1
|
RNA-Binding Proteins as Regulators of Internal Initiation of Viral mRNA Translation. Viruses 2022; 14:v14020188. [PMID: 35215780 PMCID: PMC8879377 DOI: 10.3390/v14020188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 12/17/2022] Open
Abstract
Viruses are obligate intracellular parasites that depend on the host’s protein synthesis machinery for translating their mRNAs. The viral mRNA (vRNA) competes with the host mRNA to recruit the translational machinery, including ribosomes, tRNAs, and the limited eukaryotic translation initiation factor (eIFs) pool. Many viruses utilize non-canonical strategies such as targeting host eIFs and RNA elements known as internal ribosome entry sites (IRESs) to reprogram cellular gene expression, ensuring preferential translation of vRNAs. In this review, we discuss vRNA IRES-mediated translation initiation, highlighting the role of RNA-binding proteins (RBPs), other than the canonical translation initiation factors, in regulating their activity.
Collapse
|
2
|
van den Akker GGH, Zacchini F, Housmans BAC, van der Vloet L, Caron MMJ, Montanaro L, Welting TJM. Current Practice in Bicistronic IRES Reporter Use: A Systematic Review. Int J Mol Sci 2021; 22:5193. [PMID: 34068921 PMCID: PMC8156625 DOI: 10.3390/ijms22105193] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022] Open
Abstract
Bicistronic reporter assays have been instrumental for transgene expression, understanding of internal ribosomal entry site (IRES) translation, and identification of novel cap-independent translational elements (CITE). We observed a large methodological variability in the use of bicistronic reporter assays and data presentation or normalization procedures. Therefore, we systematically searched the literature for bicistronic IRES reporter studies and analyzed methodological details, data visualization, and normalization procedures. Two hundred fifty-seven publications were identified using our search strategy (published 1994-2020). Experimental studies on eukaryotic adherent cell systems and the cell-free translation assay were included for further analysis. We evaluated the following methodological details for 176 full text articles: the bicistronic reporter design, the cell line or type, transfection methods, and time point of analyses post-transfection. For the cell-free translation assay, we focused on methods of in vitro transcription, type of translation lysate, and incubation times and assay temperature. Data can be presented in multiple ways: raw data from individual cistrons, a ratio of the two, or fold changes thereof. In addition, many different control experiments have been suggested when studying IRES-mediated translation. In addition, many different normalization and control experiments have been suggested when studying IRES-mediated translation. Therefore, we also categorized and summarized their use. Our unbiased analyses provide a representative overview of bicistronic IRES reporter use. We identified parameters that were reported inconsistently or incompletely, which could hamper data reproduction and interpretation. On the basis of our analyses, we encourage adhering to a number of practices that should improve transparency of bicistronic reporter data presentation and improve methodological descriptions to facilitate data replication.
Collapse
Affiliation(s)
- Guus Gijsbertus Hubert van den Akker
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Federico Zacchini
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, I-40138 Bologna, Italy; (F.Z.); (L.M.)
- Centro di Ricerca Biomedica Applicata—CRBA, Bologna University, Policlinico di Sant’Orsola, I-40138 Bologna, Italy
| | - Bas Adrianus Catharina Housmans
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Laura van der Vloet
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Marjolein Maria Johanna Caron
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, I-40138 Bologna, Italy; (F.Z.); (L.M.)
- Centro di Ricerca Biomedica Applicata—CRBA, Bologna University, Policlinico di Sant’Orsola, I-40138 Bologna, Italy
- Programma Dipartimentale in Medicina di Laboratorio, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Tim Johannes Maria Welting
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| |
Collapse
|
3
|
Lee J, Chan ST, Kim JY, Ou JHJ. Hepatitis C Virus Induces the Ubiquitin-Editing Enzyme A20 via Depletion of the Transcription Factor Upstream Stimulatory Factor 1 To Support Its Replication. mBio 2019; 10:e01660-19. [PMID: 31337730 PMCID: PMC6650561 DOI: 10.1128/mbio.01660-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 12/27/2022] Open
Abstract
Tumor necrosis factor alpha-induced protein 3 (TNFAIP3), also known as A20, is a ubiquitin-editing enzyme capable of ubiquitination or deubiquitination of its target proteins. In this study, we show that hepatitis C virus (HCV) infection could induce the expression of A20 via the activation of the A20 promoter. The induction of A20 by HCV coincided with the loss of upstream stimulatory factor 1 (USF-1), a transcription factor known to suppress the A20 promoter. The role of USF-1 in the regulation of the A20 promoter in HCV-infected cells was confirmed by the chromatin immunoprecipitation (ChIP) assay, and its depletion was apparently mediated by proteasomes, as USF-1 could be stabilized by the proteasome inhibitor MG132 to suppress the A20 expression. As the overexpression of A20 enhanced the replication of HCV and the silencing of A20 had the opposite effect, A20 is a positive regulator of HCV replication. Our further studies indicated that A20 enhanced the activity of the HCV internal ribosome entry site (IRES). In conclusion, our results demonstrated that HCV could induce the expression of A20 via the depletion of USF-1 to enhance its replication. Our study provided important information for further understanding the interaction between HCV and its host cells.IMPORTANCE Hepatitis C virus establishes chronic infection in approximately 85% of the patients whom it infects. However, the mechanism of how HCV evades host immunity to establish persistence is unclear. In this report, we demonstrate that HCV could induce the expression of the ubiquitin-editing enzyme A20, an important negative regulator of the tumor necrosis factor alpha (TNF-α) and NF-κB signaling pathways. This induction of A20 enhanced HCV replication as it could stimulate the HCV IRES activity to enhance the translation of HCV proteins. The induction of A20 was mediated by the depletion of USF-1, a suppressor of the A20 promoter. Our study thus provides important information for further understanding the interaction between HCV and its host cells.
