Acquired genetic and cell-state changes in IDH-mutant glioma progression

Article Acquired genetic and cell-state changes in IDH-mutant glioma progression https://doi.org/10.1038/s41586-026-10612-6 Received: 5 October 2024 Accepted: 30 April 2026 Published online: xx xx xxxx Open access Check for updates Kevin C. Johnson1,38, Avishay Spitzer2,3,38, Frederick S. Varn4,5,6,38, Masashi Nomura7,8,9,10,38, Luciano Garofano11,12,37,38, Tamrin Chowdhury1, Anuja Lipsa13, Linbin Zhang1, Ester Calvo Fernández7,8,10, Tanyeri Barak1, A. Gulhan Ercan-Sencicek1, Ayse Buket Peksen1, Kevin J. Anderson4, C. Mircea S. Tesileanu1, Samirkumar B. Amin1, Emre Kocakavuk1,14, Dacheng Zhao1, Fulvio D’Angelo12,15, Simona Migliozzi12,16,37, Lillian Bussema7,8,10, Simon Gritsch7,8,10, Hyo-Eun Moon17, Sun Ha Paek17,18, Franck Bielle19,20, Alice Laurenge20,21, Anna Luisa Di Stefano22,23, Bertrand Mathon24, Alberto Picca19,21, Marc Sanson19,21, Ann-Christin Hau13, Frank Hertel13, Kamil Grzyb13, Zheng Zhao25,26, Qianghu Wang27,28, Tao Jiang25,26, Julie J. Miller29,30, Hiroaki Wakimoto29,31, Daniel P. Cahill29,31, Jennifer Moliterno1, Murat Günel1, Beth Hermes32, Nader Sanai32,33, Anna Golebiewska13, Simone P. Niclou13, Jason Huse34, W. K. Alfred Yung35, Anna Lasorella12,16,39 ✉, Mario L. Suvà7,8,10,39 ✉, Antonio Iavarone12,17,39 ✉, Itay Tirosh2,39 ✉ & Roel G. W. Verhaak1,36,39 ✉ Gliomas with mutant isocitrate dehydrogenase (IDH) are malignant brain tumours that typically arise in early to mid-adulthood and nearly always recur following treatment1,2. However, the genetic and cellular-state changes that drive IDH-mutant glioma progression under treatment remain incompletely understood. Here we integrated single-nucleus transcriptomic profiles, chromatin accessibility profiles and bulk DNA and RNA sequencing from 75 temporally separated gliomas across 35 patients comprising both the oligodendroglioma and astrocytoma IDH-mutant glioma tumour types. We show that malignant cell states transcriptionally resemble stages of normal glial–neuronal lineage development or a reactive mesenchymal-like state, mirroring states previously described in IDH wild-type glioblastoma3,4. Malignant cell states displayed distinct chromatin accessibility profiles that were comparable between both IDH-mutant glioma types. The abundance of less differentiated malignant cells increased with grade and with genetic alterations such as PDGFRA amplification. Longitudinal analysis highlighted two major malignant cell-state transition patterns. First, reduced lineage differentiation and increased proliferative malignant cells at recurrence were enriched in gliomas that acquired recurrenceassociated genetic events. These included treatment-associated hypermutation, increased copy number changes and cell cycle alterations. Second, increased mesenchymal-like-state abundance occurred independently of acquired genetic alterations and instead coincided with elevated macrophage expression. Overall, our findings provide an integrative model that traces the cell intrinsic and extrinsic factors that shape cellular states during IDH-mutant glioma disease progression. Hotspot mutations in the IDH genes IDH1 and IDH2 define a subset of adult-type diffuse gliomas with distinct molecular, histological and clinical features1,2,5. IDH-mutant gliomas are classified into two World Health Organization (WHO) tumour types: (1) oligodendroglioma, IDH-mutant and 1p/19q co-deleted (oligodendroglioma); and (2) astrocytoma, IDH-mutant (astrocytoma)1,6. Despite treatment with surgical resection, chemotherapy and radiotherapy, both oligodendroglioma and astrocytoma inevitably recur, which leads to substantial morbidity and mortality. Previous studies have suggested that therapeutic resistance may result from a combination of intratumoural cellular heterogeneity4,7–10, acquired genetic and epigenetic aberrations9,11–13 and a shift in myeloid cell populations14. A better understanding of the complex interplay among these molecular layers and how they influence the evolutionary paths of IDH-mutant gliomas is needed to guide the development of more effective therapeutic strategies. To address these gaps, we aimed to establish a comprehensive portrait of treatment response and tumour evolution in IDH-mutant glioma through our Cellular Analysis of Resistance and Evolution (CARE) consortium. We profiled 75 longitudinally collected IDH-mutant glioma samples from 35 patients using single-nucleus RNA sequencing (snRNA-seq), complemented by matched bulk DNA sequencing (DNA-seq) and RNA sequencing (RNA-seq) and simultaneous A list of affiliations appears at the end of the paper. Nature | www.nature.com | 1 Article single-nucleus chromatin accessibility (snATAC) profiling in a subset of samples. The integrated datasets enabled us to map the trajectories that IDH-mutant gliomas follow during disease progression and highlight how malignant cell states are shaped by epigenetics, genetics, microenvironment and therapy. CARE IDH-mutant cohort We collected longitudinal glioma samples from 35 patients with an IDH-mutant oligodendroglioma (n = 13) or an IDH-mutant astrocytoma (n = 22) diagnosis based on the 2021 WHO glioma classification at 2 or 3 time points1 (n = 75 samples; Supplementary Tables 1 and 2). For each patient, we designated the two earliest samples as the initial and recurrence for longitudinal analyses. In 17 out of 35 longitudinal pairs, the initial sample was obtained at primary diagnosis, whereas for the remaining 18 cases, the initial samples were collected at a subsequent surgery. Between the initial and recurrence samples, 26 out of 35 patients received radiotherapy and/or alkylating chemotherapy, whereas no adjuvant treatment was reported for the other patients. To comprehensively investigate IDH-mutant glioma evolution, we used snRNA-seq and bulk DNA-seq and RNA-seq from the same resected glioma samples (Fig. 1a,b). A subset of these samples was profiled with simultaneous snRNA–ATAC sequencing (48 out of 75), including 22 matched longitudinal pairs, to assess epigenetic changes. In parallel, a separate subset of samples (16 out of 75) was profiled by plate-based, full-length transcriptome Smart-seq2 (Extended Data Fig. 1a–c). IDH mutations were longitudinally retained with a similar cancer cell fraction, and tumour purity was comparable at both time points (Extended Data Fig. 1d,e). We identified hypermutation associated with treatment with an alkylating agent (>10 mutations per Mb (mut per Mb)) with an enrichment for the SBS11 mutational signature (Fig. 1c and Extended Data Fig. 1f) in eight patients. Mutation burden was significantly increased at recurrence (P = 8.7 × 10–5, Wilcoxon signed-rank test; Fig. 1c), including when the analysis was restricted to samples that did not acquire a hypermutation (P = 0.01, Wilcoxon signed-rank test). We observed acquired genetic changes previously found to be enriched at recurrence11,15,16, including a >50% increase in somatic copy number alteration (SCNA) burden in ten patients, an (...truncated)