Next-generation sequencing identifies TGF-β1-associated gene expression profiles in renal epithelial cells reiterated in human diabetic nephropathy
Tài liệu tham khảo
Collins, 2011, US renal data system 2010 annual data report, Am. J. Kidney Dis., 57, e1
Reeves, 2000, Transforming growth factor beta contributes to progressive diabetic nephropathy, Proc. Natl. Acad. Sci. U. S. A., 97, 7667, 10.1073/pnas.97.14.7667
Kalluri, 2003, Epithelial–mesenchymal transition and its implications for fibrosis, J. Clin. Invest., 112, 1776, 10.1172/JCI200320530
Russo, 2007, Evidence for a role of transforming growth factor (TGF)-beta1 in the induction of postglomerular albuminuria in diabetic nephropathy: amelioration by soluble TGF-beta type II receptor, Diabetes, 56, 380, 10.2337/db06-1018
Shi, 2003, Mechanisms of TGF-beta signaling from cell membrane to the nucleus, Cell, 113, 685, 10.1016/S0092-8674(03)00432-X
Schmierer, 2007, TGFbeta-SMAD signal transduction: molecular specificity and functional flexibility, Nat. Rev. Mol. Cell Biol., 8, 970, 10.1038/nrm2297
Chaudhury, 2009, The tale of transforming growth factor-beta (TGFbeta) signaling: a soigne enigma, IUBMB Life, 61, 929, 10.1002/iub.239
Kalluri, 2009, The basics of epithelial–mesenchymal transition, J. Clin. Invest., 119, 1420, 10.1172/JCI39104
Canales, 2006, Evaluation of DNA microarray results with quantitative gene expression platforms, Nat. Biotechnol., 24, 1115, 10.1038/nbt1236
Schmid, 2006, Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy, Diabetes, 55, 2993, 10.2337/db06-0477
Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25
Benjamini, 2001, Controlling the false discovery rate in behavior genetics research, Behav. Brain Res., 125, 279, 10.1016/S0166-4328(01)00297-2
Walsh, 2008, Co-regulation of Gremlin and Notch signalling in diabetic nephropathy, Biochim. Biophys. Acta, 1782, 10, 10.1016/j.bbadis.2007.09.005
Zhijin Wu, 2004, A model-based background adjustment for oligonucleotide expression arrays, J. Am. Stat. Assoc., 99, 9
Wilson, 2005, Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis, Bioinformatics, 21, 3683, 10.1093/bioinformatics/bti605
Smyth, 2004, Linear models and empirical bayes methods for assessing differential expression in microarray experiments, Stat. Appl. Genet. Mol. Biol., 3, 10.2202/1544-6115.1027
Cohen, 2002, Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application, Kidney Int., 61, 133, 10.1046/j.1523-1755.2002.00113.x
Schmid, 2003, Gene expression profiles of podocyte-associated molecules as diagnostic markers in acquired proteinuric diseases, J. Am. Soc. Nephrol., 14, 2958, 10.1097/01.ASN.0000090745.85482.06
Zhang, 2006, Prostaglandin D2 inhibits TGF-beta1-induced epithelial-to-mesenchymal transition in MDCK cells, Am. J. Physiol. Ren. Physiol., 291, F1332, 10.1152/ajprenal.00131.2006
Ragolia, 2005, Accelerated glucose intolerance, nephropathy, and atherosclerosis in prostaglandin D2 synthase knock-out mice, J. Biol. Chem., 280, 29946, 10.1074/jbc.M502927200
Fraley, 2002, Model-based clustering, discriminant analysis, and density estimation, J. Am. Stat. Assoc., 97, 611, 10.1198/016214502760047131
Mortazavi, 2008, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nat. Meth., 5, 621, 10.1038/nmeth.1226
Martinez-Estrada, 2006, The transcription factors Slug and Snail act as repressors of claudin-1 expression in epithelial cells, Biochem. J., 394, 449, 10.1042/BJ20050591
