PATH-29. LONGITUDINAL EPIGENOMIC EVOLUTION OF IDH-WILDTYPE GLIOBLASTOMA

Abstract Glioblastoma, IDH-wildtype remains a molecularly heterogeneous disease that is refractory to current therapies. To investigate how longitudinal epigenomic evolution of glioblastoma drives tumor progression and treatment resistance, we performed comprehensive histopathologic assessment, targeted genomic sequencing, and genome-wide DNA methylation profiling of paired initial and recurrent IDH-wildtype glioblastoma samples from 98 patients, as well as a separate longitudinal cohort of IDH-mutant astrocytomas for comparison. Primary treatment-naïve IDH-wildtype glioblastomas had more globally hypomethylated genomes compared to primary IDH-mutant astrocytomas. At time of recurrence, IDH-mutant astrocytomas uniformly became more hypomethylated similar to the global methylation levels in IDH-wildtype glioblastomas. In contrast, recurrent IDH-wildtype glioblastomas were heterogeneous with subsets becoming more globally hypermethylated (27%), hypomethylated (22%), or remaining stable (51%). Accordingly, a substantial proportion (52%) of recurrent glioblastomas underwent methylation class switching compared to their matched primary tumor, with a predominance of the RTK2 epigenetic subtype at initial surgery and the Mesenchymal epigenetic subtype at recurrence. Among approximately 850,000 interrogated CpG sites, we identified only 110 and 153 sites that consistently became more hypermethylated or hypomethylated between initial and recurrent IDH-wildtype glioblastomas, which regulate genes involved in neuronal morphogenesis, oligodendrocyte differentiation, and myelination. In contrast, we identified 260 and 18,527 CpG sites that consistently became more hypermethylated or hypomethylated between initial and recurrent IDH-mutant astrocytomas, which regulate genes involved in neuronal stem-like differentiation, cell cycle control, and other biologic processes. Finally, we developed a DNA methylation evolution signature incorporating change in mean beta-methylation values from initial to recurrent tumor specimens across 347 critical CpG sites that significantly correlated with clinical outcomes for patients with IDH-wildtype glioblastoma. In summary, IDH-wildtype glioblastomas demonstrate heterogeneous epigenomic evolution patterns distinct from IDH-mutant astrocytomas. These changes in epigenetic patterns may identify unique subgroups of glioblastoma with differential treatment response and inform future therapeutic studies targeting differentially methylated gene programs.