Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension

BMC Medical Genomics

Volumn 3, Issue , 2010, Pages

  Jesmin, ^a   Rashid, Mahbubur S M ^a   Jamil, Hasan ^b   Hontecillas, Raquel ^c   Bassaganya Riera, Josep ^c  

^a UNIVERSITY OF DHAKA   (Bangladesh)

^b Wayne State University   (United States)

^c VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADIPOCYTOKINE; CHEMOKINE RECEPTOR CXCR4; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN BINDING PROTEIN; CYCLIN DEPENDENT KINASE INHIBITOR 1A; CYCLIN DEPENDENT KINASE INHIBITOR 2A; E1A ASSOCIATED P300 PROTEIN; EPIDERMAL GROWTH FACTOR RECEPTOR; HEAT SHOCK PROTEIN 90; HEAT SHOCK PROTEIN 90AA1; HISTONE ACETYLTRANSFERASE PCAF; HYPOXIA INDUCIBLE FACTOR 1ALPHA; INSULIN; JANUS KINASE; JANUS KINASE 3; MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE 3; MYC PROTEIN; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; PROTEIN P53; SOMATOMEDIN C RECEPTOR; STAT PROTEIN; STAT3 PROTEIN; STRESS ACTIVATED PROTEIN KINASE 1; TOLL LIKE RECEPTOR; TRANSCRIPTION FACTOR RELA; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG; WNT PROTEIN;

ARTICLE; DATA MINING; DISEASE ASSOCIATION; FOCAL ADHESION; GENE INTERACTION; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; HUMAN; HYPERTENSION; INFLAMMATION; NON INSULIN DEPENDENT DIABETES MELLITUS; OBESITY; OXIDATIVE STRESS; PHENOTYPE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

DATABASES, GENETIC; DIABETES MELLITUS, TYPE 2; GENE REGULATORY NETWORKS; HUMANS; HYPERTENSION; INSULIN RESISTANCE; MODELS, GENETIC; OBESITY; OXIDATIVE STRESS; PROTEIN INTERACTION MAPPING; REACTIVE OXYGEN SPECIES; SIGNAL TRANSDUCTION;

EID: 77957745068     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-3-45     Document Type: Article

References (81)

