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Journal of Virology, June 2005, p. 7558-7569, Vol. 79, No. 12
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.12.7558-7569.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Proteome Analysis of Liver Cells Expressing a Full-Length Hepatitis C Virus (HCV) Replicon and Biopsy Specimens of Posttransplantation Liver from HCV-Infected Patients

Jon M. Jacobs,^1, Deborah L. Diamond,^2, Eric Y. Chan,² Marina A. Gritsenko,¹ Weijun Qian,¹ Miroslava Stastna,¹ Tracey Baas,² David G. Camp II,¹ Robert L. Carithers Jr.,³ Richard D. Smith,¹ and Michael G. Katze^2,4*

Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington,¹ Department of Microbiology,² Hepatology Section, Department of Medicine,³ Washington National Primate Research Center, University of Washington, Seattle, Washington⁴

Received 6 October 2004/ Accepted 13 February 2005

The development of a reproducible model system for the study of hepatitis C virus (HCV) infection has the potential to significantly enhance the study of virus-host interactions and provide future direction for modeling the pathogenesis of HCV. While there are studies describing global gene expression changes associated with HCV infection, changes in the proteome have not been characterized. We report the first large-scale proteome analysis of the highly permissive Huh-7.5 cell line containing a full-length HCV replicon. We detected >4,200 proteins in this cell line, including HCV replicon proteins, using multidimensional liquid chromatographic (LC) separations coupled to mass spectrometry. Consistent with the literature, a comparison of HCV replicon-positive and -negative Huh-7.5 cells identified expression changes of proteins involved in lipid metabolism. We extended these analyses to liver biopsy material from HCV-infected patients where a total of >1,500 proteins were detected from only 2 µg of liver biopsy protein digest using the Huh-7.5 protein database and the accurate mass and time tag strategy. These findings demonstrate the utility of multidimensional proteome analysis of the HCV replicon model system for assisting in the determination of proteins/pathways affected by HCV infection. Our ability to extend these analyses to the highly complex proteome of small liver biopsies with limiting protein yields offers the unique opportunity to begin evaluating the clinical significance of protein expression changes associated with HCV infection.

Supplemental material for this article may be found at http://jvi.asm.org/.

These authors contributed equally to this work.

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