Resetting the Epigenetic Balance of Polycomb/COMPASS Function at Enhancers for Cancer Therapy

MLL3/KMT2C is a COMPASS family member and tumor suppressor that functions as a histone H3K4 mono-methyltransferase at enhancers. Human cancer genome sequencing studies have identified frequent MLL3 point mutations, however, the question of how these mutations alter MLL3 function and contribute to oncogenesis remains unanswered. Here, we have characterized a cancer mutational hot spot in the MLL3 Plant Homeo Domain (PHD) repeats that correlates with poor patient survival. Cancer-associated mutations in the MLL3-PHD disrupt interaction with the BAP1 deubiquitinase complex. BAP1 loss-of-function in cancer cells significantly reduces MLL3 recruitment to enhancers regions, resulting in reduced H3K4me1 and increased H3K27me3 levels at these loci. Notably, we find that increased H3K27me3 levels in BAP1 null cells are due to decreased MLL3/UTX/COMPASS occupancy. Reducing H3K27me3 through PRC2 catalytic inhibition resets the pattern of gene expression in cells with defective MLL3- BAP1-UTX activity and impairs tumor proliferation in cancer cells with MLL3 mutations. This study provides a molecular mechanism to explain the role of MLL3 PHD mutations in cancer pathogenesis. Therefore, based on these observations, we propose a potential therapeutic strategy for cancers harboring MLL3/COMPASS mutations by resetting the Polycomb/COMPASS epigenetic balanced state of gene expression. To examine changes in histone modification and gene expression after depletion of MLL3/BAP1/UTX or EZH2 inhibition in human cell lines.