Fig. 4: Increased percentage of expanded and plaque-enriched CD4+ T cells in the atherosclerotic plaque. | Nature Cardiovascular Research

Fig. 4: Increased percentage of expanded and plaque-enriched CD4+ T cells in the atherosclerotic plaque.

From: Single-cell T cell receptor sequencing of paired human atherosclerotic plaques and blood reveals autoimmune-like features of expanded effector T cells

Fig. 4

a, UMAP visualization of unsupervised clustering revealed 11 distinct CD4+ T cell populations (n = 17,073). b, UMAP visualization of different levels of clonotype expansion among CD4+ T cells between PBMC and plaque. c, Bar plot with quantification of clonal expansion levels between PBMC and plaque CD4+ T cells. d, Bar plot with quantification of tissue enrichment scores of clonotypes in CD4+ T cells of PBMC and plaque. e, Volcano plot with differentially expressed genes between CD4+ T cells with single clonotypes and all expanded clonotypes (Small–Large). Genes were considered significant with P <1 × 10−6 and a fold change of 0.5. For all volcano plots, Bonferroni-corrected P values were calculated based on the total number of genes in the dataset. f, Volcano plot with differentially expressed genes of PBMC-enriched versus plaque-enriched CD4+ T cells. Genes were considered significant with P <1 × 10−6 and a fold change of 0.5. g, Bar plot with quantification of tissue enrichment score of individual CD4+ T cell clusters. h, Dot plot of average expression of upregulated genes in clusters 3, 5, 7 and 8. i, Volcano plot with differentially expressed genes between Treg cells in PBMC and plaque. Genes were considered significant with P <1 × 10−6 and a fold change of 0.5. j, UMAP visualization of pseudotime analysis of CD4+ T cells. Two branches of the analysis are indicated with 1 and 2. k, UMAP visualization of RNA velocity analysis of CD4+ T cells with close-up of branches 1 and 2. l, UMAP visualization of four overlapping clonotypes between cluster 6 and cluster 3. Open circles indicate PBMC CD4+ T cells; closed circles indicate plaque CD4+ T cells. Clonotype expansion levels: Single (one occurrence), Small (≤0.1%), Medium (>0.1% and ≤1%), Large (>1% and ≤10%), percentage of all CD4+ T cells. Tissue enrichment scores: Plaque-enriched (frequency expanded clone higher in plaque versus PBMC), Single (one occurrence), Unenriched (frequency expanded clone similar in PBMC versus plaque), PBMC-enriched (frequency expanded clone higher in PBMC versus plaque).

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