Integrative molecular profiling of triple negative breast cancers identifies amplicon drivers and potential therapeutic targets (original) (raw)
Adelaide J, Finetti P, Bekhouche I, Repellini L, Geneix J, Sircoulomb F et al. (2007). Integrated profiling of basal and luminal breast cancers. Cancer Res67: 11565–11575. ArticleCASPubMed Google Scholar
Agrawal G, Chen JH, Baick CH, Chen AE, Mehta RS, Nalcioglu O et al. (2007). Pathological complete response in triple negative poorly differentiated invasive ductal breast carcinoma detected during pregnancy. J Clin Oncol25: 2618–2620. ArticlePubMed Google Scholar
Andre F, Job B, Dessen P, Tordai A, Michiels S, Liedtke C et al. (2009). Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array. Clin Cancer Res15: 441–451. ArticleCASPubMed Google Scholar
Benjamini Y, Hochberg Y . (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc57: 289–300. Google Scholar
Bernard-Pierrot I, Gruel N, Stransky N, Vincent-Salomon A, Reyal F, Raynal V et al. (2008). Characterization of the recurrent 8p11-12 amplicon identifies PPAPDC1B, a phosphatase protein, as a new therapeutic target in breast cancer. Cancer Res68: 7165–7175. ArticleCASPubMed Google Scholar
Bertucci F, Finetti P, Cervera N, Esterni B, Hermitte F, Viens P et al. (2008). How basal are triple-negative breast cancers? Int J Cancer123: 236–240. ArticleCASPubMed Google Scholar
Byron SA, Gartside MG, Wellens CL, Mallon MA, Keenan JB, Powell MA et al. (2008). Inhibition of activated fibroblast growth factor receptor 2 in endometrial cancer cells induces cell death despite PTEN abrogation. Cancer Res68: 6902–6907. ArticleCASPubMed Google Scholar
Carey LA, Dees EC, Sawyer L, Gatti L, Moore DT, Collichio F et al. (2007). The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin Cancer Res13: 2329–2334. ArticleCASPubMed Google Scholar
Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL et al. (2006). Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell10: 529–541. ArticleCASPubMed Google Scholar
Chou TC, Talalay P . (1984). Quantitative analysis of dose-effect relationships: the combined effects of multiple drugs or enzyme inhibitors. Adv Enzyme Regul22: 27–55. ArticleCASPubMed Google Scholar
Coe BP, Ylstra B, Carvalho B, Meijer GA, Macaulay C, Lam WL . (2007). Resolving the resolution of array CGH. Genomics89: 647–653. ArticleCASPubMed Google Scholar
Dent R, Hanna WM, Trudeau M, Rawlinson E, Sun P, Narod SA . (2009). Pattern of metastatic spread in triple-negative breast cancer. Breast Cancer Res Treat115: 423–428. ArticlePubMed Google Scholar
Dent R, Trudeau M, Pritchard KI, Hanna WM, Kahn HK, Sawka CA et al. (2007). Triple-negative breast cancer: clinical features and patterns of recurrence. Clin Cancer Res13: 4429–4434. ArticlePubMed Google Scholar
Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG et al. (2007). Genome-wide association study identifies novel breast cancer susceptibility loci. Nature447: 1087–1093. ArticleCASPubMedPubMed Central Google Scholar
Garcia-Closas M, Hall P, Nevanlinna H, Pooley K, Morrison J, Richesson DA et al. (2008). Heterogeneity of breast cancer associations with five susceptibility loci by clinical and pathological characteristics. PLoS Genet4: e1000054. ArticlePubMedPubMed Central Google Scholar
Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G et al. (2007). Patterns of somatic mutation in human cancer genomes. Nature446: 153–158. ArticleCASPubMedPubMed Central Google Scholar
Gunnarsson R, Staaf J, Jansson M, Ottesen AM, Goransson H, Liljedahl U et al. (2008). Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms. Genes Chromosomes Cancer47: 697–711. ArticleCASPubMed Google Scholar
