Genome-wide analysis of microRNAs expression profiling in patients with primary IgA nephropathy

Genome

Volumn 56, Issue 3, 2013, Pages 161-169

  Tan, Kuibi ^a   Chen, Jing ^b   Li, Wuxian ^c   Chen, Yuyu ^a   Sui, Weiguo ^d   Zhang, Yang ^d   Dai, Yong ^a  

^a JINAN UNIVERSITY   (China)

^b PEKING UNIVERSITY SHENZHEN HOSPITAL   (China)

^c CHONGQING MEDICAL UNIVERSITY   (China)

^d The 181th Hospital of PLA   (China)

Author keywords

Illumina sequencing; Immunoglobulin A nephropathy; MicroRNAs

Indexed keywords

MICRORNA;

ADULT; ARTICLE; CASE CONTROL STUDY; CHROMOSOME MAP; CLUSTER ANALYSIS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNOGLOBULIN A NEPHROPATHY; MALE; MIDDLE AGED; MOLECULAR GENETICS; PATHOLOGY;

ADULT; CASE-CONTROL STUDIES; CHROMOSOME MAPPING; CLUSTER ANALYSIS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME-WIDE ASSOCIATION STUDY; GLOMERULONEPHRITIS, IGA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MICRORNAS; MIDDLE AGED; MOLECULAR SEQUENCE ANNOTATION; YOUNG ADULT;

EID: 84877680544     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/gen-2012-0159     Document Type: Article

References (39)

