Fig. 6: hAEC2 transdifferentiates into KRT5⁺ basal cells through ABI cells, in vitro and in vivo.

a, scRNA-seq of freshly sorted HTII-280⁺ hAEC2s (day 0) and hAEC2s co-cultured with AHLM at days 7, 14 and 21. b–d, Pseudotime ordering of epithelial cells from day-0, 7, 14 and 21 organoids (b,c) identifies an hAEC2s → ABIs → basal → club → ciliated cell trajectory based on gene expression levels over pseudotime trajectory that was confirmed via RNA velocity (d). e, Immunofluorescence staining of day-7 hAEC2 + AHLM organoids identifies the presence of KRT17⁻/KRT8^high/SFTPC⁺ ABI1 (14%) and KRT17⁺/KRT8⁺/SFTPC^low ABI2s (23%) along with SFTPC⁺ hAEC2s (43%) and KRT17⁺/KRT5⁺ basal cells (9%). Representative of n = 2 biologically independent experiments, each performed in technical triplicate. Data are presented as the mean of biological replicates. f, IPA of the DEGs between AEC2s, ABI1 and ABI2s identifies the upregulation of alveolar signalling (NKX2-1, ETV5) in AEC2s, WNT and BMP signalling in AEC2s and ABI1 and fibrotic/airway signalling pathways (TGF-β1, HES1, extracellular matrix genes, SOX2 and TP63) in ABI2s. g,h, Re-analysis of IPF epithelium from Habermann et al.⁸ (g) to include basal cells along with PATS-like cells (encompassing transitional AEC2s and KRT17⁺/KRT5⁻ cells on UMAP) with pseudotime ordering (h). i, Heatmaps comparing lineage-specific gene expression of KRT17⁺/KRT5⁻ basaloid cells in IPF (labelled as PATS-like cells by Kobayashi et al.²⁰) and ABIs in a 3D organoid.

Source data