In silico discovery of mitosis regulation networks associated with early distant metastases in estrogen receptor positive breast cancers

Cancer Informatics

Volumn 12, Issue , 2013, Pages 31-51

  Gusev, Yuriy ^a   Riggins, Rebecca B ^b   Bhuvaneshwar, Krithika ^a   Gauba, Robinder ^a   Sheahan, Laura ^c   Clarke, Robert ^b   Madhavan, Subha ^a  

^a GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

^c ESAC Inc   (United States)

Author keywords

Early distant metastasis; Estrogen receptor alpha positive; microRNA targets; Mitotic checkpoint signaling; Mitotic regulation network

Indexed keywords

ESTROGEN RECEPTOR; MICRORNA; MICRORNA 16; MICRORNA 192; MICRORNA 193B; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; BREAST CANCER; CELL CYCLE REGULATION; COMPARATIVE STUDY; CONTROLLED STUDY; DISTANT METASTASIS; FEMALE; GENE EXPRESSION; GENE TARGETING; GENETIC ANALYSIS; GENOMIC INSTABILITY; HUMAN; MAJOR CLINICAL STUDY; MITOSIS SPINDLE; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION;

EID: 84874206230     PISSN: None     EISSN: 11769351     Source Type: Journal    
DOI: 10.4137/CIN.S10329     Document Type: Article

References (84)

