Fig. 2: Transcriptional and chromatin accessibility profiles reveal a replicative rare cell progenitor and a pre-ionocyte state.

APOU2F3+ tuft-like cells are predicted to be progenitors of mature ionocytes. UMAP embedding of scRNA-seq profiles (dots) of rare epithelial cells in our deep lung cell atlas, colored by cell annotation (left) and showing RNA velocity vectors (right) directed from tuft-like cells to ionocytes. B Human large airways and human Large ALI cultures both contain POU2F3+ cells. Antibody staining of a section of the right primary bronchus for POU2F3 (red) and DAPI (blue) and LAE ALI for POU2F3 (green) and DAPI (blue). This staining has been repeated in 3 separate samples. C–EPOU2F3+ tuft-like cells include replicating and non-replicating cells. C Mean expression (dot color, relative expression) and percentage of cells (dot size) expressing selected cell identity and cell proliferation markers (columns) in different rare epithelial cell subsets (rows). D UMAP embedding of scRNA-seq profiles (dots) of rare cells, colored by cell cycle classification (left) or cell type annotation (right). E Large ALI cultures co-stained with POU2F3 (yellow, top) and MKI67 (purple, middle). The bottom panel shows cells expressing both markers (arrows). This staining was repeated in 3 samples. F Distinct chromatin state marks POU2F3+ progenitors. UMAP embedding of large airways epithelial cell scATAC-seq profiles (dots) colored by de novo cell type annotation. Zoom of boxed rare cells highlight chromatin accessibility at select gene loci associated with tuft cells, ionocytes, and progenitor cells.