Hypermutation patterns shape tumorigenesis and immunotherapy response in mismatch repair deficient glioma

Primary mismatch repair deficient (priMMRD) glioma are deadly cancers comprising 5-10% of gliomas in children and young adults. PriMMRD glioma are characterized by universal hypermutation, resistance to chemo-irradation, and striking, but hetergeonous, responses to anti-PD1 immunotherapy. To elucidate the impact of replication-error driven mutagenesis on priMMRD glioma evolution and their heterogenous clinical courses, we analyzed genomic, methylomic, immune, and clinical data on a large cohort of priMMRD glioma (n=162) from the the International Replication Repair Deficiency Consortium. MMRD contributed to high microsatellite instability and hypermutation resulting in global DNA hypomethylation compared to non-MMRD gliomas and potentially affecting their classification. Recurrent somatic driver mutations in replicative polymerases and IDH1 stratified priMMRD gliomas into 3 distinct genetic and clinical subgroups: priMMRD1 (MMRD+ POLE/POLD1 , 56%), priMMRD2 (MMRD-only, 27%), and priMMRD3 (MMRD+ IDH1 , 17%). PriMMRD1 gliomas, which harbor complete replication repair deficiency, originated from germline biallelic MMRD (CMMRD), occurred at young ages, and exhibited ultrahypermutation. PriMMRD2 gliomas were enriched for monoallelic germline MMRD (Lynch syndrome) and older ages. Finally, IDH1 -driven priMMRD3 gliomas harboured germline mutations in MutSalpha ( MSH2 / MSH6 ), lower mutation burden, and distinct imaging patterns. Subgroups also utilized different mechanisms of genomic instability: while priMMRD1 gliomas harboured frequent point mutations in glioma drivers, priMMRD2 and priMMRD3 gliomas had higher rates of copy alteration in the same genes, including CDKN2 A (P<0.0001) and PTE N (P<0.0001). Driver mutations observed in MMRD-driven gliomagenesis could be explained by the specific trinucleotide contexts that compose MMRD mutational signatures. Hotspot mutations in TP53 and IDH1 occurred in contexts commonly mutated by MMRD, while pediatric glioma drivers ( BRAF / H3-3A) , which do not arise from frequently mutated contexts, were rare. Using mutational signatures and variant allele fractions, we built a model of MMRD gliomagenesis where TP53 mutations occur early, followed by secondary mutations in POLE/POLD1 , IDH1 , and other glioma drivers. PriMMRD glioma subgroups differed in their immune microenvironment and response to immunotherapy: priMMRD1 gliomas were associated with the highest 2-year overall survival on anti-PD1 monotherapy (75%), exhibited pro-immune expression signatures, and high CD8+ T-cell infiltration, contrasting priMMRD2 (24%) and priMMRD3 gliomas (0%). These findings suggest that MMRD mutagenesis shapes the unique landscape of priMMRD glioma through driver mutation acquisition and responses to immunotherapy, providing a rational approach for the refinement of subgroup-specific immunotherapy combinations.