1. American Cancer Society. Cancer Facts & Figures 2012. Atlanta: American Cancer Society; 2012.
2. Thorpe SM. Estrogen and progesterone receptor determinations in breast cancer. Technology, biology and clinical significance. Acta Oncol. 1988;27(1):1-19.
3. Thompson A, Brennan K, Cox A, et al. Evaluation of the current knowledge limitations in breast cancer research: a gap analysis. Breast Cancer Res. 2008;10(2):R26.
4. van't Veer LJ, Bernards R. Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature. 2008;452(7187): 564-70.
5. Chanrion M, Negre V, Fontaine H, et al. A gene expression signature that can predict the recurrence of tamoxifen-treated primary breast cancer. Clin Cancer Res. 2008;14(6):1744-52.
6. Goetz MP, Suman VJ, Ingle JN, et al. A two-gene expression ratio of homeobox 13 and interleukin-17B receptor for prediction of recurrence and survival in women receiving adjuvant tamoxifen. Clin Cancer Res. 2006; 12(7 Pt 1):2080-7.
7. Jansen MP, Foekens JA, van Staveren IL, et al. Molecular classification of tamoxifen-resistant breast carcinomas by gene expression profiling. J Clin Oncol. 2005;23(4):732-40.
8. Loi S, Haibe-Kains B, Desmedt C, et al. Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with t{stroke}amoxifen. BMC genomics. 2008;9:239.
9. Reid JF, Lusa L, De Cecco L, et al. Limits of predictive models using microarray data for breast cancer clinical treatment outcome. J Natl Cancer Inst. 2005;97(12):927-30.
10. Subramanian J, Simon R. Gene expression-based prognostic signatures in lung cancer: ready for clinical use? J Natl Cancer Inst. 2010;102(7): 464-74.
11. Madhavan S, Gusev Y, Harris M, et al. G-DOC: a systems medicine platform for personalized oncology. Neoplasia. 2011;13(9):771-83.
12. Demicheli R, Ardoino I, Boracchi P, et al. Recurrence and mortality according to estrogen receptor status for breast cancer patients undergoing conservative surgery. Ipsilateral breast tumour recurrence dynamics provides clues for tumour biology within the residual breast. BMC cancer. 2010;10:656.
13. Sotiriou C, Wirapati P, Loi S, et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst. 2006;98(4):262-72.
14. Desmedt C, Piette F, Loi S, et al. Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res. 2007;13(11):3207-14.
15. Schmidt M, Bohm D, von Torne C, et al. The humoral immune system has a key prognosticimpact in node-negative breast cancer. Cancer Res. 2008;68(13):5405-13.
16. Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4(2):249-64.
17. Tukey JW. Exploratory Data Analysis. Reading, MA: Addison-Wesley; 1977.
18. Wettenhall JM, Smyth GK. LIMMAGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics. 2004;20(18):3705-6.
19. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B. 1995;57:289-300.
20. Croft D, O'Kelly G, Wu G, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2011;39(Database issue): D691-7.
21. Szklarczyk D, Franceschini A, Kuhn M, et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011;39(Database issue):D691-7.
22. Chang J, Clark GM, Allred DC, Mohsin S, Chamness G, Elledge RM. Survival of patients with metastatic breast carcinoma: importance of prognostic markers of the primary tumor. Cancer. 2003;97(3):545-53.
23. Liberzon A, Subramanian A, Pinchback R, Thorvaldsdottir H, Tamayo P, Mesirov JP. Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011;27(12):1739-40.
24. Vergoulis T, Vlachos IS, Alexiou P, et al. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res. 2012;40(Database issue):D222-9.
25. Fountzilas G, Valavanis C, Kotoula V, et al. HER2 and TOP2A in high-risk early breast cancer patients treated with adjuvant epirubicin-based dosedense sequential chemotherapy. J Trans Med. 2012;10:10.
26. Hu K, Law J, Fotovati A, Dunn SE. Small interfering RNA library screen identified polo-like kinase-1 (PLK1) as a potential therapeutic target for breast cancer that uniquely eliminates tumour-initiating cells. Breast Cancer Res. 2012;14(1):R22.
27. Schoffski P, Blay JY, De Greve J, et al. Multicentric parallel phase II trial of the polo-like kinase 1 inhibitor BI 2536 in patients with advanced head and neck cancer, breast cancer, ovarian cancer, soft tissue sarcoma and melanoma. The first protocol of the European Organization for Research and Treatment of Cancer (EORTC) Network Of Core Institutes (NOCI). Eur J Cancer. 2010;46(12):2206-15.
28. Macarulla T, Cervantes A, Elez E, et al. Phase I study of the selective Aurora A kinase inhibitor MLN8054 in patients with advanced solid tumors: safety, pharmacokinetics, and pharmacodynamics. Mol Cancer Ther. 2010;9(10):2844-52.
29. Sehdev V, Peng D, Soutto M, et al. The Aurora Kinase A inhibitor MLN8237 enhances cisplatin-induced cell death in esophageal adenocarcinoma cells. Mol Cancer Ther. 2012;11(3):763-74.
