Identification of epigenetic factors that will overcome therapy resistance in triple-negative breast cancer

Triple Negative Breast Cancer (TNBC) is the most aggressive and recurrent type of breast cancer with a poor prognosis. Due to the lack of expression of hormone receptors (HR) and Her2, TNBC cannot be treated with targeted therapies, leaving chemotherapy as the mainstay treatment. However, acquired resistance to chemotherapy is a major challenge that, in part, causes relapse, which is thought to be driven by coordinated actions of genetic and epigenetic events. In this study, we aimed to elucidate the roles of the full spectrum of epigenetic modifiers in both naïve and chemotherapy resistant TNBC cell lines. For this, we generated an epigenome-wide CRISPR knockout library (EPIKOL) targeting all writers, readers and erasers, as well as the chromatin remodelers and structural subunits of epigenetic complexes. First, we discovered novel epigenetic modifiers that regulate TNBC cell fitness and confirmed the effects of NSL complex members (KANSL2, KANSL3, and KAT8) and SS18L2 on cell growth. Notably, in vivo screen with EPIKOL on MDA-MB-231 cell line also revealed SS18L2 as a fitness gene in two different time points of tumor growth. To generate in vitro models of chemoresistant TNBC, we exposed three different TNBC cell lines to escalating doses of an anthracycline (doxorubicin) or a taxane (paclitaxel, taxol). SUM159PT taxol resistant cells had elevated levels of ABCB1 and showed the characteristics of multidrug resistance. EPIKOL screen and a complementary epigenetic probe library screen in one of the taxol resistant SUM159PT cells in the presence of taxol identified BRPF1, a bromodomain-containing reader, as a taxol sensitizer. Upon BRPF1 inhibition or loss, transcriptome analysis revealed a significant downregulation of ribosome biogenesis pathways and a decrease in ABCB1 expression. Additionally, we demonstrated the binding of BRPF1 to the ABCB1 promoter, possibly regulating its expression in drug resistant state. Collectively, these findings provide a basis for developing combination therapies targeting specific chromatin-based epigenetic factors to counteract TNBC cell viability and chemoresistant phenotype.