Novel systems biology insights using antifibrotic approaches for diabetic kidney disease

References

• RamachandraRao SP, Zhu Y, Ravasi T et al. Pirfenidone is renoprotective in diabetic kidney disease. J. Am. Soc. Nephrol.20(8), 1765–1775 (2009).
   PubMed Web of Science ®Google Scholar
• State-specific trends in chronic kidney failure – United States, 1990–2001. MMWR Morb. Mortal. Wkly Rep.53(39), 918–920 (2004).
   PubMedGoogle Scholar
• Ewens KG, George RA, Sharma K, Ziyadeh FN, Spielman RS. Assessment of 115 candidate genes for diabetic nephropathy by transmission/disequilibrium test. Diabetes54(11), 3305–3318 (2005).
   PubMed Web of Science ®Google Scholar
• Fioretto P, Steffes MW, Brown DM, Mauer SM. An overview of renal pathology in insulin-dependent diabetes mellitus in relationship to altered glomerular hemodynamics. Am. J. Kidney Dis.20, 549–558 (1992).
   PubMed Web of Science ®Google Scholar
• Lewis EJ, Hunsicker LG, Bain RP, Rohde RD. The effect of angiotensin-converting-enzyme inhibition on diabetic nephropathy. The Collaborative Study Group. N. Engl. J. Med.329(20), 1456–1462 (1993).
   PubMed Web of Science ®Google Scholar
• Brenner BM, Cooper ME, de Zeeuw D et al. Effects of losartan on renal and cardiovascular outcomes in patients with Type 2 diabetes and nephropathy. N. Engl. J. Med.345(12), 861–869 (2001).
   PubMed Web of Science ®Google Scholar
• Lewis E, Hunsicker L, Clarke A et al. Renoprotective effect of the angiotensin-receptor antagonist irbesartan in patients with nephropathy due to Type 2 diabetes. N. Engl. J. Med.345(12), 851–860 (2001).
   PubMed Web of Science ®Google Scholar
• The Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Research Group. Retinopathy and nephropathy in patients with Type 1 diabetes 4 years after a trial of intensive therapy. N. Engl. J. Med.342(6), 381–389 (2000).
   PubMed Web of Science ®Google Scholar
• Chen S, Lee, JS, Iglesias-de la Cruz MC et al. Angiotensin II stimulates a3(IV) collagen production in mouse podocytes via TGF-β and VEGF signalling: implications for diabetic glomerulopathy. Nephrol. Dial. Transplant.20, 1320–1328 (2005).
   PubMedGoogle Scholar
• Ziyadeh FN, Sharma K. Overview: combating diabetic nephropathy. J. Am. Soc. Nephrol.14(5), 1355–1357 (2003).
   PubMed Web of Science ®Google Scholar
• Hasslacher C, Ritz E, Wahl P, Michael C. Similar risks of nephropathy in patients with Type I or Type II diabetes mellitus. Nephrol. Dial. Transplant.4, 859–863 (1989).
   PubMed Web of Science ®Google Scholar
• USRDS: the United States Renal Data System. Am. J. Kidney Dis.42(6 Suppl. 5), 1–230 (2003).
   PubMed Web of Science ®Google Scholar
• Sharma K, Lee S, Han S et al. Two-dimensional fluorescence difference gel electrophoresis analysis of the urine proteome in human diabetic nephropathy. Proteomics5(10), 2648–2655 (2005).
   PubMed Web of Science ®Google Scholar
• Thongboonkerd V, Barati MT, McLeish KR et al. Alterations in the renal elastin-elastase system in Type 1 diabetic nephropathy identified by proteomic analysis. J. Am. Soc. Nephrol.15(3), 650–662 (2004).
   PubMed Web of Science ®Google Scholar
• Ziyadeh F, Hoffman B, Han D et al. Long-term prevention of renal insufficiency excess matrix gene expression and glomerular mesangial matrix expansion by treatment with monoclonal antitransforming growth factor-β antibody in db/db diabetic mice. Proc. Natl Acad. Sci. USA97, 8015–8020 (2000).
