Comparison of HCV-associated gene expression and cell signaling pathways in cells with or without HCV replicon and in replicon-cured cells

Nishimura-Sakurai, Yuki; Sakamoto, Naoya; Mogushi, Kaoru; Nagaie, Satoshi; Nakagawa, Mina; Itsui, Yasuhiro; Tasaka-Fujita, Megumi; Onuki-Karakama, Yuko; Suda, Goki; Mishima, Kenji; Yamamoto, Mamoru; Ueyama, Mayumi; Funaoka, Yusuke; Watanabe, Tomonori; Azuma, Seishin; Sekine-Osajima, Yuko; Kakinuma, Sei; Tsuchiya, Kiichiro; Enomoto, Nobuyuki; Tanaka, Hiroshi; Watanabe, Mamoru

doi:10.1007/s00535-009-0162-3

Cited by 30 publications

(35 citation statements)

References 48 publications

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“…In this study, host genes involved in cellular metabolism and intracellular transport were also significantly regulated by JFH-1 infection. Although previous studies have shown that HCV can alter lipid metabolism (32), this study demonstrated that genes involved in protein synthesis and degradation, posttranslational modification, vesicle trafficking, and cytoskeleton function are also regulated following infection.…”

Section: Discussioncontrasting

confidence: 63%

“…Many of the genes selected were regulated in a highly coordinated manner (e.g., cholesterol biosynthesis genes, tRNA synthetase genes, and metallothionein genes), indicating that the regulation of these genes may significantly impact cellular function. By comparing the findings of this study to previously published HCV microarray studies, overlapping expression patterns were observed, including the regulation of genes involved in proliferation, apoptosis, cytokine and chemokine production, and lipid metabolism (1,2,32,53). However, many novel host genes regulated by HCV infection were also identified, including those involved in protein synthesis and degradation, posttranslational modification, and vesicular trafficking.…”

Section: Discussionsupporting

confidence: 53%

“…Genes showing at least a 2-fold change in expression and a Ͼ95% probability of being differentially expressed (P Յ 0.05) were considered to be significantly regulated by infection. These selection criteria were chosen to enable a comparison of the results in this study to those observed in previously published HCV microarray studies which used the same selection cutoff values (15,32,53). The total number of genes regulated by infection increased over time.…”

Section: Methodsmentioning

confidence: 99%

“…Microarray expression profiling has already been used to study host gene expression in cells transfected with RNA encoding either individual HCV genes, HCV subgenomic replicons, or the full-length HCV genome. These studies have demonstrated that the replication of the HCV genome results in the regulation of a small number of host genes involved in lipid metabolism, cellular immunity, proliferation, apoptosis, and molecular transport (2,5,15,32). These studies have provided interesting insights into the HCV replication cycle.…”

Section: Hepatitis C Virus (Hcv) Ismentioning

confidence: 97%

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Gene Expression Profiling Indicates the Roles of Host Oxidative Stress, Apoptosis, Lipid Metabolism, and Intracellular Transport Genes in the Replication of Hepatitis C Virus

