Extended Data Fig. 6: The analysis of the similarity of tet+ cells to other cell types in HIV+.
APOB-p18 DRB1*07:01 tetramer positive cells (Tet+ cells, solid circles) are plotted in UMAP of cell from HIV+sCVD- participants (a), from HIV+sCVD+ participants (b). Treg, Th1 and Tmem distribution are shown as contour plots of density. c, Cumulative histogram of the distances of each Tet+ cells against Tmem, Treg and Th1 in HIV-. d-f, Cumulative histograms of the distances of each of the Tet+ cells against Treg (d), Th1 (e), and Tmem (f) cells, separately for sCVD+ (yellow) and sCVD- (purple) and HIV+ in the first 6 PCA components. Significance by Kolmogorov-Smirnov test. g, A Ternary plot of relative median positions of Tet+ cells relative to pseudobulk mean of Tregs, Th1 and Tmem in the first 6 PCA components in HIV+. h, i, Volcano plots comparing gene expression in single cells of tet+ cells compared to Treg, Th1, and Tmem in HIV+sCVD- (h), and HIV+sCVD+ (i). Differential expression analysis was performed using Seurat’s non-parametric Wilcoxon rank-sum te t to extract marker genes. Significant markers were selected based on Bonferroni-adjusted P-Values <0.05. Colored dots (upregulated genes in red, and downregulated genes in blue) indicate significantly differentiated expressed genes (adjusted p-value <0.05). Dashed line indicates adjusted p-value of 0.05. Full data set shown in Supplemental Excel File 5.
