Figure 7

ACE2 and components of the KKS, RAS and CS are differentially expressed throughout alveolar epithelium differentiation dynamics. (a) Two-dimensional dbMAP embedding of 37,449 alveolar cells transcriptomes. Cells are colored by their assigned subtype. Main cell types are indicated. (b) Visualization of ACE2 expression in the dbMAP embedding. The expression pattern prioritizes AT1 cells, and less so AT2 cells. (c) Cell cycle scoring of each single-cell and its assigned cell-phase. Note how all phases are detected across the embedding, albeit at different proportions. (d) MKI67 expression visualization in the dbMAP embedding with two different coloring thresholds. AT2 cells express MKI67 at higher levels (left; arrow), and mucous, basal, club and pro-ciliated cells present lower, yet consistent levels of MKI67 expression (right; arrows). The * indicates a fixed expression level, for easier visualization. (e) AT2 progeny differentiation dynamics. The star represents the start cell used in computations. Left: pseudotime score for each cell, i.e. how much each cell is advanced in the differentiation trajectory. Right: differentiation potential for each cell, i.e. the probability that cell i transit into an adjacent cell j, also seen as entropy. Note that the intermediate states (pointed by arrows) present a higher differentiation potential than terminally differentiated cells. (f) The three terminal states detected for the AT2 progeny—alveolar type 1 (AT1), mucous and ciliated cells. The heatmaps on the left column indicate relative expression changes (left to right) throughout the differentiation trajectories shown on the right column that correspond to terminal states. (g) Gene expression trends of ACE2 and components of the KKS, RAS and CS expressed in alveolar cells. ACE2 expression is directly associated with the maturation of AT1 cells, whereas KNG1 and KLKB1 are preferentially expressed in intermediate states. REN, FGG and BDKRB1 are preferentially expressed in AT2 progenitors at the beginning of the differentiation process, and BDKRB2 expression is directly associated with the differentiation mucous cells. (i) Visualization of co-expression (yellow) by coloring overlap. KNG1 (red) is co-expressed with KLKB1 (green, top) in intermediate states corresponding to club cells, but barely co-expressed with ACE2 (green, bottom). (h) Visualization of FGG, REN and BDKRB1 expression in the dbMAP embedding. As shown in (g), these genes are preferentially expressed by AT2 progenitors, being undetected in terminally differentiated states.