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. 2022 Dec 16;13:1066176. doi: 10.3389/fimmu.2022.1066176

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Copyright © 2022 Schreibing, Hannani, Kim, Nagai, Ticconi, Fewings, Bleckwehl, Begemann, Torow, Kuppe, Kurth, Kranz, Frank, Anslinger, Ziegler, Kraus, Enczmann, Balz, Windhofer, Balfanz, Kurts, Marx, Marx, Dreher, Schneider, Saez-Rodriguez, Costa, Hayat and Kramann

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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CD8⁺ T cell exhaustion in COVID-19 (A) Relationship between T cell exhaustion and cytotoxicity. Each CD8⁺ T cell is placed in the coordinate system according to its individual exhaustion and cytotoxicity score value. To highlight the position of CD8⁺ exhausted T cells, all other CD8⁺ T cell populations are colored in gray. A version of this plot with cell type-specific and condition-specific colors is available in Figure S2A, S2B , respectively. (B) Violin plot of exhaustion scores per cell type. (C) Exhaustion scores in all CD8⁺ T cells per condition. (Kruskal-Wallis test: H (2) = 2407, p < 0.0001; healthy vs. mild: p < 0.0001; healthy vs. severe: p < 0.0001, mild vs. severe: p < 0.0001) (D) Frequencies of cells expressing different combinations of the exhaustion markers PD-1 and TIM3 in all CD8⁺ T cells as examined by flow cytometry. (TIM3⁺PD-1⁺: Kruskal-Wallis test: H(2) = 21.59, p < 0.0001; control vs. mild: p = 0.0002; control vs. severe/critical: p < 0.0001, mild vs. severe/critical: p = 0.8933; TIM3^-PD-1^-: Kruskal-Wallis test: H(2) = 6.314, p = 0.0426; control vs. mild: p = 0.036; control vs. severe/critical: p = 0.1046, mild vs. severe/critical: p = 0.1689; TIM3^-PD-1⁺: Kruskal-Wallis test: H(2) = 6.07, p = 0.0481; control vs. mild: p = 0.1303; control vs. severe/critical: p = 0.9359, mild vs. severe/critical: p = 0.0484, TIM3⁺PD-1^-: Kruskal-Wallis test: H(2) = 6.287, p = 0.0431; control vs. mild: p = 0.1369; control vs. severe/critical: p = 0.0377, mild vs. severe/critical: p = 0.4863) (E) Exhaustion score in all CD8⁺ T cells in the reference dataset per condition. (Kruskal-Wallis test: H(2) = 149.7, p < 0.0001; control vs. mild: p < 0.0001; control vs. severe/critical: p < 0.0001, mild vs. severe/critical: p < 0.0001) (F) Exhaustion score in all CD8⁺ T cells in the reference dataset per outcome. (Kruskal-Wallis test: H(2) = 1328, p < 0.0001; control vs. discharged: p < 0.0001; control vs. deceased: p < 0.0001, discharged vs. deceased: p < 0.0001) (G) Heatmap displaying the proportions of query cell types that mapped to each cluster in the integrated dataset. High values indicate that most cells of a query cluster were assigned to a distinct cluster in the reference dataset. (H) Projection of cells that mapped to exhausted CD8⁺ T cells from the query dataset onto the UMAP of the reference dataset. (I) Exhaustion scores per condition in cells from the reference dataset that mapped to exhausted CD8⁺ T cells in the query dataset. (Kruskal-Wallis test: H(2) = 31.24, p < 0.0001; control vs. mild/moderate: p = 0.1054; control vs. severe/critical: p < 0.0001, mild/moderate vs. severe/critical: p = 0.0011) (J) Exhaustion scores per condition in CD8⁺ T cells from bronchoalveolar lavage fluid. (Kolmogorov-Smirnov test: D = 0.2422, p < 0.0001) BAL, bronchoalveolar lavage. **** = p-value ± 0.0001, *** = p-value ± 0.001, ** = p-value ± 0.01, * = p-value < 0.05, ns = not significant.