Fig. 8: Antigen-specific T cells in BALF exhibit a differentiation bias toward multifunctional TRM cells after viral clearance. | Nature Immunology

Fig. 8: Antigen-specific T cells in BALF exhibit a differentiation bias toward multifunctional TRM cells after viral clearance.

From: Robust mucosal SARS-CoV-2-specific T cells effectively combat COVID-19 and establish polyfunctional resident memory in patient lungs

Fig. 8

a, The proportion of indicated specific T cell subclusters (related to Fig. 5a) in BALF varied from viral shedding stage (RNA+, n = 8) to viral clearance (RNA−, n = 8). b,c, Pseudotime trajectories for specific CD4+ (b) and CD8+ (c) T cells from 16 paired BALF and PBMC samples based on Monocle, showing three lineages on CD4+ and two lineages on CD8+ T cells. Cells are color-coded based on their phenotypes (related to a), with the arrows indicating the pseudotime trajectories. Each dot represents one cell. d,e, Trajectory inference analyses depicting the transition potential of specific CD4+ (d) and CD8+ (e) T cells from viral shedding stage (RNA+) to viral clearance (RNA−) in BALF and PBMCs. f,g, Gene expression dynamics in specific CD4+ (f) and CD8+ (g) T cells along the pseudotime in BALF. Genes were clustered into eight and 12 gene sets based on specific expression profiles, respectively, with selected marker genes shown. h,i, Density plots reflecting the number of specific CD4+ (h) and CD8+ (i) T cells among the indicated T cell subclusters stratified according to RNA+ versus RNA− in BALF. The x axis indicates pseudotime (related to f,g) and the y axis indicates probability density distribution of each T cell lineage at a different pseudotime. j, Distribution of specific T cells from BALF and PBMCs on TriMap according to RNA+ (n = 4, 5) and RNA− (n = 6, 6) stages based on the flow cytometry dataset. k, Cumulative cluster proportions of specific T cells from BALF and PBMCs at the RNA+ (n = 4, 5) and RNA− (n = 6, 6) stages were compared using pie charts. Each segment is color-coded to represent different functional clusters, as shown at the bottom (related to Fig. 3e). A two-tailed chi-squared test was used. l, Clusters that significantly increased in BALF from the RNA+ to the RNA− stages are shown. Each dot represents one sample. Data are presented as the mean ± s.e.m.; a two-tailed Mann–Whitney U-test was used.

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