Suzuki, 2004, ARK5 is a tumor invasion-associated factor downstream of Akt signaling, Mol. Cell. Biol., 24, 3526, 10.1128/MCB.24.8.3526-3535.2004
Nyhan, 2010, Jagged/Notch signalling is required for a subset of TGFbeta1 responses in human kidney epithelial cells, Biochim. Biophys. Acta, 1803, 1386, 10.1016/j.bbamcr.2010.09.001
Lin, 2011, Blocking core fucosylation of TGF-beta1 receptors downregulates their functions and attenuates the epithelial–mesenchymal transition of renal tubular cells, Am. J. Physiol. Ren. Physiol., 300, F1017, 10.1152/ajprenal.00426.2010
Xu, 2009, BMP-7 counteracts TGF-beta1-induced epithelial-to-mesenchymal transition in human renal proximal tubular epithelial cells, J. Nephrol., 22, 403
Zeisberg, 2003, BMP-7 counteracts TGF-beta1-induced epithelial-to-mesenchymal transition and reverses chronic renal injury, Nat. Med., 9, 964, 10.1038/nm888
Mezzano, 2004, NF-kappaB activation and overexpression of regulated genes in human diabetic nephropathy, Nephrol. Dial. Transplant., 19, 2505, 10.1093/ndt/gfh207
Marioni, 2008, RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays, Genome Res., 18, 1509, 10.1101/gr.079558.108
Bottomly, 2011, Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays, PLoS One, 6, e17820, 10.1371/journal.pone.0017820
Ramdas, 2004, Improving signal intensities for genes with low-expression on oligonucleotide microarrays, BMC Genomics, 5, 35, 10.1186/1471-2164-5-35
Suzuki, 2005, ARK5 is transcriptionally regulated by the Large-MAF family and mediates IGF-1-induced cell invasion in multiple myeloma: ARK5 as a new molecular determinant of malignant multiple myeloma, Oncogene, 24, 6936, 10.1038/sj.onc.1208844
Kattla, 2008, Protein kinase B/Akt activity is involved in renal TGF-beta1-driven epithelial-mesenchymal transition in vitro and in vivo, Am. J. Physiol. Ren. Physiol., 295, F215, 10.1152/ajprenal.00548.2007
Kim, 2000, Identification of motifs for cell adhesion within the repeated domains of transforming growth factor-beta-induced gene, betaig-h3, J. Biol. Chem., 275, 30907, 10.1074/jbc.M002752200
Ma, 2008, Extracellular matrix protein betaig-h3/TGFBI promotes metastasis of colon cancer by enhancing cell extravasation, Genes Dev., 22, 308, 10.1101/gad.1632008
Kajita, 2004, Aberrant expression of the transcription factors snail and slug alters the response to genotoxic stress, Mol. Cell. Biol., 24, 7559, 10.1128/MCB.24.17.7559-7566.2004
Nagalakshmi, 2010, RNA-Seq: a method for comprehensive transcriptome analysis, Curr. Protoc. Mol. Biol., 11
Wang, 2009, RNA-Seq: a revolutionary tool for transcriptomics, Nat. Rev. Genet., 10, 57, 10.1038/nrg2484
Shirley, 2009, Ectonucleotidases in the kidney, Purinergic Signal, 5, 501, 10.1007/s11302-009-9152-4
Friedman, 2007, The vascular ectonucleotidase ENTPD1 is a novel renoprotective factor in diabetic nephropathy, Diabetes, 56, 2371, 10.2337/db06-1593
Li, 2006, Ankyrin repeat: a unique motif mediating protein-protein interactions, Biochemistry, 45, 15168, 10.1021/bi062188q
Bera, 2008, A model for obesity and gigantism due to disruption of the Ankrd26 gene, Proc. Natl. Acad. Sci. U. S. A., 105, 270, 10.1073/pnas.0710978105
Raciti, 2011, Partial inactivation of Ankrd26 causes diabetes with enhanced insulin responsiveness of adipose tissue in mice, Diabetologia, 54, 2911, 10.1007/s00125-011-2263-9
Brosius, 2009, Mouse models of diabetic nephropathy, J. Am. Soc. Nephrol., 20, 2503, 10.1681/ASN.2009070721
