diabetes induces latent metabolic defects and widespread epigenetic changes in isogenic mice. Epigenetics 8:602–611. doi:10.4161/epi.24656
75. Lin SH, Yang Z, Liu HD, Tang LH, Cai ZW (2011) Beyond glucose: metabolic shifts in responses to the effects of the oral glucose tolerance test and the high-fructose diet in rats. Mol BioSyst 7:1537–1548. doi:10.1039/C0mb00246a
76. Lin LL, Huang HC, Juan HF (2015) Circadian systems biology in Metazoa. Briefings Bioinform. doi:10.1093/bib/bbv006
77. Ma J et al (2014) High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model. Nat Commun. doi:10.1038/Ncomms4889
78. Matsui N et al (2005) Ingested cocoa can prevent high-fat diet-induced obesity by regulating the expression of genes for fatty acid metabolism. Nutrition 21:594–601. doi:10.1016/j.nut.2004.10.008
79. Mc Auley MT, Wilkinson DJ, Jones JJL, Kirkwood TBL (2012) A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. BMC Syst Biol. doi:10.1186/1752-0509-6-130
80. Meng Q, Makinen VP, Luk H, Yang X (2013) Systems biology approaches and applications in obesity, diabetes, and cardiovascular diseases. Curr Cardiovasc Risk Rep 7:73–83. doi:10.1007/s12170-012-0280-y
81. Miller AM et al (2013) MiR-155 has a protective role in the development of non-alcoholic hepatosteatosis in mice. PLoS ONE. doi:10.1371/journal.pone.0072324
82. Morine MJ et al (2013) Network analysis of adipose tissue gene expression highlights altered metabolic and regulatory transcriptomic activity in high-fat-diet-fed IL-1RI knockout mice. J Nutr Biochem 24:788–795. doi:10.1016/j.jnutbio.2012.04.012
83. Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255–264. doi:10.1016/j.ygeno.2008.07.001
84. Myles IA, Fontecilla NM, Janelsins BM, Vithayathil PJ, Segre JA, Datta SK (2013) Parental dietary fat intake alters offspring microbiome and immunity. J Immunol 191:3200–3209. doi:10.4049/jimmunol.1301057
85. Ng SF, Lin RC, Maloney CA, Youngson NA, Owens JA, Morris MJ (2014) Paternal high-fat diet consumption induces common changes in the transcriptomes of retroperitoneal adipose and pancreatic islet tissues in female rat offspring. FASEB J 28:1830–1841. doi:10.1096/fj.13-244046
86. Nojima K, Sugimoto K, Ueda H, Babaya N, Ikegami H, Rakugi H (2013) Analysis of hepatic gene expression profile in a spontaneous mouse model of type 2 diabetes under a high sucrose diet. Endocr J 60:261–274
87. Oh TS, Yun JW (2012) DNA microarray analysis reveals differential gene expression in the soleus muscle between male and female rats exposed to a high fat diet. Mol Biol Rep 39:6569–6580. doi:10.1007/s11033-012-1486-2
88. Olsson AH et al (2014) Genome-wide associations between genetic and epigenetic variation influence mRNA expression and insulin secretion in human pancreatic islets. PLoS Genet. doi:10.1371/journal.pgen.1004735
89. Oster M, Murani E, Metges CC, Ponsuksili S, Wimmers K (2012a) 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. doi:10.1186/1471-2164-13-93
90. Oster M, Murani E, Metges CC, Ponsuksili S, Wimmers K (2012b) 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 Genom. doi:10.1186/1471-2164-13-93
91. O’Sulliyan A, He X, McNiven EMS, Haggarty NW, Lonnerdal B, Slupsky CM (2013) Early diet impacts infant rhesus gut microbiome, immunity, and metabolism. J Proteome Res 12:2833–2845. doi:10.1021/Pr4001702
92. Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12:87–98. doi:10.1038/Nrg2934
93. Panagiotou G, Nielsen J (2009) Nutritional systems biology: definitions and approaches. Annu Rev Nutr 29:329–339. doi:10.1146/annurev-nutr-080508-141138
94. Panasevich MR et al (2015) Modulation of the faecal microbiome of healthy adult dogs by inclusion of potato fibre in the diet. Br J Nutr 113:125–133. doi:10.1017/S0007114514003274