30. Leary RJ, Lin JC, Cummins J, et al. Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A. 2008;105(42):16224-9.
31. Hu Y, Wu G, Rusch M, et al. Integrated cross-species transcriptional network analysis of metastatic susceptibility. Proc Natl Acad Sci U S A. 2012;109(8):3184-9.
32. Wood KW, Cornwell WD, Jackson JR. Past and future of the mitotic spindle as an oncology target. Curr Opin Pharmacol. 2001;1(4):370-7.
33. Matson DR, Stukenberg PT. Spindle poisons and cell fate: a tale of two pathways. Mol Interv. 2011;11(2):141-50.
34. Bharadwaj R, Yu H. The spindle checkpoint, aneuploidy, and cancer. Oncogene. 2004;23(11):2016-27.
35. Cahill DP, Lengauer C, Yu J, et al. Mutations of mitotic checkpoint genes in human cancers. Nature. 1998;392(6673):300-3.
36. Gemma A, Hosoya Y, Seike M, et al. Genomic structure of the human MAD2 gene and mutation analysis in human lung and breast cancers. Lung Cancer. 2001;32(3):289-95.
37. Ingvarsson S, Sigbjornsdottir BI, Huiping C, et al. Mutation analysis of the CHK2 gene in breast carcinoma and other cancers. Breast Cancer Res. 2002;4(3):R4.
38. Miller CW, Ikezoe T, Krug U, et al. Mutations of the CHK2 gene are found in some osteosarcomas, but are rare in breast, lung, and ovarian tumors. Gene Chromosomes Cancer. 2002;33(1):17-21.
39. Myrie KA, Percy MJ, Azim JN, Neeley CK, Petty EM. Mutation and expression analysis of human BUB1 and BUB1B in aneuploid breast cancer cell lines. Cancer Lett. 2000;152(2):193-9.
40. Grabsch H, Takeno S, Parsons WJ, et al. Overexpression of the mitotic checkpoint genes BUB1, BUBR1, and BUB3 in gastric cancer-association with tumour cell proliferation. J Pathol. 2003;200(1):16-22.
41. Yuan B, Xu Y, Woo JH, et al. Increased expression of mitotic checkpoint genes in breast cancer cells with chromosomal instability. Clin Cancer Res. 2006;12(2):405-10.
42. Lentini L, Amato A, Schillaci T, Di Leonardo A. Simultaneous Aurora-A/ STK15 overexpression and centrosome amplification induce chromosomal instability in tumour cells with a MIN phenotype. BMC cancer. 2007; 7:212.
43. Katayama H, Sasai K, Kawai H, et al. Phosphorylation by aurora kinase A induces Mdm2-mediated destabilization and inhibition of p53. Nat Genet. 2004;36(1):55-62.
44. Zou H, McGarry TJ, Bernal T, Kirschner MW. Identification of a vertebrate sister-chromatid separation inhibitor involved in transformation and tumorigenesis. Science. 1999;285(5426):418-22.
45. Yu R, Lu W, Chen J, McCabe CJ, Melmed S. Overexpressed pituitary tumortransforming gene causes aneuploidy in live human cells. Endocrinology. 2003;144(11):4991-8.
46. Wang Z, Moro E, Kovacs K, Yu R, Melmed S. Pituitary tumor transforming gene-null male mice exhibit impaired pancreatic beta cell proliferation and diabetes. Proc Natl Acad Sci U S A. 2003;100(6):3428-32.
47. Maxwell CA, McCarthy J, Turley E. Cell-surface and mitotic-spindle RHAMM: moonlighting or dual oncogenic functions? J Cell Sci. 2008; 121(Pt 7):925-32.
48. Qian Y, Hua E, Bisht K, et al. Inhibition of Polo-like kinase 1 prevents the growth of metastatic breast cancer cells in the brain. Clin Exp Metastasis. 2011;28(8):899-908.
49. Gordon DJ, Resio B, Pellman D. Causes and consequences of aneuploidy in cancer. Nat Rev Genet. 2012;13(3):189-203.
50. Smid M, Hoes M, Sieuwerts AM, et al. Patterns and incidence of chromosomal instability and their prognostic relevance in breast cancer subtypes. Breast Cancer Res Treat. 2011;128(1):23-30.
51. Niida A, Smith AD, Imoto S, et al. Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinformatics. 2008;9:404.
52. Thomassen M, Tan Q, Kruse TA. Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer. BMC Cancer. 2008;8:394.
53. Ngwenya S, Safe S. Cell context-dependent differences in the induction of E2F-1 gene expression by 17 beta-estradiol in MCF-7 and ZR-75 cells. Endocrinology. 2003;144(5):1675-85.
54. Riggins RB, Schrecengost RS, Guerrero MS, Bouton AH. Pathways to tamoxifen resistance. Cancer Lett. 2007;256(1):1-24.
55. Vairo G, Livingston DM, Ginsberg D. Functional interaction between E2F-4 and p130: evidence for distinct mechanisms underlying growth suppression by different retinoblastoma protein family members. Genes Dev. 1995;9(7):869-81.
56. Muller H, Moroni MC, Vigo E, Petersen BO, Bartek J, Helin K. Induction of S-phase entry by E2F transcription factors depends on their nuclear localization. Mol Cell Biol. 1997;17(9):5508-20.
57. Rayman JB, Takahashi Y, Indjeian VB, et al. E2F mediates cell cycle-dependent transcriptional repression in vivo by recruitment of an HDAC1/mSin3B corepressor complex. Genes Dev. 15 2002;16(8):933-47.
58. Mady HH, Hasso S, Melhem MF. Expression of E2F-4 gene in colorectal adenocarcinoma and corresponding covering mucosa: an immunohistochemistry, image analysis, and immunoblot study. Appl Immunohistochem Mol Morphol. 2002;10(3):225-30.
