Elucidating SNF5 Regulated Gene Expression in Malignant Rhabdoid Tumor Development

Malignant Rhabdoid Tumors (MRTs), a pediatric renal cancer, lack SNF5, a subunit of the SWI/SNF chromatin remodeling complex which regulates nucleosome positioning and gene expression. MRTs offer a unique model for an epigenetically driven cancer because, unlike other cancers, they often have no other detectable mutations. Recent data on SWI/SNF mutations in cancer reveal mutations of 20 SWI/SNF subunit genes across 18 different cancers. Combined, the mutation rate of SWI/SNF complex members occurs at a frequency of 19% comparable to the 26% mutation frequency of TP53. Therefore understanding the SWI/SNF complex is highly relevant in our understanding of the mechanisms of not only tumorigenesis but also to the contribution of non-genotoxic carcinogens to this process. In these dissertation studies, we focused on the role of SNF5 inactivation in the development of MRTs. We hypothesize that SNF5 loss compromises the SWI/SNF complex resulting in aberrant targeting of the SWI/SNF complex, altered gene expression and tumorigenesis. To test this notion, we re-expressed SNF5 in MRT cell lines and examined the subsequent effects in SWI/SNF complex composition and gene expression. Our results indicated that SNF5 mediates the composition of the SWI/SNF complex, and its loss potentially disrupts SWI/SNF complex variants required for differentiation. SWI/SNF subunits are post-transcriptionally regulated in an interdependent fashion for stability. The changes in SWI/SNF complex composition also alter targeting of the complex with subsequent changes in gene expression. We validated our results using two known targets of SNF5, p21 and p16, and also through the identification of 2 two novel SNF5 targets, NOXA and CCNG2. These genes are upregulated after the reconstitution of the SWI/SNF complexes with SNF5 and may play critical roles in MRT development. These data demonstrate the intricacies of chromatin regulation and our incomplete understanding of this process in tumorigenesis. Together, this body of work serves as another milestone on our path to gain a better understanding of the relationships between chromatin structure and regulation, cancer biology, and toxicology.Doctor of Philosoph