Binding Profiles and Transcriptomes and Therapeutic Resistance, Oh My! Regulation of ERα Action in Breast Cancer

Abstract

Cancer resequencing studies have revealed epigenetic enzymes as common targets for recurrent mutations. The monomethyltransferase MLL3 is among the most recurrently mutated enzymes in ER+ breast cancer. The H3K4me1 marks created by MLL3 can define enhancers. Interestingly, in ER+ breast cancer, ERα genome binding sites are primarily distal enhancers. Thus we hypothesized that mutation of MLL3 will alter the genomic binding and transcriptional regulatory activity of ERα. We investigated the genomic consequences of knocking down MLL3 in an MLL3/PIK3CA WT ER+ breast cancer cell line. Loss of MLL3 led to large loss of H3K4me1 across the genome, and a shift in ERα binding sites, which was accompanied by a re-organization of the breast cancer transcriptome. Enrichment analyses of ERα binding sites in MLL3 KD identified endocrine therapy resistance terms, and indeed, we show that MLL3 KD cells are resistant to tamoxifen and fulvestrant. Many differentially expressed genes are controlled by new locations of H3K4me1 deposition and ERα binding, suggesting that loss of functional MLL3 leads to new transcriptional regulation of essential genes. Motif analysis of RNA-seq and ChIP-seq data highlighted SP1 as a critical transcription factor in the MLL3 KD cells. Loss of ERα binding is accompanied by a massive increase in SP1 binding at differentially expressed genes. Our data show that loss of functional MLL3 leads to endocrine therapy resistance. This highlights the importance of genotyping patient tumor samples for MLL3 mutation upon initial resection, prior to deciding upon treatment plans.