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Fig. 5 | Stem Cell Research & Therapy

Fig. 5

From: Drug metabolic activity is a critical cell-intrinsic determinant for selection of hepatocytes during long-term culture

Fig. 5

Global gene expression analysis of hepatocytes reveals a distinct hepatocyte group with proliferative capability. A Principal component analysis (PCA) for non-treated ProliHH (Puro(-)) at passage 1, 3, 6, 15 and 21), puromycin-treated ProliHH (Puro( +)) at passage 5, 15 and 25, PHH (PHH2064 and PHH2055), mature hepatocytes (MH), biliary epithelial cells (BEC: GSM4454532, GSM4454533, GSM4454534) and iPSC-derived hepatocyte-like cells (HLC-O and HLC-KI) by global gene expression. Right: Hierarchical clustering analysis of expression profiles of the samples shown in PCA. B, C Heatmaps of the liver-associated genes. Genes upregulated in mature hepatocytes (B) and bile duct epithelial cells (C) were used for the heatmap analysis (gene list: https://www.nature.com/articles/s41467-019-11266-x). The average gene expression in non-treated and puromycin-treated ProliHH was set to 0. Their expression levels were compared in groups of mature hepatocytes (MH), primary hepatocytes (PHH) and bile duct epithelial cells (BEC). The color bar indicates the signal intensity at log2 expression. D Heatmap for differentially expressed genes (1.5 < fold changes and p < 0.05) in the comparisons of PHH versus non-treated ProliHH versus puromycin-treated ProliHH. The color bars show the signal strength scaled by the z score. E Upregulated genes (1.5 < fold changes and p < 0.05) in non-treated and puromycin-treated ProliHH compared to PHH. Among the genes identified, 3,068 genes (83.6%) matched. Bar graph: Over-Representation Analysis (ORA) of 3068 genes with WebGestalt (WEB-based Gene SeT AnaLysis Toolkit) (FDR < 0.05, p < 0.01). F Heatmap showing the expression levels of top fetal hepatobiliary hybrid progenitor upregulated genes (gene list: https://www.nature.com/articles/s41467-019-11266-x) in PHH, non-treated and puromycin-treated ProliHH. The color bars show the signal strength scaled by the z score. G Gene Set Enrichment Analysis was performed to identify enriched gene sets in puromycin-treated ProliHH compared to non-treated ProliHH (FDR < 0.0001, p-value < 0.0001). H The top 15 gene sets enriched in puromycin-treated ProliHH. Gene sets that were significantly upregulated in puromycin-treated ProliHH compared to non-treated ProliHH were clustered by affinity propagation method (FDR < 0.05, p < 0.01) and ranked based on the normalized enrichment score1 (NES). I Heatmap of genes with upregulated expression during epithelial–mesenchymal transition in non-treated and puromycin-treated ProliHH (gene list: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0051136). The colored bars show the signal strength in scaled by z score. "Puro(-)": non-treated ProliHH, "Puro( +)_x1'': ProliHH treated with 1 μg/ml puromycin, "Puro( +)_x2'': ProliHH treated with 2 μg/ml puromycin

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