Integrative Single-Cell, Spatial, and Bulk Transcriptomics Characterizes an Outcome-Associated, Spatially Organized Mesenchymal Program in IDH-Mutant Glioma

IDH-mutant gliomas show variable clinical behavior that may reflect transcriptional programs organized within tumor tissue. We evaluated two curated expression scores: a differentiation-loss/Stem-NPC score (Axis1) and a mesenchymal–hypoxia score (Axis2). Public single-cell RNA-sequencing data were used to characterize malignant-cell states, and the scores were evaluated in bulk clinical cohorts using portable within-sample ranks and covariate-adjusted Cox models. Axis2 was separated into non-overlapping mesenchymal-only and hypoxia-only components. Spatial organization was tested in Visium sections from 11 patients using patient-level inference and constrained null models. The mesenchymal-only component was associated with shorter overall survival in CGGA-693 (hazard ratio per standard deviation = 1.73, 95% confidence interval 1.43–2.11) and CGGA-325 (1.41, 1.10–1.79), although molecular adjustment attenuated the association in CGGA-325. It remained spatially autocorrelated (mean Moran’s I = 0.297; p = 0.001). Removing gene overlap reduced its patient-level correlation with hypoxia from 0.798 to 0.254; residual co-organization was supported across all patients but not within either IDH subgroup. Axis1 showed no portable survival association. Thus, the mesenchymal component is outcome-associated and spatially organized, whereas the data do not establish hypoxia-driven organization, causality, or malignant-cell specificity.