Fig. 6: Persistent activation of inflammasome genes in COVID-19 CVID monocytes. | Nature Communications

Fig. 6: Persistent activation of inflammasome genes in COVID-19 CVID monocytes.

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. 6

a UMAP showing myeloid cell clusters, with cell numbers for CVID and non-CVID 1 cohorts indicated. b UMAPs showing expression of CD14 and FCGR3A; scale indicates expression levels. c Dot plot showing gene expression per myeloid cluster; circle size denotes the percentage of expressing cells and colors indicate average expression. d Heatmaps showing fold-change (baseline vs progression) of DEGs in CVID cohort, and non-CVID 1 cohort validated with non-CVID 2 cohort, across selected myeloid 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. e Table of selected significant GO categories for each cluster in d. NA indicates clusters lacking enrichment. f Heatmaps showing fold-change (baseline vs progression/convalescence) of selected DEGs in CVID, non-CVID1, and non-CVID2 cohorts, showing only COVID-19 mild samples; color indicates Log2(fold-change). g SPI1 regulon enrichment score in single-cells by NK subset. h Box plots depicting caspase-1 activity in CVID and non-CVID samples across SARS-CoV-2 infection stages. Dots correspond to 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 = 4, CV: n = 3). i Cell-cell communication analysis of BAFF and APRIL signaling pathways during SARS-CoV-2 infection. Sender cells and ligands in red, receiver cells and receptors in green. j UMAP showing myeloid clusters from spectral flow cytometry analysis. k Stacked barplot of myeloid cluster frequencies, calculated as cell counts per cluster over total live cells. l Box plots showing the MFI of selected proteins in selected monocyte clusters. Dots correspond to biological replicates from different subjects in CVID group (BL: n = 3, PG: n = 4, CV: n = 4) and non-CVID control group (BL: n = 4, PG: n = 6, CV: n = 4). Two-sided t-test was used (*p-value < 0.05). 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 for panels are provided in the Source Data Fig. 6 file.

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