Fig. 5: The formation and activity of NKG2alowCD16+ NK cells correlate with viral recrudescence following ATI.
a From PBMCs taken 24 h following the first (d6 post ATI) and the fifth PEG-IFNα dose (d37 post ATI), the expression of interferon-stimulated genes was calculated as a cross-sectional log2 fold-change between cytokine-treated (n = 8) and control (n = 5) RMs, which is represented as a double-gradient heatmap. The size of each data point corresponds inversely to the log10-transformed nominal p value with significant (p < 0.05) adjusted p values indicated by a black border. Using DESeq2, data were analyzed with a two-sided (95% CI) Wald test using the Benjamini–Hochberg method for multiple comparisons. b In PBMCs at d13 post ATI, the distribution of the differentiation subsets was measured by flow cytometry as a frequency of NK cells: Stage 0 (red, NKG2a/clowCD16–), Stage 1 (blue, NKG2a/chighCD16–), Stage 2 (orange, NKG2a/chighCD16+), and Stage 3 (purple, NKG2a/clowCD16+). NK cells isolated from PBMCs at d13 post ATI were utilized to determine c the frequency of ex vivo innate activity (CD107a surface expression) or d the Env-specific activity upon co-culture with K562 cells expressing HLA-E loaded with SIVmac Env peptides. b–d Data from individual cytokine-treated (PEG-IFNα with prior ART + IL-21 + rIFNα, blue; n = 8) and control (prior ART-only, black; n = 5) RMs (open symbols) are overlaid against the mean ± SEM (in red) and were analyzed with b, c two-sided (95% CI), two-way ANOVA with Bonferroni’s correction for cross-sectional comparisons relative to controls or d with a two-sided (95% CI) Mann–Whitney U test. e The delay in the rebound of plasma viremia was correlated against measures of SIV content, NK cell differentiation, and NK cell activity (as indicated at left; n = 13) from the final on-ART measurement (d339–374 p.i.) or during rebound following ATI (d6–13 post ATI). Per each correlation the two-tailed (95% CI) Spearman’s rank correlation coefficient (rho) is represented as a double-gradient heatmap and the size of each data point corresponds inversely to the log10-transformed Spearman’s p value. The false discovery rates (FDR) were calculated using SAS and significant values (Q < 0.05) are represented by a black border. Correlations for which data did not exist during that experimental phase are indicated as “NA”.
