Fig. 2

Among all cell-types decomposed in the TCGA and LCI bulk liver cohorts, Prol has the highest enrichment in HCC when compared to adjacent non-tumor tissue. The Prol cell-type shows consistent upregulation in HCC tumors in two independent liver bulk cohorts. a, b Proportions were estimated in the liver bulk RNA-seq data for the major cell-types identified in the single-cell level data and then tested for differential abundance between the tumor and non-tumor samples. The upper panel shows the T-statistic from a paired t-test between tumor and adjacent non-tumor tissue, with FDR-adjusted p-values calculated from a paired Wilcoxon test. The bottom panel shows a bar plot of the proportion estimates separated by tumor status. The differential abundance tests highlight the Prol cell-type as upregulated in the (a) TCGA (n = 49) and (b) LCI (n = 209) cohorts. B cell proportions were not estimated for LCI (b) as its marker genes did not show evidence of co-expression. c, d Association of the Prol cell-type with HCC tumors is highlighted by the log₂ fold-changes (log₂FC) of tumor over adjacent non-tumor samples for the marker genes of the cell-types that are indicated on the y-axis. Log₂FC values were derived from a paired differential expression (DE) analysis in (c) TCGA (n = 49) and (d) LCI (n = 209) cohorts. e–h The Prol cells/nuclei significantly express tumor-elevated genes, as shown by droplet scores in the single-cell level data for tumor-elevated genes derived from the TCGA and LCI cohorts. Genome-wide DE analysis was performed between the paired tumor and non-tumor samples, and genes with an FDR-adjusted p-value less than 0.05 and a log₂FC greater than 1 were considered tumor-elevated genes. Module scores of the tumor-elevated genes for each droplet were calculated based on their expression compared to a background set. e, f UMAP plots for (e) TCGA and (f) LCI are shown with cells and nuclei colored by their tumor module score. g, h Bar plots show the droplet tumor scores calculated from (g) TCGA and (h) LCI tumor-elevated genes separated by major cell-type. e–h Asterisks denote a significant difference in gene scores between Prol and non-Prol cells/nuclei as assessed by a Wilcoxon test. Significance levels for p-values: *p < 0.05, **p < 0.005, ***p < 0.0005