Clustering of super-enhancers for characterizing subtype identity in breast cancer

Breast cancer is a heterogeneous disease, affecting over 3.5 million women worldwide, yet the functional role of cis-regulatory elements including super-enhancers in different breast cancer subtypes remains poorly characterized. Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a poor prognosis. Here we apply integrated epigenomic and transcriptomic profiling to uncover super-enhancer heterogeneity between breast cancer subtypes, and provide clinically relevant biological insights towards TNBC. Using CRISPR/Cas9-mediated gene editing, we identify genes that are specifically regulated by TNBC-specific super-enhancers, including FOXC1, thereby unveiling a mechanism for specific overexpression of the key oncogenes in TNBC. We also identify ANLN, a gene involved in cytokinesis, as a novel TNBC-specific gene regulated by super-enhancer. Unlike FOXC1, the functional role of ANLN in breast cancer has not been studied extensively. An association between ANLN expression and cancer susceptibility has been mainly inferred by gene expression studies. Recently, ANLN was shown to regulate breast cancer cell migration and stemness. Using CRISPR/Cas9 system, we demonstrated that ANLN levels and clonogenicity were reduced significantly upon deletion of ANLN super-enhancer, indicating that the super-enhancer drives ANLN expression and TNBC progeny producing capability. Work is currently in progress to elucidate the molecular mechanisms by which super-enhancer modulates ANLN expression, which in turn regulates stemness of TNBC.