Fig. 6: Epigenetic transcriptional repression in exhausted HCV specific CD8+ T cells from chronic patients.

a Six distinct functional groups of pathways enriched in upregulated genes (red) in T1/early and displaying the opposite trend (blue) in T2/late identified by GSEA (MSigDB, C2 canonical pathways and C5 Gene Ontology sets) in HCV-specific CD8+ T cells from chronically evolving patients. NES = normalized enrichment score; FDR = False Discovery Rate. In red, above the p-value columns, is shown the total number of genes significantly upregulated in T1/early and downregulated in T2/late in each group of pathways. b Heat-maps comparing the expression profiles of leading genes belonging to the DNA repair/damage response, metabolism and cell signaling pathways in chronic and resolved infections (see also the T2 sheets in Supplementary Data 2). c Mitochondrial (left panel, JC-1 staining) and proteasomal (right panel, ProteoStat staining) functions were assessed in dextramer-stained HCV-specific CD8+ T cells from T2/late chronic and T2/late self-limited HCV infection and in healthy controls following PBMC overnight stimulation with anti-CD3/CD28. MFI, Median Fluorescence Intensity. d Heat-map comparing the expression levels (average log₂ fold change) of epigenetic regulatory complexes (derived from the EpiFactors database as detailed in Methods section) in chronic vs. self-limited infection (T1/early), chronic vs. resolved infection (T2/late) and chronic (T2/late) vs. healthy controls. e Repressive H3K9me2 (upper panels) and permissive H3K9ac2 (lower panel) histone marks determined by flow cytometry in dextramer-stained HCV specific CD8+ T cells from T2/late chronic and T2/late resolved HCV patients or healthy controls. PBMC were stimulated overnight with anti-CD3/CD28 (ex vivo staining) or for 10 days with HLA-A2-restricted HCV-specific or FLU-specific peptides. Horizontal lines in panels c and e represent median values. Differences between multiple groups in panels c and e were evaluated with the non-parametric Kruskal-Wallis test; p-values were corrected for pairwise multiple comparisons with the Dunn’s test.