Fig. 3: Defective increase of Th1-, but higher frequency of PD-1hiTIGIThi memory cells during and after SARS-CoV-2 infection in COVID-19 CVID patients.
a UMAP visualization of T cell subsets, with cell numbers for CVID and non-CVID 1 cohorts indicated. b UMAPs showing expression of selected T cell genes; scale indicates expression levels. c Heatmaps showing fold change (baseline vs progression) of DEGs in CVID cohort, and non-CVID 1 cohort validated with non-CVID 2 cohort, for selected CD4+ T cell subsets. Genes are grouped by baseline expression comparison (equal, upregulated, or downregulated in CVID vs non-CVID). Gene clusters are labeled on the left, and cluster sizes are indicated on the right. d Table of selected significant GO categories for each cluster in c. Clusters without significant enrichment are marked as NA. e Scheme of T cell polarization into Th1/Th2/Th17 with related-gene expression and subset proportions by PID, infection stage, and COVID-19 severity. Mean and standard error bars reflect biological replicates: CVID (BL: n = 5, PG: n = 5, CV: n = 5) and the non-CVID control group (BL: n = 6, PG_Mild: n = 4, CV_Mild: n = 5, PG_Severe: n = 5, CV_Severe: n = 5). f UMAP of T cell clusters from spectral flow cytometry analysis. g Stacked barplot of T cell cluster frequencies, calculated as cell counts per cluster over total live cells. h Histograms and box plots showing levels of selected proteins in CD4+ T subsets by PID and infection stage. Dots represent biological replicates from different subjects in the CVID group (BL: n = 3, PG: n = 4, CV: n = 4) and the non-CVID control group (BL: n = 4, PG: n = 6, CV: n = 4). Two-sided t-test was used (*p-value < 0.05). i Density plot of CCR4/CD25 in cluster TC#3. Box plot whiskers denote minimum and maximum values (excluding outliers), with the box spanning Q1 to Q3 and a horizontal line for the median. BL baseline, PG progression, CV convalescence. Source data are provided in Source Data Fig. 3.
