Comparison of gene expression profiles of HCV-specific CD8 T cells from resolving and chronic patients.

T cell exhaustion is a well-defined process diminishing the efficacy of the CD8 response in persistent viremia. What is less understood is whether early differences in T cell regulation already predetermine the fate of the T cell response and infection outcome. Its dichotomous outcome that is unique among human viral infections makes hepatitis C virus infection uniquely suited to compare transcriptional regulation between HCV-specific CD8 T cells that do and do not achieve viral control. Using differential gene expression and gene set enrichment analyses we validate HCV-specifcic CD8 T cell transcriptional modules. We sorted HCV-specific CD8 T cells from 3 resolving patients and 7 chronic patients at the earliest available time point during the acute phase of infection (≤21 weeks).