Investigation of mechanisms of mesenchymal stem cells for treatment of diabetic nephropathy via construction of a miRNA-TF-mRNA network

References

• Atkins RC, Zimmet P. Diabetic kidney disease: act now or pay later. Nephrol. Dial. Transplant. 2009;12:2–5.
   Google Scholar
• Sanchez AP, Sharma K. Transcription factors in the pathogenesis of diabetic nephropathy. Expert Rev Mol Med. 2009;11:e13.
   PubMed Web of Science ®Google Scholar
• Lei L, Mao Y, Meng D, et al. Percentage of circulating CD8+ T lymphocytes is associated with albuminuria in type 2 diabetes mellitus. Exp Clin Endocrinol Diabetes. 2014;122:27–30.
   PubMed Web of Science ®Google Scholar
• Lane PH, Steffes MW, Fioretto P, et al. Renal interstitial expansion in insulin-dependent diabetes mellitus. Kidney Int. 1993;43:661–667.
   PubMed Web of Science ®Google Scholar
• Ritz E, Wolf G. Comprehensive clinical nephrology: pathogenesis, clinical manifestations, and natural history of diabetic nephropathy. Netherlands: Elsevier Medicine; 2010.
   Google Scholar
• Duran-Salgado MB, Rubio-Guerra AF. Diabetic nephropathy and inflammation. World J Diabetes. 2014;5:393–398.
   PubMedGoogle Scholar
• Nguyen D, Ping F, Mu W, et al. Macrophage accumulation in human progressive diabetic nephropathy. Nephrology. 2006;11:226–231.
   PubMed Web of Science ®Google Scholar
• Katz S, Klein B, Elian I, et al. Phagocytotic activity of monocytes from diabetic patients. Diabetes Care. 1983;6:479–482.
   PubMed Web of Science ®Google Scholar
• Yang M, Gan H, Shen Q, et al. Proinflammatory CD14 + CD16+ monocytes are associated with microinflammation in patients with type 2 diabetes mellitus and diabetic nephropathy uremia. Inflammation. 2012;35:388–396.
   PubMed Web of Science ®Google Scholar
• Yang M, Gan H, Shen Q. [Effect of LPS on the level of TLR4 and on the expression of NF-kappaB and Notch1 in monocytes from patients with type 2 diabetic nephropathy]. Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2012;37:578–585.
   PubMedGoogle Scholar
• Wise AF, Williams TM, Rudd S, et al. Human mesenchymal stem cells alter the gene profile of monocytes from patients with Type 2 diabetes and end-stage renal disease. Regen Med. 2016;11:145–158.
   PubMed Web of Science ®Google Scholar
• Hof-Nahor I, Leshansky L, Shivtiel S, et al. Human mesenchymal stem cells shift CD8+ T cells towards a suppressive phenotype by inducing tolerogenic monocytes. J Cell Sci. 2012;125:4640–4650.
   PubMed Web of Science ®Google Scholar
• Samarani G, Song Y, Krasnodembskaya A, et al. Mesenchymal stem cells therapy reduces bacteremia and enhances the phagocytic activity of circulating monocytes in a mouse model of gram negative sepsis. Paper presented at: American Thoracic Society 2011 International Conference; 2011 May 13–18; Denver, Colorado.
   Google Scholar
• Jiang XX, Zhang Y, Liu B, et al. Human mesenchymal stem cells inhibit differentiation and function of monocyte-derived dendritic cells. Blood. 2005; 105:4120–4126.
   PubMed Web of Science ®Google Scholar
• Lv SS, Liu G, Wang JP, et al. Mesenchymal stem cells transplantation ameliorates glomerular injury in streptozotocin-induced diabetic nephropathy in rats via inhibiting macrophage infiltration. Int Immunopharmacol. 2013;17:275.
   PubMed Web of Science ®Google Scholar
• Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4:249–264.
   PubMed Web of Science ®Google Scholar
• Diboun I, Wernisch L, Orengo CA, et al. Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genomics. 2006;7:1–14.
   PubMed Web of Science ®Google Scholar
• Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–29.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2008;4:44–57.
   PubMed Web of Science ®Google Scholar
• Mering CV, Huynen M, Jaeggi D, et al. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003;31:258–261.
   PubMed Web of Science ®Google Scholar
• Tang Y, Li M, Wang J, et al. CytoNCA: a cytoscape plugin for centrality analysis and evaluation of protein interaction networks. Biosystems. 2015;127:67–72.
   PubMed Web of Science ®Google Scholar
• He X, Zhang J. Why do hubs tend to be essential in protein networks? Plos Genet. 2006;2:826–834.
   Web of Science ®Google Scholar
• Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003;4:2.
   PubMed Web of Science ®Google Scholar
• Garcia O, Saveanu C, Cline M, et al. GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics. 2007;23:394–396.
   PubMed Web of Science ®Google Scholar
• Zhang B, Kirov S, Snoddy J. WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005;33:741–748.
   PubMed Web of Science ®Google Scholar
• Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol. 1995;57:289–300.
   Web of Science ®Google Scholar
• Sheng H, Wang Y, Jin Y, et al. A critical role of IFNgamma in priming MSC-mediated suppression of T cell proliferation through up-regulation of B7-H1. Cell Res. 2008;18:846–857.
   PubMed Web of Science ®Google Scholar
• Ryan JM, Barry F, Murphy JM, et al. Interferon-gamma does not break, but promotes the immunosuppressive capacity of adult human mesenchymal stem cells. Clin Exp Immunol. 2007;149:353–363.
   PubMed Web of Science ®Google Scholar
• Wang H, Yu J, Zhang L, et al. RPS27a promotes proliferation, regulates cell cycle progression and inhibits apoptosis of leukemia cells. Biochem Biophys Res Commun. 2014;446:1204–1210.
   PubMed Web of Science ®Google Scholar
• Goh SH, Hong SH, Hong SH, et al. eIF3m expression influences the regulation of tumorigenesis-related genes in human colon cancer. Oncogene. 2011;30:398–409.
   PubMed Web of Science ®Google Scholar
• Teller A, Jechorek D, Hartig R, et al. Dysregulation of apoptotic signaling pathways by interaction of RPLP0 and cathepsin X/Z in gastric cancer. Pathol Res Pract. 2015;211:62–70.
   PubMed Web of Science ®Google Scholar
• Meng F, Henson R, Lang M, et al. Involvement of human micro-RNA in growth and response to chemotherapy in human cholangiocarcinoma cell lines. Gastroenterology. 2006;130:2113–2129.
   PubMed Web of Science ®Google Scholar
• Zhou H, Hasni SA, Perez P, et al. miR-150 promotes renal fibrosis in lupus nephritis by downregulating SOCS1. J Am Soc Nephrol. 2013;24:1073–1087.
   PubMed Web of Science ®Google Scholar
• Poitz DM, Stolzel F, Arabanian L, et al. MiR-134-mediated beta1 integrin expression and function in mesenchymal stem cells. Biochim Biophys Acta. 2013;1833:3396–3404.
   PubMed Web of Science ®Google Scholar
• Liu Y, Zhang M, Qian J, et al. miR-134 functions as a tumor suppressor in cell proliferation and epithelial-to-mesenchymal transition by targeting kras in renal cell carcinoma cells. DNA Cell Biol. 2015;34:429–436.
   PubMed Web of Science ®Google Scholar