Fig. 3: Abnormally activated lung monocyte-macrophages in severe COVID-19.

a The myeloid cell data from two mild and five severe COVID-19 patients who had paired PBMC and BALF samples were integrated and presented on the UMAP. b The expression of monocyte-macrophage markers FCN1, SPP1, and FABP4 were projected to UMAP from a. PM, peripheral cells of mild cases; PS, peripheral cells of severe cases; BM, BALF of mild cases; BS, BALF of severe cases. c Differentiation trajectory of the blood monocytes and BALF monocyte-macrophages from two representative COVID-19 patients, analyzed independently. d Venn diagram shows the number of upregulated and downregulated DEGs in monocyte-macrophage comparisons as indicated. logFC > 0.41 or < –0.41, adjusted P < 0.01. e Enrichment of GO biological process (BP) terms for upregulated genes (left) and downregulated genes (right) in monocyte-macrophage comparisons as indicated. Selected terms are shown, adjusted P value is indicated by the colored bar. f Heatmaps show the expression of selected interferon, cytokine, and chemokine genes in paired blood and BALF monocyte-macrophages derived from the same patient. Stars indicate that the genes are differentially expressed in BALF monocyte-macrophages between mild and severe COVID-19. Purple and green stars show that the gene expression are significantly upregulated in severe COVID-19 and mild COVID-19 groups, respectively (MAST; P < 0.01). B, BALF samples; P, PBMC samples. g The levels of selected cytokines and chemokines in paired BALF and plasma samples were measured by CBA (two-sided Wilcoxon test between BALF and PBMC of severe patients).