Time-resolved DNA methylation profiling of endocrine resistance in the T47D luminal A breast cancer cell line

Endocrine therapy is the most used treatment for hormone receptor positive breast cancers. Despite the clear benefit of endocrine therapy for patients with ER+ breast cancer, resistance to treatment is a critical clinical issue affecting a large number of patients. While many studies have shown that genetics is an important factor in therapy resistance, recent publications have also reported that epigenetics might play a major role in the acquisition of resistance to endocrine therapies. This role is exploited both at the DNA methylation level, with activation of oncogenes and silencing of tumor suppressor genes, and at the histone modification level, with changes in chromatin accessibility. DNA methylation exerts its role in resistance both by targeting the ER itself, by inducing promoter methylation, and genome wide, by changing the methylation levels of estrogen response elements. To better understand resistance acquisition in an in vitro setting, researchers developed cellular models of endocrine therapy resistance. The prevalent strategy to identify mechanisms of resistance development and novel targets involved in the process has been to study differences between resistant and sensitive cells. Here, we performed time-resolved DNA methylation profiling of development of resistance to tamoxifen treatment and to estrogen deprivation in the T47D luminal A breast cancer cell line with the aim to identify novel drivers. T47D cells were either treated with 100 nM 4-hydroxytamoxifen (TAM), long-term estrogen deprived (LTED; modelling AI treatment) or not treated (wild type (WT)) in two biological replicates cultured for 7 and 5 months, respectively. DNA was extracted after 0, 1, 2, 5 and 7 (only one replicate) months. Methylation profiling was performed using the Illumina MethylationEPIC BeadChip platform at the Genomic and Proteomic Core Facility (DKFZ, Germany). For each sample two technical replicates were measured.