HCV infection can lead to a high rate of chronicity, with 70–80% of infected persons developing persistent infection 
. The mechanisms by which HCV establishes chronic infection have been the subject of intense research. Failure of HCV-specific immune response, particularly of the T cells, has been proposed as the cause of chronicity 
. Studies in humans and chimpanzees have shown that T cell-mediated immunity is important for viral clearance 
. However, the pivotal question remains as to how the host immune response fails during the acute HCV infection so it can no longer control the virus, resulting in persistent infection. Thus it is crucial to define the molecular and cellular mechanisms by which the antiviral host response is activated and regulated during the early stage of acute HCV infection. Furthermore, because the major site of viral tropism is the liver, it is essential to study these events in the liver. One approach to elucidate this complicated process is to study the global gene expression profile in the liver during the acute phase of viral infection, and to discern unique patterns that are associated with either viral clearance or progression to chronic infection.
We previously reported the infection of three chimpanzees with an infectious HCV genotype 1b clone; one had acute self-limited infection and the other two developed chronic infection 
. We reported that regardless of the outcome of infection, peripheral T-cell responses were weak and comparable among the chimpanzees during the course of infection; however, intrahepatic T-cell response was not analyzed 
. In this study, serial liver biopsies were available in these chimpanzees and were used for cDNA microarray analysis. Analysis of these gene expression patterns revealed that a type I interferon response was induced during the early phase (4–8 weeks) of infection in all chimpanzees regardless of the outcome of infection. Various well-defined interferon stimulated genes were up-regulated in all the liver samples. This observation is consistent with previous studies describing that type I interferon response is rapidly induced in the liver in response to HCV infection 
Interestingly, several genes were specifically induced in the recovered chimpanzee during the early phase of infection but not in those chimpanzees with chronic infection. Two of the genes are interleukin enhancer binding factor 3 (ILF3) and cytotoxic granule-associated RNA binding protein (TIA1). This difference was also confirmed by quantitative RT-PCR (). Both of them are related to cellular immune response and may potentially herald the emergence of a robust T-cell response later. The other genes could be functionally clustered into cell growth/signal transduction pathways. Genes such as FOSB, JUN, JUNB, and ID2 ( and ) are typically associated with the immediate early genes during liver regeneration 
. Several studies reported that ID2 (Inhibitor of DNA binding or Differentiation) protein, a helix-loop-helix transcription factor, has important roles in cell growth, differentiation and angiogenesis 
. ID2 is also essential for NK lineage commitment from bipotent progenitors of both T and NK cells 
. Other up-regulated genes including EGR1, ETR101, CDK9 and RelA, are also related to cell growth and proliferation 
. Induction of EGR1 and ETR101 is also part of the early proliferative response in the liver. In addition, EGR1 is involved in the induction of FasL in T cells 
and the ETR101 has been implicated in T cell proliferation and maturation 
. These two genes might represent the induction of a successful T cell response against HCV in chimpanzee X0190 but not in X0142 and X0234. The induction of these genes may signify the initial phase of hepatocyte injury and proliferation, despite the absence of aminotransferase elevation and liver pathology during this stage of infection. This observation has implication with respect to the induction of adaptive immunity that is important for the subsequent control of viral infection. This pattern of gene expression in the liver may represent a successful “danger signal” that has been proposed to be a trigger for adaptive immunity. The lack of induction of these genes in chimpanzees that progress to chronic infection may actually represent a failure to amplify anti-viral T-cell response. This intriguing hypothesis awaits further studies to clarify the role of these genes during HCV infection.
Real-time PCR quantification of candidate genes involved in viral clearance and persistence.
During acute HCV infection, a rapid IFN response limits virus replication and spread in the liver until virus-infected hepatocytes are cleared by specific T-cell immune response 
. Analysis of gene expression patterns during the viral clearance phase of chimpanzee X0190 reveals the intrahepatic induction of cellular immune response. This is particularly evident with markers of CD8+ T cell response including granzyme A, CD8 antigen, T cell receptors, and interferon-gamma (). On the other hand, fewer of these genes were induced and at a lower magnitude in chimpanzees with chronic infection. These findings are consistent with a recent study on hepatic gene expression in chimpanzees during acute HCV infection 
, and support the importance of T cell immune response in controlling HCV infection 
. Other genes that were preferentially induced during the clearance phase are diverse. They do not overlap with those genes induced during the early phase of infection and may represent a more complex array of molecular and cellular events during viral clearance. All these genes returned to baseline expression after viral clearance. In contrast, many ISGs remained elevated in chimpanzees with chronic infection, indicating an ongoing type I IFN response to persistent HCV infection.
In this study, molecular profiling of gene expression patterns in chimpanzees with serial liver biopsies during the course of infection provides valuable information on the potential mechanisms of viral clearance and persistence. Although the number of animals is small, we are able to define a unique gene expression pattern associated with viral clearance and demonstrate the potential importance of induction of certain genes in a “successful” anti-HCV response. IFN-stimulated genes (ISGs) are induced similarly regardless of the outcome of infection. Early induction of a set of genes associated with cell proliferation and immune activation appears to be involved in subsequent viral clearance. Furthermore, evidence for a strong intrahepatic induction of cellular immune response in chimpanzees associated with self-limited infection is present. These findings support the importance of T-cell immune response in controlling HCV infection. Additional studies in other chimpanzees or humans with well-characterized course of acute infection are necessary to confirm these observations.