Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis

Journal of Translational Medicine

Volumn 11, Issue 1, 2013, Pages

  Chen, Jiajia ^a,b   Zhang, Daqing ^a   Zhang, Wenyu ^a   Tang, Yifei ^a   Yan, Wenying ^a   Guo, Lingchuan ^a   Shen, Bairong ^a  

^a SOOCHOW UNIVERSITY   (China)

^b SUZHOU UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Clear cell renal cell carcinoma; Heterogeneity; Meta analysis; MicroRNA; Network biomarker; Pathway analysis

Indexed keywords

AXIN; BETA CATENIN; BRCA1 PROTEIN; CYCLIN D1; FRIZZLED PROTEIN; GROWTH ARREST AND DNA DAMAGE INDUCIBLE PROTEIN 45; MICRORNA; MITOGEN ACTIVATED PROTEIN KINASE KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE P38; MYC PROTEIN; PREGNANCY SPECIFIC BETA1 GLYCOPROTEIN; PROTEIN C JUN; PROTEIN KINASE B; PROTEIN MSH2; PROTEIN P21; RETINOBLASTOMA PROTEIN; RHO KINASE; RHOA GUANINE NUCLEOTIDE BINDING PROTEIN; SOMATOMEDIN C RECEPTOR; STAT1 PROTEIN; T CELL FACTOR PROTEIN; TRANSCRIPTION FACTOR E2F1; TRANSCRIPTION FACTOR SP3; TRANSFORMING GROWTH FACTOR BETA; VASCULOTROPIN A; WNT PROTEIN;

ARTICLE; BIOINFORMATICS; CARCINOGENESIS; CELL ADHESION; CELL CYCLE PROGRESSION; CELL CYCLE REGULATION; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; DNA DAMAGE; ENZYME REGULATION; G1 PHASE CELL CYCLE CHECKPOINT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE INTERACTION; GENETIC ALGORITHM; GENETIC ASSOCIATION; HUMAN; INTRACELLULAR SIGNALING; KIDNEY CARCINOMA; MOLECULAR PATHOLOGY; NUCLEOTIDE SEQUENCE; RNA GENE; RNA SEQUENCE; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

ALGORITHMS; CARCINOMA, RENAL CELL; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; KIDNEY NEOPLASMS; MICRORNAS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION, GENETIC; TUMOR MARKERS, BIOLOGICAL;

EID: 84880021080     PISSN: None     EISSN: 14795876     Source Type: Journal    
DOI: 10.1186/1479-5876-11-169     Document Type: Article

References (50)

