Fig. 4

TNF-α and IFN-γ driven CXCL10+ CCL2+ macrophages are expanded in severe COVID-19 and other inflamed tissues. a Integrative clustering of stimulated blood-derived macrophages with tissue-level macrophages from COVID-19 BALF, UC colon, CD ileum, and RA synovium. b The previously identified tissue-level CXCL10+ CCL2+ state corresponds to cluster 1 (orange), and the FCN1+ inflammatory macrophage state corresponds to cluster 2 (yellow). Macrophages from each tissue source are displayed separately in the same UMAP coordinates as in a. c Heatmap indicates the concordance between stimulatory conditions and integrative cluster assignments. Z-score of the number of cells from each stimulatory condition to the integrative clusters is shown. d For the blood-derived stimulated macrophages, the proportions of CXCL10+ CCL2+ macrophages of total macrophages per stimulated donor are shown. e PCA analysis on the identified inflammatory macrophages. The first PC captures a gradient from the FCN1+ state to the CXCL10+ CCL2+ state. f Upon this, macrophages from severe COVID-19 mapped to PC1 present a shift in cell frequency between the FCN1+ and CXCL10+ CCL2+ (Wilcoxon rank-sum test P = 1.4e−07). The TNF-α stimulated macrophages (mean − 0.27) were projected to the left of the FCN1+ tissue macrophages (mean − 0.14), while the IFN-γ (mean 0.10), and TNF-α and IFN-γ (mean 0.23), stimulated macrophages were projected to the right of the CXCL10+ CCL2+ tissue macrophages (− 0.03). g Genes associated with CXCL10+ CCL2+ driven by PC1 show high expression levels on the severe COVID-19 macrophages and also TNF-α and IFN-γ stimulated blood-derived macrophages. We recapitulate the gradient observed in vivo across multiple diseases by stimulating macrophages ex vivo with synergistic combinations of TNF-α and IFN-γ