Fig. 1

Cellular composition and macrophage subclusters in silicotic lungs. a Flow chart of the study design and analysis. (b) UMAP plots showing the identified cell types annotated by known cell biomarkers (Supplementary Fig. S1). c Macrophage clusters (including AM and IM in (b)) were identified via Lyz2, as shown on UMAP feature plots, and the intensity of expression is indicated by purple color. d Clusters of cells expressing Lyz2 were subsets from the main dataset and reclustered, revealing five subclusters, including TRAMs, MertkhiMacs, Spp1hiMacs, S100a8/9hiMacs, and recMacs. e The percentage of macrophage subclusters in lung tissue as silicosis progresses. f Gene expression of key markers in each macrophage subcluster. g Predicted distribution of five macrophage subclusters in pulmonary niches