Fig. 4: CD16⁺ NK cell frequency in PBMCs is negatively associated with PCV13 vaccine responses.

a, Uniform manifold approximation and projection (UMAP) of PBMCs from 11 PCV13 donors (six SRs and five WRs) showing 24 clusters from 52,702 cells colored by immune cell type. Immune subsets were identified in a supervised manner. Lineage markers are shown in the dot plot; MBC, memory B cell; NBC, naive B cell; ABC, age-associated B cell; mono, monocyte; monoDC, monocyte-derived DC; HSC, hematopoietic stem cell; Mgk, megakaryocyte; MAIT, mucosal-associated invariant T cell; GZMK, granzyme K; PC, plasma cells; CTL, cytotoxic T cell. b, Stacked bar plot of immune cell frequencies in SRs and WRs. The cell types with significant differences in their frequencies between SRs and WRs are marked with a red asterisk (*; P < 0.05). c, UMAP of NK cell subsets with feature plots showing the expression NCAM1, XCL1, FCGR3A and GZMB in blue, highlighting the two NK populations: CD56^dimCD16⁺ NK cells and CD56^bright NK cells. d, Box plots of CD16⁺ NK cell and CD56^bright NK cell frequencies in SRs (n = 6) and WRs (n = 5). e, Correlation analysis between PCV13 rank and prevaccination frequencies of CD16⁺ NK and CD8⁺ naive T cells (n = 11). f, Sex differences in the prevaccination percentages of CD16⁺ NK cells in total PBMCs and in total NK cells (n = 11). Box plots display the median and IQR (25–75%), with whiskers representing the upper and lower quartiles ±1.5× IQR. A Wilcoxon rank-sum test (two sided) was used to compare cell percentages between SRs and WRs (b and d) and CD16⁺ NK cell percentages between men and women (f). Correlations were computed using the Pearson correlation metric (e), and P values were computed using two-sided t-tests; n represents the number of biological replicates.

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