Fig. 5: A distinct club cell state shows high connectivity to alveolar cell identities after injury.
a The PAGA graph visualizes potential cell-type transitions and the topology of the data manifold. Nodes represent Louvain clusters and thicker edges indicate stronger connectedness between clusters. b Principal component analysis of artificially generated cluster-specific and doublet in silico bulk samples shows that Krt8+ ADI cells map orthogonal with respect to linear activated AT2 to AT1 (left) and MHC-II + club to AT1 (right) differentiation profiles. In silico bulk samples are colored by cluster as derived from the PAGA map in (a). Artificially generated doublets are colored in black. c, d The plots visualize the UMAP embedding of Club cells colored by Louvain clustering (c) and by time point (d). e The heatmap shows the average expression levels of marker genes across the three club cell clusters. f UMAP embeddings show distinct expression patterns for selected marker genes. g Principal component analysis of artificially generated cluster-specific and doublet in silico bulk samples shows that MHCII + club cells map orthogonal with respect to a linear connection between dendritic and club cells. Dendritic cell samples and artificially generated doublets are colored in blue and black, respectively. h The bar graph shows the annotation enrichment score78 for selected examples of gene categories with significant enrichment (FDR < 5%) in either activated Club (positive scores) or Club cells (negative scores). i Immunofluorescence staining of mouse airways shows CC10+ club cells (green) and Cst3+ cells (red), DAPI (white). Note the partial overlap of Cst3+/CC10+ airway cells (highlighted by yellow arrowheads). Scale bar = 100 microns; representative images from n = 3 bleo-treated mice. j Revised model of club cell heterogeneity in mouse airways.
