Discovery pipeline for epigenetically deregulated miRNAs in cancer: Integration of primary miRNA transcription

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Hulf, Toby ^a   Sibbritt, Tennille ^a   Wiklund, Erik D ^a,b   Bert, Saul ^a   Strbenac, Dario ^a   Statham, Aaron L ^a   Robinson, Mark D ^a,c   Clark, Susan J ^a,d  

^a GARVAN INSTITUTE OF MEDICAL RESEARCH   (Australia)

^b AARHUS UNIVERSITY   (Denmark)

^c WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^d UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; HISTONE H3; HISTONE H3 ACETYLLYSINE 9; LYSINE; MICRORNA; MICRORNA 130A; MICRORNA 135B; MICRORNA 137; MICRORNA 141; MICRORNA 15B; MICRORNA 16 2; MICRORNA 196B; MICRORNA 205; MICRORNA 21; MICRORNA 24 1; MICRORNA 31; MICRORNA 376A 2; MICRORNA 423; MICRORNA 424; MICRORNA 491; MICRORNA 615; MICRORNA 618; MICRORNA 654; MICRORNA 99A; MICRORNA LET7C; RNA; UNCLASSIFIED DRUG;

ARTICLE; CANCER CELL; CONTROLLED STUDY; DNA METHYLATION; DNA MODIFICATION; EPIGENETICS; GENE ACTIVATION; GENE EXPRESSION; GENE REPRESSION; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; HUMAN; HUMAN CELL; MALE; NEOPLASM; PROSTATE CANCER; RNA TRANSCRIPTION; TRANSCRIPTION REGULATION; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; TUMOR CELL LINE;

CELL LINE, TUMOR; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MICRORNAS; NEOPLASMS;

EID: 78651538767     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-54     Document Type: Article

References (47)

