T-lymphocyte clonal expansion of the treated mice. (A) TCR clonality at single-cell resolution is portrayed with distinct colors in 2-dimensional UMAP of all T cells. T cells with TCR frequencies of 1, >1, and >4 are marked with blue, red, and yellow, respectively. T cells with no matching TCRs are marked with gray. (B) Bar plots portraying the number of T cells with TCR frequencies of 1 (blue), >1 (red), and >4 (yellow) per major T-cell category. (C-D) Box plots portraying the proportions of expanded paired α/β TCRs (expanded: α/β TCR freq of >4) among the mice treated with uTcs + IgG (n = 8), uTcs + SAR (n = 3), veTcs + IgG (n = 8), and veTcs + SAR (n = 6). (C) CD4 and CD8 T cells and (D) in CD4 and CD8 cytotoxic T-cell populations. Significantly different proportions among pairwise comparisons are denoted with asterisks (∗FDR < 0.05, ∗∗FDR < 0.01; Dirichlet regression, Benjamini-Hochberg FDR correction). (E) Heat map capturing the median freq of the expanded paired α/β TCRs (expanded: α/β TCR freq of >4) of each T-cell population for the distinct mice and Txs, represented per column. (F) Box plots capturing the median clone size abundance of the expanded paired α/β CD8 Tem/highly cytotoxic TCRs (expanded: α/β TCR freq of >4) for the distinct cohorts. Adjusted P values are displayed in significantly different proportions among pairwise comparisons (Wilcoxon rank-sum test, Benjamini-Hochberg FDR correction). (G) Heat map showing the average expression of differentially expressed genes associated with activation and exhaustion within the CD4 CTLs (CD4 CTL and CD4 CTL-IFN) between veTcs + SAR and uTcs + SAR. Distinct colors represent the different conditions, and gene expression profiles (log scale) are depicted in a blue-to-red gradient. Expr, Expression; freq, frequency; NKT, natural killer T cells; Tcm, T central memory; Temra, T effector memory RA.

T-lymphocyte clonal expansion of the treated mice. (A) TCR clonality at single-cell resolution is portrayed with distinct colors in 2-dimensional UMAP of all T cells. T cells with TCR frequencies of 1, >1, and >4 are marked with blue, red, and yellow, respectively. T cells with no matching TCRs are marked with gray. (B) Bar plots portraying the number of T cells with TCR frequencies of 1 (blue), >1 (red), and >4 (yellow) per major T-cell category. (C-D) Box plots portraying the proportions of expanded paired α/β TCRs (expanded: α/β TCR freq of >4) among the mice treated with uTcs + IgG (n = 8), uTcs + SAR (n = 3), veTcs + IgG (n = 8), and veTcs + SAR (n = 6). (C) CD4 and CD8 T cells and (D) in CD4 and CD8 cytotoxic T-cell populations. Significantly different proportions among pairwise comparisons are denoted with asterisks (∗FDR < 0.05, ∗∗FDR < 0.01; Dirichlet regression, Benjamini-Hochberg FDR correction). (E) Heat map capturing the median freq of the expanded paired α/β TCRs (expanded: α/β TCR freq of >4) of each T-cell population for the distinct mice and Txs, represented per column. (F) Box plots capturing the median clone size abundance of the expanded paired α/β CD8 Tem/highly cytotoxic TCRs (expanded: α/β TCR freq of >4) for the distinct cohorts. Adjusted P values are displayed in significantly different proportions among pairwise comparisons (Wilcoxon rank-sum test, Benjamini-Hochberg FDR correction). (G) Heat map showing the average expression of differentially expressed genes associated with activation and exhaustion within the CD4 CTLs (CD4 CTL and CD4 CTL-IFN) between veTcs + SAR and uTcs + SAR. Distinct colors represent the different conditions, and gene expression profiles (log scale) are depicted in a blue-to-red gradient. Expr, Expression; freq, frequency; NKT, natural killer T cells; Tcm, T central memory; Temra, T effector memory RA.

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