An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Nam, Seungyoon ^a,b   Long, Xinghua ^b,c   Kwon, ChangHyuk ^a   Kim, Sun ^d   Nephew, Kenneth P ^b  

^a National Cancer Center   (South Korea)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c WUHAN UNIVERSITY   (China)

^d Seoul National University   (South Korea)

Author keywords

Antiestrogen resistance; Bioinformatics; Breast cancer; MiRNA; Network

Indexed keywords

FULVESTRANT; LET 7S; MESSENGER RNA; MICRORNA; MICRORNA 125B; MICRORNA 145; MICRORNA 146A; MICRORNA 155; MICRORNA 15A; MICRORNA 21; MICRORNA 27A; TAMOXIFEN; UNCLASSIFIED DRUG;

ARTICLE; BREAST CANCER; CANCER CELL; CANCER RESISTANCE; CELL STRAIN MCF 7; CONTROLLED STUDY; GENE EXPRESSION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PREDICTION;

BREAST NEOPLASMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DRUG RESISTANCE, NEOPLASM; ESTROGENS; HUMANS; MCF-7 CELLS; MICRORNAS; MOLECULAR TARGETED THERAPY; RNA, MESSENGER;

EID: 84871572095     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-732     Document Type: Article

References (59)

1. Osborne CK, Schiff R. Mechanisms of endocrine resistance in breast cancer. Annu Rev Med 2011, 62:233-247. 10.1146/annurev-med-070909-182917, 20887199.
2. Fan M, Yan PS, Hartman-Frey C, Chen L, Paik H, Oyer SL, Salisbury JD, Cheng AS, Li L, Abbosh PH, et al. Diverse gene expression and DNA methylation profiles correlate with differential adaptation of breast cancer cells to the antiestrogens tamoxifen and fulvestrant. Cancer Res 2006, 66:11954-11966. 10.1158/0008-5472.CAN-06-1666, 17178894.
3. Esquela-Kerscher A, Slack FJ. Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 2006, 6:259-269.
4. Bang-Berthelsen CH, Pedersen L, Floyel T, Hagedorn PH, Gylvin T, Pociot F. Independent component and pathway-based analysis of miRNA-regulated gene expression in a model of type 1 diabetes. BMC Genomics 2011, 12:97. 10.1186/1471-2164-12-97, 3040732, 21294859.
5. Hulf T, Sibbritt T, Wiklund ED, Bert S, Strbenac D, Statham AL, Robinson MD, Clark SJ. Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription. BMC Genomics 2011, 12:54. 10.1186/1471-2164-12-54, 3037319, 21255435.
6. Zhou JY, Ma WL, Liang S, Zeng Y, Shi R, Yu HL, Xiao WW, Zheng WL. Analysis of microRNA expression profiles during the cell cycle in synchronized HeLa cells. BMB Rep 2009, 42:593-598. 10.5483/BMBRep.2009.42.9.593, 19788861.
7. Klinge CM. miRNAs and estrogen action. Trends Endocrinol Metab 2012, 23:223-233. 10.1016/j.tem.2012.03.002, 22503553.
8. Majumder S, Jacob ST. Emerging role of microRNAs in drug-resistant breast cancer. Gene Expr 2011, 15:141-151. 10.3727/105221611X13176664479287, 22268296.
9. Rao X, Di Leva G, Li M, Fang F, Devlin C, Hartman-Frey C, Burow ME, Ivan M, Croce CM, Nephew KP. MicroRNA-221/222 confers breast cancer fulvestrant resistance by regulating multiple signaling pathways. Oncogene 2011, 30:1082-1097. 10.1038/onc.2010.487, 3342929, 21057537.
10. Miller TE, Ghoshal K, Ramaswamy B, Roy S, Datta J, Shapiro CL, Jacob S, Majumder S. MicroRNA-221/222 confers tamoxifen resistance in breast cancer by targeting p27Kip1. J Biol Chem 2008, 283:29897-29903. 10.1074/jbc.M804612200, 2573063, 18708351.
11. Di Leva G, Gasparini P, Piovan C, Ngankeu A, Garofalo M, Taccioli C, Iorio MV, Li M, Volinia S, Alder H, et al. MicroRNA cluster 221-222 and estrogen receptor alpha interactions in breast cancer. J Natl Cancer Inst 2010, 102:706-721. 10.1093/jnci/djq102, 2873185, 20388878.
12. Nam S, Kim B, Shin S, Lee S. miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res 2008, 36:D159-164. 2238850, 17942429.
13. Jayaswal V, Lutherborrow M, Ma DD, Yang YH. Identification of microRNA-mRNA modules using microarray data. BMC Genomics 2011, 12:138. 10.1186/1471-2164-12-138, 3065435, 21375780.
14. Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP. MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res 2009, 37:W356-362. 10.1093/nar/gkp294, 2703907, 19420067.
15. Pe'er D, Hacohen N. Principles and strategies for developing network models in cancer. Cell 2011, 144:864-873. 10.1016/j.cell.2011.03.001, 3082135, 21414479.
