A New Role for ERα: Silencing via DNA Methylation of Basal, Stem Cell, and EMT Genes

Resistance to hormonal therapies is a major clinical problem in the treatment of estrogen receptor-alpha (ERalpha) positive breast cancers. Epigenetic marks namely DNA methylation of cytosine at specific CpG sites (5mCpG) are frequently associated with ERalpha-positive status in human breast cancers. Therefore, ERalpha may regulate gene expression in part via DNA methylation. This hypothesis was evaluated using a panel of breast cancer cell line models of anti-estrogen resistance. Microarray gene expression profiling was used to identify genes normally silenced in ERalpha-positive cells but de-repressed upon exposure to the demethylating agent decitabine, de-repressed upon long-term loss of ERalpha expression, and re-suppressed by gain of ERalpha activity/expression. ERalpha-dependent DNA methylation targets (n=39) were enriched for ERalpha-binding sites, basal-up/luminal-down markers, cancer stem cell (CSC), epithelial-mesenchymal transition (EMT), inflammatory and tumor suppressor genes (TSG). Kaplan-Meier survival curve and Cox proportional hazard regression analyses indicated 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 ERalpha expression/activity and contain ERalpha-binding sites. Thus, genes that are methylated in an ERalpha-dependent manner may serve as predictive biomarkers in breast cancer. Implications: ERalpha directs DNA methylation-mediated silencing of specific genes that have biomarker potential in breast cancer subtypes.