Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

Nature

Volumn 481, Issue 7381, 2012, Pages 389-393

  Ross Innes, Caryn S ^a   Stark, Rory ^a   Teschendorff, Andrew E ^b   Holmes, Kelly A ^a   Ali, H Raza ^a,g   Dunning, Mark J ^a   Brown, Gordon D ^a   Gojis, Ondrej ^c,d   Ellis, Ian O ^e   Green, Andrew R ^e   Ali, Simak ^c   Chin, Suet Feung ^a   Palmieri, Carlo ^c   Caldas, Carlos ^a,f,g,h   Carroll, Jason S ^a,f  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d CHARLES UNIVERSITY   (Czech Republic)

^e NOTTINGHAM CITY HOSPITAL   (United Kingdom)

^f UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^g ADDENBROOKE S HOSPITAL   (United Kingdom)

^h Cambridge Experimental Cancer Medicine Centre ECMC   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN RECEPTOR ALPHA; HEPATOCYTE NUCLEAR FACTOR 3ALPHA;

CANCER; CELL ORGANELLE; DISEASE PREVALENCE; DRUG RESISTANCE; ESTROGENIC COMPOUND; GENE EXPRESSION; TIMESCALE; TUMOR;

ARTICLE; BREAST CANCER; CANCER PATIENT; CANCER RELAPSE; CELL STRAIN MCF 7; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DISTANT METASTASIS; GENE MAPPING; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; HUMAN TISSUE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RECEPTOR BINDING;

BASE SEQUENCE; BREAST NEOPLASMS; CELL LINE, TUMOR; DRUG RESISTANCE, NEOPLASM; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HEPATOCYTE NUCLEAR FACTOR 3-ALPHA; HUMANS; NEOPLASM METASTASIS; PROGNOSIS; PROTEIN BINDING; RECEPTORS, ESTROGEN; REGULATORY SEQUENCES, NUCLEIC ACID; SURVIVAL ANALYSIS; TAMOXIFEN; TREATMENT OUTCOME;

EID: 84856008906     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature10730     Document Type: Article

References (30)

1. Carroll, J. S. et al. Genome-wide analysis of estrogen receptor binding sites. Nature Genet. 38, 1289-1297 (2006). (Pubitemid 44646291)
2. Lin, C. Y. et al. Whole-genome cartography of estrogen receptor a binding sites. PLoS Genet. 3, e87 (2007).
3. Welboren, W. J. et al. ChIP-Seq of ERa and RNA polymerase II defines genes differentially responding to ligands. EMBO J. 28, 1418-1428 (2009).
4. Carroll, J. S. et al. Chromosome-widemappingof estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122, 33-43 (2005). (Pubitemid 40977938)
5. Lupien, M. et al. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132, 958-970 (2008). (Pubitemid 351391952)
6. Hurtado, A., Holmes, K. A., Ross-Innes, C. S., Schmidt, D. & Carroll, J. S. FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nature Genet. 43, 27-33 (2011).
7. EBCTCG. Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials. Lancet 365, 1687-1717 (2005).
8. Kun, Y. et al. Classifying the estrogen receptor status of breast cancers by expression profiles reveals a poor prognosis subpopulation exhibiting high expression of the ERBB2 receptor. Hum. Mol. Genet. 12, 3245-3258 (2003). (Pubitemid 37541070)
9. Arpino, G. et al. Estrogen receptor-positive, progesterone receptor-negative breast cancer: association with growth factor receptor expression and tamoxifen resistance. J. Natl Cancer Inst. 97, 1254-1261 (2005). (Pubitemid 41535366)
10. Zhang, Y. et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
11. Fullwood, M. J. et al. An oestrogen-receptor-a-bound human chromatin interactome. Nature 462, 58-64 (2009).
12. Loi,S. et al.Definition of clinically distinctmolecular subtypes in estrogen receptorpositive breast carcinomas through genomic grade. J. Clin. Oncol. 25, 1239-1246 (2007). (Pubitemid 46640570)
13. Knowlden, J. M. et al. Elevated levels of epidermal growth factor receptor/c-erbB2 heterodimers mediate an autocrine growth regulatory pathway in tamoxifenresistant MCF-7 cells. Endocrinology 144, 1032-1044 (2003). (Pubitemid 36262870)
14. Lupien, M. et al. Growth factor stimulation induces a distinct ERa cistrome underlying breast cancer endocrine resistance. Genes Dev. 24, 2219-2227 (2010).
15. Nagashima, T. et al. Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation. J. Biol. Chem. 282, 4045-4056 (2007). (Pubitemid 47084498)
16. Schmidt, D. et al. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48, 240-248 (2009).
17. Gomm, J. J. et al. Isolation of pure populations of epithelial and myoepithelial cells fromthe normalhumanmammary gland usingimmunomagnetic separationwith Dynabeads. Anal. Biochem. 226, 91-99 (1995).
18. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
19. Stark, R. & Brown, G. D. DiffBind: differential binding analysis of ChIP-seq peak data. Bioconductor http://bioconductor.org/packages/release/bioc/ html/DiffBind.html.
20. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
21. Pavesi, G. et al. MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. Nucleic Acids Res. 34, W566-W570 (2006). (Pubitemid 44529833)
22. Wang, Y. et al. Gene-expression profiles to predict distant metastasis of lymphnode-negative primary breast cancer. Lancet 365, 671-679 (2005). (Pubitemid 40260888)
23. van de Vijver, M. J. et al. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347, 1999-2009 (2002). (Pubitemid 35461656)
24. Sotiriou, C. et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J. Natl. Cancer Inst. 98, 262-272 (2006). (Pubitemid 43264710)
25. Chin, K. et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10, 529-541 (2006). (Pubitemid 44854748)
26. Schmidt, M. et al. The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Res. 68, 5405-5413 (2008).
27. Buffa, F. M. et al. microRNA associated progression pathways and potential therapeutic targets identified by integrated mRNA and microRNA expression profiling in breast cancer. Cancer Res. 71, 5635 (2011).
28. Naderi, A. et al. A gene-expression signature to predict survival in breast cancer across independent data sets. Oncogene 26, 1507-1516 (2007). (Pubitemid 46340809)
29. Hoadley, K. A. et al. EGFR associated expression profiles vary with breast tumor subtype. BMC Genomics 8, 258 (2007).
30. Bair, E. & Tibshirani, R. Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol. 2, e108 (2004).