Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Jagannathan, Vidhya ^a,b   Robinson Rechavi, Marc ^a,b  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

Breast cancer; Estrogen; Meta analysis; Microarray; Pathways

Indexed keywords

ESTRADIOL;

ARTICLE; CELL CYCLE; CELL PROLIFERATION; COMPARATIVE STUDY; DNA REPAIR; DRUG EFFECT; FEMALE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; HUMAN; META ANALYSIS; METABOLISM; PROTEIN MICROARRAY; SIGNAL TRANSDUCTION; TUMOR CELL LINE;

CELL CYCLE; CELL LINE, TUMOR; CELL PROLIFERATION; DNA REPAIR; ESTRADIOL; FEMALE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; PROTEIN ARRAY ANALYSIS; SIGNAL TRANSDUCTION;

EID: 80052122015     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-138     Document Type: Article

References (40)

1. Katzenellenbogen BS. Estrogen receptors: bioactivities and interactions with cell signaling pathways. Biol Reprod 1996, 54(2):287-293. 10.1095/biolreprod54.2.287, 8788178.
2. Anderson E. The role of oestrogen and progesterone receptors in human mammary development and tumorigenesis. Breast Cancer Res 2002, 4(5):197-201. 10.1186/bcr452, 138744, 12223124.
3. Welboren WJ, Sweep FC, Span PN, Stunnenberg HG. Genomic actions of estrogen receptor alpha: what are the targets and how are they regulated?. Endocr Relat Cancer 2009, 16(4):1073-1089. 10.1677/ERC-09-0086, 19628648.
4. Welboren WJ, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FC, Span PN, Stunnenberg HG. ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands. EMBO J 2009, 28(10):1418-1428. 10.1038/emboj.2009.88, 2688537, 19339991.
5. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, et al. Genome-wide analysis of estrogen receptor binding sites. Nat Genet 2006, 38(11):1289-1297. 10.1038/ng1901, 17013392.
6. Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, et al. Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet 2007, 3(6):e87. 10.1371/journal.pgen.0030087, 1885282, 17542648.
7. Vyhlidal C, Samudio I, Kladde MP, Safe S. Transcriptional activation of transforming growth factor alpha by estradiol: requirement for both a GC-rich site and an estrogen response element half-site. J Mol Endocrinol 2000, 24(3):329-338. 10.1677/jme.0.0240329, 10828826.
8. Petz LN, Nardulli AM. Sp1 binding sites and an estrogen response element half-site are involved in regulation of the human progesterone receptor A promoter. Mol Endocrinol 2000, 14(7):972-985. 10.1210/me.14.7.972, 10894148.
9. DeNardo DG, Kim HT, Hilsenbeck S, Cuba V, Tsimelzon A, Brown PH. Global gene expression analysis of estrogen receptor transcription factor cross talk in breast cancer: identification of estrogen-induced/activator protein-1-dependent genes. Mol Endocrinol 2005, 19(2):362-378.
10. Glidewell-Kenney C, Weiss J, Lee EJ, Pillai S, Ishikawa T, Ariazi EA, Jameson JL. ERE-independent ERalpha target genes differentially expressed in human breast tumors. Mol Cell Endocrinol 2005, 245(1-2):53-59. 10.1016/j.mce.2005.10.003, 16298037.
11. Kalaitzidis D, Gilmore TD. Transcription factor cross-talk: the estrogen receptor and NF-kappaB. Trends Endocrinol Metab 2005, 16(2):46-52. 10.1016/j.tem.2005.01.004, 15734144.
12. Frasor J, Danes JM, Komm B, Chang KC, Lyttle CR, Katzenellenbogen BS. Profiling of estrogen up- and down-regulated gene expression in human breast cancer cells: insights into gene networks and pathways underlying estrogenic control of proliferation and cell phenotype. Endocrinology 2003, 144(10):4562-4574. 10.1210/en.2003-0567, 12959972.
13. Lin CY, Strom A, Vega VB, Kong SL, Yeo AL, Thomsen JS, Chan WC, Doray B, Bangarusamy DK, Ramasamy A, et al. Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells. Genome Biol 2004, 5(9):R66. 10.1186/gb-2004-5-9-r66, 522873, 15345050.
14. Kininis M, Kraus WL. A global view of transcriptional regulation by nuclear receptors: gene expression, factor localization, and DNA sequence analysis. Nucl Recept Signal 2008, 6:e005. 2254333, 18301785.
15. Cheung E, Kraus WL. Genomic analyses of hormone signaling and gene regulation. Annu Rev Physiol 72:191-218.
16. Choi JK, Yu U, Kim S, Yoo OJ. Combining multiple microarray studies and modeling interstudy variation. Bioinformatics 2003, 19(Suppl 1):i84-90. 10.1093/bioinformatics/btg1010, 12855442.
17. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, et al. Multiple-laboratory comparison of microarray platforms. Nat Methods 2005, 2(5):345-350. 10.1038/nmeth756, 15846361.
18. Hong F, Breitling R. A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics 2008, 24(3):374-382. 10.1093/bioinformatics/btm620, 18204063.
19. Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, Chory J. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics 2006, 22(22):2825-2827. 10.1093/bioinformatics/btl476, 16982708.
20. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R. NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res 2007, 35(Database issue):D760-765. 1669752, 17099226.
21. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-264. 10.1093/biostatistics/4.2.249, 12925520.
22. Wu Z, Irizarry R, Gentleman R, Martinez-Murillo F, Spencer F. A Model-Based Background Adjustment for Oligonucleotide Expression Arrays. Journal of the American Statistical Association 99(468):909.
23. Naugler WE, Karin M. NF-kappaB and cancer-identifying targets and mechanisms. Curr Opin Genet Dev 2008, 18(1):19-26. 10.1016/j.gde.2008.01.020, 2587362, 18440219.
24. Chua HL, Bhat-Nakshatri P, Clare SE, Morimiya A, Badve S, Nakshatri H. NF-kappaB represses E-cadherin expression and enhances epithelial to mesenchymal transition of mammary epithelial cells: potential involvement of ZEB-1 and ZEB-2. Oncogene 2007, 26(5):711-724. 10.1038/sj.onc.1209808, 16862183.
25. Bailey CM, Hendrix MJ. IRF6 in development and disease: a mediator of quiescence and differentiation. Cell Cycle 2008, 7(13):1925-1930. 10.4161/cc.7.13.6221, 2581479, 18604160.
26. Ochsner SA, Steffen DL, Hilsenbeck SG, Chen ES, Watkins C, McKenna NJ. GEMS (Gene Expression MetaSignatures), a Web resource for querying meta-analysis of expression microarray datasets: 17beta-estradiol in MCF-7 cells. Cancer Res 2009, 69(1):23-26. 10.1158/0008-5472.CAN-08-3492, 2782370, 19117983.
27. Molitoris KH, Kazi AA, Koos RD. Inhibition of oxygen-induced hypoxia-inducible factor-1alpha degradation unmasks estradiol induction of vascular endothelial growth factor expression in ECC-1 cancer cells in vitro. Endocrinology 2009, 150(12):5405-5414. 10.1210/en.2009-0884, 2795708, 19819950.
28. Cicatiello L, Mutarelli M, Grober OMV, 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(5):2113-2130. 10.2353/ajpath.2010.090837, 2861078, 20348243.
29. Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells. Cell 2011, 145(4):622-634. 10.1016/j.cell.2011.03.042, 21549415.
30. Matthews J, Gustafsson JA. Estrogen receptor and aryl hydrocarbon receptor signaling pathways. Nucl Recept Signal 2006, 4:e016. 1513070, 16862222.
31. Deeb KK, Michalowska AM, Yoon CY, Krummey SM, Hoenerhoff MJ, Kavanaugh C, Li MC, Demayo FJ, Linnoila I, Deng CX, et al. Identification of an integrated SV40 T/t-antigen cancer signature in aggressive human breast, prostate, and lung carcinomas with poor prognosis. Cancer Res 2007, 67(17):8065-8080. 10.1158/0008-5472.CAN-07-1515, 17804718.
32. Vanneschi L, Farinaccio A, Mauri G, Antoniotti M, Provero P, Giacobini M. A Comparison of Machine Learning Techniques for Survival Prediction in Breast Cancer. BioData Min 4(1):12.
33. Breitling R, Armengaud P, Amtmann A, Herzyk P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 2004, 573(1-3):83-92. 10.1016/j.febslet.2004.07.055, 15327980.
34. Creighton CJ, Cordero KE, Larios JM, Miller RS, Johnson MD, Chinnaiyan AM, Lippman ME, Rae JM. Genes regulated by estrogen in breast tumor cells in vitro are similarly regulated in vivo in tumor xenografts and human breast tumors. Genome Biol 2006, 7(4):R28. 10.1186/gb-2006-7-4-r28, 1557996, 16606439.
35. Chang EC, Charn TH, Park SH, Helferich WG, Komm B, Katzenellenbogen JA, Katzenellenbogen BS. Estrogen Receptors alpha and beta as determinants of gene expression: influence of ligand, dose, and chromatin binding. Mol Endocrinol 2008, 22(5):1032-1043. 10.1210/me.2007-0356, 2366177, 18258689.
36. Chang EC, Frasor J, Komm B, Katzenellenbogen BS. Impact of estrogen receptor beta on gene networks regulated by estrogen receptor alpha in breast cancer cells. Endocrinology 2006, 147(10):4831-4842. 10.1210/en.2006-0563, 16809442.
37. Gaube F, Wolfl S, Pusch L, Kroll TC, Hamburger M. Gene expression profiling reveals effects of Cimicifuga racemosa (L.) NUTT. (black cohosh) on the estrogen receptor positive human breast cancer cell line MCF-7. BMC Pharmacol 2007, 7:11. 2194763, 17880733.
38. Rae JM, Johnson MD, Scheys JO, Cordero KE, Larios JM, Lippman ME. GREB 1 is a critical regulator of hormone dependent breast cancer growth. Breast Cancer Res Treat 2005, 92(2):141-149. 10.1007/s10549-005-1483-4, 15986123.
39. Frasor J, Chang EC, Komm B, Lin CY, Vega VB, Liu ET, Miller LD, Smeds J, Bergh J, Katzenellenbogen BS. Gene expression preferentially regulated by tamoxifen in breast cancer cells and correlations with clinical outcome. Cancer Res 2006, 66(14):7334-7340. 10.1158/0008-5472.CAN-05-4269, 16849584.
40. Bourdeau V, Deschenes J, Laperriere D, Aid M, White JH, Mader S. Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells. Nucleic Acids Res 2008, 36(1):76-93. 10.1093/nar/gkn369, 2248750, 17986456.