   PubMed Web of Science ®Google Scholar
• Benigni A, Zoja C, Corna D et al. Add-on anti-TGF-β antibody to ACE inhibitor arrests progressive diabetic nephropathy in the rat. J. Am. Soc. Neph.14, 1816–1824 (2003).
   PubMed Web of Science ®Google Scholar
• Guha M, Xu ZG, Tung D, Lanting L, Natarajan R. Specific down-regulation of connective tissue growth factor attenuates progression of nephropathy in mouse models of Type 1 and Type 2 diabetes. FASEB J.21(12), 3355–3368 (2007).
   PubMed Web of Science ®Google Scholar
• Riser BL, Denichilo M, Cortes P et al. Regulation of connective tissue growth factor activity in cultured rat mesangial cells and its expression in experimental diabetic glomerulosclerosis. J. Am. Soc. Nephrol.11(1), 25–38 (2000).
   PubMed Web of Science ®Google Scholar
• Mifsud S, Kelly D, Qi W et al. Intervention with tranilast attenuates renal pathology and albuminuria in advanced experimental diabetic nephropathy. Nephron Physiol.95, 83–91 (2003).
   Google Scholar
• Martin J, Kelly DJ, Mifsud SA et al. Tranilast attenuates cardiac matrix deposition in experimental diabetes: role of transforming growth factor-β. Cardiovasc. Res.65(3), 694–701 (2005).
   PubMed Web of Science ®Google Scholar
• Best PJ, Berger PB, Davis BR et al. Impact of mild or moderate chronic kidney disease on the frequency of restenosis: results from the PRESTO trial. J. Am. Coll. Cardiol.44(9), 1786–1791 (2004).
   PubMed Web of Science ®Google Scholar
• Iyer SN, Hyde DM, Giri SN. Anti-inflammatory effect of pirfenidone in the bleomycin-hamster model of lung inflammation. Inflammation24, 477–491 (2000).
   PubMed Web of Science ®Google Scholar
• Iyer SN, Margolin SB, Hyde DM, Giri SN. Lung fibrosis is ameliorated by pirfenidone fed in diet after the second dose in a three-dose bleomycin-hamster model. Exp. Lung Res.24(1), 119–132 (1998).
   PubMed Web of Science ®Google Scholar
• Cain WC, Stuart RW, Lefkowitz DL, Starnes JD, Margolin S, Lefkowitz SS. Inhibition of tumor necrosis factor and subsequent endotoxin shock by pirfenidone. Int. J. Immunopharmacol.20(12), 685–695 (1998).
   PubMed Web of Science ®Google Scholar
• Cho ME, Smith DC, Branton MH, Penzak SR, Kopp JB. Pirfenidone slows renal function decline in patients with focal segmental glomerulosclerosis. Clin. J. Am. Soc. Nephrol.2(5), 906–913 (2007).
   PubMed Web of Science ®Google Scholar
• Azuma A, Nukiwa T, Tsuboi E et al. Double-blind, placebo-controlled trial of pirfenidone in patients with idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med.171(9), 1040–1047 (2005).
   PubMed Web of Science ®Google Scholar
• Park HS, Bao L, Kim YJ et al. Pirfenidone suppressed the development of glomerulosclerosis in the FGS/Kist mouse. J. Korean Med. Sci.18(4), 527–533 (2003).
   PubMed Web of Science ®Google Scholar
• Shimizu T, Kuroda T, Hata S, Fukagawa M, Margolin SB, Kurokawa K. Pirfenidone improves renal function and fibrosis in the post-obstructed kidney. Kidney Int.54(1), 99–109 (1998).
   PubMed Web of Science ®Google Scholar
• Iyer SN, Gurujeyalakshmi G, Giri SN. Effects of pirfenidone on transforming growth factor-β gene expression at the transcriptional level in bleomycin hamster model of lung fibrosis. J. Pharmacol. Exp. Ther.291(1), 367–373 (1999).
   PubMed Web of Science ®Google Scholar
• Oku H, Shimizu T, Kawabata T et al. Antifibrotic action of pirfenidone and prednisolone: different effects on pulmonary cytokines and growth factors in bleomycin-induced murine pulmonary fibrosis. Eur. J. Pharmacol.590(1–3), 400–408 (2008).
