Extended Data Fig. 5: Exhausted T cells do not have expected features of translational attenuation.
From: Proteotoxic stress response drives T cell exhaustion and immune evasion
a, Bar plot of protein and RNA expression changes of IRES motif-containing genes in Tex vs Teff cells 8 days post initial activation from the in vitro exhaustion model. b, Correlations of RNA and protein expression fold changes of EIF2A-dependent and EIF2A-independent genes in Tex vs Teff cells. A regression line with a shaded 95% confidence interval is shown. c, Enrichment analysis by Enrichr on proteins showing upregulation in both RNA and protein level (circled, left) in Tex versus Teff cells (one-sided Fisher’s exact test with Benjamini–Hochberg correction). A regression line with a shaded 95% confidence interval is shown in the left panel. d, PDCD4 expression across different CD8+ T cells subpopulations from in vitro exhaustion and in vivo tumor models by mass spectrometry (n = 5 for in vitro model, n = 3 for MC38 and MB49 tumor models, one-way ANOVA). Data are presented as mean (center line) and min to max (box bounds). e, The left panel is the heatmap of protein expression levels associated with selected Gene Ontology (GO) terms in in vitro-generated Teff and Tex cells 8 days post initial activation. Gene Set Enrichment Analysis (GSEA, right) compares Tex versus Teff cells, with normalized enrichment score (NES), gene rank distribution, and associated unadjusted P values are shown. P values were estimated using an adaptive multi-level split Monte Carlo scheme. f, Volcano plots of differentially expressed proteins in Tex versus Teff cells. Red: translation-related proteins; Blue: transcription-related proteins; Grey: other proteins (two-sided t-tests with Benjamini–Hochberg correction). g, Mass spectrometry analysis of protein expression levels of RPL13, eIF4E and eEF2 (n = 3 for Teff and n = 4 for Tex, two-tailed t test).