Fig. 2: Single-cell RNA-seq analysis reveals disease-specific macrophage subpopulations in FHP lungs.

A t-SNE visualization of ten macrophage subclusters. B Relative percentage of sample origins across macrophage subclusters. C t-SNE visualization of FN1^high macrophages, PLA2G7^high macrophages, MS4A6A^high macrophages, and other macrophages. D Multiplex immunofluorescence images of CD68, PLA2G7, and MS4A6A in lung tissues from the patient with FHP. Scale bar = 10 μm. White arrow, CD68⁺ MS4A6A⁺ cells(upper)/CD68⁺ PLA2G7⁺ cells(lower). E AUCell analysis of the relative gene set enrichment scores in Inflammatory response signature. F Scatter plot showing the correlation between M1 and M2 marker gene expression. G, H AUCell analyses of the relative gene set enrichment scores in M1 (G) and M2 (H) macrophage signatures. The t-SNE maps showing AUC scores of selected gene signatures (left); the box plots showing AUC scores of selected gene signatures in each cell type (middle) or sample group (right). I Trajectory analysis of FN1^high macrophages, PLA2G7^high macrophages, MS4A6A^high macrophages and other macrophages using Monocle 2. J STAT1 motif showed greater enrichment of regulon activity for PLA2G7^high and MS4A6A^high macrophages using SCENIC analysis. K t-SNE visualization of AUC values of STAT1 motif in macrophages. L Schematic developmental trajectories of macrophage subpopulations in FHP lungs. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.