Collapse
Affiliation(s)
- Jiyoung Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Stephanie T Chan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ja Yeon Kim
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jing-Hsiung James Ou
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
4
|
Ranin J, Salemovic D, Brmbolic B, Marinkovic J, Boricic I, Pesic PI, Zerjav S, Stanojevic M, Jevtovic D. Comparison of Demographic, Epidemiological, Immunological, and Clinical Characteristics of Patients with HIV Mono-infection Versus Patients Co-infected with HCV or/and HBV: A Serbian Cohort Study. Curr HIV Res 2019; 16:222-230. [PMID: 30014804 DOI: 10.2174/1570162x16666180717115614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 07/08/2018] [Accepted: 07/10/2018] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The study aimed to correlate the status of hepatitis C (HCV) and hepatitis B virus (HBV) co-infection in patients with human immunodeficiency virus (HIV) infection with clinical and demographic data prior to starting highly active antiretroviral therapy (HAART) and assess the impact of HCV and HBV co-infection on the natural history of HIV infection. PATIENTS AND METHODS The study involved a total of 836 treatment-naive patients with available serological status for HBV and HCV at the point of therapy initiation. Patients were stratified into four groups: HIV mono-infection, HIV/HCV, HIV/HBV, and HIV/HCV/HBV co-infection. Demographic, epidemiological, immunological and clinical characteristics were analyzed in order to assess the possible impact of HCV and HBV co-infection on HIV - related immunodeficiency and progression to AIDS. RESULTS The prevalence of HCV and HBV co-infection in our cohort was 25.7% and 6.3%, respectively. Triple HIV/HCV/HBV infection was recorded in 1.7% of the patients. In comparison with those co-infected with HCV, patients with HIV mono-infection had lower levels of serum liver enzymes activity and higher CD4 cell counts, and were less likely to have CD4 cell counts below100 cells/µL and clinical AIDS, with OR 0.556 and 0.561, respectively. No difference in the development of advanced immunodeficiency and/or AIDS was recorded between patients with HIV monoinfection and those co-infected with HBV, or both HCV/HBV. CONCLUSION HIV/HCV co-infection was found to be more prevalent than HIV/HBV co-infection in a Serbian cohort. Co-infection with HCV was related to more profound immunodeficiency prior to therapy initiation, reflecting a possible unfavorable impact of HCV on the natural history of HIV infection.
Collapse
Affiliation(s)
- J Ranin
- University of Belgrade Faculty of Medicine, University Hospital for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - D Salemovic
- University of Belgrade Faculty of Medicine, University Hospital for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - B Brmbolic
- University of Belgrade Faculty of Medicine, University Hospital for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - J Marinkovic
- University of Belgrade Faculty of Medicine, Institute for Medical Statistics, Belgrade, Serbia
| | - I Boricic
- University of Belgrade Faculty of Medicine, Institute for Pathohystology, Belgrade, Serbia
| | - Pavlovic I Pesic
- Virology Laboratory, Microbiology Department, Clinical Center Serbia, Belgrade, Serbia
| | - S Zerjav
- Virology Laboratory, Microbiology Department, Clinical Center Serbia, Belgrade, Serbia
| | - M Stanojevic
- University of Belgrade Faculty of Medicine, Institute of Microbiology and Immunology, Belgrade, Serbia
| | - D Jevtovic
- University of Belgrade Faculty of Medicine, University Hospital for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| |
Collapse
|
5
|
Mercuri L, Thomson EC, Hughes J, Karayiannis P. Quasispecies Changes with Distinctive Point Mutations in the Hepatitis C Virus Internal Ribosome Entry Site (IRES) Derived from PBMCs and Plasma. Adv Virol 2018; 2018:4835252. [PMID: 30581467 PMCID: PMC6276526 DOI: 10.1155/2018/4835252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/11/2018] [Indexed: 12/12/2022] Open
Abstract
The 5' untranslated region (UTR) of the hepatitis C virus (HCV) genome contains the internal ribosome entry site (IRES), a highly conserved RNA structure essential for cap-independent translation of the viral polyprotein. HCV, apart from the liver, is thought to be associated with lymphocyte subpopulations of peripheral blood mononuclear cells (PBMCs), in lymph nodes and brain tissue. In this study, RT-PCR, cloning, and sequence analysis were employed to investigate the quasispecies nature of the 5'UTR following extraction of viral RNA from PBMCs and plasma of HCV infected individuals. The nucleotide variation between IRES-derived sequences from PBMCs and plasma indicated the existence of polymorphic sites within the IRES. HCV isolates had divergent variants with unique mutations particularly at positions 107, 204, and 243 of the IRES. Most of the PBMC-derived sequences contained an A-A-A variant at these positions. The mutations associated with the IRESes suggested the presence of unique quasispecies populations in PBMCs compared with plasma.
