Fig. 3. HCV but not HBV infection impairs expression of peroxisomal genes in Huh7.5.1^dif cells and liver tissue of patients.

(A) HCV infection impairs metabolic pathways associated to peroxisomal function and lipid homeostasis. GSEA of RNA-Seq data from liver tissue of 25 chronic HCV-infected patients vs. 6 non-infected individuals²⁶, and transcriptomics and proteomics of HCV-infection time-course of Huh7.5.1^dif relative to mock-infected cells (n=2). (B) Expression of 11 peroxisomal genes is significantly (p<0.05, Wald test) suppressed by HCV in Huh7.5.1^dif and in liver tissue of patients with chronic HCV infection²⁶. Log fold change of leading-edge gene expression of the HALLMARK_PEROXISOME gene set (A). (C) Peroxisome marker expression is significantly (p=0.0048, T-Test) perturbed in HCV-infected hepatocyte-like cells. Immunofluorescence microscopy of Huh7.5.1^dif cells infected for 3 days with HCVcc. The peroxisomal marker catalase (CAT) is stained in red, nuclear DNA (DAPI) in blue and HCV (NS5A) in green (see also supplementary Fig. S5). Quantification of catalase-stained peroxisomes in 25 random HCV-infected cells and 25 mock cells is shown in box/whiskers; bar represents 200 μm. (D) HBV infection promotes peroxisome function. GSEA of transcriptomics of HBV-infection of HepG2-NTCP for 10 days (n=3), and primary human hepatocytes (n=3) infected for 40 days with HBV (genotype D) (GSE69590). NES are displayed in red (increased), blue (decreased), and gray (no significant change). Temporal analysis of infected Huh7.5.1^dif are presented as global trend (global) and individual timepoints. Statistical cut-off for GSEA of liver tissues was FDR q<0.05 and for Huh7.5.1^dif p<0.005.