Fig. 1

Composition of the mouse-derived TME in GBM PDOXs. A Schematic of the preclinical modeling of GBM tumors in PDOXs. Created with Biorender.com. See PDOX characteristics in Additional file 2: Fig S1 and Additional file 1: Table S1. B Oncoplot of glioma-specific somatic mutations, gene amplifications, and deep deletions in the PDOX cohort. Longitudinal PDOXs are highlighted with color. MGMT promoter methylation status in PDOX models in depicted. C Flow cytometric analysis showing depletion of human CD31⁺ endothelial cells and CD45⁺ immune cells upon xenografting. Examples are shown for 3 GBM patient tumors (single viable cells) and respective PDOXs models at the first passage (single viable human cells, characterized as GFP^neg population in GFP⁺ NOD/SCID mice). D Top: UMAP projection of scRNA-seq data showing the overall gene expression profile of TME cell types. scRNA-seq data combined the biological groups: nude mouse normal brain (Nu-NB), PDOXs (9 models), C57BL6/N mouse normal brain (BL6-NB), GL261 tumor (3 collection time points: early, middle, late). Bottom: Proportions of TME cell types across different tumors and normal brains. Statistical difference between PDOXs (n = 9) and GL261 (n = 3) was evaluated with two-tailed Student’s t test with Bonferroni correction (***p < 0.001, *p < 0.1); Cell types are color-coded; OPCs: oligodendrocyte progenitor cells