1. Wiklund ED, Kjems J, Clark SJ. Epigenetic architecture and microRNA: reciprocal regulators. Epigenomics 2010,
2. Siomi H, Siomi MC. Posttranscriptional regulation of microRNA biogenesis in animals. Molecular cell 2010, 38:323-332. 10.1016/j.molcel.2010.03.013, 20471939.
3. Thomson JM, Newman M, Parker JS, Morin-Kensicki EM, Wright T, Hammond SM. Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes & development 2006, 20:2202-2207.
4. Lee EJ, Baek M, Gusev Y, Brackett DJ, Nuovo GJ, Schmittgen TD. Systematic evaluation of microRNA processing patterns in tissues, cell lines, and tumors. RNA (New York, NY 2008, 14:35-42.
5. Negrini M, Nicoloso MS, Calin GA. MicroRNAs and cancer--new paradigms in molecular oncology. Current opinion in cell biology 2009, 21:470-479. 10.1016/j.ceb.2009.03.002, 19411171.
6. Guil S, Esteller M. DNA methylomes, histone codes and miRNAs: tying it all together. The international journal of biochemistry & cell biology 2009, 41:87-95.
7. Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects for epigenetic therapy. Nature 2004, 429:457-463. 10.1038/nature02625, 15164071.
8. Wilson IM, Davies JJ, Weber M, Brown CJ, Alvarez CE, MacAulay C, Schubeler D, Lam WL. Epigenomics: mapping the methylome. Cell cycle (Georgetown, Tex 2006, 5:155-158. 10.4161/cc.5.2.2367, 16397413.
9. Cooper CS, Foster CS. Concepts of epigenetics in prostate cancer development. British journal of cancer 2009, 100:240-245. 10.1038/sj.bjc.6604771, 2634711, 19002169.
10. Bartels CL, Tsongalis GJ. MicroRNAs: novel biomarkers for human cancer. Clinical chemistry 2009, 55:623-631. 10.1373/clinchem.2008.112805, 19246618.
11. Robinson MD, Stirzaker C, Statham AL, Coolen MW, Song JZ, Nair SS, Strbenac D, Speed TP, Clark SJ. Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation. Genome research 2010,
12. Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic acids research 2010, 38:391-399. 10.1093/nar/gkp992, 2811030, 19906696.
13. Ke XS, Qu Y, Rostad K, Li WC, Lin B, Halvorsen OJ, Haukaas SA, Jonassen I, Petersen K, Goldfinger N, et al. Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis. PLoS ONE 2009, 4:e4687. 10.1371/journal.pone.0004687, 2650415, 19262738.
14. Wiklund ED, Bramsen JB, Hulf T, Dyrskjot L, Ramanathan R, Hansen TB, Villadsen SB, Gao S, Ostenfeld MS, Borre M, et al. Coordinated epigenetic repression of the miR-200 family and miR-205 in invasive bladder cancer. International journal of cancer 2010,
15. Schaefer A, Jung M, Mollenkopf HJ, Wagner I, Stephan C, Jentzmik F, Miller K, Lein M, Kristiansen G, Jung K. Diagnostic and prognostic implications of microRNA profiling in prostate carcinoma. International journal of cancer 2010, 126:1166-1176.
16. Gandellini P, Folini M, Longoni N, Pennati M, Binda M, Colecchia M, Salvioni R, Supino R, Moretti R, Limonta P, et al. miR-205 Exerts tumor-suppressive functions in human prostate through down-regulation of protein kinase Cepsilon. Cancer Res 2009, 69:2287-2295. 10.1158/0008-5472.CAN-08-2894, 19244118.
17. Ribas J, Lupold SE. The transcriptional regulation of miR-21, its multiple transcripts, and their implication in prostate cancer. Cell Cycle 2010, 9:923-929. 10.4161/cc.9.5.10930, 20160498.
18. Folini M, Gandellini P, Longoni N, Profumo V, Callari M, Pennati M, Colecchia M, Supino R, Veneroni S, Salvioni R, et al. miR-21: an oncomir on strike in prostate cancer. Molecular cancer 2010, 9:12. 10.1186/1476-4598-9-12, 2823650, 20092645.
19. Iorio MV, Visone R, Di Leva G, Donati V, Petrocca F, Casalini P, Taccioli C, Volinia S, Liu CG, Alder H, et al. MicroRNA Signatures in Human Ovarian Cancer. Cancer Res 2007, 67:8699-8707. 10.1158/0008-5472.CAN-07-1936, 17875710.
20. Schotte D, Lange-Turenhout EA, Stumpel DJ, Stam RW, Buijs-Gladdines JG, Meijerink JP, Pieters R, Den Boer ML. Expression of miR-196b is not exclusively MLL-driven but is especially linked to activation of HOXA genes in pediatric acute lymphoblastic leukemia. Haematologica 2010, 95:1675-1682. 10.3324/haematol.2010.023481, 2948092, 20494936.
21. Tsai KW, Hu LY, Wu CW, Li SC, Lai CH, Kao HW, Fang WL, Lin W. Epigenetic regulation of miR-196b expression in gastric cancer. Genes, Chromosomes and Cancer 2010, 49:969-980.
22. Coolen MW, Stirzaker C, Song JZ, Statham AL, Kassir Z, Moreno CS, Young AN, Varma V, Speed TP, Cowley M, et al. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nature cell biology 2010, 12:235-246.
23. Yekta S, Tabin CJ, Bartel DP. MicroRNAs in the Hox network: an apparent link to posterior prevalence. Nature reviews 2008, 9:789-796. 10.1038/nrg2400, 2710959, 18781158.
24. Shah N, Sukumar S. The Hox genes and their roles in oncogenesis. Nat Rev Cancer 2010,
25. Hayashi H, Nagae G, Tsutsumi S, Kaneshiro K, Kozaki T, Kaneda A, Sugisaki H, Aburatani H. High-resolution mapping of DNA methylation in human genome using oligonucleotide tiling array. Hum Genet 2007, 120:701-711. 10.1007/s00439-006-0254-6, 17024368.
