DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer.

Andrew Stone,Matt Trau,Elizabeth A Musgrove,Elena Zotenko,Susan J Clark,Clare Stirzaker,Ruth Pidsley,Julia M W Gee,Darren Korbie,Ewan K A Millar,Warwick J Locke,Robert I Nicholson,Peter Graham

doi:10.1038/ncomms8758

Abstract

Expression of oestrogen receptor (ESR1) determines whether a breast cancer patient receives endocrine therapy, but does not guarantee patient response. The molecular factors that define endocrine response in ESR1-positive breast cancer patients remain poorly understood. Here we characterize the DNA methylome of endocrine sensitivity and demonstrate the potential impact of differential DNA methylation on endocrine response in breast cancer. We show that DNA hypermethylation occurs predominantly at oestrogen-responsive enhancers and is associated with reduced ESR1 binding and decreased gene expression of key regulators of ESR1 activity, thus providing a novel mechanism by which endocrine response is abated in ESR1-positive breast cancers. Conversely, we delineate that ESR1-responsive enhancer hypomethylation is critical in transition from normal mammary epithelial cells to endocrine-responsive ESR1-positive cancer. Cumulatively, these novel insights highlight the potential of ESR1-responsive enhancer methylation to both predict ESR1-positive disease and stratify ESR1-positive breast cancer patients as responders to endocrine therapy.

Highlights

Expression of oestrogen receptor (ESR1) determines whether a breast cancer patient receives endocrine therapy, but does not guarantee patient response
Density plots showing the correlation between the DNA methylation profile of parent MCF7 cells and individual endocrine-resistant cell lines indicate that the MCF7X and TAMR cells, which are both ESR1 positive[10,12], predominantly gained DNA methylation as indicated by the increased density of points above the trend line
We show for the first time that the methylation status of enhancers is associated with the inhibition of ESR1 binding in vitro and with the reduced expression of critical regulators and effectors of ESR1 activity in human disease

Summary

Introduction

Expression of oestrogen receptor (ESR1) determines whether a breast cancer patient receives endocrine therapy, but does not guarantee patient response. We show that DNA hypermethylation occurs predominantly at oestrogen-responsive enhancers and is associated with reduced ESR1 binding and decreased gene expression of key regulators of ESR1 activity, providing a novel mechanism by which endocrine response is abated in ESR1-positive breast cancers. Inappropriate activation of the ESR1 signalling network in mammary epithelial cells initiates neoplastic transformation and drives ESR1-positive breast cancer[1] Patients with this disease commonly receive adjuvant endocrine therapy, which serves to inhibit ESR1 signalling[1,5]. We show that differential DNA hypermethylation occurs predominantly at oestrogen-responsive enhancer, not promoter regions, and is associated with reduced ESR1 binding and decreased gene expression of key regulators of ESR1 activity. We demonstrate that the methylation status of these regulatory regions is associated with endocrine resistance in human disease, providing a novel mechanism by which endocrine response is abated in ESR1-positive breast cancers

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Conclusion