59. Garneau H, Alvarez L, Paquin MC, et al. Nuclear expression of E2F4 induces cell death via multiple pathways in normal human intestinal epithelial crypt cells but not in colon cancer cells. Am J Physiol Gastrointest Liver Physiol. 2007;293(4):G758-72.
60. Garneau H, Paquin MC, Carrier JC, Rivard N. E2F4 expression is required for cell cycle progression of normal intestinal crypt cells and colorectal cancer cells. J Cell Physiol. 2009;221(2):350-8.
61. Koch M, Hanl M, Wiese M. Feature extraction via composite scoring and voting in breast cancer. Breast Cancer Res Treat. 2012;135(1): 307-18.
62. de Olano N, Koo CY, Monteiro LJ, et al. The p38 MAPK-MK2 Axis Regulates E2F1 and FOXM1 Expression after Epirubicin Treatment. Mol Cancer Res. 2012;10(9):1189-202.
63. Lee KY, Lee JW, Nam HJ, Shim JH, Song Y, Kang KW. PI3-kinase/ p38 kinase-dependent E2F1 activation is critical for Pin1 induction in tamoxifen-resistant breast cancer cells. Mol Cells. 2011;32(1): 107-11.
64. Koo CY, Muir KW, Lam EW. FOXM1: From cancer initiation to progression and treatment. Biochim Biophys Acta. 2012;1819(1):28-37.
65. Jonkers J. Tracking evolution of BRCA1-associated breast cancer. Cancer Discov. 2012;2(6):486-8.
66. Zhang N, Kaur R, Akhter S, Legerski RJ. Cdc5L interacts with ATR and is required for the S-phase cell-cycle checkpoint. EMBO reports. 2009;10(9):1029-35.
67. Palmieri C, Monteverde M, Lattanzio L, et al. Site-specific CpG methylation in the CCAAT/enhancer binding protein delta (CEBPdelta) CpG island in breast cancer is associated with metastatic relapse. Br J Cancer. 2012;107(4):732-8.
68. Voets E, Wolthuis RM. MASTL is the human orthologue of Greatwall kinase that facilitates mitotic entry, anaphase and cytokinesis. Cell Cycle. 2010;9(17):3591-601.
69. Djuranovic S, Nahvi A, Green R. A parsimonious model for gene regulation by miRNAs. Science. 2011;331(6017):550-3.
70. Braun CJ, Zhang X, Savelyeva I, et al. p53-Responsive micrornas 192 and 215 are capable of inducing cell cycle arrest. Cancer Res. 2008;68(24): 10094-104.
71. Georges SA, Biery MC, Kim SY, et al. Coordinated regulation of cell cycle transcripts by p53-Inducible microRNAs, miR-192 and miR-215. Cancer Res. 2008;68(24):10105-12.
72. Kim T, Veronese A, Pichiorri F, et al. p53 regulates epithelial-mesenchymal transition through microRNAs targeting ZEB1 and ZEB2. J Exp Med. 2011;208(5):875-83.
73. Leivonen SK, Makela R, Ostling P, et al. Protein lysate microarray analysis to identify microRNAs regulating estrogen receptor signaling in breast cancer cell lines. Oncogene. 2009;28(44):3926-36.
74. Leivonen SK, Rokka A, Ostling P, et al. Identification of miR-193b targets in breast cancer cells and systems biological analysis of their functional impact. Mol Cell Proteomics. 2011;10(7):M110.005322.
75. Yoshimoto N, Toyama T, Takahashi S, et al. Distinct expressions of microRNAs that directly target estrogen receptor alpha in human breast cancer. Breast Cancer Rest Treat. 2011;130(1):331-9.
76. Cittelly DM, Das PM, Spoelstra NS, et al. Downregulation of miR-342 is associated with tamoxifen resistant breast tumors. Mol Cancer. 2010;9:317.
77. Ucar A, Vafaizadeh V, Jarry H, et al. miR-212 and miR-132 are required for epithelial stromal interactions necessary for mouse mammary gland development. Nat Genet. 2010;42(12):1101-8.
78. Park JK, Henry JC, Jiang J, et al. miR-132 and miR-212 are increased in pancreatic cancer and target the retinoblastoma tumor suppressor. Biochem Biophys Res Commun. 2011;406(4):518-23.
79. Tokiniwa H, Horiguchi J, Takata D, et al. Topoisomerase II alpha expression and the Ki-67 labeling index correlate with prognostic factors in estrogen receptor-positive and human epidermal growth factor type-2-negative breast cancer. Breast Cancer. 2012;19(4):309-14.
80. Romero A, Caldes T, Diaz-Rubio E, Martin M. Topoisomerase 2 alpha: a real predictor of anthracycline efficacy? Clin Transl Oncol. 2012;14(3):163-8.
81. Weichert W, Kristiansen G, Winzer KJ, et al. Polo-like kinase isoforms in breast cancer: expression patterns and prognostic implications. Virchows Arch. 2005;446(4):442-50.
82. Bergamaschi A, Christensen BL, Katzenellenbogen BS. Reversal of endocrine resistance in breast cancer: interrelationships among 14-3-3zeta, FOXM1, and a gene signature associated with mitosis. Breast Cancer Res. 2011;13(3):R70.
83. Haibe-Kains B, Desmedt C, Loi S, et al. A three-gene model to robustly identify breast cancer molecular subtypes. J Natl Cancer Inst. 2012;104(4): 311-25.
84. Lee HH, Zhu Y, Govindasamy KM, Gopalan G. Downregulation of Aurora-A overrides estrogen-mediated growth and chemoresistance in breast cancer cells. Endocr Relat Cancer. 2008;15(3):765-75.