ATRT-25. INTEGRATED QUANTITATIVE SWATH-MS PROTEOMICS ANALYSIS OF ATRTs UNCOVERS NEW THERAPEUTIC OPPORTUNITIES

The consequences of SMARCB1 loss in Atypical Teratoid Rhabdoid Tumors (ATRTs) have been extensively characterized at the epigenetic/transcriptomic level. In this study we detail the functional effect of SMARCB1 mutation on the MRT proteome, its relationship with RNA deregulation or lack thereof. We performed unlabeled discovery proteomics using MS-SWATH on MRT cells in which SMARCB1 was forcibly re-expressed (5 cell lines, +/-SMARCB1); analyzing changes in protein abundance within 3 fractions (total, membrane, nuclear). We generated a custom spectral library, covering >8,000 proteins, for analysis of the ATRT proteome using a pH fractionated pool of each cellular subfraction. This SMARCB1-dependent ATRT spectral library constitutes a powerful tool for profiling proteins of potentially therapeutic relevance in both model systems and primary ATRT samples. We show that whilst gene expression and protein abundance are significantly related there are many instances whereby expression changes do not reliably predict protein abundances. Several hundred proteins show significantly increased abundance (p<0.01) with no concomitant change by RNA-seq. SMARCB1 mutation is able to invoke critical changes in post-transcriptional/translational regulation as well as sub-cellular localization. By integration with whole-genome CRISPR/cas9 screening we describe functionally essential SMARCB1 dependent pathway/membrane biomarkers, evident at the protein but not the RNA level. We describe several which are druggable and suggest certain therapeutic modalities e.g. specific combinations of RTKs, RNA-binding proteins/splicing factors (SpliceosomeA, U4:U5:U6 tri-snRNP complexes). Our analysis links, for the first time in ATRT, genome-wide transcriptomic and proteome aberrations and reveals broad mechanisms underlying the effect of SMARCB1 mutation.