Fig 2: ATM and p53 pathways are activated in T1/early HCV-specific CD8+ T cells.a Interaction network of genes involved in at least five of the eight dysregulated processes identified by GSEA (outlined in Supplementary Fig. 2). The network was generated using STRING v. 10.5. Node colors refer to enriched pathways associated with the proteins represented in the network. Line thickness indicates the degree of confidence prediction of the interactions. b Intracellular staining for total p53 of dextramer positive virus-specific CD8+ T cells from patients in the acute phase of HCV infection (chronically evolving T1/early n = 19 and HCV self-limited T1/early n = 14) or from healthy controls (n = 14), performed after overnight stimulation with anti-CD3/anti-CD28 (ex vivo staining). c Intracellular staining for phospho-p53 (Ser15) of dextramer positive virus-specific CD8+ T cells from PBMCs derived from patients in the acute phase of HCV infection or from healthy controls was performed with no stimulation and after overnight anti-CD3/anti-CD28 stimuli (left and middle panels, respectively). The plot on the right represents the ratio between anti-CD3/anti-CD28 stimulated and unstimulated virus-specific CD8+ T cells. d Intracellular staining for phospho-ATM (Ser1981) of dextramer positive virus-specific CD8+ T cells as in c. e Phospho-p38 (Thr180) intracellular staining of dextramer positive virus-specific CD8+ T cells as in c. Data in panels from b to e are presented as median fluorescence intensity (MFI), with median values indicated by horizontal lines. Different numbers of patients (represented by individual dots) were tested in each assay depending on dextramer-positive cell frequencies. Representative overlay histograms are shown next to each plot in panels from b to e. All data were analyzed with the Kolmogorov-Smirnov test. Differences between multiple groups were evaluated with the nonparametric Kruskal-Wallis test; p-values were corrected for pairwise multiple comparisons with the Dunn’s test (JASP software).