Analysis of microRNAs in patients with systemic lupus erythematosus, using Solexa deep sequencing

Connective Tissue Research

Volumn 55, Issue 3, 2014, Pages 187-196

  Chen, Wenbiao ^a   Tan, Kuibi ^b   Huang, Jianrong ^a   Yu, Xiangqi ^a   Peng, Wujian ^c   Chen, Yuyu ^a   Lin, Xiaocong ^d   Chen, Deheng ^a   Dai, Yong ^a  

^a SHENZHEN PEOPLE'S HOSPITAL   (China)

^b NINGBO NO 2 HOSPITAL   (China)

^c SHENZHEN THIRD PEOPLE S HOSPITAL   (China)

^d GUANGDONG MEDICAL UNIVERSITY   (China)

Author keywords

Expression and distribution; High throughput Solexa sequencing; MicroRNA; Novel microRNA; Systemic lupus erythematosus; Target gene

Indexed keywords

MICRORNA;

ANALYZER; ARTICLE; CELL FUNCTION; CELL METABOLISM; CHROMOSOME; CLINICAL ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE LOCATION; HUMAN; HUMAN CELL; PATHOGENESIS; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA SEQUENCE; RNA TRANSCRIPTION; SEQUENCE ANALYSIS; SYSTEMIC LUPUS ERYTHEMATOSUS; DOWN REGULATION; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; PREDICTIVE VALUE; PROCEDURES; UPREGULATION;

DOWN-REGULATION; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LUPUS ERYTHEMATOSUS, SYSTEMIC; MICRORNAS; PREDICTIVE VALUE OF TESTS; UP-REGULATION;

EID: 84899829517     PISSN: 03008207     EISSN: 16078438     Source Type: Journal    
DOI: 10.3109/03008207.2014.905548     Document Type: Article

References (42)

