Defining human diabetic nephropathy on the molecular level: Integration of transcriptomic profiles with biological knowledge
Tóm tắt
Từ khóa
Tài liệu tham khảo
USRDS. 2007 Annual Data Report: Atlas of Chronic Kidney Disease and End-Stage Renal Disease in the United States. Bethseda, MD: National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases; 2007.
Ritz E, Orth SR. Nephropathy in patients with type 2 diabetes mellitus. N Engl J Med. 1999;341:1127–33. doi: 10.1056/NEJM199910073411506 .
Patel A, MacMahon S, Chalmers J, Neal B, et al. Intensive blood glucose control and vascular outcomes in patients with type 2 diabetes. N Engl J Med. 2008;358:2560–72. doi: 10.1056/NEJMicm066227 .
American Diabetes Association. Economic costs of diabetes in the U.S. in 2007. Diabetes Care 2008;31:596–615. doi: 10.2337/dc08-9017 .
Iyengar SK, Schelling JR, Sedor JR. Approaches to understanding susceptibility to nephropathy: from genetics to genomics. Kidney Int. 2002;61:S61–67. doi: 10.1046/j.1523-1755.2002.0610s1061.x .
Ng DP, Krolewski AS. Molecular genetic approaches for studying the etiology of diabetic nephropathy. Curr Mol Med. 2005;5:509–25. doi: 10.2174/1566524054553504 .
Rogus JJ, Poznik GD, Pezzolesi MG, Smiles AM, et al. High-density SNP genome wide linkage scan for susceptibility genes for diabetic nephropathy in type 1 diabetes: discordant sib-pair approach. Diabetes 2008. doi: 10.2337/db07-1086 .
Bleyer AJ, Sedor JR, Freedman BI, O’Brien A, et al. Risk factors for development and progression of diabetic kidney disease and treatment patterns among diabetic siblings of patients with diabetic kidney disease. Am J Kidney Dis. 2008;51:29–37. doi: 10.1053/j.ajkd.2007.10.029 .
Schelling JR, Abboud HE, Nicholas SB, Pahl MV, et al. Genome-wide scan for estimated glomerular filtration rate in multi-ethnic diabetic populations: the Family Investigation of Nephropathy and Diabetes (FIND). Diabetes. 2008;57:235–43. doi: 10.2337/db07-0313 .
Tanaka N, Babazono T. Assessing genetic susceptibility to diabetic nephropathy. Nephrology (Carlton) 2005;10(Suppl):S17–21. doi: 10.1111/j.1440-1797.2005.00451.x .
Iyengar SK, Adler SG. The application of the HapMap to diabetic nephropathy and other causes of chronic renal failure. Semin Nephrol. 2007;27:223–36. doi: 10.1016/j.semnephrol.2007.01.003 .
Luetscher JA, Kraemer FB, Wilson DM, Schwartz HC, et al. Increased plasma inactive renin in diabetes mellitus. A marker of microvascular complications. N Engl J Med. 1985;312:1412–7.
Sarafidis PA, Stafylas PC, Kanaki AI, Lasaridis AN. Effects of renin–angiotensin system blockers on renal outcomes and all-cause mortality in patients with diabetic nephropathy: an updated meta-analysis. Am J Hypertens. 2008;21(8):922–9.
Parving HH, Persson F, Lewis JB, Lewis EJ, et al. Aliskiren combined with losartan in type 2 diabetes and nephropathy. N Engl J Med. 2008;358:2433–46. doi: 10.1056/NEJMoa0708379 .
Rosario RF, Prabhakar S. Lipids and diabetic nephropathy. Curr Diab Rep. 2006;6:455–62. doi: 10.1007/s11892-006-0079-7 .
Forbes JM, Fukami K, Cooper ME. Diabetic nephropathy: where hemodynamics meets metabolism. Exp Clin Endocrinol Diabetes. 2007;115:69–84. doi: 10.1055/s-2007-949721 .
Maric C. Vasoactive hormones and the diabetic kidney. ScientificWorldJournal. 2008;8:470–85. doi: 10.1100/tsw.2008.57 .