1. Siegel R, Ward E, Brawley O, Jemal A. Cancer statistics, 2011: the impact of eliminating socioeconomic and racial disparities on premature cancer deaths. CA Cancer J Clin 2011, 61:212-236. 10.3322/caac.20121, 21685461.
2. Escudier B. Advanced renal cell carcinoma: current and emerging management strategies. Drugs 2007, 67:1257-1264. 10.2165/00003495-200767090-00002, 17547470.
3. Singer EA, Gupta GN, Marchalik D, Srinivasan R. Evolving therapeutic targets in renal cell carcinoma. Curr Opin Oncol 2013, 25:273-280.
4. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
5. Lossos IS, Czerwinski DK, Alizadeh AA, Wechser MA, Tibshirani R, Botstein D, Levy R. Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med 2004, 350:1828-1837. 10.1056/NEJMoa032520, 15115829.
6. Allison DB, Cui X, Page GP, Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 2006, 7:55-65. 10.1038/nrg1749, 16369572.
7. Kort EJ, Farber L, Tretiakova M, Petillo D, Furge KA, Yang XJ, Cornelius A, Teh BT. The E2F3-Oncomir-1 axis is activated in Wilms' tumor. Cancer Res 2008, 68:4034-4038. 10.1158/0008-5472.CAN-08-0592, 2442735, 18519660.
8. Jung M, Mollenkopf HJ, Grimm C, Wagner I, Albrecht M, Waller T, Pilarsky C, Johannsen M, Stephan C, Lehrach H, Nietfeld W, Rudel T, Jung K, Kristiansen G. MicroRNA profiling of clear cell renal cell cancer identifies a robust signature to define renal malignancy. J Cell Mol Med 2009, 13:3918-3928. 10.1111/j.1582-4934.2009.00705.x, 19228262.
9. Liu H, Brannon AR, Reddy AR, Alexe G, Seiler MW, Arreola A, Oza JH, Yao M, Juan D, Liou LS, Ganesan S, Levine AJ, Rathmell WK, Bhanot GV. Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. BMC Syst Biol 2009, 4:51.
10. Yi Z, Fu Y, Zhao S, Zhang X, Ma C. Differential expression of miRNA patterns in renal cell carcinoma and nontumorous tissues. J Cancer Res Clin Oncol 2009, 136:855-862.
11. White NM, Bao TT, Grigull J, Youssef YM, Girgis A, Diamandis M, Fatoohi E, Metias M, Honey RJ, Stewart R, Pace KT, Bjarnason GA. Yousef GM: miRNA profiling for clear cell renal cell carcinoma: biomarker discovery and identification of potential controls and consequences of miRNA dysregulation. J Urol 2011, 186:1077-1083. 10.1016/j.juro.2011.04.110, 21784468.
12. Huang Y, Dai Y, Yang J, Chen T, Yin Y, Tang M, Hu C, Zhang L. Microarray analysis of microRNA expression in renal clear cell carcinoma. Eur J Surg Oncol 2009, 35:1119-1123. 10.1016/j.ejso.2009.04.010, 19443172.
13. Chow TF, Youssef YM, Lianidou E, Romaschin AD, Honey RJ, Stewart R, Pace KT, Yousef GM. Differential expression profiling of microRNAs and their potential involvement in renal cell carcinoma pathogenesis. Clin Biochem 2010, 43:150-158. 10.1016/j.clinbiochem.2009.07.020, 19646430.
14. Juan D, Alexe G, Antes T, Liu H, Madabhushi A, Delisi C, Ganesan S, Bhanot G, Liou LS. Identification of a microRNA panel for clear-cell kidney cancer. Urology 2009, 75:835-841.
15. Khella HW, White NM, Faragalla H, Gabril M, Boazak M, Dorian D, Khalil B, Antonios H, Bao TT, Pasic MD, Honey RJ, Stewart R, Pace KT, Bjarnason GA, Jewett MA, Yousef GM. Exploring the role of miRNAs in renal cell carcinoma progression and metastasis through bioinformatic and experimental analyses. Tumour Biol 2011, 33:131-140.
16. Berkers J, Govaere O, Wolter P, Beuselinck B, Schoffski P, van Kempen LC, Albersen M, Van den Oord J, Roskams T, Swinnen J, Joniau S, Van Poppel H, Lerut E. A possible role for microRNA-141 down-regulation in sunitinib resistant metastatic clear cell renal cell carcinoma through induction of epithelial-to-mesenchymal transition and hypoxia resistance. J Urol 2013, 189:1930-1938. 10.1016/j.juro.2012.11.133, 23206420.
17. Osanto S, Qin Y, Buermans HP, Berkers J, Lerut E, Goeman JJ, van Poppel H. Genome-wide microRNA expression analysis of clear cell renal cell carcinoma by next generation deep sequencing. PLoS One 2012, 7:e38298. 10.1371/journal.pone.0038298, 3380046, 22745662.
18. Weng L, Wu X, Gao H, Mu B, Li X, Wang JH, Guo C, Jin JM, Chen Z, Covarrubias M, Yuan YC, Weiss LM, Wu H. MicroRNA profiling of clear cell renal cell carcinoma by whole-genome small RNA deep sequencing of paired frozen and formalin-fixed, paraffin-embedded tissue specimens. J Pathol 2010, 222:41-51.
19. Zhou L, Chen J, Li Z, Li X, Hu X, Huang Y, Zhao X, Liang C, Wang Y, Sun L, Shi M, Xu X, Shen F, Chen M, Han Z, Peng Z, Zhai Q, Zhang Z, Yang R, Ye J, Guan Z, Yang H, Gui Y, Wang J, Cai Z, Zhang X. Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma. PLoS One 2011, 5:e15224.
20. Kozomara A. Griffiths-Jones S: miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:D152-D157. 10.1093/nar/gkq1027, 3013655, 21037258.
21. MacDonald JW, Ghosh D. COPA-cancer outlier profile analysis. Bioinformatics 2006, 22:2950-2951. 10.1093/bioinformatics/btl433, 16895932.
22. Lian H. MOST: detecting cancer differential gene expression. Biostatistics 2008, 9:411-418. 10.1093/biostatistics/kxm042, 18048648.
