Abstract 2120: Interrogation of regulatory and expression changes in Malignant Rhabdoid Tumours to identify new therapeutic approaches

Abstract

Abstract Malignant Rhabdoid Tumors (MRTs) are a textbook model of epigenetic dysregulation within cancer. The biallelic inactivation of a single gene SMARCB1 in >95% of MRTs is sufficient to provoke a lethal pediatric cancer. SMARCB1 encodes a core subunit of the SWI/SNF complex and inactivation results in genome-wide deregulation of gene expression/pathways. SMARCB1 loss was previously shown to impair SWI/SNF enhancer targeting at TSS-distal enhancers and a model proposed whereby mutant residual SWI/SNF complexes preferentially binds to super-enhancers over typical-enhancers; thereby inappropriately maintaining progenitor lineage processes and blocking differentiation. This model deemphasizes the action of mutant SWI/SNF complexes upon cell cycle/oncogenic processes. We performed a consensus analysis on a cohort of novel and published ChIP-seq profiles (n=6 +/- SMARCB1 models) to define consensus SMARCB1-dependent epigenetic changes. We further used parallel RNA-seq, methylation and whole-genome CRISPR screen data to emphasize the significance of specific regulatory processes from the perspective of likely biological effects and functional essentiality. We bioinformatically identified consensus super and typical-enhancers from H3K27ac peaks, multiple datasets enabled high confidence regions to be called. SMARCB1 loss did not significantly impact SWI/SNF occupancy of super-enhancers, permutation test revealed significant (p<0.001) overlap of binding across both conditions; in agreement with residual SWI/SNF complex binding theories. However, we noted the same at typical-enhancers implying all enhancers are similarly affected. We hypothesized that the resulting SMARCB1-dependent transcriptional impact, not location of SWI/SNF binding would be paramount, InTAD and RNAseq data were used to assign target genes to enhancers. Of the SMARCB1-dependent genes linked to typical-enhancers 13% showed significantly altered expression compared to 9% for super-enhancers. Ontology analysis identified classic oncogenic pathways such as cell cycle and metabolic genes as enriched among SMARCB1-dependent enhancer targets. Gene Set Enrichment Analysis (GSEA) confirmed significant enrichment of mucopolysaccharide metabolic genes (p<0.002, NES 1.42). Correlating dysregulated gene targets to epigenetically altered enhancers/promoters we ranked loci which drive MRT tumorigenesis. We identified a 40kb upstream region of SMARCB1-dependent methylation and ChIPseq binding strongly correlated to expression of CDK6. We further employed CRISPR activation/repression tools to mimic SMARCB1 re-expression and model their effects. Successful modulation of candidate loci will help define potential future novel targeted therapeutics - e.g use of HDACi - to recapitulate the effects of SMARCB1 re-expression. Citation Format: Emma L. Lishman-Walker, Martina A. Finetti, James P. Hacking, Matthew Selby, Yura Grabovska, Stephen Crosier, Simon Bailey, Steven C. Clifford, Daniel Williamson. Interrogation of regulatory and expression changes in Malignant Rhabdoid Tumours to identify new therapeutic approaches [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2120.