Collapse
Affiliation(s)
- Luca Mercuri
- Hepatology Section, Division of Medicine, Faculty of Medicine, Imperial College, London, UK
| | - Emma C. Thomson
- University of Glasgow MRC Centre for Virus Research, Glasgow, UK
| | - Joseph Hughes
- University of Glasgow MRC Centre for Virus Research, Glasgow, UK
| | | |
Collapse
|
6
|
Chen CL, Huang JY, Wang CH, Tahara SM, Zhou L, Kondo Y, Schechter J, Su L, Lai MMC, Wakita T, Cosset FL, Jung JU, Machida K. Hepatitis C virus has a genetically determined lymphotropism through co-receptor B7.2. Nat Commun 2017; 8:13882. [PMID: 28067225 PMCID: PMC5227552 DOI: 10.1038/ncomms13882] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/08/2016] [Indexed: 12/18/2022] Open
Abstract
B-cell infection by hepatitis C virus (HCV) has been a controversial topic. To examine whether HCV has a genetically determined lymphotropism through a co-receptor specific for the infection by lymphotropic HCV, we established an infectious clone and chimeric virus of hepatotropic and lymphotropic HCV strains derived from an HCV-positive B-cell lymphoma. The viral envelope and 5'-UTR sequences of the lymphotropic HCV strain were responsible for the lymphotropism. Silencing of the virus sensor, RIGI, or overexpression of microRNA-122 promoted persistent viral replication in B cells. By cDNA library screening, we identified an immune cell-specific, co-stimulatory receptor B7.2 (CD86) as a co-receptor of lymphotropic HCV. Infection of B cells by HCV inhibited the recall reaction to antigen stimulation. Together, a co-receptor B7.2 enabled lymphotropic HCV to infect memory B cells, leading to inhibition of memory B-cell function and persistent HCV infection in HCV-infected hosts.
Collapse
Affiliation(s)
- Chia-Lin Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90033, USA
| | - Jeffrey Y. Huang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90033, USA
| | - Chun-Hsiang Wang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90033, USA
| | - Stanley M Tahara
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90033, USA
| | - Lin Zhou
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90033, USA
| | - Yasuteru Kondo
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90033, USA
| | - Joel Schechter
- Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90033, USA
| | - Lishan Su
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7290, USA
| | - Michael M C. Lai
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90033, USA
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - François-Loïc Cosset
- International Center for Infectiology Research, Team EVIR, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007 Lyon, France
| | - Jae U Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90033, USA
| | - Keigo Machida
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, California 90033, USA
| |
Collapse
|
7
|
Di Lello FA, Culasso ACA, Parodi C, Baré P, Campos RH, García G. New evidence of replication of hepatitis C virus in short-term peripheral blood mononuclear cell cultures. Virus Res 2014; 191:1-9. [PMID: 25087877 DOI: 10.1016/j.virusres.2014.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND Even though hepatocytes are the main site for hepatitis C virus (HCV) replication, peripheral blood mononuclear cells (PBMC) have also been proposed as a suitable site for HCV replication. However, this issue still remains under discussion. We have previously developed an innovative system where HCV-RNA can be recovered during PBMC culture from HCV infected patients. Thus, the aim of this work was to use this novel approach in order to observe the evolution and replication of HCV genotype 1b in the PBMC of an HIV-HCV coinfected patient. METHODS HCV-RNA was extracted from serum, uncultured PBMC and PBMC culture at day 6, 20 and 33. The evolutionary analysis was performed using the direct sequences of three viral regions: 5'UTR, E2 and NS5A. Additionally, E2 region was cloned in order to extend the evolutive analysis. RESULTS In the present work, the molecular characterization of HCV along the culture showed a clear dynamic evolving process with the appearance of several nucleotide or amino acid changes in the three regions analyzed. Furthermore, the population analysis of E2 clones showed emerging and loss of lineages which indicate the fast evolutive dynamics of this system. CONCLUSIONS Since evolution can take place only if the virus is replicating in the culture, this finding constitutes an important evidence of viral replication in PBMC. Moreover, this extrahepatic compartment could be very important due to the presence of distinctive variants that could be responsible for resistance to treatment, viral pathogenesis and other clinical implications.
