Integrated Single-Cell Analysis Reveals Treatment-Induced Epigenetic Homogenization

Triple negative breast cancers (TNBC) constitute one-sixth of invasive female breast cancer cases and are the most likely to develop resistance to treatment via genetic and/or epigenetic adaptation into drug tolerant persister (DTP) states. We applied single-cell ATAC-seq and RNA-seq to characterize the dynamic regulatory and transcriptional landscape in five basal-like TNBC cell lines in response to the MEK inhibitor Trametinib. We observed surprisingly few shared changes between lines, indicating substantial heterogeneity in the emergence of DTP states. However, we identified a shift toward a common state based on the novel observation of the preferential loss of cell line-specific regulatory elements and gene expression. Integration of the two modalities enabled a granular dissection of dynamic regulatory mechanisms, which revealed highly context-dependent roles of regulatory elements. This work highlights the heterogeneity of response, yet suggests homogenization occurs in the form of the preferential loss of epigenetic configurations unique to each BCCL.