Extended Data Fig. 10: Non-proliferating and proliferating cytotoxic T cells.

a, Principal component analysis of non-proliferating CTLs with participant density annotated along PC1 and PC2. Number of cells: P1 – 1828; P2 – 968; P3 – 1503; P4 – 670. b, Volcano plot of differentially expressed genes between the participants who control (P3/P4) and those who do not (P1/P2); implemented using a two-sided Wilcoxon rank sum test. See a for cell numbers. c, Expression of GZMB and PRF1 in all CTLs and proliferating T cells. Number of cells: CTL – 4,969; Proliferating T cells – 2,639. d, Volcano plot of differentially expressed genes between non-proliferating CTLs and proliferating T cells; implemented using a two-sided Wilcoxon rank sum test; see c for cell numbers. e, Heatmap of detected TCR-β CDR3s in proliferating T cell clusters 0 & 1 at 2 weeks, 3 weeks, and 4 weeks post-HIV detection. See Supplementary Table 10 for full list of CDR3s. f, Distribution of ranked TCR-β CDR3 clones (by total cell number) and singletons measured from all T cells (i.e. CD4⁺ T cells, CTLs, and proliferating T cells) detected at 2 weeks, 3 weeks, and 4 weeks post-HIV detection in at least two single cells in each participant. Here, except for the singletons, each sliver represents the percentage of CDR3s ascribed to the top n-n+1 clones for that timepoint and participant. g, Same as in a but over proliferating T cells. Number of cells: P1 – 483; P2 – 273; P3 – 1193; P4 – 690. h, CD8 T cell (top), γδT cell (middle), and NK cell (bottom) scores for each proliferating T cell cluster (see g for cell numbers) and 500 randomly sampled CTLs, and 500 randomly sampled NK cells. Signatures were established from differential expression over the single-cell dataset published by Gutierrez-Arcelus et al.⁴⁶. See Supplementary Table 10 for all differentially expressed genes and signature score gene lists. Box plots features depict: minimum = 25^th percentile – 1.5 * inter-quartile range (IQR; smallest value within); lower = 25^th percentile; center = 50^th percentile; upper = 75^th percentile; maximum = 75^th percentile + 1.5 * IQR (largest value within).