   PubMed Web of Science ®Google Scholar
• Salazar-Montes A, Ruiz-Corro L, Lopez-Reyes A, Castrejon-Gomez E, Armendariz-Borunda J. Potent antioxidant role of pirfenidone in experimental cirrhosis. Eur. J. Pharmacol.595(1–3), 69–77 (2008).
   PubMed Web of Science ®Google Scholar
• Misra HP, Rabideau C. Pirfenidone inhibits NADPH-dependent microsomal lipid peroxidation and scavenges hydroxyl radicals. Mol. Cell. Biochem.204(1–2), 119–126 (2000).
   PubMed Web of Science ®Google Scholar
• Iyer SN, Wild JS, Schiedt MJ, Hyde DM, Margolin SB, Giri SN. Dietary intake of pirfenidone ameliorates bleomycin-induced lung fibrosis in hamsters. J. Lab. Clin. Med.125(6), 779–785 (1995).
   PubMed Web of Science ®Google Scholar
• Davies HR, Richeldi L. Idiopathic pulmonary fibrosis: current and future treatment options. Am. J. Respir. Med.1(3), 211–224 (2002).
   PubMedGoogle Scholar
• Raghu G, Johnson WC, Lockhart D, Mageto Y. Treatment of idiopathic pulmonary fibrosis with a new antifibrotic agent, pirfenidone: results of a prospective, open-label Phase II study. Am. J. Respir. Crit. Care Med.159(4 Pt 1), 1061–1069 (1999).
   PubMed Web of Science ®Google Scholar
• Di Sario A, Bendia E, Svegliati Baroni G et al. Effect of pirfenidone on rat hepatic stellate cell proliferation and collagen production. J. Hepatol.37(5), 584–591 (2002).
   PubMed Web of Science ®Google Scholar
• Mirkovic S, Seymour AM, Fenning A et al. Attenuation of cardiac fibrosis by pirfenidone and amiloride in DOCA-salt hypertensive rats. Br. J. Pharmacol.135(4), 961–968 (2002).
   PubMed Web of Science ®Google Scholar
• Fukagawa M, Noda M, Shimizu T, Kurokawa K. Chronic progressive interstitial fibrosis in renal disease – are there novel pharmacological approaches? Nephrol. Dial. Transplant.14(12), 2793–2795 (1999).
   PubMed Web of Science ®Google Scholar
• Shimizu T, Fukagawa M, Kuroda T et al. Pirfenidone prevents collagen accumulation in the remnant kidney in rats with partial nephrectomy. Kidney Int.63(Suppl.), S239–S243 (1997).
   Google Scholar
• Shihab FS, Bennett WM, Yi H, Andoh TF. Pirfenidone treatment decreases transforming growth factor-β1 and matrix proteins and ameliorates fibrosis in chronic cyclosporine nephrotoxicity. Am. J. Transplant.2(2), 111–119 (2002).
   PubMed Web of Science ®Google Scholar
• Lee BS, Margolin SB, Nowak RA. Pirfenidone: a novel pharmacological agent that inhibits leiomyoma cell proliferation and collagen production. J. Clin. Endocrinol. Metab.83(1), 219–223 (1998).
   PubMed Web of Science ®Google Scholar
• Dosanjh AK, Wan B, Throndset W, Sherwood S, Morris RE. Pirfenidone: a novel antifibrotic agent with implications for the treatment of obliterative bronchiolitis. Transplant. Proc.30(5), 1910–1911 (1998).
   PubMed Web of Science ®Google Scholar
• Kaneko M, Inoue H, Nakazawa R et al. Pirfenidone induces intercellular adhesion molecule-1 (ICAM-1) down-regulation on cultured human synovial fibroblasts. Clin. Exp. Immunol.113(1), 72–76 (1998).
   PubMed Web of Science ®Google Scholar
• Rual JF, Venkatesan K, Hao T et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature437(7062), 1173–1178 (2005).
   PubMed Web of Science ®Google Scholar
• Stelzl U, Worm U, Lalowski M et al. A human protein–protein interaction network: a resource for annotating the proteome. Cell122(6), 957–968 (2005).
   PubMed Web of Science ®Google Scholar
• Ogawa S, Lozach J, Benner C et al. Molecular determinants of crosstalk between nuclear receptors and toll-like receptors. Cell122(5), 707–721 (2005).
