Dissecting the Mechanism of Polycomb Eviction by the BAF Complex

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PROJECT SUMMARY Thousands of cancer samples sequenced over the past decade have revealed that the chromatin remodeler complex, mSWI/SNF (BAF), is mutated in 20% of all cancers. How these mutations in BAF contribute to tumorigenesis is poorly understood, in part because the roles and functions of individual BAF subunits are not well characterized. Studies are further complicated by the combinatorial diversity of the BAF complex both within and across cell types. Together, these factors have made it difficult to define the mechanistic contribution of BAF mutations to the cancer, despite the abundance of cancer genome data. My research in the Crabtree lab will utilize a rapid, reversible assay that combines chemical-induced proximity and chromatin immunoprecipitation (ChIP) to inducibly recruit BAF to a specific genomic locus in living cells and measure immediate downstream effects. Developing this assay has been a major step forward in studying the BAF complex in vivo, as observations from previous studies in vitro have not always held up in living cells. Using this assay, our lab discovered that one mechanism by which BAF remodels chromatin is by evicting Polycomb repressive complexes (PRCs) from chromatin. Indeed, mutated BAF complexes that are catalytically inactive or found in malignant rhabdoid tumors (MRTs) are unable to evict PRCs from chromatin. Importantly, MRT patients have responded positively to PRC inhibitors in clinical trials. Thus, at least in the case of MRTs, disrupting BAF's PRC eviction function contributes to a cancer state that is treatable by PRC inhibitors. MRT is a rare cancer in which 100% of disease cases contain a null mutation in a single BAF subunit. For the vast majority of the 20% of all cancers involving BAF mutations, mutations are rather nonspecific to a particular cancer type. In this research plan I will utilize our lab's in vivo assay for studying chromatin remodelers, biochemical and genomics methods, and cancer mutation data to (1) define all BAF subunits required for PRC opposition, especially via PRC eviction; and (2) define the range of BAF subunit mutations found in cancers which produce a mutant BAF complex that cannot evict PRC from chromatin. This is an important question to answer because patients carrying such mutations that impair BAF-mediated PRC eviction would potentially respond positively to PRC inhibitors. Thus, results from this study will immediately identify potential novel cancer subsets treatable with PRC inhibitors. More broadly, understanding the critical opposition between BAF and Polycomb will identify new targets for therapeutic development.