Fig. 6: Transcriptional convergence of MHC-II+;club and AT2 cells onto the alveolar Krt8+ADI cell state.

a Velocity plot displays the UMAP embedding colored by Louvain clusters with velocity information overlaid (arrows). b Velocity plot of a subset of the data only showing alveolar identities and club cell subsets. RNA velocity shows contribution of Scgb1a1+ club cells to both Krt8+ ADI and AT2 identities. c Diffusion map of Louvain clusters 2, 10, and 9 colored by inferred terminal state likelihood reveals two distinct transdifferentiation trajectories from activated AT2 and MHC-II + club cells towards a Krt8+ cell state. d Diffusion map colored by groupings derived from Gaussian Mixed Model Clustering. Red and blue colors represent AT2 and MHC-II + club cell differentiation bridges towards the Krt8+ ADIs. Grey colors represent cells at endpoints. e The lines indicate smoothed relative frequencies across time points of cells within the AT2 (red) and MHC-II + club cell (blue) differentiation bridges. f The lines illustrate smoothed expression levels of Scgb1a1, Krt8, and Sftpc across the trajectory, marking cell identities. The dashed vertical line indicates the peak of Krt8 expression. g The heatmap shows the gene expression patterns along the differentiation trajectory based on the inferred likelihood of detection for 3036 altered genes. h Line plots show the smoothed relative expression levels of selected transcriptional regulators across the converging trajectories. The dashed vertical line indicates the peak of Krt8 expression. For (e), (f), and (h), gray colors represent the 95% confidence interval derived from the smoothing fit.