Wolf G, Ziyadeh FN. Cellular and molecular mechanisms of proteinuria in diabetic nephropathy. Nephron Physiol. 2007;106:26–31. doi: 10.1159/000101797 .
Niehof M, Borlak J. HNF4 alpha and the Ca-channel TRPC1 are novel disease candidate genes in diabetic nephropathy. Diabetes. 2008;57:1069–77. doi: 10.2337/db07-1065 .
Sieberts SK, Schadt EE. Moving toward a system genetics view of disease. Mamm Genome. 2007;18:389–401. doi: 10.1007/s00335-007-9040-6 .
Morrison N, Cochrane G, Faruque N, Tatusova T, et al. Concept of sample in OMICS technology. OMICS. 2006;10:127–37. doi: 10.1089/omi.2006.10.127 .
Malinowski DP. Multiple biomarkers in molecular oncology. II. Molecular diagnostics applications in breast cancer management. Expert Rev Mol Diagn. 2007;7:269–80. doi: 10.1586/14737159.7.3.269 .
Martinelli G, Iacobucci I, Soverini S, Cilloni D, et al. Monitoring minimal residual disease and controlling drug resistance in chronic myeloid leukaemia patients in treatment with imatinib as a guide to clinical management. Hematol Oncol. 2006;24:196–204. doi: 10.1002/hon.792 .
Sanga S, Frieboes HB, Zheng X, Gatenby R, et al. Predictive oncology: a review of multidisciplinary, multiscale in silico modeling linking phenotype, morphology and growth. Neuroimage. 2007;37(Suppl 1):S120–134. doi: 10.1016/j.neuroimage.2007.05.043 .
Wulfkuhle JD, Speer R, Pierobon M, Laird J, et al. Multiplexed cell signaling analysis of human breast cancer applications for personalized therapy. J Proteome Res. 2008;7:1508–17. doi: 10.1021/pr7008127 .
Kretzler M, Cohen CD, Doran P, Henger A, et al. Repuncturing the renal biopsy: strategies for molecular diagnosis in nephrology. J Am Soc Nephrol. 2002;13:1961–72. doi: 10.1097/01.ASN.0000020390.29418.70 .
Chabardes-Garonne D, Mejean A, Aude JC, Cheval L, et al. A panoramic view of gene expression in the human kidney. Proc Natl Acad Sci U S A. 2003;100:13710–5. doi: 10.1073/pnas.2234604100 .
Chan YH. Biostatistics. 302 Principal component and factor analysis. Singapore Med J. 2004;45:558–65.
Gasch AP, Eisen MB. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol. 2002;3(11):1–22.
Qin ZS. Clustering microarray gene expression data using weighted Chinese restaurant process. Bioinformatics. 2006;22:1988–97. doi: 10.1093/bioinformatics/btl284 .
Kanehisa M. The KEGG database. Novartis Found Symp. 2002;247:91–101. discussion 101–103, 119–128, 244–152.
Werner T. Bioinformatics applications for pathway analysis of microarray data. Curr Opin Biotechnol. 2008;19:50–4. doi: 10.1016/j.copbio.2007.11.005 .
Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467–70. doi: 10.1126/science.270.5235.467 .
Baelde HJ, Eikmans M, Doran PP, Lappin DW, et al. Gene expression profiling in glomeruli from human kidneys with diabetic nephropathy. Am J Kidney Dis. 2004;43:636–50. doi: 10.1053/j.ajkd.2003.12.028 .
Qi W, Chen X, Gilbert RE, Zhang Y, et al. High glucose-induced thioredoxin-interacting protein in renal proximal tubule cells is independent of transforming growth factor-beta1. Am J Pathol. 2007;171:744–54. doi: 10.2353/ajpath.2007.060813 .
Panchapakesan U, Sumual S, Pollock CA, Chen X. PPARgamma agonists exert antifibrotic effects in renal tubular cells exposed to high glucose. Am J Physiol Renal Physiol. 2005;289:F1153–1158. doi: 10.1152/ajprenal.00097.2005 .
