Resistance to estrogen receptor (ER)-targeted therapies (endocrine therapy) is a major clinical problem in ER+ breast cancer. We have previously identified DNA hypermethylation as a contributing mechanism to endocrine resistance[1], resulting in reduced ER binding at enhancer regions and decreased gene expression of key regulators of ER activity. This observation led us to hypothesize that epigenetic therapy using the DNA demethylating agent, decitabine, could enhance the efficacy of endocrine therapy in ER+ breast cancer.
We evaluated the efficacy of decitabine alone or in combination with an endocrine therapy on two patient-derived xenograft (PDX) models (estrogen-stimulated HCI-005 and estrogen-independent Gar15-13) derived from patients who had progressed on endocrine therapy. We show that decitabine alone effectively hampered proliferation of both PDX models and augmented the anti-tumour effect of endocrine therapy. Treated tumours were assessed for genome-wide methylation alterations using the Illumina MethylationEPIC microarray. Our results demonstrate that decitabine induced significant DNA hypomethylation, enriched primarily at promoter and enhancer elements in both models. The magnitude of demethylation was higher in the Gar15-13 model, perhaps due to elevated global DNA hypermethylation relative to HCI-005. The impact of global demethylation on ER chromatin binding was assessed using ER ChIP-sequencing. Decitabine-induced loss of ER binding occurred in both models, primarily enriched at promoter regions in Gar15-13, and at enhancer regions in HCI-005. These results indicate that remodeling of ER binding with decitabine treatment may be tumour-specific. Intriguingly, demethylation of Gar15-13 tumours was also associated with an increase in classical ER activity, as demonstrated by a gain in ER binding at enhancer regions of some ER target genes and an upregulation of an estrogen response gene signature.
Overall, our preclinical data demonstrate that epigenetic therapy can enhance the efficacy of endocrine therapy but the impact on ER binding will potentially be dependent on the epigenetic status of the individual tumours. These data warrant further development of demethylating agents as potential therapies in ER+ breast cancer.