Mechanistic Studies of a Novel Vulnerability in Pediatric Cancer

Project Abstract Rhabdoid tumors (RT) are aggressive and lethal cancers that occur in young children. These tumors are resistant to chemotherapy and have a five-year survival rate of 23%. Over 95% of RTs carry biallelic inactivating mutations in SMARCB1 (also known as SNF5/BAF47/INI1) a subunit of SWI/SNF chromatin

remodeling complexes. SWI/SNF complexes are highly conserved 2MDa complexes, composed of 12-15 subunits that co-operate with transcription factors at regulatory elements such as enhancers and promoters, where they hydrolyze ATP to remodel chromatin and regulate gene expression. It is now clear that nearly 25%

of all cancers contain mutations in a SWI/SNF-subunit encoding gene, making SWI/SNF the most frequently mutated chromatin regulator in human malignancies. Given the absence of therapeutically targetable mutations in RTs, our lab was interested in identifying genes required for the survival of RT with the aim of exploiting these targets for therapeutic opportunities and

insights into the underlying mechanisms of rhabdoid tumorigenesis. To accomplish this, our lab co-founded the Pediatric Dependency project with other investigators at the Broad Institute of Harvard and MIT (Boston, MA) to conduct near-genome-wide vulnerability screens. One gene emerged as a significant (p= 1.5e-18), rhabdoid-

specific vulnerability in all 12 RT lines from two independent CRISPR screens, but is not a vulnerability in any other cancer type. This is an unprecedented finding in our experience. Since little has been published on this gene thus far, interrogating this gene's function in addition to revealing novel biology may help identify novel

therapeutic approaches for RTs. Our lab has shown SMARCB1 loss in RTs destabilizes SWI/SNF complex integrity and also impairs SWI/SNF complex binding at enhancers. Consequently, I sought to test whether this novel vulnerability serves a role in regulation of the residual SWI/SNF complexes in SMARCB1-deficient RTs. My preliminary data

indeed shows knockdown of this gene in SMARCB1-deficient cell lines perturbs several SWI/SNF complex subunits and leads to a decrease in H3K27ac, a mark of active enhancers and promoters. Therefore, I hypothesize that in SMARCB1-deficient RTs, loss of this novel gene disrupts SWI/SNF transcriptional

regulation and results in cell death. I will address this hypothesis, and the broader function of this vulnerability in normal cells in this application. Collectively, this proposal will establish the function of this novel gene, provide new insights into the control of chromatin function, and define the mechanism by which loss of this

gene constitutes a specific vulnerability in SMARCB1-mutant RT cells, with the potential to reveal novel therapeutic targets for RTs.