Fig. 2: Characterization of mesenchymal cell activation after epithelial injury in SRC mice.

a Scheme of cell sorting and scRNA-seq strategy. Created with BioRender.com. b UMAP embedding showing mesenchymal cell types sorted from uninjured SRC mouse lungs (n = 2 mice). c Dot plot showing the average scaled expression and percentage of cells expressing cell-type specific marker genes across the mesenchymal cell populations in uninjured lungs. d UMAP embedding showing the distribution of GFP⁺-sorted dividing mesenchymal cells on day 2 (n = 12 mice) and day 3 (n = 4 mice), and non-dividing total cells on day 2 (n = 3 mice) and day 3 (n = 2 mice). The pie chart depicts the percentage of the mesenchymal cell types among the diving cells (light blue: alveolar fibroblasts, purple: adventitial fibroblasts, gray: peribronchial fibroblasts, orange: pericytes, green: SM cells). e Lung epithelial organoid cultures with adventitial fibroblasts or alveolar fibroblasts as supporting cells, taken after three weeks of culture. The inset in the upper image shows the morphology of one organoid magnified twice as much as in the main figure. Images are representative of two independent experiments. f Heatmap of differentially expressed ligands among the different mesenchymal cell types on day 0. Upregulated genes in adventitial fibroblasts are bold. g Average normalized expression of Bmp4, Tgfb3, and Mif on day 0, 2, and 3 in all mesenchymal populations. Asterisks denote significant differential expression on day 2 or 3 compared to day 0, when considering FC ≥ 1.5 and p_adj ≤ 0.05 (MAST test, all DEG had a p_adj < 0.001). adv_fibro adventitial fibroblasts, alv_fibro alveolar fibroblasts, peribr_fibro peribronchial fibroblasts, SM_cells smooth muscle cells.