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Research Papers

Network-based approach to identify prognostic biomarkers for estrogen receptor–positive breast cancer treatment with tamoxifen

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Pages 317-324 | Received 23 Sep 2014, Accepted 18 Dec 2014, Published online: 10 Mar 2015

References

  • Zhang X, Claerhout S, Prat A, Dobrolecki LE, Petrovic I, Lai Q, Landis MD, Wiechmann L, Schiff R, Giuliano M, et al. A renewable tissue resource of phenotypically stable, biologically and ethnically diverse, patient-derived human breast cancer xenograft models. Cancer Res 2013; 73:4885-97; PMID:23737486; http://dx.doi.org/10.1158/0008-5472.CAN-12-4081
  • Ferlay J, Shin HR, Bray F, Forman D, Mathers C, Parkin DM. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer J Int Du Cancer 2010; 127:2893-917; PMID:21351269; http://dx.doi.org/10.1002/ijc.25516
  • Vendrell JA, Ghayad S, Ben-Larbi S, Dumontet C, Mechti N, Cohen PA. A20/TNFAIP3, a new estrogen-regulated gene that confers tamoxifen resistance in breast cancer cells. Oncogene 2007; 26:4656-67; PMID:17297453; http://dx.doi.org/10.1038/sj.onc.1210269
  • Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003; 302:249-55; PMID:12934013; http://dx.doi.org/10.1126/science.1087447
  • Wang L, Tang H, Thayanithy V, Subramanian S, Oberg AL, Cunningham JM, Cerhan JR, Steer CJ, Thibodeau SN. Gene networks and microRNAs implicated in aggressive prostate cancer. Cancer Res 2009; 69:9490-7; PMID:19996289; http://dx.doi.org/10.1158/0008-5472.CAN-09-2183
  • Horvath S, Zhang B, Carlson M, Lu KV, Zhu S, Felciano RM, Laurance MF, Zhao W, Qi S, Chen Z, et al. Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A 2006; 103:17402-7; PMID:17090670; http://dx.doi.org/10.1073/pnas.0608396103
  • Ivliev AE, t Hoen PA, Sergeeva MG. Coexpression network analysis identifies transcriptional modules related to proastrocytic differentiation and sprouty signaling in glioma. Cancer Res 2010; 70:10060-70; PMID:21159630; http://dx.doi.org/10.1158/0008-5472.CAN-10-2465
  • Wirapati P, Sotiriou C, Kunkel S, Farmer P, Pradervand S, Haibe-Kains B, Desmedt C, Ignatiadis M, Sengstag T, Schutz F, et al. Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Res 2008; 10:28; PMID:18662380; http://dx.doi.org/10.1186/bcr2124
  • Clarke C, Madden SF, Doolan P, Aherne ST, Joyce H, O'Driscoll L, Gallagher WM, Hennessy BT, Moriarty M, Crown J, et al. Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis. Carcinogenesis 2013; 34:2300-8; PMID:23740839; http://dx.doi.org/10.1093/carcin/bgt208
  • Nishida Y, Yoshioka M, St-Amand J. Regulation of hypothalamic gene expression by glucocorticoid: implications for energy homeostasis. Physiol Genomics 2006; 25:96-104; PMID:16368873; http://dx.doi.org/10.1152/physiolgenomics.00232.2005
  • Gonzalez-Malerva L, Park J, Zou L, Hu Y, Moradpour Z, Pearlberg J, Sawyer J, Stevens H, Harlow E, LaBaer J. High-throughput ectopic expression screen for tamoxifen resistance identifies an atypical kinase that blocks autophagy. Proc Natl Acad Sci U S A 2011; 108:2058-63; PMID:21233418; http://dx.doi.org/10.1073/pnas.1018157108
  • Castellano I, Chiusa L, Vandone AM, Beatrice S, Goia M, Donadio M, Arisio R, Muscara F, Durando A, Viale G, et al. A simple and reproducible prognostic index in luminal ER-positive breast cancers. Ann Oncol: Off J Eur Soc Med Oncol/ESMO 2013; 24:2292-7; PMID:23709174; http://dx.doi.org/10.1093/annonc/mdt183
  • (EBCTCG). EBCTCG. Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials. Lancet 2005; 365:1687-717; PMID:15894097; http://dx.doi.org/10.1016/S0140-6736(05)66544-0
