Immune cell-specific gene expression signatures were used to suggest dominant inflammatory cell populations across tumor subtypes. GSEA analysis comparing the mesenchymal (Mes) to non-mesenchymal (Non-Mes) subtypes was performed in (A) adult GBM (TCGA, n = 173) and (B) pediatric GBM (grade IV, n = 38) [11]. Bars show the normalized enrichment score for each cell-specific gene signature. Black bars represent gene signatures with significant enrichment (FDR<25%), white bars represent gene signatures which did not reach significance (FDR>25%). GIM: glioma-infiltrating microglia/macrophages, HSC: hematopoietic stem cells. See Table S1 for signature gene lists and Table S4 for complete GSEA data output. (C) Numbers of microglia/macrophages per 400× field, as determined by immunostaining for Iba1, across tumor subtypes in adult GBM (n = 24). Each dot represents an individual patient tumor and the mean is denoted by the line. Microglia/macrophage cell numbers are significantly higher in the mesenchymal subtype compared to the non-mesenchymal subtype (* Mann-Whitney, p = 0.04). Representative images of Iba1 staining for the mesenchymal and non-mesenchymal subtypes are shown (Iba1 cell counts of 66.8 and 44.6, respectively), scale bars = 50 µm. (D–E) The extent of (D) hypoxia, as determined by CA9 immunostaining (n = 22), and (E) vascularity, as determined by CD34 (n = 26), was compared across tumor subtypes in adult GBM. Each dot represents an individual patient tumor and the mean is denoted by the line. The level of hypoxia is significantly higher in the mesenchymal compared to non-mesenchymal subtype (* Mann-Whitney, p = 0.027), however vascularity was not significantly different (Mann-Whitney, p = 0.173).