16. Dutkowski J, Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol 2011, 7:e1002180. 10.1371/journal.pcbi.1002180, 3182870, 21980275.
17. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113. 10.1038/nrg1272, 14735121.
18. Baliga NS, Pan M, Plaisier CL. A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res 2012, 22:2302-2314. 10.1101/gr.133991.111, 3483559, 22745231.
19. Nunez-Iglesias J, Liu CC, Morgan TE, Finch CE, Zhou XJ. Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation. PLoS One 2010, 5:e8898. 10.1371/journal.pone.0008898, 2813862, 20126538.
20. Ferraro L, Ravo M, Nassa G, Tarallo R, De Filippo MR, Giurato G, Cirillo F, Stellato C, Silvestro S, Cantarella C, et al. Effects of oestrogen on microRNA expression in hormone-responsive breast cancer cells. Horm Cancer 2012, 3:65-78. 10.1007/s12672-012-0102-1, 22274890.
21. Manavalan TT, Teng Y, Appana SN, Datta S, Kalbfleisch TS, Li Y, Klinge CM. Differential expression of microRNA expression in tamoxifen-sensitive MCF-7 versus tamoxifen-resistant LY2 human breast cancer cells. Cancer Lett 2011, 313:26-43. 10.1016/j.canlet.2011.08.018, 3214732, 21955614.
22. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 2011, 39:D163-169. 10.1093/nar/gkq1107, 3013699, 21071411.
23. Wang J, Lu M, Qiu C, Cui Q. TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res 2010, 38:D119-122. 10.1093/nar/gkp803, 2808874, 19786497.
24. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011, 144:646-674. 10.1016/j.cell.2011.02.013, 21376230.
25. Martin SA, Hewish M, Lord CJ, Ashworth A. Genomic instability and the selection of treatments for cancer. J Pathol 2010, 220:281-289.
26. Jenssen TK, Laegreid A, Komorowski J, Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 2001, 28:21-28.
27. Balch C, Nephew KP. The role of chromatin, microRNAs, and tumor stem cells in ovarian cancer. Cancer Biomark 2010, 8:203-221.
28. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011, 27:431-432. 10.1093/bioinformatics/btq675, 3031041, 21149340.
29. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics 2011, 12:436. 10.1186/1471-2105-12-436, 3262844, 22070249.
30. Lin SL, Chiang A, Chang D, Ying SY. Loss of mir-146a function in hormone-refractory prostate cancer. RNA 2008, 14:417-424. 10.1261/rna.874808, 2248249, 18174313.
31. Li Y, Vandenboom TG, Wang Z, Kong D, Ali S, Philip PA, Sarkar FH. miR-146a suppresses invasion of pancreatic cancer cells. Cancer Res 2010, 70:1486-1495. 10.1158/0008-5472.CAN-09-2792, 2978025, 20124483.
32. Rusca N, Monticelli S. MiR-146a in Immunity and Disease. Mol Biol Int 2011, 2011:437301. 3200075, 22091404.
33. Deng CX. BRCA1: cell cycle checkpoint, genetic instability, DNA damage response and cancer evolution. Nucleic Acids Res 2006, 34:1416-1426. 10.1093/nar/gkl010, 1390683, 16522651.
34. Roy R, Chun J, Powell SN. BRCA1 and BRCA2: different roles in a common pathway of genome protection. Nat Rev Cancer 2012, 12:68-78.
35. Guirouilh-Barbat JK, Wilhelm T, Lopez BS. AKT1/BRCA1 in the control of homologous recombination and genetic stability: the missing link between hereditary and sporadic breast cancers. Oncotarget 2010, 1:691-699. 3157734, 21321378.
36. Wang L, Zhang Q, Zhang J, Sun S, Guo H, Jia Z, Wang B, Shao Z, Wang Z, Hu X. PI3K pathway activation results in low efficacy of both trastuzumab and lapatinib. BMC Cancer 2011, 11:11-248. 10.1186/1471-2407-11-11, 3032749, 21223585.
37. Miller TW, Rexer BN, Garrett JT, Arteaga CL. Mutations in the phosphatidylinositol 3-kinase pathway: role in tumor progression and therapeutic implications in breast cancer. Breast Cancer Res 2011, 13:224. 10.1186/bcr3039, 3315683, 22114931.
38. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 2011, 39:D945-950. 10.1093/nar/gkq929, 3013785, 20952405.
39. Puc J, Keniry M, Li HS, Pandita TK, Choudhury AD, Memeo L, Mansukhani M, Murty VV, Gaciong Z, Meek SE, et al. Lack of PTEN sequesters CHK1 and initiates genetic instability. Cancer Cell 2005, 7:193-204. 10.1016/j.ccr.2005.01.009, 15710331.
