Fig. 2: Time-resolved scRNA-seq data of mesothelial cells in the lung Bleomycin-induced fibrosis model.

a Schematic of the sample preparation for the high-resolution mesothelial cell scRNA-seq dataset. Wild type mice received a single shot of Bleomycin at day 0. Lungs were harvested on the selected days (day 2 to day 54) and digested. Single cell suspensions were then sorted using Max sorting (negative gating for Cd45, Cd31, Ter119, Lyve1). Single cell suspensions were analyzed using scRNAseq. b UMAP of the time-scaled high-resolution mouse Bleomycin mesothelial cell dataset, color-coded for the newly identified lineages. c UMAP of the novel mesothelial cell lineages, highlighting the expression of the gene markers of the different clusters: Klf9 for Healthy, Ifi27l2a for metabolically active, Dcn for proteolytic, Saa3 for immune-modulator and Mgp for fibrogenic. d Partition-based graphic abstraction of the trajectories between the different identified populations. Upon Bleomycin installation, mesothelial cells differentiate to metabolically active cells. These metabolically active cells give rise to proteolytic cells. The proteolytic cells differentiate into immune modulator cells then into fibrogenic cells which eventually revert back to metabolically active cells. e Graphic predicting trajectory of interconversion of different mesothelial cell population relative abundance during Bleomycin-induced injury (x axis, day 0 to day 54). Up-regulated genes are shown for each step in the illustration underneath. f Gene driver plot, produced using the CellRank package, of the differentiation from metabolically active to proteolytic (right plot) and from Immune modulator to Fibrogenic. Plots highlight the most distinguishing genes corrrelating with the phenotype differentiation process. Created in BioRender. Kadri, S. (2025) https://BioRender.com/onyksnk.