DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection

Abstract

Hepatitis C virus (HCV) poses a worldwide health problem in that the majority of individuals exposed to HCV become chronically infected and are predisposed for developing significant liver disease. DNA microarray technology provides an opportunity to survey transcription modulation in the context of an infectious disease and is a particularly attractive approach in characterizing HCV-host interactions, since the mechanisms underlying viral persistence and disease progression are not understood and are difficult to study. Here, we describe the changes in liver gene expression during the course of an acute-resolving HCV infection in a chimpanzee. Clearance of viremia in this animal occurred between weeks 6 and 8, while clearance of residual infected hepatocytes did not occur until 14 weeks postinfection. The most notable changes in gene expression occurred in numerous interferon response genes (including all three classical interferon antiviral pathways) that increased dramatically, some as early as day 2 postinfection. The data suggest a biphasic mechanism of viral clearance dependent on both the innate and adaptive immune responses and provide insight into the response of the liver to a hepatotropic viral infection.

FIG. 1

HCV infection profile of the chimpanzee used in DNA microarray studies. Chimpanzee 4x0271 was inoculated with HCV genotype 1a, H77 strain, and serial serum and liver biopsy samples were obtained during the course of infection. Serum ALT values were measured as an indication of liver damage (● ; horizontal line indicates upper limit of normal). Quantitative RT-PCR (TaqMan) values for viral RNA in the serum or liver are given as genome equivalents per milliliter of serum (shaded bars) or micrograms of total liver RNA (unshaded bars), respectively. Seroconversion for anti-HCV antibodies was monitored by third-generation ELISA (+ and −). d, day.

FIG. 2

Microarray analysis of changes in liver gene expression during acute HCV infection. FC of 3.5 or greater compared to the preinoculation values for a subset of genes are shown in rows from days (d) 2 and 7 and weeks 2, 4, 6, 8, and 14. Genes are listed by open reading frame (ORF) (GenBank accession number or TIGR database HT number) and name and are grouped into functional classes (titles in gray). IFN-inducible genes (22) are in red. Yellow boxes, FC of 5.0 to 9.9; green boxes, FC of 10.0 to 20.0; blue boxes, FC of >20; red boxes, FC of >90.0. Genes represented on the array multiple times (e.g., FAS/APO-1) reflect probe sets obtained from different accession numbers.

FIG. 3

IFN-inducible genes are expressed in distinct temporal patterns. Many of the IFN-inducible genes have overlapping patterns of expression, although several exhibit distinct temporal changes in peak expression levels. At least three distinct patterns were observed: genes with an early maximum expression level (□ [ISG15] and ◊ [16-Jun]), genes with a late peak in expression level (● [IP-10] and ▴ [MK]), and genes with an intermediate pattern in which maximum levels were reached early and were sustained (X [p27]). d, day.