Functional Dissection of mSWI/SNF Protein Complexes Using Fitness Screening and Epigenome Profiling

Abstract

The functional characterization of mammalian protein complexes is critical to understanding the molecular basis of many human diseases. One particular protein complex of interest is the evolutionarily conserved SWI/SNF (BAF) chromatin remodeling complex. Although this protein complex is mutated in ~20% of human cancers, we do not yet fully understand how perturbations to subunits of this protein complex affect cellular fitness and promote tumorigenesis. In this work, we first develop a framework for inferring gene-gene relationships between subunits of protein complexes by using correlated fitness profiles from genome-wide screens on hundreds of cancer cell lines. Using this approach, we reconstructed a wide range of genetic networks for gold-standard as well as computationally predicted protein complexes. By applying this strategy to the mSWI/SNF complex, we resolved three functionally distinct genetic modules with different biochemical profiles as well as distinct mutational patterns across human cancer. Next, we coupled biochemical approaches with genome-wide assays of mSWI/SNF complex localization and chromatin accessibility to characterize a rare mSWI/SNF-deficient cancer: small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). This cancer is defined by the dual loss of the paralogous ATPase subunits of the complex, SMARCA4 and SMARCA2. Through studies using cell line models of this disease, we observed that the loss of these ATPase subunits results in the collateral degradation of a subset of mSWI/SNF subunits, suggesting that they form a structural ATPase module within the subunit interaction network. Through rescue of wild-type and mutant alleles of the ATPase subunit, we found that the ATPase module is critical for maintaining the landscape of enhancer elements in SCCOHT cells, linking the loss of this structural module to an epigenetic state permissive for unconstrained cellular division.