Srinivasan S, Bolick DT, Hatley ME, Natarajan R, et al. Glucose regulates interleukin-8 production in aortic endothelial cells through activation of the p38 mitogen-activated protein kinase pathway in diabetes. J Biol Chem. 2004;279:31930–6. doi: 10.1074/jbc.M400753200 .
Mora C, Navarro JF. Inflammation and diabetic nephropathy. Curr Diab Rep. 2006;6:463–8. doi: 10.1007/s11892-006-0080-1 .
Moczulski DK, Fojcik H, Wielgorecki A, Trautsolt W, et al. Expression pattern of genes in peripheral blood mononuclear cells in diabetic nephropathy. Diabet Med. 2007;24:266–71. doi: 10.1111/j.1464-5491.2006.02067.x .
Tone A, Shikata K, Ogawa D, Sasaki S, et al. Changes of gene expression profiles in macrophages stimulated by angiotensin II–angiotensin II induces MCP-2 through AT1-receptor. J Renin Angiotensin Aldosterone Syst. 2007;8:45–50. doi: 10.3317/jraas.2007.007 .
Huang C, Kim Y, Caramori ML, Moore JH, et al. Diabetic nephropathy is associated with gene expression levels of oxidative phosphorylation and related pathways. Diabetes. 2006;55:1826–31. doi: 10.2337/db05-1438 .
de Borst MH, Benigni A, Remuzzi G. Primer: strategies for identifying genes involved in renal disease. Nat Clin Pract Nephrol. 2008;4:265–76. doi: 10.1038/ncpneph0785 .
Werner T, Fessele S, Maier H, Nelson PJ. Computer modeling of promoter organization as a tool to study transcriptional coregulation. FASEB J. 2003;17:1228–37. doi: 10.1096/fj.02-0955rev .
Schmid H, Boucherot A, Yasuda Y, Henger A, et al. Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes. 2006;55:2993–3003. doi: 10.2337/db06-0477 .
Mezzano S, Aros C, Droguett A, Burgos ME, et al. NF-kappaB activation and overexpression of regulated genes in human diabetic nephropathy. Nephrol Dial Transplant. 2004;19:2505–12. doi: 10.1093/ndt/gfh207 .
Sakai N, Wada T, Furuichi K, Iwata Y, et al. Involvement of extracellular signal-regulated kinase and p38 in human diabetic nephropathy. Am J Kidney Dis. 2005;45:54–65. doi: 10.1053/j.ajkd.2004.08.039 .
Yang B, Hodgkinson A, Oates PJ, Millward BA, et al. High glucose induction of DNA-binding activity of the transcription factor NFkappaB in patients with diabetic nephropathy. Biochim Biophys Acta. 2008;1782:295–302.
Nagai N, Izumi-Nagai K, Oike Y, Koto T, et al. Suppression of diabetes-induced retinal inflammation by blocking the angiotensin II type 1 receptor or its downstream nuclear factor-kappaB pathway. Invest Ophthalmol Vis Sci. 2007;48:4342–50. doi: 10.1167/iovs.06-1473 .
Yoshida A, Yoshida S, Ishibashi T, Kuwano M, et al. Suppression of retinal neovascularization by the NF-kappaB inhibitor pyrrolidine dithiocarbamate in mice. Invest Ophthalmol Vis Sci. 1999;40:1624–9.
Chen L, Zhang J, Zhang Y, Wang Y, et al. Improvement of inflammatory responses associated with NF-kappaB pathway in kidneys from diabetic rats. Inflamm Res 2008;57(5):199–204.
Saisho Y, Hirose H, Horimai C, Miyashita K, et al. Effects of DHMEQ, a novel nuclear factor-kappab inhibitor, on beta cell dysfunction in INS-1 cells. Endocr J. 2008;55:433–8. doi: 10.1507/endocrj.K07E-036 .
Lorz C, Benito-Martin A, Boucherot A, Ucero AC, et al. The death ligand TRAIL in diabetic nephropathy. J Am Soc Nephrol. 2008;19:904–14. doi: 10.1681/ASN.2007050581 .
Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, et al. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia. 2007;9:166–80. doi: 10.1593/neo.07112 .