Fig. 1: Modeling the clinical prognostic liver signature (PLS) in a cell-based system.
a Experimental approach. b Analysis of HCV infection by qRT-PCR (log10 of relative RNA quantity normalized to GAPDH mRNA; mean ± SD, n = 3). Immunodetection of HCV E2 protein 10 days post infection. Scale bar: 50 µm. c PLS assay in Huh7.5.1dif cells. Heatmap shows expression of poor- and good-prognosis genes (186 gene signature). Results are representative of one out of three independent experiments performed in triplicate. d Analysis of the PLS after HCV Jc1 infection and antiviral treatment. PLS induction was determined by GSEA analysis using “mock” non-infected cells as reference. Simplified heatmaps show PLS global status and PLS poor- and good-prognosis gene expression. Results from two experiments performed in triplicate are shown. FDR false discovery rate, NES normalized enrichment score. e scRNA-Seq profiling reveals HCV-dependent induction of the PLS in Huh7.5.1dif cells. Heatmaps show: PLS global status and modulation of the poor-prognosis (FDR = 0.013) and good-prognosis genes (FDR = 0.016). White: non-infected cells, n = 17; black: infected cells, n = 23. f Enrichment scores of PLS gene modulation for their correlation with the HCV viral load measured at the single-cell level (Pearson correlation tests). g PLS assays in the cell-based models. Cell-based models were infected with different viruses or exposed to metabolic cues. HBV infection was performed in HepG2-NTCP cells and free fatty acids (FFA) treatment was performed in Huh7.5.1dif cells cocultured with LX2. Results are from three independent experiments. h PLS in clinical liver tissues from patient cohorts. HCV-related cirrhosis (Italy, n = 216 GSE156546; US, n = 145 GSE541027), HBV-related liver cancer (n = 199, GSE14520), alcoholic hepatitis (n = 22, GSE28619), and NASH (n = 72, GSE49541). Induction of the PLS was assessed by comparing diseased tissues with non-diseased tissues. i Induction of the PLS in cell-based systems was compared to liver transcriptome profiles from clinical cohorts using Subclass Mapping. j PLS deconvolution showing mean gene expression of the poor- and the good-prognosis genes in the main cell compartment within the liver. The scRNA-Seq dataset was extracted from GSE11546915. Source data are provided as a Source data file.