95. Parks BW et al (2013) Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab 17:141–152. doi:10.1016/j.cmet.2012.12.007
96. Parks BW et al (2015) Genetic architecture of insulin resistance in the mouse. Cell Metab 21:334–346. doi:10.1016/j.cmet.2015.01.002
97. Patsouris D, Reddy JK, Muller M, Kersten S (2006) Peroxisome proliferator-activated receptor alpha mediates the effects of high-fat diet on hepatic gene expression. Endocrinology 147:1508–1516. doi:10.1210/en.2005-1132
98. Petersen AK et al (2014) Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits. Hum Mol Genet 23:534–545. doi:10.1093/Hmg/Ddt430
99. Pioli K, Barbieri C, Cann I, Mackie R, Beverly J (2013) High protein diet reduces food intake and adiposity and alters GI microbiome. FASEB J 27:1056.14
100. Primeaux SD, Braymer HD, Bray GA (2013) High fat diet differentially regulates the expression of olfactory receptors in the duodenum of obesity-prone and obesity-resistant rats. Dig Dis Sci 58:72–76. doi:10.1007/s10620-012-2421-z
101. Pritchard CC, Cheng HH, Tewari M (2012) MicroRNA profiling: approaches and considerations. Nat Rev Genet 13:358–369. doi:10.1038/Nrg3198
102. Qin JJ et al (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490:55–60. doi:10.1038/Nature11450
103. Rasmussen LG et al (2012) Assessment of the effect of high or low protein diet on the human urine metabolome as measured by NMR. Nutrients 4:112–131. doi:10.3390/Nu4020112
104. Rivera CM, Ren B (2013) Mapping human epigenomes. Cell 155:39–55. doi:10.1016/j.cell.2013.09.011
105. Roat R et al (2014) Alterations of pancreatic islet structure, metabolism and gene expression in diet-induced obese C57BL/6J Mice. PLoS ONE. doi:10.1371/journal.pone.0086815
106. Romao JM, Jin WW, Dodson MV, Hausman GJ, Moore SS, Guan LL (2011) MicroRNA regulation in mammalian adipogenesis. Exp Biol Med 236:997–1004. doi:10.1258/ebm.2011.011101
107. Ross SA, Davis CD (2014) The emerging role of microRNAs and nutrition in modulating health and disease. Annu Rev Nutr 34(34):305–336. doi:10.1146/annurev-nutr-071813-105729
108. Sahajpal V, Ashton N (2003) Renal function and angiotensin AT(1) receptor expression in young rats following intrauterine exposure to a maternal low-protein diet. Clin Sci 104:607–614. doi:10.1042/Cs20020355
109. Samuel BS, Gordon JI (2006) A humanized gnotobiotic mouse model of host–archaeal–bacterial mutualism. Proc Natl Acad Sci 103:10011–10016
110. Sauer S, Luge T (2015) Nutriproteomics: facts, concepts, and perspectives. Proteomics 15:997–1013. doi:10.1002/pmic.201400383
111. Sims EK et al (2013) Divergent compensatory responses to high-fat diet between C57BL6/J and C57BLKS/J inbred mouse strains. Am J Physiol-Endocrinol Metab 305:E1495–E1511. doi:10.1152/ajpendo.00366.2013
112. Sparks LM, Xie H, Koza RA, Mynatt R, Hulver MW, Bray GA, Smith SR (2005) A high-fat diet coordinately downregulates genes required for mitochondrial oxidative phosphorylation in skeletal muscle. Diabetes 54:1926–1933
113. Suez J et al (2014) Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature 514:181–186. doi:10.1038/nature13793
114. Sun SY, Ji YW, Kersten S, Qi L (2012) Mechanisms of inflammatory responses in obese adipose tissue. Annu Rev Nutr 32(32):261. doi:10.1146/annurev-nutr-071811-150623
115. Sundsten T, Ortsater H (2009) Proteomics in diabetes research. Mol Cell Endocrinol 297:93–103. doi:10.1016/j.mce.2008.06.018
116. Sverdlov AL et al (2015) High fat, high sucrose diet causes cardiac mitochondrial dysfunction due in part to oxidative post-translational modification of mitochondrial complex II. J Mol Cell Cardiol 78:165–173
