Identification of genes that are differentially regulated during chronic hepatitis C virus infection of the liver using RNA-Seq

Robinson, M. and Domingues, P. and Gatherer, Derek and Mills, P. and Patel, A. and McLauchlan, J. (2012) Identification of genes that are differentially regulated during chronic hepatitis C virus infection of the liver using RNA-Seq. Immunology, 137 (Suppl.). p. 117. ISSN 0019-2805

Abstract

Purpose/Objective: Hepatitis C virus (HCV) establishes a chronic infection in approximately 80% of infected individuals and is a leading cause of liver disease. Knowledge gaps exist with regard to the mechanisms of viral replication within hepatocytes and disease progression during chronic infection. The present study aimed to explore the regulation of gene expression during chronic HCV infection in liver biopsy samples. Materials and methods: RNA was isolated from liver biopsies from patients who were chronically infected with HCV. Biopsies from noninfected patients with other liver diseases were used as controls to focus on HCV-associated changes in hepatic gene expression. This excluded altered gene expression patterns resulting from either inflammation or fibrosis. We applied high-throughput RNA-Seq technology to provide a more complete overview of the interactions between HCV and the host. Differential gene expression was analysed using DESeq and edgeR and gene enrichment analysis was performed with GSEA and Gestalt. Results: Expression profiling identified 181 genes that were differentially regulated (P < 0.05 after adjusting for multiple testing) between infected and uninfected biopsies. These genes fell into distinct regulatory pathways including immune response, antigen processing and interferon*stimulated genes (ISGs). Of note a significant enrichment of the IFIT and PARP gene families was observed as well as upregulation of multiple genes involved in the ISGylation pathway such as ISG15, UBE2L6 and HERC5. Validation of these gene targets was carried out in liver biopsies and tissue culture cells. Functional analysis of ISG15 indicated that depleting mRNA levels resulted in increased HCV RNA abundance. On-going studies are underway to explore the role of IFIT and PARP family members during chronic HCV. Conclusions: High-throughput sequencing has shed new light on the pathways that may regulate HCV replication and associated pathology during chronic infection. Future studies will address how HCV is able to persist in the presence of a stimulated IFN response within the liver.