The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancer

Molecular Biology Reports

Volumn 39, Issue 2, 2012, Pages 1627-1637

  Xu, Yan ^a   DuanMu, Huizi ^a   Chang, Zhiqiang ^a   Zhang, Shanzhen ^a   Li, Zhenqi ^a   Li, Zihui ^a   Liu, Yufeng ^a   Li, Kening ^a   Qiu, Fujun ^a   Li, Xia ^a  

^a Medical University   (China)

Author keywords

Breast cancer; Copy number variation; Functional modules; Synergistic action

Indexed keywords

ARTICLE; BREAST CANCER; COPY NUMBER VARIATION; GENE EXPRESSION PROFILING; GENE INTERACTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; ONCOGENE; PATHOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; BREAST TUMOR; FEMALE; GENE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM;

BREAST NEOPLASMS; DNA COPY NUMBER VARIATIONS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; GENES; HUMANS; MICROARRAY ANALYSIS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84860343391     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-011-0902-3     Document Type: Article

References (74)

1. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C (2004) Detection of large-scale variation in the human genome. Nat Genet 36(9):949-951 (Pubitemid 39167488)
2. Lee M, Lee Y, Cho H-J, Hong J, Kwon S-J, Park C-G, Lee H-Y, Son J-W, Kang J (2011) Copy number variations of chromosome 17p13.1 might be linked to high risk of lung cancer in heavy smokers. Mol Biol Rep. doi:10.1007/s11033-010-0672- 3
3. Baik SH, Jee BK, Choi JS, Yoon HK, Lee KH, Kim YH, Lim Y (2009) DNA profiling by array comparative genomic hybridization (CGH) of peripheral blood mononuclear cells (PBMC) and tumor tissue cell in non-small cell lung cancer (NSCLC). Mol Biol Rep 36(7):1767-1778
4. Zhang SG, Song WQ, Gao YT, Yang B, Du Z (2010) CD1d gene is a target for a novel amplicon at 1q22-23.1 in human hepato-cellular carcinoma. Mol Biol Rep 37(1):381-387
5. Menezes RX, Boetzer M, Sieswerda M, van Ommen GJ, Boer JM (2009) Integrated analysis of DNA copy number and gene expression microarray data using gene sets. BMC Bioinformatics 10:203
6. Margareto J, Leis O, Larrarte E, Pomposo IC, Garibi JM, Lafuente JV (2009) DNA copy number variation and gene expression analyses reveal the implication of specific oncogenes and genes in GBM. Cancer Invest 27(5):541-548
7. Kadota M, Sato M, Duncan B, Ooshima A, Yang HH, Diaz-Meyer N, Gere S, Kageyama S, Fukuoka J, Nagata T, Tsukada K, Dunn BK, Wakefield LM, Lee MP (2009) Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA. Cancer Res 69(18):7357-7365
8. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavare S, Deloukas P, Hurles ME, Dermitzakis ET (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315(5813):848-853
9. Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN, Li C, Golub TR, Rimm DL, Meyerson ML, Fisher DE, Sellers WR (2005) Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436(7047):117-122 (Pubitemid 40966196)
10. Adler AS, Lin M, Horlings H, Nuyten DS, van de Vijver MJ, Chang HY (2006) Genetic regulators of large-scale transcrip-tional signatures in cancer. Nat Genet 38(4):421-430
11. Torkamani A, Schork NJ (2009) Identification of rare cancer driver mutations by network reconstruction. Genome Res 19(9): 1570-1578
12. Parkin DM, Bray F, Ferlay J, Pisani P (2005) Global cancer statistics, 2002. CA Cancer J Clin 55(2):74-108 (Pubitemid 40372904)
13. Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR, Meyerson M (2004) An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 64(9):3060-3071 (Pubitemid 38581405)
14. Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Han-gaishi A, Kurokawa M, Chiba S, Bailey DK, Kennedy GC, Og-awa S (2005) A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 65(14):6071-6079 (Pubitemid 40994391)
15. Komura D, Shen F, Ishikawa S, Fitch KR, Chen W, Zhang J, Liu G, Ihara S, Nakamura H, Hurles ME, Lee C, Scherer SW, Jones KW, Shapero MH, Huang J, Aburatani H (2006) Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res 16(12):1575-1584 (Pubitemid 44878496)
16. Hoeflich KP, O'Brien C, Boyd Z, Cavet G, Guerrero S, Jung K, Januario T, Savage H, Punnoose E, Truong T, Zhou W, Berry L, Murray L, Amler L, Belvin M, Friedman LS, Lackner MR (2009) In vivo antitumor activity of MEK and phosphatidylinositol 3-kinase inhibitors in basal-like breast cancer models. Clin Cancer Res 15(14):4649-4664
17. Pandit TS, Kennette W, Mackenzie L, Zhang G, Al-Katib W, Andrews J, Vantyghem SA, Ormond DG, Allan AL, Rodenhiser DI, Chambers AF, Tuck AB (2009) Lymphatic metastasis of breast cancer cells is associated with differential gene expression profiles that predict cancer stem cell-like properties and the ability to survive, establish and grow in a foreign environment. Int J Oncol 35(2):297-308
18. Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA Jr, Marks JR, Dressman HK, West M, Nevins JR (2006) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439(7074):353-357 (Pubitemid 43128862)
19. Budczies J, Weichert W, Noske A, Muller BM, Weller C, Wittenberger T, Hofmann HP, Dietel M, Denkert C, Gekeler V (2011) Genome-wide gene expression profiling of formalin-fixed paraffin-embedded breast cancer core biopsies using microarrays. J Histochem Cytochem 59(2):146-157
20. BourdeauV, DeschenesJ, LaperriereD, AidM, White JH, Mader S (2008) Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells. Nucleic Acids Res 36(1):76-93
21. Mori S, Chang JT, Andrechek ER, Matsumura N, Baba T, Yao G, Kim JW, Gatza M, Murphy S, Nevins JR (2009) Anchorage-independent cell growth signature identifies tumors with meta-static potential. Oncogene 28(31):2796-2805
22. Ince TA, Richardson AL, Bell GW, Saitoh M, Godar S, Karnoub AE, Iglehart JD, Weinberg RA (2007) Transformation of different human breast epithelial cell types leads to distinct tumor phenotypes. Cancer Cell 12(2):160-170 (Pubitemid 47199120)
23. Karnoub AE, Dash AB, Vo AP, Sullivan A, Brooks MW, Bell GW, Richardson AL, Polyak K, Tubo R, Weinberg RA (2007) Mesenchymal stem cells within tumour stroma promote breast cancer metastasis. Nature 449(7162):557-563 (Pubitemid 47525152)
24. Marty B, Maire V, Gravier E, Rigaill G, Vincent-Salomon A, Kappler M, Lebigot I, Djelti F, Tourdes A, Gestraud P, Hupe P, Barillot E, Cruzalegui F, Tucker GC, Stern MH, Thiery JP, Hickman JA, Dubois T (2008) Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells. Breast Cancer Res 10(6):R101
25. Richardson AL, Wang ZC, De Nicolo A, Lu X, Brown M, Miron A, Liao X, Iglehart JD, Livingston DM, Ganesan S (2006) X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell 9(2):121-132 (Pubitemid 43202662)
26. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7(Suppl 1):S7
27. Zhang B, Horvath S (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4, Article 17
28. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498-2504 (Pubitemid 37428274)
29. Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2
30. Maslov S, Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296(5569):910-913 (Pubitemid 34464896)
31. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25-29 (Pubitemid 30257031)
32. Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, Skaug J, Shago M, Moessner R, Pinto D, Ren Y, Thiruvahindrapduram B, Fiebig A, Schreiber S, Friedman J, Ketelaars CE, Vos YJ, Fici-cioglu C, Kirkpatrick S, Nicolson R, Sloman L, Summers A, Gibbons CA, Teebi A, Chitayat D, Weksberg R, Thompson A, Vardy C, Crosbie V, Luscombe S, Baatjes R, Zwaigenbaum L, Roberts W, Fernandez B, Szatmari P, Scherer SW (2008) Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet 82(2):477-488
33. Hartwell LH, Kastan MB (1994) Cell cycle control and cancer. Science 266(5192):1821-1828
34. Preston-Martin S, Pike MC, Ross RK, Jones PA, Henderson BE (1990) Increased cell division as a cause of human cancer. Cancer Res 50(23):7415-7421
35. Weaver BA, Cleveland DW (2005) Decoding the links between mitosis, cancer, and chemotherapy: the mitotic checkpoint, adaptation, and cell death. Cancer Cell 8(1):7-12 (Pubitemid 40991810)
36. Ueki T, Park JH, Nishidate T, Kijima K, Hirata K, Nakamura Y, Katagiri T (2009) Ubiquitination and downregulation of BRCA1 by ubiquitin-conjugating enzyme E2T overexpression in human breast cancer cells. Cancer Res 69(22):8752-8760
37. Ma XJ, Salunga R, Tuggle JT, Gaudet J, Enright E, McQuary P, Payette T, Pistone M, Stecker K, Zhang BM, Zhou YX, Varnholt H, Smith B, Gadd M, Chatfield E, Kessler J, Baer TM, Erlander MG, Sgroi DC (2003) Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA 100(10): 5974-5979 (Pubitemid 36576916)
38. Hayward DG, Clarke RB, Faragher AJ, Pillai MR, Hagan IM, Fry AM (2004) The centrosomal kinase Nek2 displays elevated levels of protein expression in human breast cancer. Cancer Res 64(20):7370-7376 (Pubitemid 39372076)
39. Hu Y, Sun H, Drake J, Kittrell F, Abba MC, Deng L, Gaddis S, Sahin A, Baggerly K, Medina D, Aldaz CM (2004) From mice to humans: identification of commonly deregulated genes in mammary cancer via comparative SAGE studies. Cancer Res 64(21): 7748-7755 (Pubitemid 39446906)
40. Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton MR, Wooster R (2004) The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer 91(2):355-358 (Pubitemid 39037083)
41. Percy MJ, Myrie KA, Neeley CK, Azim JN, Ethier SP, Petty EM (2000) Expression and mutational analyses of the human MAD2L1 gene in breast cancer cells. Genes Chromosom Cancer 29(4):356-362
42. Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nord-gren H, Farmer P, Praz V, Haibe-Kains B, Desmedt C, Larsimont D, Cardoso F, Peterse H, Nuyten D, Buyse M, Van de Vijver MJ, Bergh J, Piccart M, Delorenzi M (2006) Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 98(4): 262-272 (Pubitemid 43264710)
43. Park JH, Lin ML, Nishidate T, Nakamura Y, Katagiri T (2006) PDZ-binding kinase/T-LAK cell-originated protein kinase, a putative cancer/testis antigen with an oncogenic activity in breast cancer. Cancer Res 66(18):9186-9195 (Pubitemid 44521139)
44. Langerod A, Zhao H, Borgan O, Nesland JM, Bukholm IR, Ik-dahl T, Karesen R, Borresen-Dale AL, Jeffrey SS (2007) TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer. Breast Cancer Res 9(3):R30
45. de Visser KE, Eichten A, Coussens LM (2006) Paradoxical roles of the immune system during cancer development. Nat Rev Cancer 6(1):24-37 (Pubitemid 43053650)
46. Balkwill F, Mantovani A (2001) Inflammation and cancer: back to Virchow? Lancet 357(9255):539-545 (Pubitemid 32173595)
47. Clark GJ, Der CJ (1995) Aberrant function of the Ras signal transduction pathway in human breast cancer. Breast Cancer Res Treat 35(1):133-144
