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SMARCB1 Missense Mutants Destabilize SWI/SNF Complex Stability and Remodeling Activity

Study Design and Aims: This study utilizes a comprehensive deep mutational scanning (DMS) approach to systematically assess the functional consequences of 8,418 amino acid substitutions in the SMARCB1 gene, a core subunit of the SWI/SNF chromatin remodeling complex. The primary aim is to evaluate how missense mutations affect SMARCB1's tumor suppressor function and its role in the assembly and activity of distinct SWI/SNF subcomplexes (cBAF, PBAF, and GBAF). By addressing functional impacts across the entire coding sequence of SMARCB1, the study seeks to elucidate the molecular mechanisms underlying chromatin remodeling deficiencies caused by SMARCB1 missense mutations and their implications for cancer biology and diagnostics.

Population Information: The study focuses on functional variants of SMARCB1, specifically addressing the mutational landscape relevant to cancers such as malignant rhabdoid tumor (MRTK), atypical teratoid rhabdoid tumor (ATRT), and renal medullary carcinoma (RMC). Variants are modeled using in vitro systems to characterize their functional consequences.

Molecular Technologies: This study first uses DMS for the systematic identification of functionally disruptive mutations in SMARCB1. Top hits identified through DMS were validated using complementary molecular technologies. These included RNA sequencing (RNA-Seq) to evaluate transcriptional changes associated with specific mutations, ATAC-sequencing (ATAC-seq) to assess chromatin accessibility and remodeling activity, and mass spectrometry to analyze SWI/SNF complex composition in the presence of specific mutations.

Principal Findings: The study identifies a subset of missense mutations within the RPT2 domain of SMARCB1 that impair SWI/SNF complex stability and chromatin remodeling, despite retaining detectable protein expression. Notably, these findings challenge current diagnostic methods that rely solely on immunohistochemistry to assess protein presence, as some functionally disruptive mutations retain detectable expression.

Data Available through dbGaP: The dataset includes RNA-Seq and ATAC-seq data detailing transcriptional and chromatin accessibility changes associated with validated mutations, mass spectrometry data documenting SWI/SNF complex composition and stability in the context of specific mutations, and functional assay results for all SMARCB1 variants assessed via DMS. This dataset provides a valuable resource for understanding SMARCB1's role in chromatin biology and for improving the classification of variants of uncertain significance (VUS) in clinical diagnostics.