1. World Diabetes. World Health Organization, Fact sheet N312 2008
2. Global burden of diabetes 1995-2025. H King RE Aubert WH Herman, Diabetes Care 1998 21 1414 1431 10.2337/diacare.21.9.1414 9727886
3. Cause-specific excess deaths associated with underweight, overweight, and obesity. KM Flegal BI Graubard DF Williamson MH Gail, JAMA 2007 298 2028 37 10.1001/jama.298.17.2028 17986696
4. A Systems Biology Approach Identifies Inflammatory Abnormalities between Mouse Strains Prior to Development of Metabolic Disease. MA Mori M Liu O Bezy K Almind H Shapiro S Kasif CR Kahn, Diabetes 2010 59
5. Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases. K Wang M Narayanan H Zhong M Tompa EE Schadt J Zhu, PLoS Comput Biol 2009 5 12 1000616 10.1371/journal.pcbi. 1000616 20019805
6. Meta-Analysis Approach identifies Candidate Genes and associated Molecular Networks for Type-2 Diabetes Mellitus. U Sengupta S Ukil N Dimitrova S Agrawal, BMC Genomics 2008 9 310 10.1186/1471-2164-9-310 18590522
7. Network-based analysis of affected biological processes in type 2 diabetes models. M Liu A Liberzon SW Kong WR Lai PJ Park IS Kohane S Kasif, PLoS Genet 2007 3 96 10.1371/journal.pgen.0030096 17571924
8. High-performance information extraction with Alibaba. P Palaga L Nguyen Uif Leser J Hakenberg, EDBT ACM 2009 360 1140 1143 full-text
9. UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. G Chaurasia S Malhotra J Russ S Schnoegl C Hänig EE Wanker ME Futschik, Nucleic Acids Res 2009 37 Database 657 60 10.1093/nar/gkn841 18984619
10. KEGG for linking genomes to life and the environment. M Kanehisa M Araki S Goto M Hattori M Hirakawa M Itoh T Katayama S Kawashima S Okuda T Tokimatsu Y Yamanishi, Nucleic Acids Res 2008 36 480 D484 10.1093/nar/gkm882 18077471
11. Human protein reference database-2006 update. GR Mishra M Suresh K Kumaran N Kannabiran S Suresh P Bala K Shivakumar N Anuradha R Reddy MT Raghavan, Nucleic Acids Res 2006 34 411 D414 10.1093/nar/gkj141 16381900
12. Comparison of human protein-protein interaction maps. ME Futschik G Chaurasia H Herzel, Bioinf 2007 23 605 611 10.1093/bioinformatics/btl683 (Pubitemid 46522594)
13. Cytoscape: a software environment for integrated models of biomolecular interaction networks. p Shannon A Markiel O Ozier NS Baliga JT Wang D Ramage N Amin B Schwikowski T Ideker, Genome Res 2003 13 2498 504 10.1101/gr.1239303 14597658
14. Phenopedia and Genopedia: Disease-centered and Gene-centered Views of the Evolving Knowledge of Human Genetic Associations. W Yu M Clyne MJ Khoury M Gwinn, Bioinformatics 2010 26 1 145 6 10.1093/bioinformatics/btp618 19864262
15. Reactome: a knowledgebase of biological pathways. G Joshi-Tope M Gillespie I Vastrik P DEustachio E Schmidt B Bono B Jassal GR Gopinath GR Wu L Matthews S Lewis E Birney L Stein, Nucleic Acids Res 2005 33 428 432 10.1093/nar/gki072 15608231
16. Kyoto Encyclopedia of Genes and Genomes. M Kanehisa S Goto KEGG, Nucleic Acids Res 2000 28 27 30 10.1093/nar/28.1.27 10592173
17. Computational prediction of human metabolic pathways from the complete human genome. P Romero J Wagg ML Green D Kaiser M Krummenacker PD Karp, Genome Biology 2004 6 2 10.1186/gb-2004-6-1-r2 15642094
18. Deletion of nicotinamide nucleotide transhydrogenase: a new quantitive trait locus accounting for glucose intolerance in C57BL/6J mice. HC Freeman A Hugill NT Dear FM Ashcroft RD Cox, Diabetes 2006 55 2153 2156 10.2337/db06-0358 16804088
19. Genomic analysis of regulatory network dynamics reveals large topological changes. NM Luscombe M Babu H Yu M Snyder SA Teichmann M Gerstein, Nature 2004 431 308 312 10.1038/nature02782 15372033
20. Computational discovery of gene modules and regulatory networks. ARZ Joseph GK Gerber TI Lee NJ Rinaldi JY Yoo F Robert DB Gordon E Fraenkel TS Jaakkola RA Young, Nat Biotechnol 2003 21 1337 1342 10.1038/nbt890 14555958
21. Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data. E Segal M Shapira A Regev D Pe'er D Boststein D Koller N Friedman, Nat Genet 2003 34 166 176 10.1038/ng1165 12740579
22. A Protein-Protein Interaction Network for Human Inherited Ataxias and Disorders of Purkinje cell degeneration. J Lim T Hao C Shaw AJ Patel G Szabo JF Rual JC Fisk N Li A Smolyar DE Hill, Cell 2006 125 801 814 10.1016/j.cell.2006. 03.032 16713569