1. Beerman I. Novak J. Wyatt R.J. Julian B.A. Gharavi A.G. 2007. The genetics of IgA nephropathy. Nat. Clin. Pract. Nephrol. 3 (6): 325-338. 10.1038/ncpneph0492. 17525715.
2. Berezikov E. Cuppen E. Plasterk R.H. 2006. Approaches to microRNA discovery. Nat. Genet. 38 (Suppl.): S2-S7. 10.1038/ng1794.
3. Bianchi I. Lleo A. Gershwin M.E. Invernizzi P. 2012. The X chromosome and immune associated genes. J. Autoimmun. 38 (2-3): J187-J192. 10.1016/j.jaut.2011.11.012. 22178198.
4. Bisceglia L. Cerullo G. Forabosco P. Torres D.D. Scolari F. Di Perna M. et al. 2006. Genetic heterogeneity in Italian families with IgA nephropathy: suggestive linkage for two novel IgA nephropathy loci. Am. J. Hum. Genet. 79 (6): 1130-1134. 10.1086/510135. 17186473.
5. Cai G.-Y. Chen X.-M. 2009. Immunoglobulin A nephropathy in China: progress and challenges. Am. J. Nephrol. 30 (3): 268-273. 10.1159/000225563. 19521068.
6. Cao H.-X. Li M. Nie J. Wang W. Zhou S.-F. Yu X.-Q. 2008. Human leukocyte antigen DRB1 alleles predict risk and disease progression of immunoglobulin A nephropathy in Han Chinese. Am. J. Nephrol. 28 (4): 684-691. 10.1159/000122111. 18367833.
7. Chen Y.-H. Wang S.-Q. Wu X.-L. Shen M. Chen Z.-G. Chen X.-G. et al. 2013. Characterization of microRNAs expression profiling in one group of Chinese urothelial cell carcinoma identified by Solexa sequencing. Urol. Oncol. 31 (2): 219-227. 10.1016/j.urolonc.2010.11.007.
8. Cullen B.R. 2004. Transcription and processing of human microRNA precursors. Mol. Cell, 16 (6): 861-865. 10.1016/j.molcel.2004.12.002.
9. Dai Y. Sui W. Lan H. Yan Q. Huang H. Huang Y. 2008. Microarray analysis of micro-ribonucleic acid expression in primary immunoglobulin A nephropathy. Saudi. Med. J. 29 (10): 1388-1393. 18946560.
10. Gharavi A.G. Yan Y. Scolari F. Schena F.P. Frasca G.M. Ghiggeri G.M. et al. 2000. IgA nephropathy, the most common cause of glomerulonephritis, is linked to 6q22-23. Nat. Genet. 26 (3): 354-357. 10.1038/81677. 11062479.
11. Gharavi A.G. Moldoveanu Z. Wyatt R.J. Barker C.V. Woodford S.Y. Lifton R.P. et al. 2008. Aberrant IgA1 glycosylation is inherited in familial and sporadic IgA nephropathy. J. Am. Soc. Nephrol. 19 (5): 1008-1014. 10.1681/ASN.2007091052. 18272841.
12. Glassock R.J. 2011. The pathogenesis of IgA nephropathy. Curr. Opin. Nephrol. Hypertens. 20 (2): 153-160. 10.1097/MNH.0b013e3283436f5c. 21301336.
13. Gregory P.A. Bracken C.P. Bert A.G. Goodall G.J. 2008. MicroRNAs as regulators of epithelial-mesenchymal transition. Cell Cycle, 7 (20): 3112-3117. 10.4161/cc.7.20.6851. 18927505.
14. Hafner M. Landgraf P. Ludwig J. Rice A. Ojo T. Lin C. et al. 2008. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods, 44 (1): 3-12. 10.1016/j.ymeth.2007.09.009. 18158127.
15. Hsu S.I. 2008. Racial and genetic factors in IgA nephropathy. Semin. Nephrol. 28 (1): 48-57. 10.1016/j.semnephrol.2007.10.006. 18222346.
16. Jeffries C.D. Perkins D.O. Guan X. 2010. Gene processing control loops suggested by sequencing, splicing, and RNA folding. BMC Bioinformatics, 11: 602. 10.1186/1471-2105-11-602. 21167075.
17. Kiryluk K. Julian B.A. Wyatt R.J. Scolari F. Zhang H. Novak J. Gharavi A.G. 2010. Genetic studies of IgA nephropathy: past, present, and future. Pediatr. Nephrol. 25 (11): 2257-2268. 10.1007/s00467-010-1500-7. 20386929.
18. Lee H.S. Lee M.S. Lee S.M. Lee S.Y. Lee E.S. Lee E.Y. et al. 2005. Histological grading of IgA nephropathy predicting renal outcome: revisiting H.S. Lee's glomerular grading system. Nephrol. Dial. Transplant. 20 (2): 342-348. 10.1093/ndt/gfh633.
19. Lewis B.P. Shih I.H. Jones-Rhoades M.W. Bartel D.P. Burge C.B. 2003. Prediction of mammalian microRNA targets. Cell, 115 (7): 787-798. 10.1016/S0092-8674(03)01018-3. 14697198.
20. Lewis B.P. Burge C.B. Bartel D.P. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120 (1): 15-20. 10.1016/j.cell.2004.12.035. 15652477.
21. Li G.-S. Zhang H. Lv J.-C. Shen Y. Wang H.-Y. 2007. Variants of C1GALT1 gene are associated with the genetic susceptibility to IgA nephropathy. Kidney Int. 71 (5): 448-453. 10.1038/sj.ki.5002088. 17228361.
