Fig. 3: Sorted CD44^Hi Sftpc^C121G AT2s are enriched in profibrotic mediators.

a UMAP representation of Cd44 expression in aberrant intermediate cells. b (left) Representative (n = 3 biological replicates) immunofluorescence staining of Sftpc^WT and non-fibrotic and fibrotic regions of Sftpc^C121G lungs (identified by picrosirius red (PSR) staining; see Supplementary Fig. 6) showing CD44+ /KRT8+ cells in fibrotic regions (scale bar = 50 μm). (right) Quantification of KRT8+ /CD44− and KRT8+ /CD44+ cells per 350 μm × 550 μm high-power field. Ordinary one-way ANOVA with adjustments (Tukey’s) made for multiple comparisons for total KRT8+ cells per HPF (*) and CD44+ /KRT8+ cells per HPF (#). Data are presented as mean values ± SEM. c Flow cytometry approach to CD44 AT2s. Total lung epithelial cells (EpCAM+ /CD45−/PECAM−) were gated for AT2s (CD200+ /CD104−) before isolating CD44^Hi/^Lo cells from Sftpc^WT and Sftpc^C121G lungs. d Percent AT2s that are CD44^Hi in Sftpc^WT and Sftpc^C121G mice. Two-way Student’s t test; n = 4 biological replicates. Data are presented as mean values ± SEM. e PCA demonstrating bulk transcriptomic differences between CD44^Hi/Lo AT2s from Sftpc^WT and Sftpc^C121G mice. f Heatmap of all differentially expressed genes across all conditions (>1.5 fold change, adjusted p value < 0.05, adjustments were made for multiple comparisons), grouped by k-means clustering. Select genes are highlighted within each cluster. g Heatmap of murine aberrant basaloid and AT2 marker genes grouped by k-means clustering. h Gene expression by RT-qPCR from freshly sorted AT2s. Ordinary one-way ANOVA with adjustments (Tukey’s) made for multiple comparisons; n = 3 biological replicates from Sftpc^WT and n = 4 from Sftpc^C121G. Data are presented as mean values ± SEM. i Volcano plot showing differentially upregulated (red) and downregulated (blue) genes (>1.5 fold change (vertical lines), adjusted p value < 0.05 (horizontal line), adjustments were made for multiple comparisons) between CD44^Hi and CD44^Lo Sftpc^C121G AT2s annotated with AT2 marker genes, profibrotic marker genes, and mouse aberrant basaloid genes. j Gene ontology analysis for upregulated biological processes in CD44^Hi Sftpc^C121G compared to CD44^Lo Sftpc^C121G AT2s. k Heatmap of the KRT5-/KRT17+ gene list grouped by k-means clustering. Source data are provided as a Source Data file. p value is shown if p  <  0.05.