Mutational signature stratification of recurrent gliomas reveals distinct patterns of genomic traits

Background: Although temozolomide (TMZ) is widely used for glioma treatment, its therapeutic benefit is limited by acquired resistance and recurrence, facilitated by intratumor heterogeneity. Mutational signatures can inform tumor evolution and reveal alterations associated with treatment response. Methods: We performed a molecular analysis of 96 glioma recurrences with sufficient private single-base substitution (SBS) relative to their matched primary tumors, stratified by their dominant SBS. Results: Four groups were identified: SBS11 (TMZ, n=38), SBS1/5 (aging, n=32), SBS6/15/21/26 (microsatellite instability (MSI), n=13), and other dominant SBSs (n=13). Recurrences with dominant SBS11 showed markedly higher acquired mutational counts than the other groups (1338 vs 59 (aging) vs 57 (MSI) vs 57 (other); p<0.01). Mutations in SYNE2 , SZT2 , and FBN3 were exclusive to recurrences with dominant or second-dominant SBS11 (n=41), and 85% (35/41) harbored a mutation in at least one of these genes. Among TMZ-associated recurrences, SBS23 was frequent (44%, 18/41) and was associated with higher acquired mutational counts (2089 vs 1188; p=0.018) and more IDH-wildtype tumors (67% vs 30%; p=0.037) compared with cases lacking SBS23 dominance. MAPKBP1 mutations were enriched in SBS23-positive recurrences (56% (10/18) vs 0% (0/23); p<0.001). Aging-dominant recurrences showed more frequent acquired chromosome 16q losses (22% vs 8% (TMZ) vs 0% (MSI) vs 0% (other); p<0.05), which were associated with an increased fraction of the genome altered when compared with diploid chromosome 16q (15% vs 7%; p=0.01). Conclusions: Collectively, these findings show that signature-based grouping of recurrences can refine molecular characterization after therapy and nominate candidate biomarkers linked to resistance.