Collapse
Affiliation(s)
- Federico Alejandro Di Lello
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | | | - Cecilia Parodi
- Instituto de Investigaciones Hematológicas "Mariano R. Castex", Instituto de Medicina Experimental (IMEx), Academia Nacional de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Patricia Baré
- Instituto de Investigaciones Hematológicas "Mariano R. Castex", Instituto de Medicina Experimental (IMEx), Academia Nacional de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rodolfo Héctor Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gabriel García
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
8
|
Blackard JT, Ma G, Sengupta S, Martin CM, Powell EA, Shata MT, Sherman KE. Evidence of distinct populations of hepatitis C virus in the liver and plasma of patients co-infected with HIV and HCV. J Med Virol 2014; 86:1332-41. [PMID: 24788693 DOI: 10.1002/jmv.23968] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2014] [Indexed: 12/15/2022]
Abstract
Viral diversity is an important predictor of hepatitis C virus (HCV) treatment response and may influence viral pathogenesis. HIV influences HCV variability in the plasma; however, limited data on viral variability are available from distinct tissue/cell compartments in patients co-infected with HIV and HCV. Thus, this exploratory study evaluated diversity of the hypervariable region 1 (HVR1) of HCV in the plasma and liver for 14 patients co-infected with HIV and HCV. Median intra-patient genetic distances and entropy values were similar in the plasma and liver compartments. Positive immune selection pressure was observed in the plasma for five individuals and in the liver for three individuals. Statistical evidence supporting viral compartmentalization was found in five individuals. Linear regression identified ALT (P = 0.0104) and AST (P = 0.0130) as predictors of viral compartmentalization. A total of 12 signature amino acids that distinguish liver from plasma E1/HVR1 were identified. One signature amino acid was shared by at least two individuals. These findings suggest that HCV compartmentalization is relatively common among patients co-infected with HIV and HCV. These data also imply that evaluating viral diversity, including drug resistance patterns, in the serum/plasma only may not adequately represent viruses replicating with in the liver and, thus, deserves careful consideration in future studies.
Collapse
Affiliation(s)
- Jason T Blackard
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | | | | | | | | | | | | |
Collapse
|
9
|
Stamataki Z. Hepatitis C infection of B lymphocytes: more tools to address pending questions. Expert Rev Anti Infect Ther 2014; 8:977-80. [DOI: 10.1586/eri.10.86] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
10
|
Bolcic F, Laufer N, Torres C, Cassino L, Reynoso R, Quarleri J. Longitudinal analysis of the 5'UTR, E2-PePHD and NS5A-PKRBD genomic regions of hepatitis C virus genotype 1a in association with the response to peginterferon and ribavirin therapy in HIV-coinfected patients. Antiviral Res 2012; 95:72-81. [PMID: 22683884 DOI: 10.1016/j.antiviral.2012.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 05/22/2012] [Accepted: 05/26/2012] [Indexed: 12/16/2022]
Abstract
BACKGROUND The rate of non-response to pegylated interferon plus ribavirin (peg-IFN+RBV) in HCV/HIV coinfected patients is higher than in HCV-monoinfected patients. In this sense, the contribution of HCV genetic variability is unknown. The 5' untranslated (5'UTR), the nonstructural 5A (NS5A) and the second envelope (E2) HCV genomic regions have been implicated to peg-IFN therapy response. The proteins appear to block interferon (IFN)-induced RNA-dependent protein kinase (PKR) and the 5'UTR may influence the viral lymphotropism. METHODS We examined comparatively the pretreatment HCV variability between HIV coinfected and HCV monoinfected patients as well as assessed longitudinally the impact of peg-IFN+RBV on HCV variability when HIV is co-present. For this purpose, 15 HIV coinfected and 20 HCV monoinfected patients were compared. They were peg-IFN+RBV non-responders and infected with HCV 1a. RESULTS Irrespectively of the HIV-coexistence, at baseline the amino acid variation in the NS5A-related domains was significantly higher than in the E2-PePHD (p<0.001). The number of amino acid variations (mean±SD) at the NS5A-ISDR domain was higher among HCV/HIV patients than HCV-monoinfected ones (1.80±0.77 vs. 0.95±1.05; p=0.009) but such difference was slightly lower when comparing NS5A-PKRBD sequences (2.47±1.13 vs. 1.60±1.57; p=0.06). No differences were found at the E2-PePHD (0±0 vs. 0.2±0.4). At intra-HIV coinfected patient level, only minor (HCV genetic analysis) or no (HCV substitution rate and quasispecies heterogeneity) changes were observed during therapy (basal, 24h, 4weeks, and 12weeks). CONCLUSIONS Among HCV-1a/HIV coinfected and HCV-monoinfected peg-IFN+RBV non-responder patients, the HCV variability at the 5'UTR, E2-PePHD and NS5A-PKRBD/ISDR domains was mostly comparable exhibiting a low number of variations. Four well-defined amino acid substitutions in NS5A-ISDR domain appeared most frequently when HIV coexists. The interferon-based therapy did not exert any effect in the variation, selection or diversity in the above mentioned HCV regions that could influence clinical responsiveness to IFN therapy.
