Clonal evolution drives
cancer progression and therapeutic resistance. Recent studies have revealed divergent longitudinal trajectories in
gliomas, but early molecular features steering posttreatment
cancer evolution remain unclear. Here, we collected sequencing and clinical data of initial-recurrent
tumor pairs from 544 adult diffuse
gliomas and performed multivariate analysis to identify early molecular predictors of
tumor evolution in three diffuse
glioma subtypes. We found that CDKN2A deletion at initial diagnosis preceded
tumor necrosis and microvascular proliferation that occur at later stages of IDH-mutant
glioma. Ki67 expression at diagnosis was positively correlated with acquiring hypermutation at recurrence in the IDH-wild-type
glioma. In all
glioma subtypes, MYC gain or MYC-target activation at diagnosis was associated with treatment-induced hypermutation at recurrence. To predict
glioma evolution, we constructed CELLO2 (
Cancer EvoLution for LOngitudinal data version 2), a machine learning model integrating features at diagnosis to forecast hypermutation and progression
after treatment. CELLO2 successfully stratified patients into subgroups with distinct prognoses and identified a high-risk patient group featured by MYC gain with worse post-progression survival, from the low-grade IDH-mutant-noncodel subtype. We then performed chronic
temozolomide-induction experiments in
glioma cell lines and isogenic patient-derived gliomaspheres and demonstrated that MYC drives
temozolomide resistance by promoting hypermutation. Mechanistically, we demonstrated that, by binding to open
chromatin and transcriptionally active genomic regions, c-MYC increases the vulnerability of key mismatch repair genes to treatment-induced mutagenesis, thus triggering hypermutation. This study reveals early predictors of
cancer evolution under
therapy and provides a resource for precision oncology targeting
cancer dynamics in diffuse
gliomas.