48. Feng Y, Sun B, Li X, Zhang L, Niu Y, Xiao C, Ning L, Fang Z, Wang Y, Cheng J, Zhang W, Hao X (2007) Differentially expressed genes between primary cancer and paired lymph node metastases predict clinical outcome of node-positive breast cancer patients. Breast Cancer Res Treat 103(3):319-329 (Pubitemid 46944516)
49. Turgut Cosan D, Soyocak A, Basaran A, Degirmenci I, Gunes HV, Mutlu Sahin F (2011) Effects of various agents on DNA fragmentation and telomerase enzyme activities in adenocarci-noma cell lines. Mol Biol Rep 38(4):2463-2469
50. Hoskins JM, Carey LA, McLeod HL (2009) CYP2D6 and tamoxifen: DNA matters in breast cancer. Nat Rev Cancer 9(8):576-586
51. Kleer CG, Bloushtain-Qimron N, Chen YH, Carrasco D, Hu M, Yao J, Kraeft SK, Collins LC, Sabel MS, Argani P, Gelman R, Schnitt SJ, Krop IE, Polyak K (2008) Epithelial and stromal cathepsin K and CXCL14 expression in breast tumor progression. Clin Cancer Res 14(17):5357-5367
52. Galamb O, Sipos F, Solymosi N, Spisak S, Krenacs T, Toth K, Tulassay Z, Molnar B (2008) Diagnostic mRNA expression patterns of inflamed, benign, and malignant colorectal biopsy specimen and their correlation with peripheral blood results. Cancer Epidemiol Biomarkers Prev 17(10):2835-2845
53. Lee HJ, Lee YJ, Kang CM, Bae S, Jeoung D, Jang JJ, Lee SS, Cho CK, Lee YS (2008) Differential gene signatures in rat mammary tumors induced by DMBA and those induced by fractionated gamma radiation. Radiat Res 170(5):579-590
54. Gorbenko O, Kuznetsov V, Kukharenko O, Zhyvoloup A, Pan-asyuk G, Nemazanyy I, Filonenko V, Gout I (2004) Identification of a novel binding partners for tumor suppressor PTEN by a yeast two-hybrid approach. Eksp Onkol 26(1):15-19
55. Schuetz CS, Bonin M, Clare SE, Nieselt K, Sotlar K, Walter M, Fehm T, Solomayer E, Riess O, Wallwiener D, Kurek R, Neubauer HJ (2006) Progression-specific genes identified by expression profiling of matched ductal carcinomas in situ and invasive breast tumors, combining laser capture microdissection and oligonucleotide microarray analysis. Cancer Res 66(10): 5278-5286 (Pubitemid 43844952)
56. Iacobuzio-Donahue CA, Argani P, Hempen PM, Jones J, Kern SE (2002) The desmoplastic response to infiltrating breast carcinoma: gene expression at the site of primary invasion and implications for comparisons between tumor types. Cancer Res 62(18):5351-5357 (Pubitemid 35024612)
57. Oh DS, Troester MA, Usary J, Hu Z, He X, Fan C, Wu J, Carey LA, Perou CM (2006) Estrogen-regulated genes predict survival in hormone receptor-positive breast cancers. J Clin Oncol 24(11): 1656-1664 (Pubitemid 46622136)
58. Sachdev D, Li SL, Hartell JS, Fujita-Yamaguchi Y, Miller JS, Yee D (2003) A chimeric humanized single-chain antibody against the type I insulin-like growth factor (IGF) receptor renders breast cancer cells refractory to the mitogenic effects of IGF-I. Cancer Res 63(3):627-635 (Pubitemid 36158140)
59. Al-Zahrani A, Sandhu MS, Luben RN, Thompson D, Baynes C, Pooley KA, Luccarini C, Munday H, Perkins B, Smith P, Pharoah PD, Wareham NJ, Easton DF, Ponder BA, Dunning AM (2006) IGF1 and IGFBP3 tagging polymorphisms are associated with circulating levels of IGF1, IGFBP3 and risk of breast cancer. Hum Mol Genet 15(1):1-10 (Pubitemid 43020099)
60. Datta D, Flaxenburg JA, Laxmanan S, Geehan C, Grimm M, Waaga-Gasser AM, Briscoe DM, Pal S (2006) Ras-induced modulation of CXCL10 and its receptor splice variant CXCR3-B in MDA-MB-435 and MCF-7 cells: relevance for the development of human breast cancer. Cancer Res 66(19):9509-9518 (Pubitemid 44623649)
