Fig. 2: Self-reactive CD8+ T cells express a gene program of T-cell exhaustion.
From: Persistence of self-reactive CD8+ T cells in the CNS requires TOX-dependent chromatin remodeling
104 naive P14 cells were adoptively transferred into WT and MOG-GP mice. One day later (day 0), mice were challenged i.c. with 104 PFU rLCMV-GP33. Brain infiltrating P14 cells were FACS sorted for RNA-seq (a–d) and ATAC-seq (d) 21 days later or isolated for flow cytometric analysis at indicated days post infection (e–g). a Volcano plot of differentially expressed genes (DEGs) (FC ≥ 1.5; FDR < 0.05) in AL vs. VL (n = 3 mice/group). b Gene set enrichment analysis (GSEA) of a signature of exhaustion (chronic LCMV clone 13 infection24) in a ranked list of genes differentially expressed by AL vs. VL. NES: normalized enrichment score. c Heatmap of the significantly enriched WikiPathways for DEGs identified in (a). d Heatmap illustrating ATAC-seq Z-score and the RNA-seq Log2 FC of genes (FDR < 0.05) found adjacent to differentially accessible ChARs (Log2 FC ≥1; FDR < 0.05). e Representative flow cytometry histograms of inhibitory receptor expression in AL and VL P14 cells 28 days post i.c. rLCMV-GP33 infection. f TOX protein expression in P14 cells at day 7 and 21 following i.c. rLCMV-GP33 infection in WT and MOG-GP mice. Representative flow cytometry histograms (left) and summary data (right) (WT mice at day 7, n = 3, p = 0.0043; WT mice at day 21, n = 3, p = 0.0113; MOG-GP at day 7, n = 5; p = 0.0018; MOG-GP mice at day 21, n = 4). Light gray histograms indicate the control staining obtained with Tox−/− P14 cells. Flow cytometry data are expressed as background-corrected gMFI (ΔgMFI). ΔgMFI values were obtained after subtraction of gMFI values derived from Tox−/− P14 cells. Bars represent mean ± SEM. gMFI: geometric mean fluorescence intensity. g Stratification of inhibitory receptor expression in TOXhi (blue histograms) and TOXlo (red histograms) AL P14 cells 21 days following i.c. rLCMV-GP33 infection. Flow cytometric analysis of TOX vs. PD-1 expression, inhibitory receptors expression (left) and summary data (right) (n = 4 mice/group; PD-1 (p = 0.0049); TIGIT (p = 0.0204); TIM-3 (p = 0.1748); LAG-3 (p = 0.0192). ns, not significant; *p ≤ 0.05; **p ≤ 0.01 (one-way ANOVA with Tukey’s post-test for f, two-tailed paired t test for g). Data are representative of at least 2 independent experiments (e–g). Source data are provided as a Source data file.
