Abstract B011: Sex-specific chromatin remodeling drives tumorigenesis in glioblastoma

Abstract SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodelling complexes are potent regulators of cellular differentiation that are encoded by some of the most frequently altered genes in cancer. Within this family, the ATP-dependent (BRG-1/BRM associated factor (BAF) chromatin remodelling complex is altered in roughly 20% of human cancers including gliomas. However, its role in gliomagenesis and progression remains largely unknown. The complex exists in three forms: canonical BAF (BAF), polybromo-associated BAF (PBAF) and a non-canonical BAF cmplex (ncBAF), with specific subunits specifying the distinct complexes. We hypothesize a BAF switch as a driver of glioma proliferation and invasiveness. Analysis of 18 human gliomas specimens revealed that BAF complexes were differentially expressed based on World Health Organization (WHO) grade. Specifically, the expression levels of PBAF components (BRD7 and SMARCB1) decreased significantly as WHO grade increased. Conversely, the canonical BAF complex component SMARCE1, and the ncBAF complex component BRD9 were upregulated in high grade vs low grade gliomas. We used CRISPRi to investigate the role of BAF complex in glioblastoma (GBM) tumorigenesis using control and knockdown murine male and female GBM astrocytes. Growth assays demonstrated distinct sex-dependent effects of the three different BAF complex knockouts on GBM astrocyte proliferation. Depletion of SMARCE1 and SMARCB1 resulted in a significant increase in astrocyte growth in male cells, suggesting a potential inhibitory role of canonical BAF in male GBM astrocyte proliferation. Surprisingly, SMARCE1 knockdown led to markedly decreased cell growth in female cells. Knockdown of BRD9 had no effect on proliferation in either male or female GBM cells, suggesting that BRD-9-containing ncBAF may not play a role in the regulation of gliomagenesis. However, knockdown of BRD7 (PBAF) resulted in marked increase in astrocyte growth in both male and female cells. To investigate the clonogenic capacity of the BAF component depleted cells, we performed extreme limiting dilution analysis (ELDA). There was a significant increase in sphere-forming capacity in BRD7 KD cells in both males and females. There was a significant increase in clonogenic frequency in SMARCE1 and SMARCB1 KD in males only, with a significant decrease in sphere formation in SMARCE1 KD in females. Knockdown of BRD9 showed no effect on sphere forming capacity in mouse GBM cells. This data was consistent with tumor cell growth assays and demonstrated a role of BAF in regulation of clonogenic capacity GBM astrocytes. To define the epitranscriptomic effect of BAF complex depletion in GBM cells, we are conducting ChIP- and RNA-seq for the control and BAF depleted GBM cells and characterizing the effect of subunit depletion on BAF complex assembly and composition using affinity purification and mass spectrometry. Understanding the mechanisms underlying the sex-dependent effects of the BAF chromatin remodelling complex in gliomas could be valuable for the development of new precision therapeutics. Citation Format: Adham Halaoui, Najla Kfoury-Beaumont, Thomas Beaumont. Sex-specific chromatin remodeling drives tumorigenesis in glioblastoma abstract. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84 (5 Suppl₁): Abstract nr B011.