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ISSN: 2153-0777
Journal of Bioengineering and Bioelectronics
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Genome-wide Gene Expression Profiling: An Excellent Tool to Study Virus- Host Interactions

Limin Chen1,2*, Shilin Li1, Yujia Li1, Xiaoqiong Duan1 and Ian McGilvray1,2
1Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
2Toronto General Research Institute, University of Toronto, Toronto, ON, Canada
Corresponding Author : Dr. Limin Chen
Toronto General Research Institute
University of Toronto
Toronto, ON, Canada
Tel: 1-416-946-3435, 011-86-28- 61648530
E-mail: [email protected], [email protected]
Received November 19, 2012; Accepted November 21, 2012; Published November 23, 2012
Citation: Chen L, Li S, Li Y, Duan X, McGilvray I (2012) Genome-wide Gene Expression Profiling: An Excellent Tool to Study Virus-Host Interactions. J Biochips Tiss Chips 2:e118. doi:10.4172/2153-0777.1000e118
Copyright: © 2012 Chen L, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Virus infection is one of the major issues threatening our health, leading to chronic infections and viral persistence in many cases. Unlike bacteria infection, anti-viral drugs are not as much effective as antibiotics. For example, for Hepatitis C Virus (HCV) infection, upto 70% of those infected will develop into chronic infections and almost half of them will not respond to current standard treatment with pegylated interferon and ribavirin [1,2]. Although most recently the addition of the HCV specific protease inhibitors (triple-therapy) increased the overall response rate upto 70%, there is still a significant portion of the patients will not respond, not to mention the rapid development of viral resistance to these Direct-acting Agents (DAAs) widely observed in clinic [3]. One of the major reasons for lacking the effective antiviral drugs is that the molecular mechanisms of the viral resistance to these drugs are poorly understood.
Virus-host interaction provides much information for us to understand how a specific virus infects the host cells and how the host cells respond to the infection. Previously, a lot of data have been gathered as to how the virus responds to host immune attack, especially to counteract the innate and adaptive immune responses. The virus can utilize many mechanisms to evade host immune surveillance, such as by rapid mutation, by interfering with the recognition step of the virus invasion and induction of the innate immunity as the first-line defense, and also by dampening the antiviral effect of the antiviral molecules [4]. However, how the host cells respond to the virus infection at the whole genomic level is not well defined.
Microarray gene-expression profiling, a high throughput method that allows simultaneously examine gene expression changes at the transcript (mRNA) level, makes it possible to look at the host response to any given virus infection at the whole genomic scale. Combined with data analysis tools, these large gene expression data sets provided insights into the molecular mechanisms of viral resistance. Novel antiviral drug targets can be identified and further developed.
By comparing the pretreatment hepatic gene expression levels between treatment responders and non-responders of patients chronically infected with HCV, Chen et al. [5] identified 18 genes (out of 19,000 host genes or transcripts) whose expression levels are significantly and statistically different between the two groups. Most of these 18 genes are Interferon-stimulated (-sensitive) Genes (ISGs) and they are more highly expressed in the pretreatment liver tissues of treatment non-responders. Therefore, they proposed that the pre-activation of the interferon signaling pathway leading to the increased expression of a subset of ISGs is involved in HCV resistance to interferon therapy [5]. This hypothesis has now been confirmed by many other groups and was generally accepted in the file [6,7]. More interestingly, based on the gene expression data and the 18 differentially-expressed gene set, they identified a novel ubiquitin-like pathway (ISG15/USP18) whose activation is related to HCV resistance [5]. Silencing USP18, a specific protease to strip ISG15 from its conjugation proteins, potentiated the anti-HCV effect of Interferon Alpha (IFNa) by 40-100 fold [8]. Furthermore, they demonstrated that the cell-type specific protein expression of some ISGs, such as ISG15 and MxA, in the pretreatment liver tissues of HCV patients correlated well with treatment outcomes [9]: predominant expression in hepatocytes predicts non-response while in macrophages predicts treatment response, with prediction accuracy higher than that predicted by the polymorphism of IL28B [10], which was identified by large-scale Genome-wide Association Studies (GWAS) [11-14].
This is an excellent example on how genome-wide gene expression study can be used to delineate virus-host interactions, especially to understand how the host responds to virus infection at the whole genomic level. Not only a novel pathway (ISG15/USP18 ubiquitin-like pathway) but also new drug targets have been identified [15]. These studies and novel data opens a new avenue of research into HCV-host interactions, especially into the molecular mechanisms of the host role in HCV resistance to interferon therapy, leading the hope to develop novel anti-HCV drugs.
Although the microarray gene-expression profiling method is robust, with enormous data being generated from a single experiment, the key to arrive at any significant conclusion depends on the successful use of various data analysis software [5]. We believe more ready-touse data mining tools will be readily available in the future, which will definitely facilitate the application of this high throughput gene expression tool to study how host responds to virus infections at the whole genomic scale. Data from these studies will shed light on the detailed molecular mechanisms of viral resistance, leading to new drug target identification and development, and eventually wipe out the virus infection.
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