40. Plo I, Laulier C, Gauthier L, Lebrun F, Calvo F, Lopez BS. AKT1 inhibits homologous recombination by inducing cytoplasmic retention of BRCA1 and RAD51. Cancer Res 2008, 68:9404-9412. 10.1158/0008-5472.CAN-08-0861, 19010915.
41. Li Z, Hu S, Wang J, Cai J, Xiao L, Yu L, Wang Z. MiR-27a modulates MDR1/P-glycoprotein expression by targeting HIPK2 in human ovarian cancer cells. Gynecol Oncol 2010, 119:125-130. 10.1016/j.ygyno.2010.06.004, 20624637.
42. Peng X, Guo W, Liu T, Wang X, Tu X, Xiong D, Chen S, Lai Y, Du H, Chen G, et al. Identification of miRs-143 and -145 that is associated with bone metastasis of prostate cancer and involved in the regulation of EMT. PLoS One 2011, 6:e20341. 10.1371/journal.pone.0020341, 3103579, 21647377.
43. Gregersen LH, Jacobsen AB, Frankel LB, Wen J, Krogh A, Lund AH. MicroRNA-145 targets YES and STAT1 in colon cancer cells. PLoS One 2010, 5:e8836. 10.1371/journal.pone.0008836, 2809101, 20098684.
44. La Rocca G, Badin M, Shi B, Xu SQ, Deangelis T, Sepp-Lorenzinoi L, Baserga R. Mechanism of growth inhibition by MicroRNA 145: the role of the IGF-I receptor signaling pathway. J Cell Physiol 2009, 220:485-491. 10.1002/jcp.21796, 19391107.
45. Han M, Liu M, Wang Y, Mo Z, Bi X, Liu Z, Fan Y, Chen X, Wu C. Re-expression of miR-21 contributes to migration and invasion by inducing epithelial-mesenchymal transition consistent with cancer stem cell characteristics in MCF-7 cells. Mol Cell Biochem 2012, 363:427-436. 10.1007/s11010-011-1195-5, 22187223.
46. Cottonham CL, Kaneko S, Xu L. miR-21 and miR-31 converge on TIAM1 to regulate migration and invasion of colon carcinoma cells. J Biol Chem 2010, 285:35293-35302. 10.1074/jbc.M110.160069, 2975153, 20826792.
47. Yang Y, Chaerkady R, Beer MA, Mendell JT, Pandey A. Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics 2009, 9:1374-1384. 10.1002/pmic.200800551, 3030979, 19253296.
48. Jiang S, Zhang HW, Lu MH, He XH, Li Y, Gu H, Liu MF, Wang ED. MicroRNA-155 functions as an OncomiR in breast cancer by targeting the suppressor of cytokine signaling 1 gene. Cancer Res 2010, 70:3119-3127. 10.1158/0008-5472.CAN-09-4250, 20354188.
49. Li CL, Nie H, Wang M, Su LP, Li JF, Yu YY, Yan M, Qu QL, Zhu ZG, Liu BY. microRNA-155 is downregulated in gastric cancer cells and involved in cell metastasis. Oncol Rep 2012, 27:1960-1966.
50. Dorsett Y, McBride KM, Jankovic M, Gazumyan A, Thai TH, Robbiani DF, Di Virgilio M, Reina San-Martin B, Heidkamp G, Schwickert TA, et al. MicroRNA-155 suppresses activation-induced cytidine 0deaminase-mediated Myc-Igh translocation. Immunity 2008, 28:630-638. 10.1016/j.immuni.2008.04.002, 2713656, 18455451.
51. Zhou M, Liu Z, Zhao Y, Ding Y, Liu H, Xi Y, Xiong W, Li G, Lu J, Fodstad O, et al. MicroRNA-125b confers the resistance of breast cancer cells to paclitaxel through suppression of pro-apoptotic Bcl-2 antagonist killer 1 (Bak1) expression. J Biol Chem 2010, 285:21496-21507. 10.1074/jbc.M109.083337, 2898411, 20460378.
52. Budhu A, Ji J, Wang XW. The clinical potential of microRNAs. J Hematol Oncol 2010, 3:37. 10.1186/1756-8722-3-37, 2958878, 20925959.
53. Pradhan MP, Prasad NK, Palakal MJ. A systems biology approach to the global analysis of transcription factors in colorectal cancer. BMC Cancer 2012, 12:331. 10.1186/1471-2407-12-331, 3539921, 22852817.
54. Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 2010, 16:991-1006. 10.1261/rna.1947110, 2856892, 20360395.
55. Chen Y, Gelfond JA, McManus LM, Shireman PK. Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis. BMC Genomics 2009, 10:407. 10.1186/1471-2164-10-407, 2753550, 19715577.
56. Thomson JM, Parker J, Perou CM, Hammond SM. A custom microarray platform for analysis of microRNA gene expression. Nat Methods 2004, 1:47-53. 10.1038/nmeth704, 15782152.
57. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
58. Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. UCSC genome browser tutorial. Genomics 2008, 92:75-84. 10.1016/j.ygeno.2008.02.003, 18514479.
59. Hobert O. Common logic of transcription factor and microRNA action. Trends Biochem Sci 2004, 29:462-468. 10.1016/j.tibs.2004.07.001, 15337119.