Abstract Adult gliomas exhibit substantial molecular and pathological variation. Prior single-cell studies have characterized intratumoral heterogeneity; in glioblastoma, tumor cells adopt lineage-associated programs—such as oligodendrocyte- and neuro- progenitor (OPC, NPC), astrocyte (AC) and mesenchymal (MES) like states. However, how these states recur across other gliomas remains unclear. Given their shared environment, defining conserved versus entity-specific tumor characteristics is essential for understanding glioma heterogeneity. Here, we analyzed 310 tumor cores from 284 patients spanning oligodendroglioma, astrocytoma, glioblastoma, and ependymoma, using single-cell spatial transcriptomics with a 344-gene panel (10x Xenium). This approach yielded a dataset of 2.8 million cells, including 18 tumor microenvironment (TME) cell types. To further probe local interactions, we profiled a validation cohort of astrocytomas using a 5,096-genes panel and multiplexed immunofluorescence (57 proteins). Our data revealed 9 recurrent tumor states across gliomas, organized into neighborhoods shaped by local cellular interactions. These formed structured layers, with OPC-/NPC-like tumors near cortical interfaces and AC-like regions forming a continuum with MES1-gliosis. Neighborhoods were largely subtype-specific suggesting that tissue organization and not cell composition alone, underlies glioma heterogeneity. Consistently, methylation classification—central to subtype definition in gliomas—stratified the cohort into 13 classes with distinct neighborhood profiles, including characteristic architectures in RTK1, RTK2, and MES glioblastomas. Neighborhoods also showed distinct TME variation: P2RY12+ microglia were enriched in AC-like and MES1-gliosis regions, while CD163+ myeloid cells concentrated in MES1-gliosis and MES2-hypoxia niches. These immune patterns corresponded to neighborhood-specific inflammatory programs and at the entity level to myeloid-dominated inflammation in ependymoma and low inflammation in oligodendroglioma. Beyond neighborhood definition, we evaluated their diagnostic potential. In astrocytoma, AC-like enrichment marked favorable prognosis, whereas MES1-like prevalence defined high-risk patients. Given this, we asked whether neighborhoods show histopathological correlates in routine H Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4953.
Mathioudaki et al. (2026) studied this question.