  • Fisher B, Costantino JP, Wickerham DL, Redmond CK, Kavanah M, Cronin WM, Vogel V, Robidoux A, Dimitrov N, Atkins J, et al. Tamoxifen for prevention of breast cancer: report of the national surgical adjuvant breast and bowel project P-1 study. J Natl Cancer Inst 1998; 90:1371-88; PMID:9747868; http://dx.doi.org/10.1093/jnci/90.18.1371
  • 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; 66:7334-40; PMID:16849584; http://dx.doi.org/10.1158/0008-5472.CAN-05-4269
  • 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; 66:11954-66; PMID:17178894; http://dx.doi.org/10.1158/0008-5472.CAN-06-1666
  • Chanrion M, Negre V, Fontaine H, Salvetat N, Bibeau F, Mac Grogan G, Mauriac L, Katsaros D, Molina F, Theillet C, et al. A gene expression signature that can predict the recurrence of tamoxifen-treated primary breast cancer. Clin Cancer Res 2008; 14:1744-52; PMID:18347175; http://dx.doi.org/10.1158/1078-0432.CCR-07-1833
  • Jansen MP, Foekens JA, van Staveren IL, Dirkzwager-Kiel MM, Ritstier K, Look MP, Meijer-van Gelder ME, Sieuwerts AM, Portengen H, Dorssers LC, et al. Molecular classification of tamoxifen-resistant breast carcinomas by gene expression profiling. J Clin Oncol 2005; 23:732-40; PMID:15681518; http://dx.doi.org/10.1200/JCO.2005.05.145
  • Sgroi DC, Sestak I, Cuzick J, Zhang Y, Schnabel CA, Schroeder B, Erlander MG, Dunbier A, Sidhu K, Lopez-Knowles E, et al. Prediction of late distant recurrence in patients with oestrogen-receptor-positive breast cancer: a prospective comparison of the breast-cancer index (BCI) assay, 21-gene recurrence score, and IHC4 in the TransATAC study population. Lancet Oncol 2013; 14:1067-76; PMID:24035531; http://dx.doi.org/10.1016/S1470-2045(13)70387-5
  • Guo S, Li Y, Tong Q, Gu F, Zhu T, Fu L, Yang S. deltaEF1 down-regulates ER-alpha expression and confers tamoxifen resistance in breast cancer. PloS one 2012; 7:e52380; PMID:23285017; http://dx.doi.org/10.1371/journal.pone.0052380
  • Johansson HJ, Sanchez BC, Mundt F, Forshed J, Kovacs A, Panizza E, Hultin-Rosenberg L, Lundgren B, Martens U, Mathe G, et al. Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer. Nat Commun 2013; 4:2175; PMID:23868472; http://dx.doi.org/10.1038/ncomms3175
  • Gao T, Han Y, Yu L, Ao S, Li Z, Ji J. CCNA2 is a prognostic biomarker for ER+ breast cancer and tamoxifen resistance. PloS One 2014; 9:e91771; PMID:24622579; http://dx.doi.org/10.1371/journal.pone.0091771
  • Ding K, Li W, Zou Z, Zou X, Wang C. CCNB1 is a prognostic biomarker for ER+ breast cancer. Med Hypotheses 2014; 83:359-64; PMID:25044212; http://dx.doi.org/10.1016/j.mehy.2014.06.013
  • Ma XJ, Wang Z, Ryan PD, Isakoff SJ, Barmettler A, Fuller A, Muir B, Mohapatra G, Salunga R, Tuggle JT, et al. A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 2004; 5:607-16; PMID:15193263; http://dx.doi.org/10.1016/j.ccr.2004.05.015
  • Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. New Engl J Med 2004; 351:2817-26; PMID:15591335; http://dx.doi.org/10.1056/NEJMoa041588
  • Xu XL, Chen SZ, Chen W, Zheng WH, Xia XH, Yang HJ, Li B, Mao WM. The impact of cyclin D1 overexpression on the prognosis of ER-positive breast cancers: a meta-analysis. Breast Cancer Res Treat 2013; 139:329-39; PMID:23670132; http://dx.doi.org/10.1007/s10549-013-2563-5
  • Marie SK, Okamoto OK, Uno M, Hasegawa AP, Oba-Shinjo SM, Cohen T, Camargo AA, Kosoy A, Carlotti CG Jr, Toledo S, et al. Maternal embryonic leucine zipper kinase transcript abundance correlates with malignancy grade in human astrocytomas. Int J Cancer J Int Du Cancer 2008; 122:807-15; PMID:17960622; http://dx.doi.org/10.1002/ijc.23189
  • Nakano I, Masterman-Smith M, Saigusa K, Paucar AA, Horvath S, Shoemaker L, Watanabe M, Negro A, Bajpai R, Howes A, et al. Maternal embryonic leucine zipper kinase is a key regulator of the proliferation of malignant brain tumors, including brain tumor stem cells. J Neurosci Res 2008; 86:48-60; PMID:17722061; http://dx.doi.org/10.1002/jnr.21471
