RNA-seq of DEX induced and ethanol control Basal-like breast cancer cell lines
Breast cancers can be divided into subtypes with different prognoses and treatment responses based on global gene expression differences.   This study utilized integrated analysis of DNA methylation, chromatin accessibility, transcription factor binding, and gene expression in large collections of breast cancer cell lines and patient tumors to identify transcription factors responsible for the basal-like gene expression program. The results of this study indicate that glucocorticoid receptor (GR) and signal transducer and activator of transcription 3 (STAT3) bind to the same genomic regulatory regions that are specifically open and unmethylated in basal-like breast cancer. These transcription factors cooperate to regulate expression of hundreds of genes in the basal-like gene expression signature and these downstream genes are associated with poor prognosis in patients. Overall design: To determine which genes are regulated by GR and STAT3, RNA-seq was performed on two basal-like cell lines (HCC70 and MDA-MB-231) treated with 100nM dexamethasone or an equal volume of 100% ethanol vehicle control for 4 hours.