Chemical screens identify HDAC6 as an epigenetic vulnerability in acquired Temozolomide-resistant models of glioblastoma

Glioblastoma (GBM) is an aggressive primary brain tumor associated with a median survival of approximately 15 months following diagnosis. Current standard-of-care treatment includes surgical resection followed by radiotherapy and chemotherapy with the DNA-alkylating agent temozolomide (TMZ). However, tumor recurrence in a therapy-resistant state remains a major driver of poor patient outcomes. To investigate the molecular mechanisms underlying TMZ resistance, we generated in vitro models of acquired resistance by exposing initially TMZ-sensitive GBM cells to escalating doses of TMZ. Transcriptomic and chromatin accessibility profiling revealed extensive remodeling of DNA damage response (DDR) and DNA repair pathways that favored protection against TMZ-induced genotoxic stress. Although upregulation of O-6-methylguanine-DNA methyltransferase (MGMT) emerged as a dominant determinant of resistance in our models, the data suggested that additional adaptive resistance mechanisms contribute to the resistant phenotype. To identify targetable epigenetic dependencies associated with TMZ resistance, we performed a chemical screen using an epigenetic probe library. This screen identified multiple histone deacetylase (HDAC) inhibitors that selectively impaired the viability of TMZ-resistant cells, either as monotherapy or in combination with TMZ. Among these, HDAC6-selective inhibitors, including Ricolinostat, were particularly effective at inducing cell death in TMZ-resistant GBM models. Mechanistically, HDAC6 inhibition reduced the expression of key DDR-associated genes, while MGMT responses varied depending on cellular context and treatment duration. Furthermore, pharmacological inhibition and loss-of-function studies demonstrated that targeting HDAC6 could restore TMZ sensitivity by altering the balance of DNA repair pathway activity, potentially acting as a compensatory mechanism for MGMT-mediated resistance. Collectively, our findings identify HDAC6 as an epigenetic vulnerability in acquired TMZ-resistant GBM and support the therapeutic potential of HDAC6 inhibition as a strategy to overcome TMZ resistance in glioblastoma patients.