26. Shi H, Wei SH, Leu YW, Rahmatpanah F, Liu JC, Yan PS, Nephew KP, Huang TH. Triple analysis of the cancer epigenome: an integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation. Cancer Res 2003, 63:2164-2171.
27. Meiers I, Shanks JH, Bostwick DG. Glutathione S-transferase pi (GSTP1) hypermethylation in prostate cancer: review 2007. Pathology 2007, 39:299-304. 10.1080/00313020701329906, 17558856.
28. Stirzaker C, Song JZ, Davidson B, Clark SJ. Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells. Cancer Res 2004, 64:3871-3877. 10.1158/0008-5472.CAN-03-3690, 15172996.
29. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:Article3.
30. Song JZ, Stirzaker C, Harrison J, Melki JR, Clark SJ. Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells. Oncogene 2002, 21:1048-1061. 10.1038/sj.onc.1205153, 11850822.
31. Coolen MW, Stirzaker C, Song JZ, Statham AL, Kassir Z, Moreno CS, Young AN, Varma V, Speed TP, Cowley M, et al. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nature cell biology 12:235-246.
32. Oliveros JC. VENNY. An interactive tool for comparing lists with Venn Diagrams. 2007, 2223552, 18039769., http://bioinfogp.cnb.csic.es/tools/venny/index.html
33. Ozen M, Creighton CJ, Ozdemir M, Ittmann M. Widespread deregulation of microRNA expression in human prostate cancer. Oncogene 2008, 27:1788-1793. 10.1038/sj.onc.1210809, 17891175.
34. Vrba L, Jensen TJ, Garbe JC, Heimark RL, Cress AE, Dickinson S, Stampfer MR, Futscher BW. Role for DNA methylation in the regulation of miR-200c and miR-141 expression in normal and cancer cells. PLoS ONE 2010, 5:e8697. 10.1371/journal.pone.0008697, 2805718, 20084174.
35. Satzger I, Mattern A, Kuettler U, Weinspach D, Voelker B, Kapp A, Gutzmer R. MicroRNA-15b represents an independent prognostic parameter and is correlated with tumor cell proliferation and apoptosis in malignant melanoma. International journal of cancer 2010, 126:2553-2562.
36. Hu Y, Correa AM, Hoque A, Guan B, Ye F, Huang J, Swisher SG, Wu TT, Ajani JA, Xu XC. Prognostic significance of differentially expressed miRNAs in esophageal cancer. International journal of cancer 2010,
37. Hui AB, Lenarduzzi M, Krushel T, Waldron L, Pintilie M, Shi W, Perez-Ordonez B, Jurisica I, O'Sullivan B, Waldron J, et al. Comprehensive MicroRNA profiling for head and neck squamous cell carcinomas. Clin Cancer Res 2010, 16:1129-1139. 10.1158/1078-0432.CCR-09-2166, 20145181.
38. Nakano H, Miyazawa T, Kinoshita K, Yamada Y, Yoshida T. Functional screening identifies a microRNA, miR-491 that induces apoptosis by targeting Bcl-X(L) in colorectal cancer cells. International journal of cancer 2009,
39. Cicatiello L, Mutarelli M, Grober OM, Paris O, Ferraro L, Ravo M, Tarallo R, Luo S, Schroth GP, Seifert M, et al. Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. The American journal of pathology 2010, 176:2113-2130. 10.2353/ajpath.2010.090837, 20348243.
40. Zhang H, Luo XQ, Zhang P, Huang LB, Zheng YS, Wu J, Zhou H, Qu LH, Xu L, Chen YQ. MicroRNA patterns associated with clinical prognostic parameters and CNS relapse prediction in pediatric acute leukemia. PLoS ONE 2009, 4:e7826. 10.1371/journal.pone.0007826, 2773830, 19915715.
41. Chen Y, Gorski DH. Regulation of angiogenesis through a microRNA (miR-130a) that down-regulates antiangiogenic homeobox genes GAX and HOXA5. Blood 2008, 111:1217-1226. 10.1182/blood-2007-07-104133, 2214763, 17957028.
42. Sarver AL, French AJ, Borralho PM, Thayanithy V, Oberg AL, Silverstein KA, Morlan BW, Riska SM, Boardman LA, Cunningham JM, et al. Human colon cancer profiles show differential microRNA expression depending on mismatch repair status and are characteristic of undifferentiated proliferative states. BMC Cancer 2009, 9:401. 10.1186/1471-2407-9-401, 2787532, 19922656.
43. Bandres E, Agirre X, Bitarte N, Ramirez N, Zarate R, Roman-Gomez J, Prosper F, Garcia-Foncillas J. Epigenetic regulation of microRNA expression in colorectal cancer. International journal of cancer 2009, 125:2737-2743.
44. Popovic R, Riesbeck LE, Velu CS, Chaubey A, Zhang J, Achille NJ, Erfurth FE, Eaton K, Lu J, Grimes HL, et al. Regulation of mir-196b by MLL and its overexpression by MLL fusions contributes to immortalization. Blood 2009, 113:3314-3322. 10.1182/blood-2008-04-154310, 2665896, 19188669.
45. Qin W, Shi Y, Zhao B, Yao C, Jin L, Ma J, Jin Y. miR-24 regulates apoptosis by targeting the open reading frame (ORF) region of FAF1 in cancer cells. PLoS ONE 2010, 5:e9429. 10.1371/journal.pone.0009429, 2828487, 20195546.
46. Valastyan S, Reinhardt F, Benaich N, Calogrias D, Szasz AM, Wang ZC, Brock JE, Richardson AL, Weinberg RA. A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis. Cell 2009, 137:1032-1046. 10.1016/j.cell.2009.03.047, 2766609, 19524507.
47. Lee EJ, Gusev Y, Jiang J, Nuovo GJ, Lerner MR, Frankel WL, Morgan DL, Postier RG, Brackett DJ, Schmittgen TD. Expression profiling identifies microRNA signature in pancreatic cancer. International journal of cancer 2007, 120:1046-1054.