Genomic signature of BRCA1 deficiency in sporadic basal-like breast tumors

Genes Chromosomes and Cancer

Volumn 50, Issue 2, 2011, Pages 71-81

  Joosse, Simon A ^a,b   Brandwijk, Kim I M ^a   Mulder, Lennart ^a   Wesseling, Jelle ^a   Hannemann, Juliane ^a,b   Nederlof, Petra M ^a  

^a NETHERLANDS CANCER INSTITUTE   (Netherlands)

^b UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN; MESSENGER RNA;

ADULT; ARTICLE; BREAST TUMOR; CHROMOSOME 3Q; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA REPAIR; FEMALE; GENE EXPRESSION; GENE LOSS; GENE MUTATION; GENOMICS; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; METHYLATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MICROARRAY; REAL TIME POLYMERASE CHAIN REACTION;

ADULT; AGED; AGED, 80 AND OVER; BRCA1 PROTEIN; BREAST NEOPLASMS; CHROMOSOME ABERRATIONS; CHROMOSOMES, HUMAN, PAIR 3; DNA COPY NUMBER VARIATIONS; DNA METHYLATION; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HISTONES; HUMANS; MIDDLE AGED; MUTATION; NEOPLASMS, BASAL CELL; PROMOTER REGIONS, GENETIC; TUMOR SUPPRESSOR PROTEINS;

EID: 78650026917     PISSN: 10452257     EISSN: 10982264     Source Type: Journal    
DOI: 10.1002/gcc.20833     Document Type: Article

References (45)