Han W, Jung EM, Cho J, Lee JW, Hwang KT, Yang SJ et al. (2008). DNA copy number alterations and expression of relevant genes in triple-negative breast cancer. Genes Chromosomes Cancer47: 490–499. ArticleCASPubMed Google Scholar
Hannemann J, Velds A, Halfwerk JB, Kreike B, Peterse JL, van de Vijver MJ . (2006). Classification of ductal carcinoma in situ by gene expression profiling. Breast Cancer Res8: R61. ArticlePubMedPubMed Central Google Scholar
Harris LN, Broadwater G, Lin NU, Miron A, Schnitt SJ, Cowan D et al. (2006). Molecular subtypes of breast cancer in relation to paclitaxel response and outcomes in women with metastatic disease: results from CALGB 9342. Breast Cancer Res8: R66. ArticlePubMedPubMed Central Google Scholar
Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E et al. (2006). Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res16: 1465–1479. ArticleCASPubMedPubMed Central Google Scholar
Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF et al. (2006). The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics7: 96. ArticlePubMedPubMed Central Google Scholar
Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, Slade D et al. (2000). Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet25: 333–337. ArticleCASPubMed Google Scholar
Jonsson G, Naylor TL, Vallon-Christersson J, Staaf J, Huang J, Ward MR et al. (2005). Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization. Cancer Res65: 7612–7621. ArticlePubMed Google Scholar
Kreike B, van Kouwenhove M, Horlings H, Weigelt B, Peterse H, Bartelink H et al. (2007). Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res9: R65. ArticlePubMedPubMed Central Google Scholar
Lambros MB, Simpson PT, Jones C, Natrajan R, Westbury C, Steele D et al. (2006). Unlocking pathology archives for molecular genetic studies: a reliable method to generate probes for chromogenic and fluorescent in situ hybridization. Lab Invest86: 398–408. ArticleCASPubMed Google Scholar
Mackay A, Tamber N, Fenwick K, Iravani M, Grigoriadis A, Dexter T et al. (2009). A high-resolution integrated analysis of genetic and expression profiles of breast cancer cell lines. Breast Cancer Res Treat118: 481–498. ArticleCASPubMed Google Scholar
Maira SM, Stauffer F, Brueggen J, Furet P, Schnell C, Fritsch C et al. (2008). Identification and characterization of NVP-BEZ235, a new orally available dual phosphatidylinositol 3-kinase/mammalian target of rapamycin inhibitor with potent in vivo antitumor activity. Mol Cancer Ther7: 1851–1863. ArticleCASPubMed Google Scholar
Marchio C, Natrajan R, Shiu KK, Lambros MB, Rodriguez-Pinilla SM, Tan DS et al. (2008). The genomic profile of HER2-amplified breast cancers: the influence of ER status. J Pathol216: 399–407. ArticleCASPubMed Google Scholar
Mohammadi M, Froum S, Hamby JM, Schroeder MC, Panek RL, Lu GH et al. (1998). Crystal structure of an angiogenesis inhibitor bound to the FGF receptor tyrosine kinase domain. EMBO J17: 5896–5904. ArticleCASPubMedPubMed Central Google Scholar
Natrajan R, Lambros MB, Rodriguez-Pinilla SM, Moreno-Bueno G, Tan DS, Marchio C et al. (2009a). Tiling path genomic profiling of grade 3 invasive ductal breast cancers. Clin Cancer Res15: 2711–2722. ArticleCASPubMed Google Scholar
Natrajan R, Weigelt B, Mackay A, Geyer FC, Grigoriadis A, Tan DS et al. (2009b). An integrative genomic and transcriptomic analysis reveals molecular pathways and networks regulated by copy number aberrations in basal-like, HER2 and luminal cancers. Breast Cancer Res Treat (e-pub ahead of print 18 August 2009).
