Extended Data Fig. 8: Single-cell gene expression analysis of CD8⁺ and CD4⁺ T cells in paired blood and plaque.

(a, b) Volcano plot of the top 5000 Differentially Expressed Genes (DEGs) (determined by two-sided Welch’s T- Test and Benjamini-Hochberg correction) in (a) CD4⁺ T Cells and (b) CD8⁺ T Cells T cells of plaque or blood. (c, d) Pathway analysis of (c) CD4⁺ and (d) CD8⁺ T cell DEGs with q < 0.05 (CD4⁺, n = 930 genes; CD8⁺, n = 310 genes) upregulated in blood (left) and plaque (right). The combined score metric corresponds to the P value (two-sided Fisher’s exact test) multiplied by the Z-score of the deviation from the expected rank, and q values determined by Benjamini-Hochberg correction. (e, f) Heatmap of hierarchically clustered top 50 variable genes across (e) CD4⁺ (n = 1,830 total cells, n = 347 plaque cells, n = 1,483 blood cells) and (f) CD8⁺ (n = 579 total cells, n = 420 plaque cells, n = 159 blood cells) T cells in plaque and blood. Rows: z-scored gene expression values; columns: individual cells. Above the heatmap, categories of identified cell clusters (top) cell’s origin from plaque or blood (bottom). Below the heatmap, cluster enrichment in tissue type is displayed with p values (two-sided binomial proportions test). Boxes (right) list key genes found in clusters. (g, h) Canonical signaling pathway analysis of the top 5000 DEGs in the indicated cell clusters from (g) CD4⁺ and (h) CD8⁺ T cells.