Collapse
Affiliation(s)
- Federico Bolcic
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida, Facultad de Medicina, Universidad de Buenos Aires, Argentina
| | | | | | | | | | | |
Collapse
|
11
|
Blackard JT, Ma G, Welge JA, Martin CM, Sherman KE, Taylor LE, Mayer KH, Jamieson DJ. Analysis of a non-structural gene reveals evidence of possible hepatitis C virus (HCV) compartmentalization. J Med Virol 2012; 84:242-52. [PMID: 22170544 DOI: 10.1002/jmv.22269] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Viral diversity is a hallmark of hepatitis C virus (HCV) infection; however, only limited data are available regarding HCV variability in extrahepatic sites, and none have systematically compared diversity in non-structural and structural genomic regions. Therefore, HCV diversity in the NS5B and envelope 1 (E1) hypervariable region 1 (HVR1) genes was evaluated in matched sera and peripheral blood mononuclear cells (PBMCs) obtained from 13 HCV-infected women. Multiple clonal sequences were compared to evaluate quasispecies diversity and viral compartmentalization in PBMCs. Genetic distances were higher for E1/HVR1 compared to NS5B in both the sera and PBMCs (P = 0.0511 and 0.0284). Genetic distances were higher in serum NS5B compared to PBMC NS5B (P = 0.0003); however, they were not different when comparing E1/HVR1 in sera to PBMCs. By phylogenetic analysis of NS5B, evidence of possible PBMC compartmentalization was observed for one woman, while statistical methods were consistent with PBMC compartmentalization for six women. Evidence of compartmentalization within a non-structural genomic region may suggest that viral adaptation to a unique extracellular microenvironment(s) may be required for efficient replication and could contribute to HCV persistence.
Collapse
Affiliation(s)
- Jason T Blackard
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Novel nucleotide and amino acid covariation between the 5'UTR and the NS2/NS3 proteins of hepatitis C virus: bioinformatic and functional analyses. PLoS One 2011; 6:e25530. [PMID: 21980483 PMCID: PMC3182228 DOI: 10.1371/journal.pone.0025530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 09/06/2011] [Indexed: 01/02/2023] Open
Abstract
Molecular covariation of highly polymorphic viruses is thought to have crucial effects on viral replication and fitness. This study employs association rule data mining of hepatitis C virus (HCV) sequences to search for specific evolutionary covariation and then tests functional relevance on HCV replication. Data mining is performed between nucleotides in the untranslated regions 5′ and 3′UTR, and the amino acid residues in the non-structural proteins NS2, NS3 and NS5B. Results indicate covariance of the 243rd nucleotide of the 5′UTR with the 14th, 41st, 76th, 110th, 211th and 212th residues of NS2 and with the 71st, 175th and 621st residues of NS3. Real-time experiments using an HCV subgenomic system to quantify viral replication confirm replication regulation for each covariant pair between 5′UTR243 and NS2-41, -76, -110, -211, and NS3-71, -175. The HCV subgenomic system with/without the NS2 region shows that regulatory effects vanish without NS2, so replicative modulation mediated by HCV 5′UTR243 depends on NS2. Strong binding of the NS2 variants to HCV RNA correlates with reduced HCV replication whereas weak binding correlates with restoration of HCV replication efficiency, as determined by RNA-protein immunoprecipitation assay band intensity. The dominant haplotype 5′UTR243-NS2-41-76-110-211-NS3-71-175 differs according to the HCV genotype: G-Ile-Ile-Ile-Gly-Ile-Met for genotype 1b and A-Leu-Val-Leu-Ser-Val-Leu for genotypes 1a, 2a and 2b. In conclusion, 5′UTR243 co-varies with specific NS2/3 protein amino acid residues, which may have significant structural and functional consequences for HCV replication. This unreported mechanism involving HCV replication possibly can be exploited in the development of advanced anti-HCV medication.
Collapse
|
13
|
Human cell types important for hepatitis C virus replication in vivo and in vitro: old assertions and current evidence. Virol J 2011; 8:346. [PMID: 21745397 PMCID: PMC3142522 DOI: 10.1186/1743-422x-8-346] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 07/11/2011] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C Virus (HCV) is a single stranded RNA virus which produces negative strand RNA as a replicative intermediate. We analyzed 75 RT-PCR studies that tested for negative strand HCV RNA in liver and other human tissues. 85% of the studies that investigated extrahepatic replication of HCV found one or more samples positive for replicative RNA. Studies using in situ hybridization, immunofluorescence, immunohistochemistry, and quasispecies analysis also demonstrated the presence of replicating HCV in various extrahepatic human tissues, and provide evidence that HCV replicates in macrophages, B cells, T cells, and other extrahepatic tissues. We also analyzed both short term and long term in vitro systems used to culture HCV. These systems vary in their purposes and methods, but long term culturing of HCV in B cells, T cells, and other cell types has been used to analyze replication. It is therefore now possible to study HIV-HCV co-infections and HCV replication in vitro.