22. Li R. Li Y. Kristiansen K. Wang J. 2008. SOAP: short oligonucleotide alignment program. Bioinformatics, 24 (5): 713-714. 10.1093/bioinformatics/ btn025. 18227114.
23. Mestecky J. Tomana M. Moldoveanu Z. Julian B.A. Suzuki H. Matousovic K. et al. 2008. Role of aberrant glycosylation of IgA1 molecules in the pathogenesis of IgA nephropathy. Kidney Blood Pressure Res. 31 (1): 29-37. 10.1159/000112922. 18182777.
24. Paterson A.D. Liu X.-Q. Wang K. Magistroni R. Song X. Kappel J. et al. 2007. Genome-wide linkage scan of a large family with IgA nephropathy localizes a novel susceptibility locus to chromosome 2q36. J. Am. Soc. Nephrol. 18 (8): 2408-2415. 10.1681/ASN.2007020241. 17634434.
25. Paterson E.L. Kolesnikoff N. Gregory P.A. Bert A.G. Khew-Goodall Y. Goodall G.J. 2008. The microRNA-200 family regulates epithelial to mesenchymal transition. Sci. World J. 8: 901-904. 10.1100/tsw.2008.115. 18836656.
26. Pauley K.M. Chan E.K. 2008. MicroRNAs and their emerging roles in immunology. Ann. N.Y. Acad. Sci. 1143: 226-239. 10.1196/annals.1443.009. 19076353.
27. Preston G.A. Waga I. Alcorta D.A. Sasai H. Munger W.E. Sullivan P. et al. 2004. Gene expression profiles of circulating leukocytes correlate with renal disease activity in IgA nephropathy. Kidney Int. 65 (2): 420-430. 10.1111/j.1523-1755.2004.00398.x. 14717912.
28. Qin W. Zhou Q. Yang L.-C. Li Z. Su B.-H. Luo H. Fan J.-M. 2005. Peripheral B lymphocyte β1,3-galactosyltransferase and chaperone expression in immunoglobulin A nephropathy. J. Intern. Med. 258 (5): 467-477. 10.1111/j.1365-2796.2005.01558.x. 16238683.
29. Serino G. Sallustio F. Cox S.N. Pesce F. Schena F.P. 2012. Abnormal miR-148b expression promotes aberrant glycosylation of IgA1 in IgA nephropathy. J. Am. Soc. Nephrol. 23 (5): 814-824. 10.1681/asn.2011060567.
30. Smith A.C. Molyneux K. Feehally J. Barratt J. 2006. O-glycosylation of serum IgA1 antibodies against mucosal and systemic antigens in IgA nephropathy. J. Am. Soc. Nephrol. 17 (12): 3520-3528. 10.1681/ASN.2006060658. 17093066.
31. Sommer C.A. Pavarino-Bertelli E.C. Goloni-Bertollo E.M. Henrique-Silva F. 2008. Identification of dysregulated genes in lymphocytes from children with Down syndrome. Genome, 51 (1): 19-29. 10.1139/G07-100. 18356936.
32. Sui W. Dai Y. Zhang Y. Chen J. Liu H. Huang H. Zou G. 2010. Proteomic profiling of immunoglobulin A nephropathy in serum using magnetic bead based sample fractionation and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Saudi Med. J. 31 (12): 1378-1379. 21136007.
33. Tanaka M. Seki G. Someya T. Nagata M. Fujita T. 2011. Aberrantly glycosylated IgA1 as a factor in the pathogenesis of IgA nephropathy. Clin. Dev. Immunol. 2011: 470803. 10.1155/2011/470803. 21318178.
34. Walsh M. Sar A. Lee D. Yilmaz S. Benediktsson H. Manns B. Hemmelgarn B. 2010. Histopathologic features aid in predicting risk for progression of IgA nephropathy. Clin. J. Am. Soc. Nephrol. 5 (3): 425-430. 10.2215/CJN.06530909. 20089495.
35. Wang G. Kwan B.C.-H. Lai F.M.-M. Choi P.C.-L. Chow K.-M. Li P.K.-T. Szeto C.-C. 2010 a. Intrarenal expression of microRNAs in patients with IgA nephropathy. Lab. Invest. 90 (1): 98-103. 10.1038/labinvest.2009.118. 19901913.
36. Wang G. Kwan B.C.-H. Lai F.M.-M. Chow K.-M. Li P.K.-T. Szeto C.-C. 2010 b. Expression of microRNAs in the urinary sediment of patients with IgA nephropathy. Dis. Markers, 28 (2): 79-86. 10.3233/dma-2010-0687.
37. Wang G. Kwan B.C.-H. Lai F.M.-M. Chow K.-M. Li P.K.-T. Szeto C.-C. 2011. Elevated levels of miR-146a and miR-155 in kidney biopsy and urine from patients with IgA nephropathy. Dis. Markers, 30 (4): 171-179. 10.3233/dma-2011-0766.
38. Zhang H. Yang J.H. Zheng Y.S. Zhang P. Chen X. Wu J. et al. 2009. Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach. PLoS One, 4 (9): e6849. 10.1371/journal.pone.0006849.
39. Zuo L. Wang M. 2010. Current burden and probable increasing incidence of ESRD in China. Clin. Nephrol. 74 (Suppl. 1): S20-S22. 20979958.