Blackham

Baillie

Al-Hababi

et al. 2010

J Virol

130

122

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Hepatitis C virus (HCV) isHepatitis C virus (HCV) is a leading cause of chronic liver disease, which affects around 170 million people worldwide. Infections are initially acute, and in many cases the symptoms are mild. However, around 80% of patients eventually develop a persistent chronic infection which can result in steatosis, fibrosis, cirrhosis, liver failure, and, in some cases, hepatocellular carcinoma. The main treatments currently available for chronically infected patients use a combination of pegylated alpha interferon and ribavirin, but these still result in a sustained antiviral response in only about 50% of genotype 1 infections (4). Consequently, more effective antivirals that target either the virus proteins directly or the host cell proteins required during HCV replication are currently being developed. In order to ensure that successful antivirals are generated, it is important that all aspects of the HCV life cycle and HCV-associated pathology are well understood.One way in which the different host processes that are an essential part of the HCV replication cycle can be studied is to investigate the effect that HCV infection has on cellular gene expression. RNA microarray hybridization is routinely used to investigate host gene expression and allows the entire transcriptomic profile of the cell to be characterized. Microarray analysis of HCV-infected cells can provide an insight into the genes involved in host cell antiviral responses, genes that are essential for the HCV replication cycle, and genes that contribute to HCV-associated liver pathology. Microarray expression profiling has already been used to study host gene expression in cells transfected with RNA encoding either individual HCV genes, HCV subgenomic replicons, or the full-length HCV genome. These studies have demonstrated that the replication of the HCV genome results in the regulation of a small number of host genes involved in lipid metabolism, cellular immunity, proliferation, apoptosis, and molecular transport (2,5,15,32). These studies have provided interesting insights into the HCV replication cycle. However, the biological significance of gene expression patterns identified is less clear, since the full virus replication cycle, including the processes of viral entry, assembly, and exit, does not take place.The recent discovery of JFH-1, a genotype 2a HCV clone that can undergo a complete infection cycle in cell culture, provides the opportunity to characterize the true effect of HCV infection on host gene expression (51). A recent study investigated the effects that a J6/JFH-1 chimera had on the gene expression profile of Huh7.5 cells during a time course infection with time points of 24, 48, 72, 96, and 120 h (53). The number of host genes regulated during infection was much higher than that previously observed for cells permitting only genome replication, indicating that the full replication cycle has additional effects on host gene expression.In this study, we present the results from an investigation

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Section: Discussioncontrasting

confidence: 63%

Section: Discussionsupporting

confidence: 53%

Section: Methodsmentioning

confidence: 99%

Section: Hepatitis C Virus (Hcv) Ismentioning

confidence: 97%

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Gene Expression Profiling Indicates the Roles of Host Oxidative Stress, Apoptosis, Lipid Metabolism, and Intracellular Transport Genes in the Replication of Hepatitis C Virus

Blackham

Baillie

Al-Hababi

et al. 2010

J Virol

130

122

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“…Such patients show higher levels of hepatic SOCS3 ex- pression than those without obesity or insulin resistance (34,61). We reported previously that a series of genes involved in fatty acid and cholesterol synthesis are upregulated in HCV replicon-expressing and HCV-JFH1-infected cells and increased cellular LDs (39). Such lipogenic cellular processes may be the cause of the upregulated expression of IL-6.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Interferon Signaling by Infectious Hepatitis C Virus Clones with Substitutions of Core Amino Acids 70 and 91

Funaoka

Sakamoto

Suda

et al. 2011

J Virol

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Substitution of amino acids 70 and 91 in the hepatitis C virus (HCV) core region is a significant predictor of poor responses to peginterferon-plus-ribavirin therapy, while their molecular mechanisms remain unclear. Here we investigated these differences in the response to alpha interferon (IFN) by using HCV cell culture with R70Q, R70H, and L91M substitutions. IFN treatment of cells transfected or infected with the wild type or the mutant HCV clones showed that the R70Q, R70H, and L91M core mutants were significantly more resistant than the wild type. Among HCV-transfected cells, intracellular HCV RNA levels were significantly higher for the core mutants than for the wild type, while HCV RNA in culture supernatant was significantly lower for these mutants than for the wild type. IFN-induced phosphorylation of STAT1 and STAT2 and expression of the interferon-inducible genes were significantly lower for the core mutants than for the wild type, suggesting cellular unresponsiveness to IFN. The expression level of an interferon signal attenuator, SOCS3, was significantly higher for the R70Q, R70H, and L91M mutants than for the wild type. Interleukin 6 (IL-6), which upregulates SOCS3, was significantly higher for the R70Q, R70H, and L91M mutants than for the wild type, suggesting interferon resistance, possibly through IL-6-induced, SOCS3-mediated suppression of interferon signaling. Expression levels of endoplasmic reticulum (ER) stress proteins were significantly higher in cells transfected with a core mutant than in those transfected with the wild type. In conclusion, HCV R70 and L91 core mutants were resistant to interferon in vitro, and the resistance may be induced by IL-6-induced upregulation of SOCS3. Those mechanisms may explain clinical interferon resistance of HCV core mutants.Hepatitis C virus (HCV) is one of the most important pathogens causing liver-related morbidity and mortality. Approximately 3% of the worldwide population is infected with HCV, which represents 170 million people, and 3 million to 4 million individuals are newly infected each year (33,47,62). There is no therapeutic or prophylactic vaccine available for HCV. Antiviral treatment has been shown to improve liver histology and decrease the incidence of hepatocellular carcinoma in chronic hepatitis C (CHC) (17, 64). Current therapies for CHC consist of treatment with pegylated interferon (peg-IFN), which acts both as an antiviral and as an immunoregulatory cytokine, and ribavirin (RBV), an antiviral prodrug that interferes with RNA metabolism (16, 31). However, less than 50% of patients infected with HCV genotype 1 treated in this way achieve a sustained virological response (SVR) or a cure of the infection (14, 16). Given this situations, gaining a detailed understanding of the molecular mechanisms of interferon (IFN) resistance has been a high priority in academia and industry.The response to peg-IFN-plus-RBV treatment is affected by several viral and host factors, including age, gender (22, 23), grade of liver fibrosis (21, 42), HCV ge...

