ANewRole forERa: SilencingviaDNAMethylation of Basal, Stem Cell, and EMT Genes

Resistance to hormonal therapies is a major clinical problem in the treatment of estrogen receptor a–positive (ERaþ) breast cancers. Epigenetic marks, namely DNA methylation of cytosine at specific CpG sites (5mCpG), are frequently associated with ERaþ status in human breast cancers. Therefore, ERa may regulate gene expression in part via DNA methylation. This hypothesis was evaluated using a panel of breast cancer cell line models of antiestrogen resistance. Microarray gene expression profiling was used to identify genes normally silenced in ERaþ cells but derepressed upon exposure to the demethylating agent decitabine, derepressed upon long-term loss of ERa expression, and resuppressed by gain of ERa activity/expression. ERadependent DNA methylation targets (n 1⁄4 39) were enriched for ERa-binding sites, basal-up/luminal-down markers, cancer stem cell, epithelial–mesenchymal transition, and inflammatory and tumor suppressor genes. Kaplan–Meier survival curve and Cox proportional hazards regression analyses indicated that these targets predicted poor distant metastasis–free survival among a large cohort of breast cancer patients. The basal breast cancer subtype markers LCN2 and IFI27 showed the greatest inverse relationship with ERa expression/activity and contain ERa-binding sites. Thus, genes that are methylated in an ERa-dependent manner may serve as predictive biomarkers in breast cancer. Implications: ERa directs DNA methylation–mediated silencing of specific genes that have biomarker potential in breast cancer subtypes. Mol Cancer Res; 15(2); 152–64. 2016 AACR.