1. Elkon KB, Stone VV. Type I interferon and systemic lupus erythematosus. J Interferon Cytokine Res 2011;31:803-12.
2. Apostolidis SA, Lieberman LA, Kis-Toth K, Crispin JC, Tsokos GC. The dysregulation of cytokine networks in systemic lupus erythematosus. J Interferon Cytokine Res 2011;31:769-79.
3. Askanase A, Shum K, Mitnick H. Systemic lupus erythematosus: An overview. Soc Work Health Care 2012;51:576-86.
4. Stojan G, Baer AN. Flares of systemic lupus erythematosus during pregnancy and the puerperium: Prevention, diagnosis and management. Expert Rev Clin Immunol 2012;8:439-53.
5. Bezalel S, Asher I, Elbirt D, Sthoeger ZM. Novel biological treatments for systemic lupus erythematosus: Current and future modalities. Isr Med Assoc J 2012;14:508-14.
6. Khan WA, Uddin M, Khan MW, Chabbra HS. Catecholoestrogens: Possible role in systemic lupus erythematosus. Rheumatology (Oxford) 2009;48:1345-51.
7. Maidhof W, Hilas O. Lupus: An overview of the disease and management options. P T 2012;37:240-9.
8. Cojocaru M, Cojocaru IM, Silosi I, Vrabie CD. Manifestations of systemic lupus erythematosus. Maedica (Buchar) 2011;6:330-6.
9. Bartel DP. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 2004;116:281-97.
10. Dai Y, Sui W, Lan H, Yan Q, Huang H, Huang Y. Comprehensive analysis of microRNA expression patterns in renal biopsies of lupus nephritis patients. Rheumatol Int 2009;29:749-54.
11. Liang D, Shen N. MicroRNA involvement in lupus: The beginning of a new tale. Curr Opin Rheumatol 2012;24:489-98.
12. Chang TC, Mendell JT. microRNAs in vertebrate physiology and human disease. Annu Rev Genomics Hum Genet 2007;8:215-39.
13. Zen K, Zhang CY. Circulating microRNAs: A novel class of biomarkers to diagnose and monitor human cancers. Med Res Rev 2012;32:326-48.
14. Berezikov E, Cuppen E, Plasterk RH. Approaches to microRNA discovery. Nat Genet 2006;38 Suppl:S2-7.
15. Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q. MicroRNAs of Bombyx mori identified by Solexa sequencing. BMC Genomics 2010;11: 148.
16. Audic S, Claverie JM. The significance of digital gene expression profiles. Genome Res 1997;7:986-95.
17. Tino P. Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays. BMC Bioinformatics 2009;10: 310.
18. Dennis Jr. G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol 2003;4:P3.
19. Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Clifford Lane H, Lempicki RA. DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res 2007;35:W169-75.
20. Kazubek M, Dlugosz A, Pawlik K. [Application of PCR techniques in toxicology]. Postepy Hig Med Dosw (Online) 2010;64:482-9.
21. Provenzano M, Mocellin S. Complementary techniques: Validation of gene expression data by quantitative real time PCR. Adv Exp Med Biol 2007;593:66-73.
22. Te JL, Dozmorov IM, Guthridge JM, Nguyen KL, Cavett JW, Kelly JA, Bruner GR, Harley JB, Ojwang JO. Identification of unique microRNA signature associated with lupus nephritis. PLoS One 2010;5:e10344.
23. Dai Y, Huang YS, Tang M, Lv TY, Hu CX, Tan YH, Xu ZM, Yin YB. Microarray analysis of microRNA expression in peripheral blood cells of systemic lupus erythematosus patients. Lupus 2007; 16:939-46.
24. Garchow BG, Bartulos Encinas O, Leung YT, Tsao PY, Eisenberg RA, Caricchio R, Obad S, Petri A, Kauppinen S, Kiriakidou M. Silencing of microRNA-21 in vivo ameliorates autoimmune splenomegaly in lupus mice. EMBO Mol Med 2011;3: 605-15.
25. Pan W, Zhu S, Yuan M, Cui H, Wang L, Luo X, Li J, Zhou H, Tang Y, Shen N. MicroRNA-21 and microRNA-148a contribute to DNA hypomethylation in lupus CD4+ T cells by directly and indirectly targeting DNA methyltransferase 1. J Immunol 2010;184: 6773-81.
26. Tang Y, Luo X, Cui H, Ni X, Yuan M, Guo Y, Huang X, Zhou H, de Vries N, Tak PP, Chen S, Shen N. MicroRNA-146A contributes to abnormal activation of the type I interferon pathway in human lupus by targeting the key signaling proteins. Arthritis Rheum 2009;60:1065-75.
27. Luo X, Yang W, Ye DQ, Cui H, Zhang Y, Hirankarn N, Qian X, Tang Y, Lau YL, de Vries N, Tak PP, Tsao BP, Shen N. A functional variant in microRNA-146a promoter modulates its expression and confers disease risk for systemic lupus erythematosus. PLoS Genet 2011;7:e1002128.
28. Li YT, Chen SY, Wang CR, Liu MF, Lin CC, Jou IM, Shiau AL, Wu CL. Brief report: Amelioration of collagen-induced arthritis in mice by lentivirus-mediated silencing of microRNA-223. Arthritis Rheum 2012;64:3240-5.
29. Dai R, Ahmed SA. MicroRNA, a new paradigm for understanding immunoregulation, inflammation, and autoimmune diseases. Transl Res 2011;157:163-79.
30. Vinuesa CG, Rigby RJ, Yu D. Logic and extent of miRNAmediated control of autoimmune gene expression. Int Rev Immunol 2009;28:112-38.
31. Ding S, Liang Y, Zhao M, Liang G, Long H, Zhao S, Wang Y, Yin H, Zhang P, Zhang Q, Lu Q. Decreased microRNA-142-3p/5p expression causes CD4+ T cell activation and B cell hyperstimulation in systemic lupus erythematosus. Arthritis Rheum 2012;64:2953-63.
32. Makino K, Jinnin M, Kajihara I, Honda N, Sakai K, Masuguchi S, Fukushima S, Inoue Y, Ihn H. Circulating miR-142-3p levels in patients with systemic sclerosis. Clin Exp Dermatol 2012;37:34-9.
33. Chen YH, Wang SQ, Wu XL, Shen M, Chen ZG, Chen XG, Liu YX, Zhu XL, Guo F, Duan XZ, Han XC, Tao ZH. Characterization of microRNAs expression profiling in one group of Chinese urothelial cell carcinoma identified by Solexa sequencing. Urol Oncol 2013;31:219-27.
34. Mohan C, Yu Y, Morel L, Yang P, Wakeland EK. Genetic dissection of SLE pathogenesis: SLE3 on murine chromosome 7 impacts T cell activation, differentiation, and cell death. J Immunol 1999;162:6492-502.
35. Sommer CA, Pavarino-Bertelli EC, Goloni-Bertollo EM, Henrique-Silva F. Identification of dysregulated genes in lymphocytes from children with Down syndrome. Genome 2008;51:19-29.
36. Gordon C, Bradley H, Waring RH, Emery P. Abnormal sulphur oxidation in systemic lupus erythematosus. Lancet 1992;339: 25-6.
37. Rovin BH. The chemokine network in systemic lupus erythematous nephritis. Front Biosci 2008;13:904-22.
38. Pereira-Lopes S, Celhar T, Sans-Fons G, Serra M, Fairhurst AM, Lloberas J, Celada A. The exonuclease Trex1 restrains macrophage proinflammatory activation. J Immunol 2013;191:6128-35.
39. Nielsen CT. Circulating microparticles in systemic Lupus erythematosus. Dan Med J 2012;59:B4548.
40. McPhee CG, Bubier JA, Sproule TJ, Park G, Steinbuck MP, Schott WH, Christianson GJ, Morse HC 3rd, Roopenian DC. IL-21 is a double-edged sword in the systemic lupus erythematosus-like disease of BXSB.Yaa mice. J Immunol 2013;191:4581-8.
41. Tan K, Chen J, Li W, Chen Y, Sui W, Zhang Y, Dai Y. Genomewide analysis of microRNAs expression profiling in patients with primary IgA nephropathy. Genome 2013;56:161-9.
42. El-Osta A, Wolffe AP. DNA methylation and histone deacetylation in the control of gene expression: Basic biochemistry to human development and disease. Gene Expr 2000;9:63-75.