Collapse
|
14
|
Hubbard JJ, Kottilil S. Extra-hepatic replication of the hepatitis C virus: current issues and future directions. Future Virol 2011. [DOI: 10.2217/fvl.11.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jonathan J Hubbard
- Immunopathogenesis Section, Laboratory of Immunoregulation, National institute of Allergy & Infectious Diseases, National Institutes of Health, Department of Health & Human Sciences, Bldg 10, Room 11N204, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | | |
Collapse
|
15
|
Natarajan V, Kottilil S, Hazen A, Adelsberger J, Murphy AA, Polis MA, Kovacs JA. HCV in peripheral blood mononuclear cells are predominantly carried on the surface of cells in HIV/HCV co-infected individuals. J Med Virol 2011; 82:2032-7. [PMID: 20981790 DOI: 10.1002/jmv.21906] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
HCV replication in extra-hepatic reservoirs has been suggested to occur in many tissues including PBMCs. A recent study showed evidence for compartmentalization and evolution of HCV in PBMCs. However, the cells that support HCV replication in PBMCs have not been identified. In this study we have fractionated the PBMC from HIV/HCV co-infected patients into T, monocytes, B and NK cells, and most of the HCV was located in CD3-cell fractions. Protease treatment of PBMCs to remove cell surface receptors resulted in the loss of HCV RNA suggesting that most of the HCV is present on the cell surface. PBMCs were treated by freeze-thaw nuclease method that would protect the HCV RNA in the virus but not the intracellular viral RNA. Data from this analysis support the conclusion that most of HCV is present on the cell surface. Even though the presence of minus strand RNA in PBMCs suggests that a low level HCV replication takes place within the PBMCs of HIV/HCV co-infected individuals, HCV in PBMC is present mainly on the surface of non-T cells, mostly on NK, monocytes and B cells. These results suggest a unique pathogenic role of NK, monocyte and B cells as carriers of HCV.
Collapse
Affiliation(s)
- Ven Natarajan
- Laboratory of Molecular Cell Biology, SAIC-Frederick, Inc., Frederick, Maryland, USA
| | | | | | | | | | | | | |
Collapse
|
16
|
Zhou Z, Wang N, Woodson SE, Dong Q, Wang J, Liang Y, Rijnbrand R, Wei L, Nichols JE, Guo JT, Holbrook MR, Lemon SM, Li K. Antiviral activities of ISG20 in positive-strand RNA virus infections. Virology 2010; 409:175-88. [PMID: 21036379 PMCID: PMC3018280 DOI: 10.1016/j.virol.2010.10.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 08/05/2010] [Accepted: 10/06/2010] [Indexed: 01/19/2023]
Abstract
ISG20 is an interferon-inducible 3′–5′ exonuclease that inhibits replication of several human and animal RNA viruses. However, the specificities of ISG20's antiviral action remain poorly defined. Here we determine the impact of ectopic expression of ISG20 on replication of several positive-strand RNA viruses from distinct viral families. ISG20 inhibited infections by cell culture-derived hepatitis C virus (HCV) and a pestivirus, bovine viral diarrhea virus and a picornavirus, hepatitis A virus. Moreover, ISG20 demonstrated cell-type specific antiviral activity against yellow fever virus, a classical flavivirus. Overexpression of ISG20, however, did not inhibit propagation of severe acute respiratory syndrome coronavirus, a highly-pathogenic human coronavirus in Huh7.5 cells. The antiviral effects of ISG20 were all dependent on its exonuclease activity. The closely related cellular exonucleases, ISG20L1 and ISG20L2, did not inhibit HCV replication. Together, these data may help better understand the antiviral specificity and action of ISG20.
Collapse
Affiliation(s)
- Zhi Zhou
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Carter JR, Fraser TS, Fraser MJ. Examining the relative activity of several dicistrovirus intergenic internal ribosome entry site elements in uninfected insect and mammalian cell lines. J Gen Virol 2009; 89:3150-3155. [PMID: 19008405 DOI: 10.1099/vir.0.2008/003921-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Comparisons of the relative activities of 11 intergenic region (IGR) internal ribosome entry site (IRES) elements of insect dicistrovirus with 5' IRES elements of the hepatitis C and encephalomyocarditis viruses were performed in insect and mammalian cells. Dual luciferase assays were performed to determine the most effective dicistrovirus IGR IRES in the lepidopteran cell lines Sf9 (Spodoptera frugiperda) and BmN (Bombyx mori), and the dipteran cell lines S2 (Drosophila melanogaster) and ATC-10 (Aedes aegypti). Evaluation of dual luciferase expression from DNA plasmids and in vitro-transcribed RNA revealed apparent splicing with certain IRES elements. Though IRES activity depended upon the cell line examined, the black queen cell and Drosophila C dicistrovirus intergenic IRES elements were most effective for coupled gene expression in the diverse insect cell lines examined.
