Fig. 4

MES-like states association with T cell states. A Scatterplot showing the correlations of 406 T cell-specific genes (dots) with estimated T cell abundance (X-axis), as defined by average expression of canonical marker genes (CD2, CD3D, CD3E, CD3G), and with the core MES score (Y-axis), across TCGA bulk RNA-seq samples. Line indicates a LOESS regression and confidence intervals are shown in grey. Dot colors indicate marker genes for T cell subtypes (cytotoxic, Treg, exhaustion). (B-C) Bars show correlations or partial correlations between core MES scores and T cell-related scores: T cell abundance as defined above (B), or the difference between cytotoxicity and exhaustion scores (C). Partial correlations control for the MES-Hyp (yellow) or MES-Ast (brown) scores, across TCGA bulk RNA-seq samples. Error bars correspond to first and third quartiles, calculated by sampling 75 tumors with 1000 iterations; the difference between averages is significant by Wilcoxon rank sum test (***, p = 0.0003; **** p< 2.2e−16). D Model depicting the three MES states in GBM. Cells in IDH-WT GBM (left) can be found in four states, one of them is the MES state (colored), while IDH-mutant gliomas (right) do not contain MES cells. MES cells all express a core MES program and can be found in three main flavors: a MES-Hyp state (light yellow), MES-Ast state (brown), and intermediate states (orange). The MES-Hyp state is associated with macrophage abundance and a high macrophage-microglia and M2-M1 activation. The MES-Ast state is associated with higher T cell abundance and T cell cytotoxicity