The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

Nature - Tập 486 Số 7403 - Trang 346-352 - 2012
Christina Curtis1,2, Sohrab P. Shah3, Suet‐Feung Chin1, Gulisa Turashvili3, Oscar M. Rueda1, Mark Dunning4, Doug Speed5,2, Andy G. Lynch1, Shamith A. Samarajiwa1, Yinyin Yuan1, Stefan Gräf1, Gavin Ha3, Gholamreza Haffari3, Ali Bashashati3, Roslin Russell4, Steven McKinney3, Anita Grigoriadis6, Andrew R. Green7, Elena Provenzano8, Gordon Wishart8, Sarah E. Pinder9, Peter H. Watson3,10, Florian Markowetz1, Leigh C. Murphy10, Ian O. Ellis7, Arnie Purushotham9,11, Anne‐Lise Børresen‐Dale6,12, James Hadfield4, Simon Tavaré1, Carlos Caldas1, Samuel Aparício3
1Department of Oncology, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK
2Present addresses: Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA (Ch.C.); University College London, Genetics Institute, WC1E 6BT, UK (D.S.).,
3Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
4Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
5Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Centre for Mathematical Sciences, Cambridge CB3 0WA, UK,
6Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Montebello, 0310 Oslo, Norway,
7Department of Histopathology, School of Molecular Medical Sciences, University of Nottingham, Nottingham, NG5 1PB, UK
8Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
9King's College London, Breakthrough Breast Cancer Research Unit, London WC2R 2LS, UK
10Manitoba Institute of Cell Biology, University of Manitoba, Manitoba, R3E 0V9, Canada.
11NIHR Comprehensive Biomedical Research Centre at Guy's and St. Thomas NHS Foundation Trust and King's College London, London WC2R 2LS, UK
12Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0316 Oslo, Norway ,

Tóm tắt

Từ khóa


Tài liệu tham khảo

Leary, R. J. et al. Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc. Natl Acad. Sci. USA 105, 16224–16229 (2008)

Bignell, G. R. et al. Signatures of mutation and selection in the cancer genome. Nature 463, 893–898 (2010)

Perou, C. M. et al. Molecular portraits of human breast tumours. Nature 406, 747–752 (2000)

Sørlie, T. et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA 98, 10869–10874 (2001)

Chin, K. et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10, 529–541 (2006)

Chin, S. F. et al. High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol. 8, R215 (2007)

Parker, J. S. et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J. Clin. Oncol. 27, 1160–1167 (2009)

Stranger, B. E. et al. Genome-wide associations of gene expression variation in humans. PLoS Genet. 1, e78 (2005)

Gilad, Y., Rifkin, S. A. & Pritchard, J. K. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet. 24, 408–415 (2008)

Teschendorff, A. E., Naderi, A., Barbosa-Morais, N. L. & Caldas, C. PACK: Profile analysis using clustering and kurtosis to find molecular classifiers in cancer. Bioinformatics 22, 2269–2275 (2006)

Holland, D. et al. ZNF703 is a common Luminal B breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium. EMBO Mol. Med. 3, 167–180 (2011)

Li, J. et al. PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 275, 1943–1947 (1997)

Santarius, T., Shiply, J., Brewer, D., Stratton, M. R. & Cooper, C. S. A census of amplified and overexpressed human cancer genes. Nature Rev. Cancer 10, 59–64 (2010)

Jones, S. et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330, 228–231 (2010)

McConechy, M. K. et al. Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas. J. Pathol. 223, 567–573 (2011)

Tan, J. et al. B55β-associated PP2A complex controls PDK1-directed MYC signaling and modulates rapamycin sensitivity in colorectal cancer. Cancer Cell 18, 459–471 (2010)

Christopher, S. A., Diegelman, P., Porter, C. W. & Kruger, W. D. Methylthioadenosine phosphorylase, a gene frequently codeleted with p16 (CDKN2A/ARF), acts as a tumor suppressor in a breast cancer cell line. Cancer Res. 62, 6639–6644 (2002)

Teng, D. H. et al. Human mitogen-activated protein kinase kinase 4 as a candidate tumor suppressor. Cancer Res. 57, 4177–4182 (1997)

Hollestelle, A. et al. Distinct gene mutation profiles among luminal-type and basal-type breast cancer cell lines. Breast Cancer Res. Treat. 121, 53–64 (2010)

Shen, R., Olshen, A. B. & Ladanyi, M. Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics 25, 2906–2912 (2009)

Tibshirani, R., Hastie, T., Narasimhan, B. & Chu, G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl Acad. Sci. USA 99, 6567–6572 (2002)

Kapp, A. V. & Tibshirani, R. Are clusters found in one dataset present in another dataset? Biostatistics 8, 9–31 (2007)

Hughes-Davies, L. et al. EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer. Cell 115, 523–535 (2003)

Brown, L. A. et al. Amplification of 11q13 in ovarian carcinoma. Genes Chromosom. Cancer 47, 481–489 (2008)

Russnes, H. G. et al. Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Sci. Transl. Med. 2, 38ra47 (2010)

Blows, F. M. et al. Subtyping of breast cancer by immunohistochemistry to investigate a relationship between subtype and short and long term survival: a collaborative analysis of data for 10,159 cases from 12 studies. PLoS Med. 7, e1000279 (2010)

Mahmoud, S. M. A. et al. Tumor-infiltrating CD8+ lymphocytes predict clinical outcome in breast cancer. J. Clin. Oncol. 29, 1949–1955 (2011)

Daniel, J., Coulter, J., Woo, J.-H., Wilsbach, K. & Gabrielson, E. High levels of the Mps1 checkpoint protein are protective of aneuploidy in breast cancer cells. Proc. Natl Acad. Sci. USA 108, 5384–5389 (2011)

Chen, Y. et al. Variations in DNA elucidate molecular networks that cause disease. Nature 452, 429–435 (2008)