ID #304 Molecular hijacking of developmental master regulators through BRD4-driven super-enhancers in pediatric and AYA gliomas

Abstract Pediatric and adolescent/young adult (AYA) gliomas remain among the deadliest childhood cancers. Key subtypes include H3.3 G34R/V diffuse hemispheric glioma (DHG), IDH-mutant gliomas, and H3 K27M diffuse midline gliomas (DMG), with ATRX loss occurring at a high frequency in DHG and IDH-mutant tumors (80-90%), but less frequently in DMG (15-30%). While these aggressive tumor types each exhibit stalled neurodevelopmental programs as a central feature of their respective pathogeneses, the molecular mechanisms by which ATRX deficiency and associated mutations in either H3.3 or IDH1/2 drive this developmental dysregulation remain unknown. We hypothesize that the epigenomic consequences of these combined molecular alterations effectively hijack master transcriptional regulators to induce and maintain aberrant neuro-progenitor states. Using isogenic neural stem cell (NSC) models harboring the defining alterations of ATRX-deficient glioma variants, along with integrated epigenomic and transcriptomic profiling, we discovered that ATRX deficiency activates transcription of SOX2, SOX4, and POU3F2 through the formation of BRD4-occupied super-enhancers. Furthermore, loss of repressive epigenetic marks in these models allows aberrant enhancer accessibility at specific neuroprogenitor gene loci. Integrative H3K27ac analysis of pediatric and adult glioma datasets [DHG, n = 10; DMG, n = 5; GBM, n = 4] validated these master regulators and identified subtype-specific core regulatory circuits (CRCs): autoregulatory transcriptional networks that sustain oncogenic neuro-progenitor identity. Notably, ATRX-deficient models and patient-derived cell lines showed a selective sensitivity to BRD4 inhibition (IC50 = 0.2 μM vs. 0.8 μM in ATRX-WT), strongly suggesting that this biology could be targeted therapeutically. These findings reveal ATRX loss as a key epigenetic driver that engages developmental master regulators and their respective CRCs through super-enhancer remodeling, establishing a novel therapeutic vulnerability in pediatric and AYA gliomas.