1. Abd El-Rehim DM, Ball G, Pinder SE, Rakha E, Paish C, Robertson JF, Macmillan D, Blamey RW, Ellis IO. 2005. High-throughput protein expression analysis using tissue microarray technology of a large well-characterised series identifies biologically distinct classes of breast cancer confirming recent cDNA expression analyses. Int J Cancer 3: 340-350.
2. Bergamaschi A, Kim YH, Wang P, Sorlie T, Hernandez-Boussard T, Lonning PE, Tibshirani R, Borresen-Dale AL, Pollack JR. 2006. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 11: 1033-1040.
3. Chen Y, Zhou J, Xu Y, Li Z, Wen X, Yao L, Xie Y, Deng D. 2009. BRCA1 promoter methylation associated with poor survival in Chinese patients with sporadic breast cancer. Cancer Sci 9: 1663-1667.
4. Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, van de Wiel MA, Green AR, Ellis IO, Porter PL, Tavare S, Brenton JD, Ylstra B, Caldas C. 2007. High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol 10: R215.
5. de Ronde JJ, Hannemann J, Halfwerk H, Mulder L, Straver ME, Vrancken Peeters MJ, Wesseling J, van dV, Wessels LF, Rodenhuis S. 2009. Concordance of clinical and molecular breast cancer subtyping in the context of preoperative chemotherapy response. Breast Cancer Res Treat 1: 119-126.
6. Dennis GJr., Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. 2003. DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol 5: 3.
7. Foulkes WD, Stefansson IM, Chappuis PO, Begin LR, Goffin JR, Wong N, Trudel M, Akslen LA. 2003. Germline BRCA1 mutations and a basal epithelial phenotype in breast cancer. J Natl Cancer Inst 19: 1482-1485.
8. Galizia E, Giorgetti G, Piccinini G, Santinelli A, Loretelli C, Bianchi F, Gagliardini D, Carbonari G, Pisa E, Belvederesi L, Bracci R, Ferretti C, Corradini F, Cellerino R. 2010. BRCA1 expression in triple negative sporadic breast cancers. Am J Epidemiol 1: 24-29.
9. Genestie C, Zafrani B, Asselain B, Fourquet A, Rozan S, Validire P, Vincent-Salomon A, Sastre-Garau X. 1998. Comparison of the prognostic value of Scarff-Bloom-Richardson and Nottingham histological grades in a series of 825 cases of breast cancer: Major importance of the mitotic count as a component of both grading systems. Anticancer Res B 1: 571-576.
10. Holstege H, Joosse SA, van Oostrom CT, Nederlof PM, de Vries A, Jonkers J. 2009. High incidence of protein-truncating TP53 mutations in BRCA1-related breast cancer. Cancer Res 69: 3625-3633.
11. Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF, Livasy C, Carey LA, Reynolds E, Dressler L, Nobel A, Parker J, Ewend MG, Sawyer LR, Wu J, Liu Y, Nanda R, Tretiakova M, Ruiz OA, Dreher D, Palazzo JP, Perreard L, Nelson E, Mone M, Hansen H, Mullins M, Quackenbush JF, Ellis MJ, Olopade OI, Bernard PS, Perou CM. 2006. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genom 96.
12. James CR, Quinn JE, Mullan PB, Johnston PG, Harkin DP. 2007. BRCA1, a potential predictive biomarker in the treatment of breast cancer. Oncologist 2: 142-150.
13. Jonsson G, Naylor TL, Vallon-Christersson J, Staaf J, Huang J, Ward MR, Greshock JD, Luts L, Olsson H, Rahman N, Stratton M, Ringner M, Borg A, Weber BL. 2005. Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization. Cancer Res 17: 7612-7621.
14. Joosse SA. 2010. 4x2 Fisher's exact test. Available from
15. Joosse SA, van Beers EH, Nederlof PM. 2007. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer 43.
16. Joosse SA, van Beers EH, Tielen IH, Horlings H, Peterse JL, Hoogerbrugge N, Ligtenberg MJ, Wessels LF, Axwijk P, Verhoef S, Hogervorst FB, Nederlof PM. 2009. Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res Treat 3: 479-489.
17. Joosse SA, Brandwijk KI, Devilee P, Wesseling J, Hogervorst FB, Verhoef S, Nederlof PM. 2010. Prediction of BRCA2-association in hereditary breast carcinomas using array-CGH. Breast Cancer Res Treat [Epub ahead of print].
18. Kreike B, van Kouwenhove M, Horlings H, Weigelt B, Peterse H, Bartelink H, van de Vijver MJ. 2007. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 5: R65.
19. Lakhani SR, Reis-Filho JS, Fulford L, Penault-Llorca F, van der Vijver M, Parry S, Bishop T, Benitez J, Rivas C, Bignon YJ, Chang-Claude J, Hamann U, Cornelisse CJ, Devilee P, Beckmann MW, Nestle-Kramling C, Daly PA, Haites N, Varley J, Lalloo F, Evans G, Maugard C, Meijers-Heijboer H, Klijn JG, Olah E, Gusterson BA, Pilotti S, Radice P, Scherneck S, Sobol H, Jacquemier J, Wagner T, Peto J, Stratton MR, McGuffog L, Easton DF. 2005. Prediction of BRCA1 status in patients with breast cancer using estrogen receptor and basal phenotype. Clin Cancer Res 14: 5175-5180.
20. Linn SC, van't Veer LJ. 2009. Clinical relevance of the triple-negative breast cancer concept: Genetic basis and clinical utility of the concept. Eur J Cancer 11-26.
21. Manie E, Vincent-Salomon A, Lehmann-Che J, Pierron G, Turpin E, Warcoin M, Gruel N, Lebigot I, Sastre-Garau X, Lidereau R, Remenieras A, Feunteun J, Delattre O, de TH, Stoppa-Lyonnet D, Stern MH. 2009. High frequency of TP53 mutation in BRCA1 and sporadic basal-like carcinomas but not in BRCA1 luminal breast tumors. Cancer Res 2: 663-671.
22. Melchor L, Benitez J. 2008. An integrative hypothesis about the origin and development of sporadic and familial breast cancer subtypes. Carcinogenesis 8: 1475-1482.
