Fig. 4: Multiomic demonstration of progenitor cell characteristics.
A Paired heatmaps of progenitor-related genes with high accessibility (GAS) and high integrated expression (GIS) in SH5 compared with homeostasis hepatocytes (HH1, HH2, HH3, HH4). Those genes were called progenitor cell related genes (PRGs). P was calculated by Wilcoxon. B GO term enrichments for genes with high accessibility and high integrated expression in SH5 compared with homeostasis hepatocytes (HH1, HH2, HH3, HH4). C Line plots showing the module score of PRGs for Stereo-seq data. The color of lines representing time point. The nine points on the curve representing liver zonation (1 and 2 pericentral,3–6 midzonal and 7–9 periportal). ***P < 0.001. P was calculated by T-test. Error bars: mean ± SD. Each point represents one zonation layer along the CV-PV axis (Data points correspond to 9 zonation layers (CV-PV axis), each resolved into 10 sub-regions). D K-means clustering (k = 2) of Stereo-seq data based on PRGs module scores identifies distinct expression domains. Color gradient represents PRG expression levels. Deep red represent high expression (PRGhigh) and light red represent low-expression (PRGlow). E Genes expression for Tnfrsf12a and Sox9 (F) in the Stereo-seq data grouped by PRGs module score. P was calculated by T-test. (***P < 0.001). The horizontal line within each violin plot denotes the average gene expression level. G UMAP showing the hepatocytes clusters in the 8 h post-PHx scRNA-seq grouped by PRGs. H Gene expression for Sox9 and Tnfrsf12a across hepatocytes clusters. Color indicates relative expression across all clusters and dot size indicates the percentage of cells in that cluster expressing the gene. P was calculated by Wilcoxon. I The model score of DAGs of SH5 for scRNA-seq hepatocytes clusters. The lines in the middle of the boxplots mean the median. P was calculated by T-test. (***P < 0.001). J The expression of progenitor-related genes (Portion) in scRNA-seq hepatocytes clusters. Color indicates relative expression across all clusters and dot size indicates the percentage of cells in that cluster expressing the gene. P was calculated by Wilcoxon. K GO term enrichments for genes high expression in Cluster2. L The number of shared DAGs between hepatocyte subtypes in PHx model and LPLCs in DDC model. M The module score of DAGs of LPLCs for hepatocyte subtypes. The lines in the middle of the boxplots mean the median. ***P < 0.001 (SH5 vs other hepatocyte subtypes). P was calculated by T-test.