23. Genome Project: a unified framework for functional annotation across species. PE Bourne, PLoS Comput Biol 2009 5 7 1000431 10.1371/journal.pcbi. 1000431 19578431
24. Gluco-lipotoxicity of the pancreatic beta cell. V Poitout I Briaud C Kelpe D Hagman, Annales d'Endocrinologie 2004 65 1 37 41 15122090
25. Loss of ARNT/HIF1 mediates altered gene expression and pancreatic-islet dysfunction in human type 2 diabetes. JE Gunton RN Kulkarni S Yim,, et al. Cell 2005 122 3 337 349 10.1016/j.cell.2005.05.027 16096055
26. Chronic oxidative stress as a central mechanism for glucose toxicity in pancreatic islet beta cells in diabetes. AP Robertson, J of Biol Chem 2004 279 41 42351 42354 10.1074/jbc.R400019200 (Pubitemid 39372114)
27. Endoplasmic reticulum stress contributes to beta cell apoptosis in type 2 diabetes. DR Laybutt AM Preston MCA Kerfeldt,, et al. Diabetologia 2007 50 4 752 763 10.1007/s00125-006-0590-z 17268797
28. Both Wnt and mTOR signaling pathways are involved in insulin-stimulated proto-oncogene expression in intestinal cells. J Sun T Jin, Cell Signal 2008 20 219 229 10.1016/j.cellsig.2007.10.010 17993259
29. P-21-activated protein kinase-1 functions as a linker between insulin and Wnt signaling pathways in the intestine. J Sun S Khalid M Rozakis-Adcock IG Fantus T Jin, Oncogene 2009 28 3132 3144 10.1038/onc.2009.167 19581924
30. Insulin and IGF-1 stimulate the beta-catenin pathway through two signalling cascades involving GSK-3beta inhibition and Ras activation. C Desbois-Mouthon A Cadoret MJ Blivet-VanEggelpoel F Bertrand G Cherqui C Perret J Capeau, Oncogene 2001 20 252 259 10.1038/sj.onc.1204064 11313952
31. Beta-catenin is involved in insulin-like growth factor 1-mediated transactivation of the androgen receptor. M Verras Z Sun, Mol Endocrinol 2005 19 391 398 10.1210/me.2004-0208 15514031
32. TSC2 integrates Wnt and energy signals via a coordinated phosphorylation by AMPK and GSK3 to regulate cell growth. K Inoki H Ouyang T Zhu C Lindvall Y Wang X Zhang Q Yang C Bennett Y Harada K Stankunas CY Wang X He OA MacDougald M You BO Williams KL Guan, Cell 2006 126 955 968 10.1016/j.cell.2006.06.055 16959574
33. Insulin alters the expression of components of the Wnt signaling pathway including TCF-4 in the intestinal cells. J Sun D Wang T Jin, Biochim Biophys Acta 2010 1800 3 344 51 20056134
34. Expression and characterization of glycogen synthase kinase-3 mutants and their effect on glycogen synthase activity in intact cells. H Eldar-Finkelman GM Argast O Foord EH Fischer EG Krebs, Proc Natl Acad Sci USA 1996 93 10228 10233 10.1073/pnas.93.19.10228 8816781
35. Mice with beta cell overexpression of glycogen synthase kinase-3beta have reduced beta cell mass and proliferation. Z Liu K Tanabe E Bernal-Mizrachi MA Permutt, Diabetologia 2008 51 623 631 10.1007/s00125-007-0914-7 18219478
36. Genetic deficiency of glycogen synthase kinase-3beta corrects diabetes in mouse models of insulin resistance. K Tanabe Z Liu S Patel BW Doble L Li C Cras-Méneur SC Martinez CM Welling MF White E Bernal-Mizrachi JR Woodgett MA Permutt, PLoS Biol 2008 6 37 10.1371/journal.pbio.0060037 18288891
37. Forkhead transcription factor FOXO3a protects quiescent cells from oxidative stress. GJ Kops TB Dansen PE Polderman I Saarloos KW Wirtz PJ Coffer TT Huang JL Bos RH Medema BM Burgering, Nature 2002 419 316 321 10.1038/nature01036 12239572
38. Wnt signaling stimulates osteoblastogenesis of mesenchymal precursors by suppressing CCAAT/enhancer-binding protein alpha and peroxisome proliferator-activated receptor gamma. S Kang CN Bennett I Gerin LA Rapp KD Hankenson OA Macdougald, J Biol Chem 2007 282 14515 14524 10.1074/jbc.M700030200 17351296
39. Adipogenesis and WNT signalling. C Christodoulides C Lagathu JK Sethi A Vidal-Puig, Trends Endocrinol Metab 2009 20 16 24 10.1016/j.tem.2008.09.002 19008118
40. COUP-TFII acts downstream of Wnt/beta-catenin signal to silence PPARgamma gene expression and repress adipogenesis. M Okamura H Kudo K Wakabayashi T Tanaka A Nonaka A Uchida S Tsutsumi I Sakakibara M Naito TF Osborne T Hamakubo S Ito H Aburatani M Yanagisawa T Kodama J Sakai, Proc Natl Acad Sci USA 2009 106 5819 5824 10.1073/pnas.0901676106 19307559
