Fig. 5: Impaired differentiation, preserved cytotoxic and increased immune checkpoint molecules by NK cells from COVID-19 CVID patients. | Nature Communications

Fig. 5: Impaired differentiation, preserved cytotoxic and increased immune checkpoint molecules by NK cells from COVID-19 CVID patients.

From: COVID-19 progression and convalescence in common variable immunodeficiency patients show dysregulated adaptive immune responses and persistent type I interferon and inflammasome activation

Fig. 5

a UMAP showing NK cell clusters, with cell numbers for CVID and non-CVID 1 cohorts indicated. b Dot plot showing gene expression per NK cell subpopulation; circle size denotes the percentage of expressing cells and colors indicate scaled gene expression. c Heatmaps showing fold-change (baseline vs progression) of DEGs in CVID cohort, and non-CVID 1 cohorts validated with non-CVID 2 cohort, for selected NK cell subsets. Genes are grouped by baseline expression comparison (equal, upregulated, or downregulated in CVID vs non-CVID). Gene clusters (left) and cluster sizes (right) are labeled. d Table of selected significant GO categories for each cluster in c. NA indicates clusters lacking enrichment. e UMAP and box plots showing cell trajectory of NK cells. Scale refers to pseudotime trajectory. f Enrichment scores for IRF9, STAT1 and STAT2 in single-cells by NK cell subset. g Box plots showing ‘cytotoxic response’ score for selected NK cell subsets in CVID, non-CVID 1, and non-CVID 2 cohorts. Dots correspond to biological replicates from different subjects in CVID (BL: n = 5, PG: n = 5, CV: n = 5), non-CVID1 (BL: n = 6, PG_Mild: n = 4, CV_Mild: n = 5, PG_Severe: n = 5, CV_Severe: n = 5) and non-CVID 2 control group (BL: n = 14, PG_Mild: n = 11, CV_Mild: n = 8, PG_Severe: n = 8, CV_Severe: n = 5). h UMAP of NK cells from spectral flow cytometry analysis. i Stacked barplot of NK cell cluster frequencies, calculated as cell counts per cluster over total live cells. j Box plots showing frequencies of selected NK cell clusters. k Histograms and box plots showing granzyme B and perforin levels in selected NK cells. Panels j and k show biological replicates for CVID (BL: n = 3, PG: n = 4, CV: n = 4) and non-CVID controls (BL: n = 4, PG: n = 6, CV: n = 4). Two-sided t-tests were used (*p-value < 0.05). Box plot whiskers denote minimum and maximum values (excluding outliers), with box spanning Q1 to Q3 and horizontal line for the median. BL baseline, PG progression, CV convalescence. Source data for panels are provided in the Source Data Fig. 5 file.

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