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Title:
Differential oestrogen receptor binding is associated with clinical outcome in breast cancer | Nature
Description:
Genome-wide mapping of oestrogen receptor-ฮฑ binding sites in primary breast cancer tissues shows that oestrogen receptor binding is dynamically regulated and that the expression of genes near differentially bound regulatory regions is associated with clinical outcome. Most breast tumours express the oestrogen receptor-ฮฑ (ER), and this transcription factor is seen as an important drug target for the treatment of breast cancer. Jason Carroll and colleagues have mapped ER binding sites in solid primary cancers for the first time, and find distinct ER-binding profiles that are mediated in part by the FoxA1 DNA-binding protein and are associated with better or worse clinical outcome. As well as providing a potentially useful method of prognosis, this work may help to answer one of the major questions in breast cancer biology: how some ER+ tumours become drug resistant. Oestrogen receptor-ฮฑ (ER) is the defining and driving transcription factor in the majority of breast cancers and its target genes dictate cell growth and endocrine response, yet genomic understanding of ER function has been restricted to model systems1,2,3. Here we map genome-wide ER-binding events, by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), in primary breast cancers from patients with different clinical outcomes and in distant ER-positive metastases. We find that drug-resistant cancers still recruit ER to the chromatin, but that ER binding is a dynamic process, with the acquisition of unique ER-binding regions in tumours from patients that are likely to relapse. The acquired ER regulatory regions associated with poor clinical outcome observed in primary tumours reveal gene signatures that predict clinical outcome in ER-positive disease exclusively. We find that the differential ER-binding programme observed in tumours from patients with poor outcome is not due to the selection of a rare subpopulation of cells, but is due to the FOXA1-mediated reprogramming of ER binding on a rapid timescale. The parallel redistribution of ER and FOXA1 binding events in drug-resistant cellular contexts is supported by histological co-expression of ER and FOXA1 in metastatic samples. By establishing transcription-factor mapping in primary tumour material, we show that there is plasticity in ER-binding capacity, with distinct combinations of cis-regulatory elements linked with the different clinical outcomes.
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nature portfolio permissions reprints privacy policy org/packages/release/bioc/html/diffbind enhancer-driven lineage-specific transcription author information authors accession number gse32222 advertising mod tools cambridge research institute nature genet social media cancer research uk translational research fellowship gene expression omnibus node-negative breast cancer nature 462 nature 481 nature oestrogen receptor-ฮฑ gene expression data prevents aging-related euchromatinization discover proteinโdna interactions chip-seq peak data cis-regulatory elements linked establishing transcription-factor mapping unique er-binding regions er-positive disease exclusively distant er-positive metastases foxa1 dna-binding protein drug-resistant cellular contexts tamoxifen-resistant mcf-7 cells estrogen receptor-positive springerlink instant access predict distant metastasis independent data sets expression profiles reveals estrogen receptor status primary breast cancers permissions breast cancer biology breast tumor subtype gene-expression profiles foxa1-mediated reprogramming estrogen receptor function gene-expression signature gene expression profiling solid primary cancers prognostic gene signatures primary tumour material
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headline:Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
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headline:Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
description:Genome-wide mapping of oestrogen receptor-รยฑ binding sites in primary breast cancer tissues shows that oestrogen receptor binding is dynamically regulated and that the expression of genes near differentially bound regulatory regions is associated with clinical outcome. Most breast tumours express the oestrogen receptor-รยฑ (ER), and this transcription factor is seen as an important drug target for the treatment of breast cancer. Jason Carroll and colleagues have mapped ER binding sites in solid primary cancers for the first time, and find distinct ER-binding profiles that are mediated in part by the FoxA1 DNA-binding protein and are associated with better or worse clinical outcome. As well as providing a potentially useful method of prognosis, this work may help to answer one of the major questions in breast cancer biology: how some ER+ tumours become drug resistant. Oestrogen receptor-รยฑ (ER) is the defining and driving transcription factor in the majority of breast cancers and its target genes dictate cell growth and endocrine response, yet genomic understanding of ER function has been restricted to model systems1,2,3. Here we map genome-wide ER-binding events, by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), in primary breast cancers from patients with different clinical outcomes and in distant ER-positive metastases. We find that drug-resistant cancers still recruit ER to the chromatin, but that ER binding is a dynamic process, with the acquisition of unique ER-binding regions in tumours from patients that are likely to relapse. The acquired ER regulatory regions associated with poor clinical outcome observed in primary tumours reveal gene signatures that predict clinical outcome in ER-positive disease exclusively. We find that the differential ER-binding programme observed in tumours from patients with poor outcome is not due to the selection of a rare subpopulation of cells, but is due to the FOXA1-mediated reprogramming of ER binding on a rapid timescale. The parallel redistribution of ER and FOXA1 binding events in drug-resistant cellular contexts is supported by histological co-expression of ER and FOXA1 in metastatic samples. By establishing transcription-factor mapping in primary tumour material, we show that there is plasticity in ER-binding capacity, with distinct combinations of cis-regulatory elements linked with the different clinical outcomes.
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