23. Wu B. Cancer outlier differential gene expression detection. Biostatistics 2007, 8:566-575.
24. Tibshirani R, Hastie T. Outlier sums for differential gene expression analysis. Biostatistics 2007, 8:2-8. 10.1093/biostatistics/kxl005, 16702229.
25. Wang Y, Rekaya R. LSOSS: Detection of Cancer Outlier Differential Gene Expression. Biomark Insights 2010, 5:69-78. 2918352, 20703321.
26. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003, 115:787-798. 10.1016/S0092-8674(03)01018-3, 14697198.
27. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N. Combinatorial microRNA target predictions. Nat Genet 2005, 37:495-500. 10.1038/ng1536, 15806104.
28. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004, 2:e363. 10.1371/journal.pbio.0020363, 521178, 15502875.
29. Xiao F, Zuo Z, Cai G, Kang S, Gao X. Li T: miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009, 37:D105-D110. 10.1093/nar/gkn851, 2686554, 18996891.
30. da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
31. Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005, 310:644-648. 10.1126/science.1117679, 16254181.
32. Tang Y, Chen J, Luo C, Kaipia A, Shen B. MicroRNA expression analysis reveals significant biological pathways in human prostate cancer 2011, 203-210. Zhuhai, China: EEE Computer Society, In 5th IEEE International Conference on Systems Biology, ISB 2011; 2-4 Sept. 2011.
33. Zhang W, Zhuang Y, Jin X, Guo F, Shen B. Identification of novel miRNA biomarkers for prostate cancer diagnosis from gene expression data. in press.
34. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
35. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008, 36:D480-484. 2238879, 18077471.
36. Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavtigian S, Liu Q, Cochran C, Bennett LM, Ding W. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 1994, 266:66-71. 10.1126/science.7545954, 7545954.
37. Gao X, Porter AT, Honn KV. Involvement of the multiple tumor suppressor genes and 12-lipoxygenase in human prostate cancer. Therapeutic implications. Adv Exp Med Biol 1997, 407:41-53. 10.1007/978-1-4899-1813-0_7, 9321930.
38. Zink D, Mayr C, Janz C, Wiesmuller L. Association of p53 and MSH2 with recombinative repair complexes during S phase. Oncogene 2002, 21:4788-4800. 10.1038/sj.onc.1205614, 12101417.
39. Yun J, Lee WH. Degradation of transcription repressor ZBRK1 through the ubiquitin-proteasome pathway relieves repression of Gadd45a upon DNA damage. Mol Cell Biol 2003, 23:7305-7314. 10.1128/MCB.23.20.7305-7314.2003, 230312, 14517299.
40. Fan W, Jin S, Tong T, Zhao H, Fan F, Antinore MJ, Rajasekaran B, Wu M, Zhan Q. BRCA1 regulates GADD45 through its interactions with the OCT-1 and CAAT motifs. J Biol Chem 2002, 277:8061-8067. 10.1074/jbc.M110225200, 11777930.
41. Chen IT, Smith ML, O'Connor PM, Fornace AJ. Direct interaction of Gadd45 with PCNA and evidence for competitive interaction of Gadd45 and p21Waf1/Cip1 with PCNA. Oncogene 1995, 11:1931-1937.
42. Jin S, Antinore MJ, Lung FD, Dong X, Zhao H, Fan F, Colchagie AB, Blanck P, Roller PP, Fornace AJ, Zhan Q. The GADD45 inhibition of Cdc2 kinase correlates with GADD45-mediated growth suppression. J Biol Chem 2000, 275:16602-16608. 10.1074/jbc.M000284200, 10747892.
43. Sancar A, Lindsey-Boltz LA, Unsal-Kacmaz K, Linn S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu Rev Biochem 2004, 73:39-85. 10.1146/annurev.biochem.73.011303.073723, 15189136.
44. Yin XY, Grove L, Datta NS, Katula K, Long MW, Prochownik EV. Inverse regulation of cyclin B1 by c-Myc and p53 and induction of tetraploidy by cyclin B1 overexpression. Cancer Res 2001, 61:6487-6493.
45. Chen J, Zhang D, Zhang W, Tang Y, Guo L, Shen B. An integrative framework for identifying consistent microRNA expression signatures associated with clear cell renal cell carcinoma 2012, 37-42. Xian, China: IEEE, In Systems Biology (ISB), 2012 IEEE 6th International Conference on; 20-22 Aug. 2012.
46. Chen J, Chen L, Shen B. Identification of Network Biomarkers for Cancer Diagnosis. Bioinformatics of Human Proteomics 2012, 257-275. Springer.
47. Chen J, Wang Y, Shen B, Zhang D. Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data. Computational and mathematical methods in medicine 2013, 2013:8.
48. Wang Y, Chen J, Li Q, Wang H, Liu G, Jing Q, Shen B. Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. Comput Biol Chem 2011, 35:151-158. 10.1016/j.compbiolchem.2011.04.003, 21704261.
49. Zhang M, Yao C, Guo Z, Zou J, Zhang L, Xiao H, Wang D, Yang D, Gong X, Zhu J, Li Y, Li X. Apparently low reproducibility of true differential expression discoveries in microarray studies. Bioinformatics 2008, 24:2057-2063. 10.1093/bioinformatics/btn365, 18632747.
50. Liu Q, Fu H, Sun F, Zhang H, Tie Y, Zhu J, Xing R, Sun Z. Zheng X: miR-16 family induces cell cycle arrest by regulating multiple cell cycle genes. Nucleic Acids Res 2008, 36:5391-5404. 10.1093/nar/gkn522, 2532718, 18701644.