Fig. 2: Cell-type-specific analysis of T cell diversity and functionality in SjD. | Nature Communications

Fig. 2: Cell-type-specific analysis of T cell diversity and functionality in SjD.

From: Comparative single-cell and spatial profiling of anti-SSA-positive and anti-centromere-positive Sjögren’s disease reveals common and distinct immune activation and fibroblast-mediated inflammation

Fig. 2

a The UMAP plot displays T cell subsets in salivary glands. b Expression levels of markers across T cell subsets. c Clonal expansion of T cells. d TCR repertoire diversity by cell clusters, with the left plot quantifying diversity scores and the right plot depicting connectivity diagrams of TCR clonotypes for different T cell subsets. Data are presented as mean values ±  standard deviation (SD) derived from 200 bootstrap replicates for each group. e Subtype analysis of top 20 expanded clones in CD8+ and CD4+ T cells across different SjD autoantibody profiles. f TCR repertoire diversity as a smooth function (D) of a single parameter q by autoantibody status. As the parameter q increases from 0 to + ∞ the diversity index (D) depends less on rare clones and more on common (abundant) ones. Large diversity index (D) are interpreted as high diversity in clonal populations. Lines represent mean diversity values, and shaded areas indicate 95% confidence intervals estimated from 200 bootstrap replicates. g Differentially expressed gene (DEG) analysis in CD4+ and CD8 + T cells across SjD subgroups compared to Sicca using the Wilcoxon rank-sum test (two-sided). Volcano plots show log₂ fold changes (logFC) (x-axis) and –log₁₀ adjusted p-values (y-axis) for DEGs between each SjD subgroup and Sicca controls in CD4+ (left three panels) and CD8 + T cells (right three panels). Upregulated genes (red) and downregulated genes (blue) are highlighted with selected key genes annotated. Genes not reaching significance are shown in grey. h Differential abundance profiles of T cell populations in SjD subtypes. Beeswarm plots showing the distribution of logFC in neighborhoods in different cell type clusters in T cells. Each plot compares the abundance in SjD overall, SSA+, CENT+, and SSA + CENT+ subtypes versus Sicca or each other. Significant changes (false discovery rate (FDR) < 0.05) are highlighted, indicating enriched or depleted in each case. Source data are provided as a Source Data file.

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