Recurrent copy number alterations in BRCA1-mutated ovarian tumors alter biological pathways

Human Mutation

Volumn 30, Issue 12, 2009, Pages 1693-1702

  Leunen, Karin ^a   Gevaert, Olivier ^b   Daemen, Anneleen ^b   Vanspauwen, Vanessa ^a   Michils, Geneviève ^a   De Moor, Bart ^b   Moerman, Philippe ^a   Vergote, Ignace ^a   Legius, Eric ^a  

^a UNIVERSITY HOSPITALS LEUVEN   (Belgium)

^b UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

Array CGH; BRCA1; Hidden Markov model; Ovarian cancer; Recurrent copy number alterations

Indexed keywords

ESTROGEN; METALLOPROTEINASE;

ARTICLE; CELL ADHESION; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; COMPLEMENT ACTIVATION; CONTROLLED STUDY; FEMALE; GENE MUTATION; GENOME; GENOMIC INSTABILITY; HOX GENE; HUMAN; ONCOGENE; OVARY CANCER; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TUMOR SUPPRESSOR GENE;

BRCA1 PROTEIN; CHROMOSOMES, HUMAN; FEMALE; GENE DOSAGE; GENES, NEOPLASM; HUMANS; KARYOTYPING; MARKOV CHAINS; MUTATION; OVARIAN NEOPLASMS; SIGNAL TRANSDUCTION;

EID: 71749102289     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.21135     Document Type: Article

References (41)

1. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B 57:289-300.
2. Buller RE, Lallas TA, Shahin MS, Sood AK, Hatterman-Zogg M, Anderson B, Sorosky JI, Kirby PA. 2001. The p53 mutational spectrum associated with BRCA1 mutant ovarian cancer. Clin Cancer Res 7:831-838. (Pubitemid 32708718)
3. Crijns APG, Duiker EW, de Jong S, Willemse PHB, van der Zee AGJ, de Vries EGE. 2006. Molecular prognostic markers in ovarian cancer: toward patient-tailored therapy. Int J Gynecol Cancer 16:152-165.
4. Cunat S, Hoffmann P, Pujol P. 2004. Estrogens and epithelial ovarian cancer. Gynecol Oncol 94:25-32.
5. Davies J, Wilson I, Lam W. 2005. Array CGH technologies and their applications to cancer genomes. Chromosome Res 13:237-248.
6. Dhar KK, Branigan K, Parkes J, Howells REJ, Hand P, Musgrove C, Strange RC, Fryer AA, Redman CWE, Hoban PR. 1999. Expression and subcellular localization of cyclin D1 protein in epithelial ovarian tumour cells. Br J Cancer 81:1174-1181.
7. Diebold J, Suchy B, Baretton GB, Blasenbreu S, Meier W, Schmidt M, Rabes H, Lohrs U. 1996. DNA ploidy and MYC DNA amplification in ovarian carcinomas - correlation with p53 and bcl-2 expression, proliferative activity and prognosis. Virchrows Arch 429:221-227. (Pubitemid 26402664)
8. Evers B, Jonkers J. 2006. Mouse models of BRCA1 and BRCA2 deficiency: past lessons, current understanding and future prospects. Oncogene 25:5885-5897. (Pubitemid 44453444)
9. Fan S, Wang JA, Yuan R, Ma Y, Meng Q, Erdos MR, Pestell RG, Yuan F, Auborn KJ, Goldberg ID, Rosen EM. 1999. BRCA1 inhibition of estrogen receptor signaling in transfected cells. Science 284:1354-1356. (Pubitemid 29289660)
10. Frietze S, Lupien M, Silver PA, Brown M. 2008. CARM1 regulates estrogen-stimulated breast cancer growth through up-regulation of E2F1. Cancer Res 68:301-306.
11. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR. 2004. A census of human cancer genes. Nat Rev Cancer 4:177-183.
12. Gorringe KL, Jacobs S, Thompson ER, Sridhar A, Qiu W, Choong DY, Campbell IG. 2007. High-resolution single nucleotide polymorphism array analysis of epithelial ovarian cancer reveals numerous microdeletions and amplifications. Clin Cancer Res 13:4731-4739. (Pubitemid 47294779)
13. Grier D, Thompson A, Kwasniewska A, Mcgonigle G, Halliday H, Lappin T. 2005. The pathophysiology of HOX genes and their role in cancer. J Pathol 205:154. (Pubitemid 40227988)
14. Haverty PM, Hon LS, Kaminker JS, Chant J, Zhang Z. 2009. High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors. BMC Med Genomics 2:21.
15. Hennessy BT, Mills GB. 2006. Ovarian cancer: homeobox genes, autocrine/paracrine growth, and kinase signaling. Int J Biochem Cell Biol 38:1450-1456.
16. Hua KQ, Feng WW, Cao Q, Zhou XR, Lu X, Feng YJ. 2008. Estrogen and progestin regulate metastasis through the PI3K/AKT pathway in human ovarian cancer. Int J Oncol 33:959-967.
17. Huang E, Ishida S, Pittman J, Dressman H, Bild A, Kloos M, D'Amico M, Pestell RG, West M, Nevins JR. 2003. Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat Genet 34:226-230. (Pubitemid 36666937)
18. Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P. 2009. Ensembl 2009. Nucleic Acids Res 37:D690-D697.
19. Israeli O, Gotlieb WH, Friedman E, Goldman B, Ben-Baruch G, viram-Goldring A, Rienstein S. 2003. Familial vs sporadic ovarian tumors: characteristic genomic alterations analyzed by CGH. Gynecol Oncol 90:629-636.
20. Jazaeri A, Yee C, Sotiriou C, Brantley K, Boyd J, Liu E. 2002. Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. J Natl Cancer Inst 94:990-1000. (Pubitemid 34814728)
21. Lai WR, Johnson MD, Kucherlapati R, Park PJ. 2005. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 21:3763-3770. (Pubitemid 41535525)
22. Lau KM, Mok SC, Ho SM. 1999. Expression of human estrogen receptor-alpha and -beta, progesterone receptor, and androgen receptor mRNA in normal and malignant ovarian epithelial cells. Proc Natl Acad Sci USA 96:5722-5727.
23. Lindgren PR, Cajander S, Backstrom T, Gustafsson JA, Makela S, Olofsson JI. 2004. Estrogen and progesterone receptors in ovarian epithelial tumors. Mol Cell Endocrinol 221:97-104. (Pubitemid 38829727)
24. Liu Y, Ganesan TS. 2002. Tumour suppressor genes in sporadic epithelial ovarian cancer. Reproduction 123:341-353. (Pubitemid 34223880)
25. North BV, Curtis D, Sham PC. 2002. A note on the calculation of empirical P values from Monte Carlo procedures. Am J Hum Genet 71:439-441. (Pubitemid 34800261)
26. Nowee ME, Snijders AM, Rockx DA, de Wit RM, Kosma VM, Hamalainen K, Schouten JP, Verheijen RH, van Diest PJ, Albertson DG, Dorsman JC. 2007. DNA profiling of primary serous ovarian and fallopian tube carcinomas with array comparative genomic hybridization and multiplex ligation-dependent probe amplification. J Pathol 213:46-55. (Pubitemid 47354565)
27. Orsulic S, Li Y, Soslow RA, Vitale-Cross LA, Gutkind JS, Varmus HE. 2002. Induction of ovarian cancer by defined multiple genetic changes in a mouse model system. Cancer Cell 1:53-62. (Pubitemid 41039176)
28. Paliouras M, Borgono C, Diamandis EP. 2007. Human tissue kallikreins: the cancer biomarker family. Cancer Lett 249:61-79. (Pubitemid 46427999)
29. Patael-Karasik Y, Daniely M, Gotlieb WH, Ben-Baruch G, Schiby J, Barakai G, Goldman B, Aviram A, Friedman E. 2000. Comparative genomic hybridization in inherited and sporadic ovarian tumors in Israel. Cancer Genet Cytogenet 121:26-32. (Pubitemid 30665737)
30. Prat J, Ribe A, Gallardo A. 2005. Hereditary ovarian cancer. Hum Pathol 36:861-870.
31. Risinger JI, Berchuck A, Kohler MF, Boyd J. 1994. Mutations of the E-cadherin gene in human gynecologic cancers. Nat Genet 7:98-102. (Pubitemid 24232388)
32. Shah SP, Lam WL, Ng RT, Murphy KP. 2007. Modeling recurrent DNA copy number alterations in array CGH data. Bioinformatics 23.
33. Shah SP, Xuan X, Deleeuw RJ, Khojasteh M, Lam WL, Ng R, Murphy KP. 2006. Integrating copy number polymorphisms into array CGH analysis using a robust HMM. Bioinformatics 22. (Pubitemid 44288313)
34. Shayesteh L, Lu Y, Kuo WL, Baldocchi R, Godfrey T, Collins C, Pinkel D, Powell B, Mills GB, Gray JW. 1999. PIK3CA is implicated as an oncogene in ovarian cancer. Nat Genet 21:99-102. (Pubitemid 29036292)
35. Song H, Hogdall E, Ramus SJ, DiCioccio RA, Hogdall C, Quaye L, McGuire V, Whittemore AS, Shah M, Greenberg D, Easton D, Kjaer SK, Pharoah PDP, Gayther SA. 2008. Effects of common germ-line genetic variation in cell cycle genes on ovarian cancer survival. Clin Cancer Res 14:1090-1095. (Pubitemid 351302555)
36. Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M, Paulovich A, Pomeroy S, Golub T, Lander E, Mesirov J. 2005. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545-15550. (Pubitemid 41528093)
37. Tapper J, Sarantaus L, Vahteristo P, Nevanlinna H, Hemmer S, Seppala M, Knuutila S, Butzow R. 1998. Genetic changes in inherited and sporadic ovarian carcinomas by comparative genomic hybridization: extensive similarity except for a difference at chromosome 2q24-q32. Cancer Res 58:2715-2719. (Pubitemid 28311896)
38. Venter DJ, Ramus SJ, Hammet FM, de Silva M, Hutchins AM, Petrovic V, Price G, Armes JE. 2005. Complex CGH alterations on chromosome arm 8p at candidate tumor suppressor gene loci in breast cancer cell lines. Cancer Genet Cytogenet 160:134-140. (Pubitemid 40910048)
39. Walsh CS, Ogawa S, Scoles DR, Miller CW, Kawamata N, Narod SA, Koeffler HP, Karlan BY. 2008. Genome-wide loss of heterozygosity and uniparental disomy in BRCA1/2-associated ovarian carcinomas. Clin Cancer Res 14:7645-7651.
40. Xing D, Orsulic S. 2006. A mouse model for the molecular characterization of brca1-associated ovarian carcinoma. Cancer Res 66:8949-8953. (Pubitemid 44521109)
41. Zweemer RP, Ryan A, Snijders AM, Hermsen MA, Meijer GA, Beller U, Menko FH, Jacobs IJ, Baak JP, Verheijen RH, Kenemans P, van Diest PJ. 2001. Comparative genomic hybridization of microdissected familial ovarian carcinoma: two deleted regions on chromosome 15q not previously identified in sporadic ovarian carcinoma. Lab Invest 81:1363-1370. (Pubitemid 32980159)