Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance
Fig 3
The peripheral immune response to acute HCV infection is characterized by upregulated innate antiviral/interferon signatures.
(A) Barcode plots depicting differential enrichment of a PBMC ISG set for the indicated acute HCV time points relative to Pre-Infection. Red-blue color bar represents all genes ordered by differential expression statistics (moderated t statistic) for the designated contrast. PBMC ISG set member genes are highlighted by vertical black lines. Corresponding line plot displays sliding average of set enrichment. MROAST and CAMERA test p-values for PBMC ISG set enrichment are presented with each plot. (B) Heatmap displaying scaled expression values (normalized log2 read counts per million, scaled to z-scores by gene) for acute HCV PBMC ISG signature genes (as described in text) at Pre-Infection and Early acute time points. Select ISGs are annotated. Sidebars designate differential ISG expression in the indicated transcriptomics study (red indicates concordant upregulation): Type I IFN–PBMC and Type II IFN–PBMC [30], Acute HCV–Liver (Human) [19], Acute HCV–Liver (Chimpanzee) [25]. See also S4 Table. (C) Plasma CXCL10 concentration (pg/mL) for the indicated acute HCV time points. Each color (points/lines) denotes data from a single patient. (D) Plasma CXCL10 concentration (pg/mL) and CXCL10 RNA-Seq gene expression measures (regularized log transformed counts) from corresponding PBMC samples. Point color denotes time point analysis group, point shape denotes HCV viremia status (presence/absence of viral RNA by RT-PCR).