Fig. 3: Alveolosphere scRNA-seq detects Fn1+ aberrant epithelial cells. | Communications Biology

Fig. 3: Alveolosphere scRNA-seq detects Fn1+ aberrant epithelial cells.

From: Triggering AHR resolves TGF-β1 induced fibroblast activation and promotes AT1 cell regeneration in alveolar organoids

Fig. 3

A: Single cell suspension from alveolosphere assay were analyzed using scRNA-seq at indicated timepoints post assay setup. Untreated control (Day 0) and three treatment groups (DMSO, 10 µM DB-11-BE87, 10 µM QA-92-TQ17) were included to understand DB-11-BE87’s influence on TGF-β1 treated alveolosphere culture. 4 cell categories containing 117, 450 integrated cells from all samples are colored on UMAP. B Cell proportions of major cell categories for the indicated timepoint and compound treatment in the alveolosphere assay. C UMAP for all epithelial cells integrated from all conditions. 8 cell types and states were identified. D Expression of canonical epithelial cell type markers. E RNA velocity vectors projected over UMAP plot of AT1, AT2, Krt8 + ADI, and Transitional AT2 epithelial cell types, from all samples. F Expression of individual genes among cells from (E). G Degree of similarity between indicated cell types/states from patient derived samples (x-axis) and alveolosphere culture (y-axis). Color code indicates scaled spearman correlation coefficient (z-score) of two transcriptomes. H Fraction of Krt8 + ADI cells that expressed Fn1, across individual samples collected on day 11. I Violin plot of Fn1 expression in Krt8 + ADI cells from samples in three treatment groups.

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