Fig. 5: Single-cell RNA-sequencing of M198–206-specific CD8+ T cells.

a UMAP analysis displays transcriptomic landscape of M_198–206-specific CD8⁺ T cells. Each dot corresponds a single cell and is colored according to the cluster. b Heatmap representation of top 50 differentially expressed genes of each cluster (each cluster vs. rest). c Mean expression (color) and frequency of expressing cells (size) of the featured genes were shown in the graph. d UMAPs are illustrating mRNA expression of the indicated genes. The expression level of the indicated genes of each cluster was shown in the violin plot. e Volcano plot shows fold changes of differentially expressed genes between cluster (1, 2, 3, 4, 7) and the rest. f Violin plot shows mRNA expression of indicated genes in cluster (1, 2, 3, 4, 7) (n = 2727 cells) and the rest (n = 1656 cells). Box represents 25–75 percentiles and median (straight line) and mean (dotted line) are indicated. g, h UMAPs indicate cytotoxicity (g) and exhaustion (h) signature score (see Methods). i Trajectory analysis shows transition of the cell state of indicated cells within cluster 0 and cluster 6. j Graph shows relative frequency of T_cyto-eff/mem and T_EX cells from moderate (n = 3) or severe convalescents (n = 3). Data represent mean ± SD. k Frequency of PD-1⁺TIGIT⁺ cells from moderate (n = 5) and severe (n = 4) convalescents in M_198–206-tetramer⁺ CD8⁺ T cells were examined by flow cytometry analysis. Data represent mean ± SD. p values were calculated by two-sided Mann–Whitney test. *p = 0.032.