  • Pickard MR, Green AR, Ellis IO, Caldas C, Hedge VL, Mourtada-Maarabouni M, Williams GT. Dysregulated expression of Fau and MELK is associated with poor prognosis in breast cancer. Breast Cancer Res 2009; 11:11; PMID:19671159; http://dx.doi.org/10.1186/bcr2350
  • Lin ML, Park JH, Nishidate T, Nakamura Y, Katagiri T. Involvement of maternal embryonic leucine zipper kinase (MELK) in mammary carcinogenesis through interaction with Bcl-G, a pro-apoptotic member of the Bcl-2 family. Breast Cancer Res 2007; 9:R17; PMID:17280616;
  • Li Y, Tang H, Sun Z, Bungum AO, Edell ES, Lingle WL, Stoddard SM, Zhang M, Jen J, Yang P, et al. Network-based approach identified cell cycle genes as predictor of overall survival in lung adenocarcinoma patients. Lung Cancer 2013; 80:91-8; PMID:23357462; http://dx.doi.org/10.1016/j.lungcan.2012.12.022
  • Chen X, Thiaville MM, Chen L, Stoeck A, Xuan J, Gao M, Shih Ie M, Wang TL. Defining NOTCH3 target genes in ovarian cancer. Cancer Res 2012; 72:2294-303; PMID:22396495; http://dx.doi.org/10.1158/0008-5472.CAN-11-2181
  • Pavlou MP, Dimitromanolakis A, Martinez-Morillo E, Smid M, Foekens JA, Diamandis EP. Integrating meta-analysis of microarray data and targeted proteomics for biomarker identification: application in breast cancer. J Proteome Res 2014; 13:2897-909; PMID:24799281; http://dx.doi.org/10.1021/pr500352e
  • Kang J, Sergio CM, Sutherland RL, Musgrove EA. Targeting cyclin-dependent kinase 1 (CDK1) but not CDK4/6 or CDK2 is selectively lethal to MYC-dependent human breast cancer cells. BMC Cancer 2014; 14:1471-2407; PMID:24444383; http://dx.doi.org/10.1186/1471-2407-14-32
  • Kretschmer C, Sterner-Kock A, Siedentopf F, Schoenegg W, Schlag PM, Kemmner W. Identification of early molecular markers for breast cancer. Mol Cancer 2011; 10:15; PMID:21314937; http://dx.doi.org/10.1186/1476-4598-10-15
  • Putluri N, Maity S, Kommangani R, Creighton CJ, Putluri V, Chen F, Nanda S, Bhowmik SK, Terunuma A, Dorsey T, et al. Pathway-centric integrative analysis identifies RRM2 as a prognostic marker in breast cancer associated with poor survival and tamoxifen resistance. Neoplasia 2014; 16:390-402; PMID:25016594; http://dx.doi.org/10.1016/j.neo.2014.05.007
  • Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, Ellis P, Harris A, Bergh J, Foekens JA, et al. Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol 2007; 25:1239-46; PMID:17401012; http://dx.doi.org/10.1200/JCO.2006.07.1522
  • Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, et al. Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics 2008; 9:1471-2164; PMID:18498629; http://dx.doi.org/10.1186/1471-2164-9-239
  • Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, et al. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A 2005; 102:13550-5; PMID:16141321; http://dx.doi.org/10.1073/pnas.0506230102
  • Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 2006; 98:262-72; PMID:16478745; http://dx.doi.org/10.1093/jnci/djj052
  • Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 2009; 27:1160-7; PMID:19204204; http://dx.doi.org/10.1200/JCO.2008.18.1370
  • Miller J, Cai C, Langfelder P, Geschwind D, Kurian S, Salomon D, Horvath S. Strategies for aggregating gene expression data: the collapseRows R function. BMC Bioinformatics 2011; 12:322; PMID:21816037; http://dx.doi.org/10.1186/1471-2105-12-322
  • Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 2005; 4:Article17; PMID:16646834; http://dx.doi.org/10.2202/1544-6115.1128
  • Dennis G, Sherman B, Hosack D, Yang J, Gao W, Lane HC, Lempicki R. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003; 4:P3; PMID:12734009; http://dx.doi.org/10.1186/gb-2003-4-5-p3

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