117. Takamura T et al (2008) Obesity upregulates genes involved in oxidative phosphorylation in livers of diabetic patients. Obesity 16:2601–2609. doi:10.1038/Oby.2008.419
118. Telese F, Gamliel A, Skowronska-Krawczyk D, Garcia-Bassets I, Rosenfeld MG (2013) “Seq-ing” insights into the epigenetics of neuronal gene regulation. Neuron 77:606–623. doi:10.1016/j.neuron.2013.01.034
119. Temelkova-Kurktschiev T, Stefanov T (2012) Lifestyle and genetics in obesity and type 2 diabetes. Exp Clin Endocrinol Diabetes 120:1–6. doi:10.1055/s-0031-1285832
120. Tilgner H, Grubert F, Sharon D, Snyder MP (2014) Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci USA 111:9869–9874. doi:10.1073/pnas.1400447111
121. van de Bunt M et al (2013) The miRNA profile of human pancreatic islets and beta-cells and relationship to type 2 diabetes pathogenesis. PLoS ONE 8:e55272
122. van den Berghe G, Bronfman M, Vanneste R, Hers HG (1977) The mechanism of adenosine triphosphate depletion in the liver after a load of fructose. A kinetic study of liver adenylate deaminase. Biochem J 162:601–609
123. Via M (2012) The malnutrition of obesity: micronutrient deficiencies that promote diabetes. ISRN Endocrinol 2012:103472
124. Volkmar M et al (2012) DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients. EMBO J 31:1405–1426. doi:10.1038/emboj.2011.503
125. Vrieze A et al (2012) Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 143(913–916):e917. doi:10.1053/j.gastro.2012.06.031
126. Walker A et al (2014) Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet. ISME J 8:2380–2396. doi:10.1038/ismej.2014.79
127. Waller-Evans H et al (2013a) Nutrigenomics of high fat diet induced obesity in mice suggests relationships between susceptibility to fatty liver disease and the proteasome. PLoS ONE. doi:10.1371/journal.pone.0082825
128. Waller-Evans H et al (2013b) Nutrigenomics of high fat diet induced obesity in mice suggests relationships between susceptibility to fatty liver disease and the proteasome. PLoS ONE. doi:10.1371/journal.pone.0082825
129. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63. doi:10.1038/Nrg2484
130. Wang TJ et al (2011) Metabolite profiles and the risk of developing diabetes. Nat Med 17:448–U483. doi:10.1038/Nm.2307
131. Wen HT et al (2011) Fatty acid-induced NLRP3-ASC inflammasome activation interferes with insulin signaling. Nat Immunol 12:408–U461. doi:10.1038/Ni.2022
132. Wolden-Kirk H et al (2013) Unraveling the effects of 1,25(OH)(2)D-3 on global gene expression in pancreatic islets. J Steroid Biochem Mol Biol 136:68–79. doi:10.1016/j.jsbmb.2012.10.017
133. Wolden-Kirk H et al (2014) Discovery of molecular pathways mediating 1,25-dihydroxyvitamin D3 protection against cytokine-induced inflammation and damage of human and male mouse islets of Langerhans. Endocrinology 155:736–747. doi:10.1210/en.2013-1409
134. Wu GD et al (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105–108. doi:10.1126/science.1208344
135. Wu YB et al (2014) Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell 158:1415–1430. doi:10.1016/j.cell.2014.07.039
136. Xia J et al (2014) Transcriptome analysis on the inflammatory cell infiltration of nonalcoholic steatohepatitis in Bama minipigs induced by a long-term high-fat, high-sucrose diet. PLoS ONE 9:e113724. doi:10.1371/journal.pone.0113724
137. Zhang LH, Perdomo G, Kim DH, Qu S, Ringquist S, Trucco M, Dong HH (2008) Proteomic analysis of fructose-induced fatty liver in hamsters. Metab-Clin Exp 57:1115–1124. doi:10.1016/j.metabol.2008.03.017
138. Zhao YQ, Huang JF (2011) Reconstruction and analysis of human heart-specific metabolic network based on transcriptome and proteome data. Biochem Biophys Res Commun 415:450–454. doi:10.1016/j.bbrc.2011.10.090