Peer-reviewed article

DIPG-19. BAF COMPLEX PERTURBATION AS A NOVEL THERAPEUTIC OPPORTUNITY IN H3K27M PEDIATRIC GLIOMA

· 1 Jun 2023

Abstract

Abstract Epigenetic dysregulation resulting in stalled development plays a crucial role in pediatric cancer tumorigenesis. Diffuse midline gliomas (DMG) are universally fatal pediatric brain cancers refractory to standard of care treatment modalities. These malignancies are driven by heterozygous mutations in genes encoding histone 3 (H3K27M) which create an aberrant epigenetic landscape that keeps glioma cells in an undifferentiated stem-like state. Consequently, targeting epigenetic regulators to restore the epigenome and force glioma cells to exit this stem-like cell state represents a promising new therapeutic strategy for H3K27M-DMG. To interrogate for epigenetic dependencies, we performed a CRISPR/Cas9 inactivation screen in patient-derived H3K27M-DMG neurospheres using an epigenetically focused sgRNA library and identified several core components of the mammalian BAF (SWI/SNF) chromatin remodeling complex as genetic vulnerabilities. Validation assays revealed that knockout of the BAF catalytic subunit BRG1 results in decreased glioma cell proliferation and tumor growth in orthotopic mouse models. Mechanistically, genome wide localization and DNA accessibility studies combined with regulatory network analysis demonstrated that BRG1 controls the transcription factor and enhancer landscapes that maintain H3K27M-DMG cells in a cycling, oligodendrocyte precursor cell-like state. Single cell transcriptome analysis in vitro and immunofluorescence studies in vivo confirmed that genetic perturbation of this chromatin remodeler promotes progression of differentiation along the astrocytic lineage. Similarly, pharmacological suppression of BRG1 activity, using both catalytic inhibitors as well as recently developed degraders, opposes tumor cell proliferation, stimulates cell state transition, and improves overall survival of patient-derived xenograft models. Interestingly, these effects seem to be restricted to H3K27M mutant glioma, as H3 wildtype glioma cells were less sensitive to BRG1 inhibition both in vitro and in vivo. In summary, we demonstrate that the BAF complex contributes to the maintenance of glioma cells in a proliferative stem-like state and that its therapeutic inhibition has translational potential for children bearing H3K27M-DMG.