Enhancing radiotherapy efficacy in glioblastoma by inhibiting BRD9

Glioblastoma (GBM) remains one of the most aggressive and treatment-resistant forms of brain cancer, marked by high heterogeneity, invasive growth, and limited therapeutic options. Despite current standard therapies such as surgical resection, radiotherapy, and temozolomide chemotherapy (Stupp protocol), recurrence and resistance are still frequently seen. In this study, we aimed to enhance the radiotherapeutic response in GBM by targeting the epigenetic regulator BRD9, a bromodomain-containing protein implicated in chromatin remodeling and transcriptional control. Using U373 and U87MG cells, we combined a selective inhibitor (I‑BRD9) and CRISPR‑mediated BRD9 knockout with ionizing radiation (IR). BRD9 loss impaired viability and further reduced clonogenic survival in combination with IR. To capture early chromatin effects, we performed a histone Western‑blot panel that included BRD9‑linked acetylation marks, revealing a global reduction in active‑chromatin signatures upon BRD9 inhibition/knockout. These data indicated that BRD9 remodeling the epigenetic landscape may underlie the observed radiosensitization. To uncover the pathways altered by BRD9 loss, we next carried out transcriptomic profiling in two glioblastoma models (U373 and U87MG) exposed either to BRD9 inhibition or genetic knockout. Due to the downregulatory effect of BRD9, our studies focused more on genes with decreased expression that are intersecting in four different RNA sequencings. 31 downregulated genes were common in different conditions, which were linked to MYC signaling and translation machinery as a result of pathway analysis. BRD9 perturbation consistently rewired translation, MYC signaling, and ribosome biogenesis programs, with 31 genes reproducibly downregulated; many encode components of the translational machinery and tRNA aminoacylation. We focused on a MYC‑associated axis involving aminoacyl‑tRNA synthetases (AARS1, CARS1, GARS1, WARS1, YARS1) and EIF2S2. qPCR validated the coordinated suppression of these targets. Mechanistically, our data support a functional BRD9–MYC axis that coordinates aaRS/EIF2S2 expression and ribosome biogenesis. MYC overexpression restored translation‑related transcripts and ribosome‑biogenesis markers, reversing the effects of BRD9 inhibition and reinforcing this dependency. In parallel, transcripts for rRNA species essential to ribosome production (47S, 28S, 18S, 5.8S, 5S) decreased upon BRD9 inhibition/knockout, aligning with the epigenetic shift and supporting a model in which BRD9 sustains translational capacity. Together, these findings nominate BRD9 as an epigenetic regulator that regulates chromatin accessibility for protein synthesis in GBM and suggest that targeting BRD9 can disrupt the translational machinery and enhance radiotherapeutic response. Further studies will elucidate the direct genomic occupancy for BRD9 and MYC while also revealing the interacting partners of BRD9. Moreover, test in vivo whether disrupting the BRD9–MYC–aaRS/EIF2S2 circuit durably sensitizes GBM to radiation.