Fig. 1: Single-cell RNA-seq analysis of primary tumor material illustrates fetal and embryonal tumor signatures.

a UMAP plot based on unsupervised clustering, annotated per cell type or tumor signature (left) and patient identity (right) of epithelial cell subsets from the Song et al.²¹ dataset. The table shows the number of cells per signature per patient. b Heatmaps showing the top differentially expressed genes between tumor cell populations and hepatocytes. WNT signaling pathway target genes are upregulated, especially in the WNT-high embryonal tumor subpopulation, and marked in red. c Violin plots showing expression of select markers. d Gene set enrichment analysis showing hallmark gene sets significantly enriched in the fetal and embryonal clusters, compared to each other. NES: normalized enrichment score. Adjusted p-value < 0.05, calculated using the fgsea package. e UMAP plot showing embryonal and fetal cells identified in an external snRNA-seq dataset (Hirsch et al.¹⁷) from a single tumor (left). Violin plots showing TF regulon activity scores for HNF4A and LEF1 for these clusters (right). f UMAP plot showing embryonal and fetal cells identified in scRNA-seq data of tumors from PT9 and PT13 (left). Violin plots showing TF regulon activity scores for HNF4A and LEF1 for these clusters (right). g Venn diagrams showing the amount of overlap between the top 200 differentially expressed genes of the scRNA clusters described in this paper, the snRNA-seq data of Hirsch et al.¹⁷ and scRNA-seq data of PT9 and PT13 (“PMC tissues”). h Violin plots showing embryonal and fetal signature scores (50 genes each) derived from histology-guided laser microdissection RNA-seq of 17 patients (Wu et al.³⁰) on our tumor clusters (left). Venn diagrams show the amount of overlap between the signatures from Wu et al. (50 markers each) and ours (200 markers each) for fetal and embryonal cells. i Violin plots showing regulon activity scores for hepatic TFs (above) enriched in fetal tumor cells and WNT/β-catenin co-factors (below) in embryonal tumor cells. j UMAP plot based on the SCENIC regulon activity scores.