Investigating essential chromatin regulators in cancers with SWI/SNF mutations

PROJECT SUMMARY Genes that encode subunits of SWI/SNF chromatin remodeling complexes are mutated in nearly 25% of cancers. Additionally, germline mutations in SWI/SNF subunits cause several neurodevelopmental disorders. However, the mechanisms by which these mutations drive cancer and disease are poorly understood. SWI/SNF complexes mobilize nucleosomes at enhancers and promoters to modulate transcription. Biallelic inactivation of SMARCB1, a gene encoding a SWI/SNF complex subunit, causes pediatric rhabdoid tumors (RTs). These highly aggressive soft tissue tumors occur in infants and young children and have extremely poor outcomes. Since RT genomes are diploid and lack other mutations, they are ideal for studying SWI/SNF-specific mechanisms driving cancer and for identifying novel therapeutic targets. My mentor and his collaborators initiated the Pediatric Cancer Dependency Project to identify novel drivers and therapeutic targets in pediatric cancers, including RT. Performing genome-wide CRISPR screens in 10 RT cell lines compared to over 800 other cancer cell lines revealed a novel gene that SMARCB1-deficient RT specifically depend upon for survival. This proposal seeks to investigate the function of this putative chromatin regulator and to determine why it constitutes a specific dependency in RT. Overexpression of this gene is associated with poor prognosis in several cancers and thus pharmacological efforts are already underway to develop chemical inhibitors. Intriguingly, preliminary experiments suggest that this protein may control histone post-translational modifications (PTMs) that dictate remodeling by SWI/SNF complexes and gene expression. Understanding why RT cells depend on this protein for survival will reveal novel mechanisms of chromatin regulation and may identify a new therapeutic target in these lethal cancers. My central hypothesis is that this protein controls histone PTMs and is required for the chromatin recruitment of the sole family of SWI/SNF complexes that lack SMARCB1, thus making it essential in RT. This proposal will investigate how this regulator, which lacks enzymatic activity, controls these histone PTMs and how this influences chromatin accessibility. Additionally, it will determine how this regulator influences remodeling and gene expression controlled by SWI/SNF complexes. Collectively, this proposal will uncover the function of this relatively understudied protein, provide novel insight into how chromatin function is regulated, explain why RTs selectively depend on this protein for survival, and potentially identify a novel therapeutic target in the lethal pediatric rhabdoid tumor. Additionally, this proposal is designed to address my training goal of becoming proficient in studying chromatin biology both experimentally and computationally.