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

ABSTRACT 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.