23. Nielsen TO, Hsu FD, Jensen K, Cheang M, Karaca G, Hu Z, Hernandez-Boussard T, Livasy C, Cowan D, Dressler L, Akslen LA, Ragaz J, Gown AM, Gilks CB, van de Rijn M, Perou CM. 2004. Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clin Cancer Res 16: 5367-5374.
24. Oncoline. Oncoline Guidelines. Accessed 1 September 2008.
25. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D. 2000. Molecular portraits of human breast tumours. Nature 6797: 747-752.
26. Picard F, Robin S, Lavielle M, Vaisse C, Daudin JJ. 2005. A statistical approach for array CGH data analysis. BMC Bioinform 27.
27. Rakha EA, Reis-Filho JS, Ellis IO. 2008. Basal-like breast cancer: A critical review. J Clin Oncol 15: 2568-2581.
28. Reis-Filho JS, Tutt AN. 2008. Triple negative tumours: A critical review. Histopathology 1: 108-118.
29. Reis-Filho JS, Simpson PT, Gale T, Lakhani SR. 2005. The molecular genetics of breast cancer: The contribution of comparative genomic hybridization. Pathol Res Pract 11: 713-725.
30. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lonning PE, Brown PO, Borresen-Dale AL, Botstein D. 2003. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 14: 8418-8423.
31. Stefansson OA, Jonasson JG, Johannsson OT, Olafsdottir K, Steinarsdottir M, Valgeirsdottir S, Eyfjord JE. 2009. Genomic profiling of breast tumours in relation to BRCA abnormalities and phenotypes. Breast Cancer Res 4: R47.
32. Su C, Gao G, Schneider S, Helt C, Weiss C, O'Reilly MA, Bohmann D, Zhao J. 2004. DNA damage induces downregulation of histone gene expression through the G1 checkpoint pathway. EMBO J 5: 1133-1143.
33. Suijkerbuijk KP, Fackler MJ, Sukumar S, van Gils CH, van LT, van der WE, Vooijs M, van Diest PJ. 2008. Methylation is less abundant in BRCA1-associated compared with sporadic breast cancer. Ann Oncol 11: 1870-1874.
34. Tirkkonen M, Johannsson O, Agnarsson BA, Olsson H, Ingvarsson S, Karhu R, Tanner M, Isola J, Barkardottir RB, Borg A, Kallioniemi OP. 1997. Distinct somatic genetic changes associated with tumor progression in carriers of BRCA1 and BRCA2 germ-line mutations. Cancer Res 7: 1222-1227.
35. Turner NC, Reis-Filho JS. 2006. Basal-like breast cancer and the BRCA1 phenotype. Oncogene 43: 5846-5853.
36. Turner NC, Reis-Filho JS, Russell AM, Springall RJ, Ryder K, Steele D, Savage K, Gillett CE, Schmitt FC, Ashworth A, Tutt AN. 2007. BRCA1 dysfunction in sporadic basal-like breast cancer. Oncogene 14: 2126-2132.
37. Tusher VG, Tibshirani R, Chu G. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 9: 5116-5121.
38. van Beers EH, van Welsem T, Wessels LF, Li Y, Oldenburg RA, Devilee P, Cornelisse CJ, Verhoef S, Hogervorst FB, van't Veer LJ, Nederlof PM. 2005. Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations. Cancer Res 3: 822-827.
39. van Beers EH, Joosse SA, Ligtenberg MJ, Fles R, Hogervorst FB, Verhoef S, Nederlof PM. 2006. A multiplex PCR predictor for aCGH success of FFPE samples. Br J Cancer 2: 333-337.
40. Vasilatos SN, Broadwater G, Barry WT, Baker JC Jr., Lem S, Dietze EC, Bean GR, Bryson AD, Pilie PG, Goldenberg V, Skaar D, Paisie C, Torres-Hernandez A, Grant TL, Wilke LG, Ibarra-Drendall C, Ostrander JH, D'Amato NC, Zalles C, Jirtle R, Weaver VM, Seewaldt VL. 2009. CpG island tumor suppressor promoter methylation in non-BRCA-associated early mammary carcinogenesis. Cancer Epidemiol Biomark Prev 3: 901-914.
41. Viale G, Regan MM, Maiorano E, Mastropasqua MG, Dell'Orto P, Rasmussen BB, Raffoul J, Neven P, Orosz Z, Braye S, Ohlschlegel C, Thurlimann B, Gelber RD, Castiglione-Gertsch M, Price KN, Goldhirsch A, Gusterson BA, Coates AS. 2007. Prognostic and predictive value of centrally reviewed expression of estrogen and progesterone receptors in a randomized trial comparing letrozole and tamoxifen adjuvant therapy for postmenopausal early breast cancer: BIG 1-98. J Clin Oncol 25: 3846-3852.
42. Vincent-Salomon A, Gruel N, Lucchesi C, MacGrogan G, Dendale R, Sigal-Zafrani B, Longy M, Raynal V, Pierron G, de Mascarel I, Taris C, Stoppa-Lyonnet D, Pierga JY, Salmon R, Sastre-Garau X, Fourquet A, Delattre O, de Cremoux P, Aurias A. 2007. Identification of typical medullary breast carcinoma as a genomic sub-group of basal-like carcinomas, a heterogeneous new molecular entity. Breast Cancer Res 2: R24.
43. Wessels LF, van Welsem T, Hart AA, van't Veer LJ, Reinders MJ, Nederlof PM. 2002. Molecular classification of breast carcinomas by comparative genomic hybridization: A specific somatic genetic profile for BRCA1 tumors. Cancer Res 23: 7110-7117.
44. Wolff AC, Hammond ME, Schwartz JN, Hagerty KL, Allred DC, Cote RJ, Dowsett M, Fitzgibbons PL, Hanna WM, Langer A, McShane LM, Paik S, Pegram MD, Perez EA, Press MF, Rhodes A, Sturgeon C, Taube SE, Tubbs R, Vance GH, van d, V, Wheeler TM, Hayes DF. 2007. American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer. J Clin Oncol 1: 118-145.
45. Young SR, Pilarski RT, Donenberg T, Shapiro C, Hammond LS, Miller J, Brooks KA, Cohen S, Tenenholz B, Desai D, Zandvakili I, Royer R, Li S, Narod SA. 2009. The prevalence of BRCA1 mutations among young women with triple-negative breast cancer. BMC Cancer 86.