Collapse
Affiliation(s)
- James R Carter
- 214 Galvin Life Sciences, Department of Biological Sciences, Center for Tropical Diseases Research and Training, University of Notre Dame, PO Box 369, Notre Dame, IN 46556-0369, USA
| | - Tresa S Fraser
- 214 Galvin Life Sciences, Department of Biological Sciences, Center for Tropical Diseases Research and Training, University of Notre Dame, PO Box 369, Notre Dame, IN 46556-0369, USA
| | - Malcolm J Fraser
- 214 Galvin Life Sciences, Department of Biological Sciences, Center for Tropical Diseases Research and Training, University of Notre Dame, PO Box 369, Notre Dame, IN 46556-0369, USA
| |
Collapse
|
18
|
Pham TNQ, King D, Macparland SA, McGrath JS, Reddy SB, Bursey FR, Michalak TI. Hepatitis C virus replicates in the same immune cell subsets in chronic hepatitis C and occult infection. Gastroenterology 2008; 134:812-22. [PMID: 18243182 DOI: 10.1053/j.gastro.2007.12.011] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Accepted: 11/26/2007] [Indexed: 12/23/2022]
Abstract
BACKGROUND & AIMS Infection of the lymphatic system by hepatitis C virus (HCV) appears to be an intrinsic characteristic of chronic hepatitis C (CHC) and low-level (occult) HCV infection, but the subsets of immune cells involved were not defined. The aim of this study was to characterize HCV replication status and to assess virus compartmentalization in CD4+ and CD8+ T lymphocytes, B cells, and monocytes in CHC, and silent infection persisting after resolution of hepatitis C. METHODS Immune cell subtypes isolated from 7 patients with CHC and 7 individuals with occult infection were analyzed for HCV-RNA-positive and -negative strands and, in selected cases, nonstructural protein 5A display and HCV variants. RESULTS All subtypes of immune cells investigated support HCV replication in both forms of infection, although significant differences were found between patients, and virus loads in the cells were greater in CHC than in occult infection. Although HCV RNA occurred at a comparable frequency in all cell subtypes in CHC, monocytes contained the greatest loads. In contrast, B cells tended to carry the highest virus quantities in occult infection, whereas monocytes appeared to be the least frequently infected. Detection of HCV nonstructural protein 5A and HCV variants that were not found in plasma confirmed virus replication in different immune cell types. CONCLUSIONS This work documents that the immune system supports HCV replication regardless of clinical appearance of infection and identifies immune cells that are reservoirs of HCV in symptomatic and occult infections.
Collapse
Affiliation(s)
- Tram N Q Pham
- Molecular Virology and Hepatology Research, Division of BioMedical Sciences, Memorial University, St. John,s, Newfoundland and Labrador, Canada
| | | | | | | | | | | | | |
Collapse
|
19
|
Moratorio G, Martínez M, Gutiérrez MF, González K, Colina R, López-Tort F, López L, Recarey R, Schijman AG, Moreno MP, García-Aguirre L, Manascero AR, Cristina J. Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region. Virol J 2007; 4:79. [PMID: 17683527 PMCID: PMC1973069 DOI: 10.1186/1743-422x-4-79] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 08/02/2007] [Indexed: 12/21/2022] Open
Abstract
Background Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Previous and recent studies have suggested a diversification of type 1 HCV in the South American region. The degree of genetic variation among HCV strains circulating in Bolivia and Colombia is currently unknown. In order to get insight into these matters, we performed a phylogenetic analysis of HCV 5' non-coding region (5'NCR) sequences from strains isolated in Bolivia, Colombia and Uruguay, as well as available comparable sequences of HCV strains isolated in South America. Methods Phylogenetic tree analysis was performed using the neighbor-joining method under a matrix of genetic distances established under the Kimura-two parameter model. Signature pattern analysis, which identifies particular sites in nucleic acid alignments of variable sequences that are distinctly representative relative to a background set, was performed using the method of Korber & Myers, as implemented in the VESPA program. Prediction of RNA secondary structures was done by the method of Zuker & Turner, as implemented in the mfold program. Results Phylogenetic tree analysis of HCV strains isolated in the South American region revealed the presence of a distinct genetic lineage inside genotype 1. Signature pattern analysis revealed that the presence of this lineage is consistent with the presence of a sequence signature in the 5'NCR of HCV strains isolated in South America. Comparisons of these results with the ones found for Europe or North America revealed that this sequence signature is characteristic of the South American region. Conclusion Phylogentic analysis revealed the presence of a sequence signature in the 5'NCR of type 1 HCV strains isolated in South America. This signature is frequent enough in type 1 HCV populations circulating South America to be detected in a phylogenetic tree analysis as a distinct type 1 sub-population. The coexistence of distinct type 1 HCV subpopulations is consistent with quasispecies dynamics, and suggests that multiple coexisting subpopulations may allow the virus to adapt to its human host populations.
