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

Oestrogen receptor-a (ER) is the defining and driving transcrip- tion factor in the majority of breast cancers and its target genes dictate cell growth and endocrine response, yet genomic under- standing of ER function has been restricted to model systems1­3. 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 time- scale. The parallel redistribution of ER and FOXA1 cis-regulatory elements 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. Oestrogen receptor alpha (ER) binding was mapped genome wide in 15 primary ER-positive breast tumours and 3 ER-positive distant metastases. As a control, ER binding was also mapped in 2 ER-negative breast tumours. For cell line experiments, ER was mapped, in at least duplicate, in three ER-positive cell lines that respond to tamoxifen treatment, and 2 ER-positive cell lines that are resistant to tamoxifen treatment. Both ER and FOXA1 binding was mapped in MCF-7 cells, in duplicate, before and after treatment with a cocktail of mitogens (i.e. IGF-1, TNF-alpha, EGF and IL-6).