Gene expression profile at single cell level of virus-specific CD8+ T cells in subjects with past or current HCV infection.

CD8+ T cells play a central role in antiviral control. We used single cell RNA sequencing (scRNA-seq) to analyze the differences of HCV-specific CD8+ T cells isolated from subjects that are chronically infected by HCV, individuals that spontaneously resolved an acute HCV infection, and chronic HCV patients in treatment with direct-acting antiviral (DAA). We also profiled non-HCV virus-specific cells (CMV and FLU) to analyze the impact of HCV infection on the adaptive immune response. We selected our cohort from our biobank. We included 4 subjects with chronic HCV, 4 subjects with self-limiting HCV infection, 3 non-HCV-exposed non-diseased controls. We also evaluated 3 patients that went through 12 weeks of DAA therapy in 4 different time points: pre-treatment (Pre-tx), 2-4 weeks into the treatment (Early-tx), 8 weeks of therapy (Late-tx), and 12 weeks after therapy completion (Post-tx). We used the stored PBMCs to isolate virus-specific CD8+ T cells by sorting cells CD8+ CD3+ CD4- CD56- that were positive for barcoded-dextramers (dCODE Dextramers, Immudex). The sorted cells were partitioned for scRNAseq (10x Genomics), and gene expression and surface protein libraries were prepared using Chromium Next GEM Single Cell 5' Kit v1.1 (10x Genomics, Pleasanton, CA).