SMARCB1-Mediated chromatin remodeling underlies sex differences in gliomagenesis

Glioblastoma (GBM), the most prevalent primary malignant brain tumor has significant sex disparities with a higher incidence and poorer prognosis in males. SMARCB1 is a key component of SWI/SNF chromatin remodeling complexes, including canonical BAF (BAF) and polybromo-associated BAF (PBAF), and has been shown to have tumor-suppressive functions in a wide range of cancers. Using a panel of 20 human glioma samples, we have shown that SMARCB1 expression is significantly downregulated in GBM compared to IDH wild-type gliomas. However, its role in GBM development remains unclear. Using a murine model of GBM, we performed SMARCA4 immunoprecipitation coupled with mass spectrometry in syngeneic male and female tumor cells and demonstrated BAF complex assembly. We then performed knockdown (KD) of SMARCB1 using CRISPR CRISPRi in male and female tumor cells. Growth assays revealed strong sex-dependent differences, as depletion of SMARCB1 markedly increased proliferation and clonogenic potential in male cells, while having the opposite effect in female cells. RNA-seq analysis uncovered sex-specific transcriptional reprogramming following SMARCB1 knockdown. Gene set enrichment analyses revealed strong enrichment (NES = 2.08-2.19, FWER < 0.001) in proliferation- and oncogenesis-associated pathways in male tumor cells, and an inflammatory pathway (NES = 1.73-2.72, FWER = 0) in female cells. Additionally, we observed pronounced sex-dependent expression in O‑6‑methylguanine‑DNA methyltransferase (MGMT) gene expression wherein male cells displayed three‑fold higher MGMT expression compared to females. Importantly, SMARCB1 KD further amplified this sex-biased MGMT expression. Based on this observation, we treated male and female tumor cells with Temozolomide (TMZ), the standard-of-care chemotherapy for patient with GBM and performed a metabolic viability assay. Consistent with the expression profiling data, female cells exhibited a 25 % greater reduction in metabolic activity following TMZ treatment than their male counterparts, indicating heightened intrinsic sensitivity. MGMT expression levels correlate with the relative TMZ resistance of male cells, implicating a potential sex‑specific response to treatment. To further assess sex-specific SMARCB1 function at the epigenetic level, we performed ATAC-seq and ChIP-seq experiments on male and female control and SMARCB1 KD GBM cells. These experiments demonstrated increased chromatin access at the MGMT locus in male cells and facultative heterochromatin in female cells. Additionally, 3D-genome studies using HiC are underway to identify sex-specific topographical associated domains (TADs). Collectively, our data underscore an important sex-specific role for SMARCB1 in GBM tumorigenesis and identifies a potential new biomarker for TMZ responsiveness during treatment.