Fig. 7: The immune landscape of gliomas.

A Heatmap illustrating cell type compositions and activities of selected individual genes/proteins and pathways across immune clusters. First section: immune/stromal signatures based on xCell scores. Second section: the GSVA scores in terms of proteome data for subgroup upregulated biological pathways. Remaining section: the expression patterns of subgroup upregulated proteins, respectively. B Kaplan–Meier curves for OS based on immune subtypes (log-rank test, analyzed patients: n = 187). C Heatmap showed the comparison between immune clusters (columns) with proteomic subtypes and different histological types (rows). D Contour plot of two-dimensional density based on immune scores (y-axis) and stromal scores (x-axis) for different immune groups. For each immune group, key upregulated pathways and molecules were reported based on RNA-seq (R), proteomics (P), and phosphoproteomics (Ph) in the annotation boxes. E The boxplots indicated the mRNA and protein expression of PD-L1 among the three immune subtypes. F The plot indicated the mutational frequency of EGFR (left, two-sided fisher exact test), the expression of its cognate mRNA (middle) and protein (right) among the three immune subtypes. For boxplots in E and F, p values: two-sided Wilcoxon test, mRNA: Im-S-1: n = 25, Im-S-2: n = 33, Im-S-3: n = 33, protein: Im-S−1: n = 58, Im-S-2: n = 60, Im-S-3: n = 69). G The box plot indicated the mRNA (left, EGFR^Amp&Mut: n = 14, EGFR^Amp: n = 14, WT: n = 35) and protein expression (right, EGFR^Amp&Mut: n = 14, EGFR^Amp: n = 97, EGFR^Mut: n = 5, WT: n = 25) of PD-L1 among samples (two-sided Wilcoxon test). H The heatmap indicated protein expression patterns of EGFR significantly associated proteins. I The scatter plot described the correlation between the inferred TF activity of NFKB1 and the protein expression of NFκB1 (left) or the mRNA expression of PD-L1(right). Samples were color coded based on their immune subtypes (p value: Spearman-rank correlation). J Immunohistochemistry of PD-L1 in EGFR-mutant and WT samples (analyzed patients: n = 4). Scale bar = 100 μm. K Systematic diagram summarizing patients with EGFR^Am&Mut might better respond to PD-L1 treatment. In the box plots E, F and G the middle bar represents the median, and the box represents the interquartile range; bars extend to 1.5× the interquartile range. Source data are provided as Source Data files.