   PubMed Web of Science ®Google Scholar
• Alfarano C, Andrade CE, Anthony K et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res.33, D418–D424 (2005).
   PubMed Web of Science ®Google Scholar
• Joshi-Tope G, Gillespie M, Vastrik I et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res.33, D428–D432 (2005).
   PubMed Web of Science ®Google Scholar
• Peri S, Navarro JD, Amanchy R et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res.13(10), 2363–2371 (2003).
   PubMed Web of Science ®Google Scholar
• Vastrik I, D’Eustachio P, Schmidt E et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biol.8(3), R39 (2007).
   PubMed Web of Science ®Google Scholar
• Remm M, Storm CE, Sonnhammer EL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol.314(5), 1041–1052 (2001).
   PubMed Web of Science ®Google Scholar
• Tatusov RL, Fedorova ND, Jackson JD et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics4, 41 (2003).
   PubMed Web of Science ®Google Scholar
• Chen F, Mackey AJ, Stoeckert CJ Jr, Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res.34, D363–D368 (2006).
   PubMed Web of Science ®Google Scholar
• Jensen LJ, Julien P, Kuhn M et al. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res.36, D250–D254 (2008).
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res.13(11), 2498–2504 (2003).
   PubMed Web of Science ®Google Scholar
• Dennis G Jr, Sherman BT, Hosack DA et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol.4(5), P3 (2003).
   PubMed Web of Science ®Google Scholar
• Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc.4(1), 44–57 (2009).
   PubMed Web of Science ®Google Scholar
• Choi WI, Kim Y, Kim Y et al. Eukaryotic translation initiator protein 1A isoform, CCS-3, enhances the transcriptional repression of p21CIP1 by proto-oncogene FBI-1 (Pokemon/ZBTB7A). Cell Physiol. Biochem.23(4–6), 359–370 (2009).
   PubMedGoogle Scholar
• Feliers D, Lee MJ, Ghosh-Choudhury G, Bomsztyk K, Kasinath BS. Heterogeneous nuclear ribonucleoprotein K contributes to angiotensin II stimulation of vascular endothelial growth factor mRNA translation. Am. J. Physiol. Renal Physiol.293(2), F607–F615 (2007).
   Google Scholar
• Lee MJ, Feliers D, Mariappan MM et al. A role for AMP-activated protein kinase in diabetes-induced renal hypertrophy. Am. J. Physiol. Renal Physiol.292(2), F617–F627 (2007).
   PubMed Web of Science ®Google Scholar
• Kasinath BS, Mariappan MM, Sataranatarajan K, Lee MJ, Feliers D. mRNA translation: unexplored territory in renal science. J. Am. Soc. Nephrol.17(12), 3281–3292 (2006).
   PubMedGoogle Scholar
• Mariappan MM, Shetty M, Sataranatarajan K, Choudhury GG, Kasinath BS. Glycogen synthase kinase 3b is a novel regulator of high glucose- and high insulin-induced extracellular matrix protein synthesis in renal proximal tubular epithelial cells. J. Biol. Chem.283(45), 30566–30575 (2008).
   PubMedGoogle Scholar
• Sataranatarajan K, Mariappan MM, Lee MJ et al. Regulation of elongation phase of mRNA translation in diabetic nephropathy: amelioration by rapamycin. Am. J. Pathol.171(6), 1733–1742 (2007).
   PubMed Web of Science ®Google Scholar
• Walker PD. The renal biopsy. Arch. Pathol. Lab. Med.133(2), 181–188 (2009).
   PubMed Web of Science ®Google Scholar
• Lu B, Motoyama A, Ruse C, Venable J, Yates JR 3rd. Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data. Anal. Chem.80(6), 2018–2025 (2008).
   PubMedGoogle Scholar
• Sharma K, Jin Y, Guo J, Ziyadeh FN. Neutralization of TGF-β by anti-TGF-β antibody attenuates kidney hypertrophy and the enhanced extracellular matrix gene expression in STZ-induced diabetic mice. Diabetes45(4), 522–530 (1996).
   PubMed Web of Science ®Google Scholar