A State-Resolved Single-Cell and Spatial Atlas Reveals IDH-Associated Differences in Malignant and Immune Architecture in Diffuse Glioma.

Adult-type diffuse gliomas are defined by the isocitrate-dehydrogenase (IDH) axis, yet how this biology constrains malignant cell-state repertoires and their immune-modulatory potential remains unclear. We profiled 69 tumors using single-cell RNA sequencing (scRNA-seq), single-nucleus RNA sequencing (snRNA-seq), and spatial transcriptomics, and resolved seven recurrent malignant cell states: astrocyte-like progenitor cells (ALPC), hypoxia, cycling G1/S, cycling G2/M, oligo-lineage, neuro-oligo-lineage, and neuro-lineage. The IDH axis strongly biased state occupancy and malignant-immune composition, with IDH-mutant tumors dominated by differentiated lineage-like states and reduced immune infiltration, whereas glioblastoma (GBM) showed expansion of ALPC and hypoxia states alongside increased myeloid and lymphoid infiltration. Orthogonal analyses supported that ALPC-associated markers are expressed in situ and in patient-derived stem cell-permissive cultures, consistent with a stem-like, differentiation-competent malignant phenotype. State-resolved pathway analysis identified mitochondrial oxidative phosphorylation programs enriched in GBM ALPC and extracellular matrix remodeling, and chemotaxis-associated programs enriched in GBM hypoxia. Composition-controlled, patient-level interaction modeling identified a greater malignant-myeloid signaling interface in GBM, driven by SPP1-CD44/integrin signaling and confirmed by differential expression; GBM networks also featured TGFB and NECTIN modules, whereas IDH-mutant networks were dominated by APP/APOE-TREM2/TYROBP and MIF modules. These data suggest that the IDH axis shapes glioma behavior by constraining malignant state repertoires and biasing the deployment of state-specific metabolic and immunomodulatory programs.