41. Peroxisome proliferator-activated receptor gamma activation can regulate beta-catenin levels via a proteasome-mediated and adenomatous polyposis coli-independent pathway. C Sharma A Pradeep L Wong A Rana B Rana, J Biol Chem 2004 279 35583 35594 10.1074/jbc.M403143200 15190077
42. Inhibition of PPAR2 gene expression by the HIF-1-regulated gene DEC1/Stra13: a mechanism for regulation of adipogenesis by hypoxia. Z Yun HL Maecker RS Johnson AJ Giaccia, Dev Cell 2002 2 331 341 10.1016/S1534-5807(02) 00131-4 11879638
43. 2tensions and the prevention of differentiation of hES cells. T Ezashi P Das RM Roberts, Proc Natl Acad Sci USA 2005 102 4783 4788 10.1073/pnas.0501283102 15772165
44. Low oxygen tension inhibits osteogenic differentiation and enhances stemness of human MIAMI cells. G D'Ippolito S Diabira GA Howard BA Roos PC Schiller, Bone 2006 39 513 522 10.1016/j.bone.2006.02.061 16616713
45. Low oxygen expansion improves subsequent chondrogenesis of ovine bone-marrow-derived mesenchymal stem cells in collagen type I hydrogel. M Zscharnack C Poesel J Galle A Bader, Cells Tissues Organs 2009 190 2 81 93 10.1159/000178024 19033681
46. Interaction between -catenin and HIF-1 promotes cellular adaptation to hypoxia. A Kaidi AC Williams C Paraskeva, Nat Cell Biol 2007 9 210 217 10.1038/ncb1534 17220880
47. Glucagon-like peptide-1 activation of TCF7L2-dependent Wnt signaling enhances pancreatic cell proliferation. Z Liu JF Habener, J Biol Chem 2008 283 8723 8735 10.1074/jbc.M706105200 18216022
48. Oxygen: a master regulator of pancreatic development? CA Fraker C Ricordi L Inverardi Domínguez-Bendala, J Biol Cell 2009 101 8 431 40 10.1042/BC20080178
49. A crucial role for adipose tissue p53 in the regulation of insulin resistance. T Minamino M Orimo I Shimizu T Kunieda M Yokoyama T Ito A Nojima A Nabetani Y Oike H Matsubara F Ishikawa I Komuro, Nature med 2009 15 9 1082 87 10.1038/nm.2014 19718037
50. Increased oxidative stress in obesity and its impact on metabolic syndrome. S Furukawa T Fujita M Shimabukuro M Iwaki Y Yamada Y Nakajima O Nakayama M Makishima M Matsuda I Shimomura, J Clin Invest 2004 114 1752 1761 15599400
51. Molecular mechanisms of cardiovascular disease in OSAHS: the oxidative stress link. L Lavie P Lavie, Eur Respir J 2009 33 6 1467 84 10.1183/09031936.00086608 19483049
52. Free radicals and antioxidants in normal physiological functions and human disease. M Valko D Leibfritz J Moncol MT Cronin M Mazur J Telser, J Biochem Cell Biol 2007 39 44 84 10.1016/j.biocel.2006.07.001 (Pubitemid 44566469)
53. Free radicals in the physiological control of cell function. W Droge, Physiol Rev 2002 82 47 95 11773609
54. Inter mittent hypoxia: the culprit of oxidative stress, vascular inflammation and dyslipidemia in obstructive sleep apnea. L Lavie, Expert Rev Respir Med 2008 2 75 84 10.1586/17476348.2.1.75 20477224
55. Connecting obesity, aging and diabetes. RS Ahima, Nat Med 2009 15 9 996 7 10.1038/nm0909-996 19734871
56. Oxidative stress in mice is dependent on the free glucose content of the diet. V Folmer JC Soares JB Rocha, Int J Biochem Cell Biol 2002 34 1279 1285 10.1016/S1357-2725(02)00065-1 12127578
57. Free radical generation by early glycation products: a mechanism for accelerated atherogenesis in diabetes. CJ Mullarkey D Edelstein M Brownlee, Biochem Biophys Res Commun 1990 173 932 939 10.1016/S0006-291X(05)80875-7 2176495
58. Hyperactivity and increased hydrogen peroxide formation in platelets of NIDDM patients. G Leoncini MG Signorello A Piana, Thromb Res 1997 86 153 160 10.1016/S0049-3848(97)00058-3 9175236
59. Oxygen-regulated transcription factors and their role in pulmonary disease. GL Semenza, Respir Res 2000 1 159 162 10.1186/rr27 11667980
60. Heterozygous HIF-1a deficiency impairs carotid body-mediated systemic responses and reactive oxygen species generation in mice exposed to intermittent hypoxia. YJ Peng G Yuan D Ramakrishnan SD Sharma M Bosch-Marce GK Kumar GL Semenza NR Prabhakar, J Physiol 2006 577 705 716 10.1113/jphysiol.2006.114033 16973705
