Fig 2: Activated MAIT cells can limit HCV replication.Sorted MAIT cells (CD8+CD161++Vα7.2+) were rested or activated in a TCR-independent manner (IL-12+IL-18 stimulation, MAIT+) for 24 h. (a) IFN-γ expression by MAIT cells (gated on live CD3+CD8+CD161++Vα7.2+ cells) was analysed by flow cytometry. (b,c) Neat or diluted supernatants were transferred to hepatocyte lines infected with HCV expressing luciferase and viral replication measured 4 days post infection. (d) Supernatants were transferred to hepatocyte lines infected with HCV expressing luciferase repeated in the presence of an isotype control or anti-IFN-γ antibody. Data are representative from at least two independent experiments. Bars represent means±s.e.m. Statistical significance was determined with a Wilcoxon matched-paired test (c) or the Mann–Whitney test (d). **P≤0.01. −, unstimulated; luc, luciferase; RLU, relative light units; sup, supernatant.

Fig 3: Spatial cross presentation in human STS is prognostic for patient survival. (a) Microphotograph with double immunohistochemistry (IHC) visualizing direct cell–cell interactions between CD11c+ cells and CD8+ cells; (b) Kaplan–Meier survival analysis using the log-rank test for comparison between absence or presence of CD11c–CD8 cellular interactions detected by double IHC in tumors from the Karolinska STS cohort. * p < 0.05; p < 0.05 is considered significant; (c) Double IF (Opal multiplexing) visualizing representative single-positive CD11c+ cells and single-positive CD8+ cells. Blue pseudocolor = nuclei; (d) QuPath digital image quantification of CD11c+ cells with or without coexpression of the macrophage markers CD68 (left) and CD163 (right). Each bar represents an individual case displaying CD11-CD8 interactions; (e) Flow cytometry for CD8 and CD3 in a preparation of freshly isolated CD45+ cells from a 76-year-old male with UPS, G3 displaying intratumoral CD11c–CD8 interactions in sections from the same tumor.

Fig 4: High gene expression levels of ITGAX together with CD8A are prognostic by transcriptomics, irrespective of FOXP3 levels, in human STS. (a) Contrast group analysis of gene expression levels of ITGAX (CD11c) and CD8A (CD8) in the TCGA sarcoma cohort; (b) Contrast group analysis of gene expression levels of ITGAX (CD11c) and CD8A (CD8) in the TCGA sarcoma cohort where FOXP3low and FOXP3high indicate subgroupings according to total FOXP3 levels in the TME. * p < 0.05, ** p < 0.01; p < 0.05 is considered significant.

Fig 5: Enhanced Autophagy Levels Are Linked to Effector Function and Mitochondrial Fitness in Human T Cells(A) Example plots of IFN-?, LC3, granzyme B (GzB), and perforin (perf; gated on CD8+ T cells) and histograms of LC3 staining for PBMC ex vivo or after anti-CD3/CD28 stimulation (3 days; see also Figure S3).(B) LC3 staining of CD8+ T cells from unstimulated PBMCs (IFN-?-), IFN-?- and IFN-?+ CD8+ T cells after anti-CD3/CD28 stimulation (3 days; eight biological replicates).(C and D) LC3 staining on GzB and perf-expressing CD8+ T cells ex vivo (C) and after anti-CD3/CD28 stimulation (D) (3 days; eight biological replicates; box whisker, Tukey).(E) Example mitochondrial staining of CD8+ T cells in blood (PBMCs; black) and liver (IHLs; red) and summary data for the ex vivo percentage of total CD8+ T cells with depolarized mitochondria (mitoTracker deep red [MtDR]lo; see also Figure S4; PBMCs, 10; and IHLs, 15 biological replicates).(F) Ex vivo percentage of CD8+ TRM cell subsets in the liver with depolarized mitochondria (14 biological replicates; box whisker, Tukey; outliers shown as dots).(G) The percentage of total CD8+ T cells or CD8+ TRM cell subsets with depolarized mitochondria after overnight culture of IHLs with DMSO (untreated), MRT68921 dihydrochloride (10 µM), bafA1 (0.1 µM), or reagent A (chloroquine diphosphate, 1:1000, FlowCellect LC3 kit; 13–15 biological replicates).Cells were treated with bafA1 (A–D). Bars at mean (B, E, and G). Friedman test (ANOVA) with Dunn’s post hoc test for pairwise multiple comparisons (B, C, D, and F). Kruskal-Wallis test with Dunn’s post hoc test for unpaired multiple comparisons (G). Mann-Whitney unpaired t test for total CD8+ PBMCs versus IHLs (E). Wilcoxon paired t test for untreated versus that treated with MRT68921 (G). Bars at mean (E and G). *p < 0.05, **p < 0.005, ***p < 0.001, ****p < 0.0001.