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Alteration of hepatic nuclear receptor-mediated signaling pathways in hepatitis C virus patients with and without a history of alcohol drinking

Gilroy

Taylor

et al. 2011

Hepatology

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The current study tests a hypothesis that nuclear receptor signaling is altered in chronic hepatitis C patients and that the altered pattern is alcohol drinking history specific. The expression of a panel of more than 100 genes encoding nuclear receptors, co-regulators, and their direct/indirect targets was studied in human livers. (1) Gene expression pattern was compared between 15 normal donor livers and 23 HCV genotype 1 positive livers from patients without a drinking history (age, gender, and BMI matched). HCV infection increased the expression of nuclear receptors small heterodimer partner and constitutive androstane receptor (CAR) as well as genes involved in fatty acid trafficking, bile acid synthesis and uptake, and inflammatory response. However, the expression of retinoid x receptor (RXR) α, peroxisomal proliferator activated receptor (PPAR) α and β as well as SREBP-1c was decreased in HCV-infected livers. (2) Gene expression pattern was compared in chronic hepatitis C patients with (21) and without (13) a drinking history. Alcohol drinking increased the expression of genes involved in fatty acid uptake, trafficking, and oxidation, but decreased the expression of genes responsible for gluconeogenesis. These changes were consistent with reduced fasting plasma glucose levels and altered expression of upstream regulators that include RXRα, PPARα, and CAR. (3) The mRNA levels of fibroblast growth factor 21, IL-10, and fatty acid synthase, which are all regulated by nuclear receptors, showed independent correlation with hepatic HCV RNA levels. Our findings suggest that those genes and pathways that showed altered expression could potentially be therapeutic targets for HCV infection and/or alcohol drinking-induced liver injury.

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Comparison of HCV-associated gene expression and cell signaling pathways in cells with or without HCV replicon and in replicon-cured cells

Abstract: Comprehensive gene expression and pathway analyses show that lipid biosynthesis pathways are crucial to support proficient virus replication. These metabolic pathways could constitute novel antiviral targets against HCV.

Cited by 30 publications

References 48 publications

Gene Expression Profiling Indicates the Roles of Host Oxidative Stress, Apoptosis, Lipid Metabolism, and Intracellular Transport Genes in the Replication of Hepatitis C Virus

Gene Expression Profiling Indicates the Roles of Host Oxidative Stress, Apoptosis, Lipid Metabolism, and Intracellular Transport Genes in the Replication of Hepatitis C Virus

Analysis of Interferon Signaling by Infectious Hepatitis C Virus Clones with Substitutions of Core Amino Acids 70 and 91

Alteration of hepatic nuclear receptor-mediated signaling pathways in hepatitis C virus patients with and without a history of alcohol drinking

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