61. Altered metabolic responses to intermittent hypoxia in mice with partial deficiency of hypoxia-inducible factor-1a. J Li M Bosch-Marce A Nanayakkara V Savransky SK Fried GL Semenza VY Polotsky, Physiol Genomics 2006 25 450 457 10.1152/physiolgenomics.00293.2005 16507783
62. Glucose induces de novo lipogenesis in rat muscle satellite cells through a sterolregulatory- element-binding-protein-1c-dependent pathway. I Guillet-Deniau AL Pichard A Kone C Esnous M Nieruchalski J Girard C Prip-Buus, J Cell Sci 2004 117 1937 1944 10.1242/jcs.01069 15039461
63. Inflammatory responses underlying the microvascular dysfunction associated with obesity and insulin resistance. G Singer DN Granger, Microcirculation 2007 14 375 387 10.1080/10739680701283158 17613809
64. The Wnt signalling pathway in development and disease. CY Logan R Nusse, Annu Rev Cell Dev Biol 2004 20 781 810 10.1146/annurev.cellbio.20.010403.113126 15473860
65. Wnt-signalling and the metabolic syndrome. S Schinner, Horm Metab Res 2009 41 2 159 63 10.1055/s-0028-1119408 19214925
66. Nutrient availability and growth: regulation of insulin signaling by dFOXO/FOXO1. O Puig R Tjian, Cell Cycle 2006 5 503 505 16552183
67. FOXO transcription factor activation by oxidative stress mediated by the small GTPase Ral and JNK. MA Essers S Weijzen AM de Vries-Smits I Saarloos ND de Ruiter JL Bos BM Burgering, EMBO J 2004 23 4802 4812 10.1038/sj.emboj.7600476 15538382
68. Interaction of FOXO with beta-catenin inhibits beta-catenin/TCF activity. D Hoogeboom MA Essers PE Polderman E Voets LM Smits BM Burgering, J Biol Chem 2008 283 9224 9230 10.1074/jbc.M706638200 18250171
69. Neonatal growth and regeneration of -cells regulate by the Wnt/-catenin signaling in normal and diabetic rats. F Figeac B Uzan M Faro N Chelali B Portha J Movassat, Am J Physiol Endocrnol Metab 2010 298 245 E256 10.1152/ajpendo. 00538.2009
70. The WNT signaling pathway and diabetes mellitus. T Jin, Diabetologia 2008 51 1771 80 10.1007/s00125-008-1084-y 18696049
71. Regulation of insulin secretion, glucokinase gene transcription and beta cell proliferation by adipocyte-derived Wnt signalling molecules. S Schinner F Ulgen C Papewalis M Schott A Woelk A Vidal-Puig WA Scherbaum, Diabetologia 2008 51 147 154 10.1007/s00125-007-0848-0 17994217
72. Mechanisms by which common variants in the TCF7L2 gene increase risk of type 2 diabetes. V Lyssenko R Lupi P Marchetti V Lyssenko R Lupi P Marchetti, J Clin Invest 2007 117 2155 2163 10.1172/JCI30706 17671651
73. Beta-catenin directly displaces Groucho/TLE repressors from Tcf/Lef in Wnt-mediated transcription activation. DL Daniels WI Weis, Nat Struct Mol Biol 2005 12 364 371 10.1038/nsmb912 15768032
74. The p300/CBP acetyltransferases function as transcriptional coactivators of beta-catenin in vertebrates. A Hecht K Vleminckx MP Stemmler FV Roy R Kemler, EMBO J 2000 19 1839 1850 10.1093/emboj/19.8.1839 10775268
75. The transcriptional coactivator CBP interacts with beta-catenin to activate gene expression. KI Takemaru RT Moon, J Cell Biol 2000 149 249 254 10.1083/jcb.149.2.249 10769018
76. Insulin and IGF-1 stimulate the beta-catenin pathway through two signalling cascades involving GSK-3beta inhibition and Ras activation. C Desbois-Mouthon A Cadoret MJ Blivet-Van Eggelpoel F Bertrand G Cherqui C Perret J Capeau, Oncogene 2001 20 2 252 259 10.1038/sj.onc.1204064 11313952
77. Insulin-like growth factor 1 regulates the location, stability, and transcriptional activity of beta-catenin. MP Playford D Bicknell WF Bodmer VM Macaulay, Proc Natl Acad Sci USA 2000 97 12103 12108 10.1073/pnas.210394297 11035789
78. A novel component of the metabolic syndrome: The oxidative stress. E Hopps D Noto G Caimi MR Averna, Nutrition, Metabolism & Cardiovascular Diseases 2010 20 72 e77
79. Activation of the Wnt Pathway Plays a Pathogenic Role in Diabetic Retinopathy in Humans and Animal Models. Y Chen Y Hu Ti Zhou KK Zhou R Mott M Wu M Boulton TJ Lyons G Gao J Ma, AJP 2009 175 6 2676 2685 19893025
80. Postprandial glycemia and cardiovascular disease in diabetes mellitus. BL Wajchenberg, Arq Bras Endocrinol Metabol 2007 51 212 21 17505628
81. Postprandial hyperglycemia and diabetes complications: is it time to treat? A Ceriello, Diabetes 2005 54 1 7 10.2337/diabetes.54.1.1 15616004