Fig. 4.

scRNA-seq reveals YAP induction in EC and KC subclusters. A Scheme illustrating the experimental setup. Livers from WT, YAP^KO, TAZ^KO, and DKO mice were digested in situ to achieve pure and viable murine HCs (20–30 µm), smaller NPCs, and infiltrating immune cells. Cell fractions were mixed at a ratio of 7:3 and applied to the 10x  scRNA-seq platform. Figure 4A was modified using Servier Medical Art (http://smart.servier.com). B T-distributed stochastic neighbor embedding (t-SNE) plot showing annotated and color-coded cell types derived from WT, YAP^KO, TAZ^KO, and DKO livers. HC hepatocytes, HSC hepatic stellate cells, NK natural killer cells, B B cells, MAC macrophages, DC1 dendritic cells cluster 1, BEC biliary epithelial cells, EC endothelial cells, KC Kupffer cells, DC2 dendritic cells cluster 2, Mix cells not expressing distinct marker genes. C t-SNE plot illustrating eight subtypes of ECs. The different EC subclusters are characterized by specific marker genes and cellular processes such as EC-0 (CDH13, WNT2, KIT, PLPP1 representing pericentral ECs) and EC-1/EC-6 (EFNB1, LTBP4, LY6A, NTN4, representing periportal ECs). D Violin plot showing YAP induction in the subclusters EC-2 and EC-7 from YAP^KO and DKO animals but not WT and TAZ^KO mice. Other EC subclusters did not show a comparable YAP expression pattern. E t-SNE plot illustrating five subtypes of KCs. The different KC subclusters are characterized by specific marker genes and cellular processes, such as KC-0 (M1 polarization-like phenotype) and KC-1 (lipid metabolism). F Violin plot for subcluster KC-4 demonstrating the induction of YAP in liver tissues from YAP^KO and DKO mice. Other KC subclusters did not show a comparable YAP pattern (exemplified for KC-1)