Ng G, Huang J, Roberts I, Coleman N . (2006). Defining ploidy-specific thresholds in array comparative genomic hybridization to improve the sensitivity of detection of single copy alterations in cell lines. J Mol Diagn8: 449–458. ArticleCASPubMedPubMed Central Google Scholar
Orsetti B, Nugoli M, Cervera N, Lasorsa L, Chuchana P, Ursule L et al. (2004). Genomic and expression profiling of chromosome 17 in breast cancer reveals complex patterns of alterations and novel candidate genes. Cancer Res64: 6453–6460. ArticleCASPubMed Google Scholar
Reis-Filho JS, Drury S, Lambros MB, Marchio C, Johnson N, Natrajan R et al. (2008). ESR1 gene amplification in breast cancer: a common phenomenon? Nat Genet40: 809–810; author reply 810–812. ArticleCASPubMed Google Scholar
Reis-Filho JS, Simpson PT, Turner NC, Lambros MB, Jones C, Mackay A et al. (2006). FGFR1 emerges as a potential therapeutic target for lobular breast carcinomas. Clin Cancer Res12: 6652–6662. ArticleCASPubMed Google Scholar
Reis-Filho JS, Tutt AN . (2008). Triple negative tumours: a critical review. Histopathology52: 108–118. ArticleCASPubMed Google Scholar
Schneider BP, Winer EP, Foulkes WD, Garber J, Perou CM, Richardson A et al. (2008). Triple-negative breast cancer: risk factors to potential targets. Clin Cancer Res14: 8010–8018. ArticleCASPubMed Google Scholar
Tan DS, Lambros MB, Natrajan R, Reis-Filho JS . (2007). Getting it right: designing microarray (and not ‘microawry’) comparative genomic hybridization studies for cancer research. Lab Invest87: 737–754. ArticleCASPubMed Google Scholar
Tannheimer SL, Rehemtulla A, Ethier SP . (2000). Characterization of fibroblast growth factor receptor 2 overexpression in the human breast cancer cell line SUM-52PE. Breast Cancer Res2: 311–320. ArticleCASPubMedPubMed Central Google Scholar
Tischkowitz MD, Foulkes WD . (2006). The basal phenotype of BRCA1-related breast cancer: past, present and future. Cell Cycle5: 963–967. ArticleCASPubMed Google Scholar
Turner N, Tutt A, Ashworth A . (2004). Hallmarks of ‘BRCAness’ in sporadic cancers. Nat Rev Cancer4: 814–819. ArticleCASPubMed Google Scholar
Turner NC, Lord CJ, Iorns E, Brough R, Swift S, Elliott R et al. (2008). A synthetic lethal siRNA screen identifying genes mediating sensitivity to a PARP inhibitor. EMBO J27: 1368–1377. ArticleCASPubMedPubMed Central Google Scholar
Weigelt B, Horlings HM, Kreike B, Hayes MM, Hauptmann M, Wessels LF et al. (2008). Refinement of breast cancer classification by molecular characterization of histological special types. J Pathol216: 141–150. ArticleCASPubMed Google Scholar
Yamaguchi N, Oyama T, Ito E, Satoh H, Azuma S, Hayashi M et al. (2008). NOTCH3 signaling pathway plays crucial roles in the proliferation of ErbB2-negative human breast cancer cells. Cancer Res68: 1881–1888. ArticleCASPubMed Google Scholar
Yuan B, Xu Y, Woo JH, Wang Y, Bae YK, Yoon DS et al. (2006). Increased expression of mitotic checkpoint genes in breast cancer cells with chromosomal instability. Clin Cancer Res12: 405–410. ArticleCASPubMed Google Scholar
Zhao JJ, Liu Z, Wang L, Shin E, Loda MF, Roberts TM . (2005). The oncogenic properties of mutant p110alpha and p110beta phosphatidylinositol 3-kinases in human mammary epithelial cells. Proc Natl Acad Sci USA102: 18443–18448. ArticleCASPubMedPubMed Central Google Scholar