Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer
This paper, which maps ERα binding via ChIP-seq in tumour tissue from twenty ER+ breast cancer patients, relies on a concurrently developed Bioconductor package, DiffBind, which provides a framework for quantitative differential analysis of protein/DNA binding events. Here we use DiffBind to identify ERα sites significantly differentially bound between those found in tumours from patients with good prognosis vs. those with poor prognosis and metastases. Gene signatures that predict clinical outcome in ER+ disease, validated in publically available breast cancer gene expression datasets, are derived from these sites. These signatures are enriched for genes with relevant proximal cis-regulatory events. Statistical characterization of differentially bound ERα sites enables further downstream analysis, including identification of a differentially enriched motif for the transcription factor FoxA1. Further differential analysis in five ER+ breast cancer cell lines shows how ERα binding is extensively shifted in tamoxifen-resistance, with the FoxA1 motif enriched proximal to ERα binding sites differentially bound in cells resistant to treatment. Analysis of FoxA1 binding at mitogen-induced ERα sites demonstrates that the observed differential ER binding program is not due to the selection of a rare subpopulation of cells, but rather to the FoxA1-mediated reprogramming of ER binding on a rapid time scale. Focusing our analysis on differential binding in primary tumour material allows us to show the plasticity of ERα binding capacity, with distinct combinations of cis-regulatory elements linked with the different clinical outcomes. These techniques are applicable to other cancers (and indeed other diseases) where master transcription factor regulators are known.