61. Gach K, Szemraj J, Wyrebska A, Janecka A (2011) The influence of opioids on matrix metalloproteinase-2 and -9 secretion and mRNA levels in MCF-7 breast cancer cell line. Mol Biol Rep 38(2):1231-1236
62. Kruszyna L, Lianeri M, Rubis B, Knula H, Rybczynska M, Grodecka-Gazdecka S, Jagodzinski PP (2011) CCL2-2518 A/G single nucleotide polymorphism as a risk factor for breast cancer. Mol Biol Rep 38(2):1263-1267
63. Leek RD, Harris AL (2002) Tumor-associated macrophages in breast cancer. J Mammary Gland Biol Neoplasia 7(2):177-189 (Pubitemid 38420774)
64. Dahl E, Sadr-Nabavi A, Klopocki E, Betz B, Grube S, Kreutzfeld R, Himmelfarb M, An HX, Gelling S, Klaman I, Hinzmann B, Kristiansen G, Grutzmann R, Kuner R, Petschke B, Rhiem K, Wiechen K, Sers C, Wiestler O, Schneider A, Hofler H, Nahrig J, Dietel M, Schafer R, Rosenthal A, Schmutzler R, Durst M, Meindl A, Niederacher D (2005) Systematic identification and molecular characterization of genes differentially expressed in breast and ovarian cancer. J Pathol 205(1):21-28 (Pubitemid 40029089)
65. Beck AH, Espinosa I, Edris B, Li R, Montgomery K, Zhu S, Varma S, Marinelli RJ, van de Rijn M, West RB (2009) The macrophage colony-stimulating factor 1 response signature in breast carcinoma. Clin Cancer Res 15(3):778-787
66. Yacyshyn MB, Poppema S, Berg A, MacLean GD, Reddish MA, Meikle A, Longenecker BM (1995) CD69? and HLA-DR activation antigens on peripheral blood lymphocyte populations in metastatic breast and ovarian cancer patients: correlations with survival following active specific immunotherapy. Int J Cancer 61(4):470-474
67. Mukhopadhyay D, Jung J, Murmu N, Houchen CW, Dieckgraefe BK, Anant S (2003) CUGBP2 plays a critical role in apoptosis of breast cancer cells in response to genotoxic injury. Ann N Y Acad Sci 1010:504-509 (Pubitemid 38265034)
68. Strieter RM (2001) Chemokines: not just leukocyte chemoat-tractants in the promotion of cancer. Nat Immunol 2(4):285-286 (Pubitemid 33706336)
69. Bergamaschi A, Tagliabue E, Sorlie T, Naume B, Triulzi T, Orlandi R, Russnes HG, Nesland JM, Tammi R, Auvinen P, Kosma VM, Menard S, Borresen-Dale AL (2008) Extracellular matrix signature identifies breast cancer subgroups with different clinical outcome. J Pathol 214(3):357-367 (Pubitemid 351212391)
70. Forsti A, Jin Q, Altieri A, Johansson R, Wagner K, Enquist K, Grzybowska E, Pamula J, Pekala W, Hallmans G, Lenner P, Hemminki K (2007) Polymorphisms in the KDR and POSTN genes: association with breast cancer susceptibility and prognosis. Breast Cancer Res Treat 101(1):83-93 (Pubitemid 47555326)
71. Chan KY, Wong N, Lai PB, Squire JA, Macgregor PF, Beheshti B, Albert M, To KF, Johnson PJ (2005) Transcriptional profiling on chromosome 19p indicated frequent downregulation of ACP5 expression in hepatocellular carcinoma. Int J Cancer 114(6): 902-908
72. Jaeger E, Webb E, Howarth K, Carvajal-Carmona L, Rowan A, Broderick P, Walther A, Spain S, Pittman A, Kemp Z, Sullivan K, Heinimann K, Lubbe S, Domingo E, Barclay E, Martin L, Gorman M, Chandler I, Vijayakrishnan J, Wood W, Papaemmanuil E, Penegar S, Qureshi M, Farrington S, Tenesa A, Cazier JB, Kerr D, Gray R, Peto J, Dunlop M, Campbell H, Thomas H, Houlston R, Tomlinson I (2008) Common genetic variants at the CRAC1 (HMPS) locus on chromosome 15q13.3 influence colorectal cancer risk. Nat Genet 40(1):26-28
73. Wain LV, Armour JA, Tobin MD (2009) Genomic copy number variation, human health, and disease. Lancet 374(9686):340-350
74. Hyvarinen AK, Pohjoismaki JL, Holt IJ, Jacobs HT (2011) Overexpression of MTERFD1 or MTERFD3 impairs the completion of mitochondrial DNA replication. Mol Biol Rep 38(2):1321-1328