Fig. 4: Comparison of rhesus and human macrophage subsets.

a UMAP of macrophage subsets in lungs from six healthy human donors (GEO: GSE135893). b UMAP of macrophage subsets in lungs from three healthy rhesus macaques (GEO: GSE149758). c DotPlots showing the expression of marker genes. The color gradient represents the level of expression and the size of the dot represents the percentage of cells expressing a given gene. d UMAP of BAL samples from human donors that are healthy (n = 3), or suffering from moderate (n = 3) or severe (n = 6) COVID-19 (GEO: GSE145926) mapped to the healthy lung reference using the Seurat MapQuery function. e Percent of predicted cell types out of all macrophage/monocytes in each human BAL sample. The black bar indicates the median. Statistical analysis was performed using pairwise two-tailed Mann–Whitney U test in R v4.2.2. p value * = 0.02. Contribution of each predicted macrophage/monocyte subsets in human BAL toward the production of the pro-inflammatory genes and ISG—pooled (f) and individual (g). The percentage contribution was calculated by dividing the sum of normalized expression of a given gene in a macrophage/monocyte subset by the sum of the normalized expression of the gene in all macrophage/monocyte subsets. The black bars represent the median. Statistical analysis was performed using two-tailed Wilcoxon signed rank test in R v4.2.2. *p value 0.03 for all except FABP4 vs. Proliferating for IL6, IL1B, TNF, CXCL3, CXCL8 and SPP1hi vs. Proliferating for CCR2: p value = 0.04. Source data (e–g) are provided as a Source Data file.