Collapse
Affiliation(s)
- Gonzalo Moratorio
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Mariela Martínez
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - María F Gutiérrez
- Laboratorio de Virología, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7 # 43-82 Ed 50 of 313, Bogotá, Colombia
| | - Katiuska González
- Facultad de Ciencias Médicas y Bioquímicas, Universidad Mayor de San Andrés, Av. Villazón No. 1995 Monoblock Central, La Paz, Bolivia
| | - Rodney Colina
- Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, Quebec, Canada H3G 1Y6
| | - Fernando López-Tort
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Lilia López
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ricardo Recarey
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Alejandro G Schijman
- Laboratorio de Biología Molecular, Grupo CentraLab, Buenos Aires, Argentina
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Vuelta de Obligado 2490, Second Floor, 1428 Buenos Aires, Argentina
| | - María P Moreno
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Laura García-Aguirre
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| | - Aura R Manascero
- Laboratorio de Virología, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7 # 43-82 Ed 50 of 313, Bogotá, Colombia
| | - Juan Cristina
- Laboratorio de Virología Molecular. Centro de Investigaciones Nucleares. Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
| |
Collapse
|
20
|
Thélu MA, Leroy V, Ramzan M, Dufeu-Duchesne T, Marche P, Zarski JP. IRES complexity before IFN-alpha treatment and evolution of the viral load at the early stage of treatment in peripheral blood mononuclear cells from chronic hepatitis C patients. J Med Virol 2007; 79:242-53. [PMID: 17245718 DOI: 10.1002/jmv.20792] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
At the early stage of treatment, IFN alpha-2a induces inhibition of HCV replication. The viral load reflects mainly the degradation rate of the viruses. However, differences in the behavior of the viral population depend on changes, which occurred in the HCV-IRES genome. In this study, cloning and sequencing strategies permitted the generation of a large number of IRES sequences from the PBMCs of 18 patients (5 women, 13 men) with chronic hepatitis C. The HCV IRES appeared to be highly conserved structurally. However, some variability was found between the different isolates obtained: 467 substitutions with a median of 7 variants/patients. No relationship was observed between pre-treatment IRES complexity and the viral load at the beginning. However, on review of the evolution of viral load in the PBMCs during the first 3 days of IFN alpha-2a treatment, patients could be classified into two groups: Group 1, in which the viral population continued to replicate and Group 2, in which the viral load decreased significantly (P = 0.01727). Positioning of the mutations on the predicted IRES secondary structure showed that the distribution of the mutations and their apparition frequency were different between the two groups. At the early stage of treatment, IFN alpha-2a was efficient in reducing the viral replication in a significant number of patients; mechanisms of response might affect the virus directly. However, pre-treatment genomic variations observed in the 5'NCR of HCV were not a parameter of a later response to antiviral therapy in chronic hepatitis C patients. (244)
Collapse
Affiliation(s)
- M A Thélu
- Département d'Hépato-Gastroentérologie, Hôpital Albert Michallon, Grenoble, France
| | | | | | | | | | | |
Collapse
|
21
|
Laskus T, Operskalski EA, Radkowski M, Wilkinson J, Mack WJ, deGiacomo M, Al-Harthi L, Chen Z, Xu J, Kovacs A. Negative-strand hepatitis C virus (HCV) RNA in peripheral blood mononuclear cells from anti-HCV-positive/HIV-infected women. J Infect Dis 2006; 195:124-33. [PMID: 17152016 PMCID: PMC3319123 DOI: 10.1086/509897] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Accepted: 08/31/2006] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) has been reported to replicate in peripheral blood mononuclear cells (PBMCs), particularly in patients coinfected with HCV and human immunodeficiency virus (HIV). However, there are limited data regarding the prevalence of and the factors associated with extrahepatic replication. METHODS The presence of negative-strand HCV RNA in PBMCs was evaluated by a strand-specific assay for 144 anti-HCV-positive/HIV-infected women enrolled in the Women's Interagency HIV Study. One to 5 PBMC samples obtained from each woman were tested. Multivariate analyses were used to assess for associations with the clinical and demographic characteristics of the women. RESULTS Negative-strand HCV RNA was detected in 78 (25%) of 315 specimens, and, for 61 women (42%), > or = 1 specimen was found to have positive results. The presence of negative-strand HCV RNA in PBMCs was significantly positively associated with an HCV RNA plasma level of > or = 6.75 log copies/mL (P=.04) and consumption of > or = 7 alcoholic drinks per week (P=.02). It was also negatively associated with injection drug use occurring in the past 6 months (P=.03). A negative association with a CD4+ CD38+ DR+ cell percentage of > 10% and a positive association with acquired immunodeficiency syndrome were borderline significant (P=.05). CONCLUSIONS HCV replication in PBMCs is common among HIV-coinfected women and appears to be a dynamic process related to lifestyle, virologic, and immunologic factors.
Collapse
Affiliation(s)
- Tomasz Laskus
- Department of Medicine, St. Joseph's Hospital and Medical Center, Phoenix, AZ 85013, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Revie D, Alberti MO, Braich RS, Chelyapov N, Bayles D, Prichard JG, Salahuddin SZ. Analysis of in vitro replicated human hepatitis C virus (HCV) for the determination of genotypes and quasispecies. Virol J 2006; 3:81. [PMID: 17010197 PMCID: PMC1609102 DOI: 10.1186/1743-422x-3-81] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 09/29/2006] [Indexed: 12/13/2022] Open
Abstract
Isolation and self-replication of infectious HCV has been a difficult task. However, this is needed for the purposes of developing rational drugs and for the analysis of the natural virus. Our recent report of an in vitro system for the isolation of human HCV from infected patients and their replication in tissue culture addresses this challenge. At California Institute of Molecular Medicine several isolates of HCV, called CIMM-HCV, were grown for over three years in cell culture. This is a report of the analysis of CIMM-HCV isolates for subtypes and quasispecies using a 269 bp segment of the 5'UTR. HCV RNA from three patients and eleven CIMM-HCV were analyzed for this purpose. All isolates were essentially identical. Isolates of HCV from one patient were serially transmitted into fresh cells up to eight times and the progeny viruses from each transmission were compared to each other and also to the primary isolates from the patient's serum. Some isolates were also transmitted to different cell types, while others were cultured continuously without retransmission for over three years. We noted minor sequence changes when HCV was cultured for extended periods of time. HCV in T-cells and non-committed lymphoid cells showed a few differences when compared to isolates obtained from immortalized B-cells. These viruses maintained close similarity despite repeated transmissions and passage of time. There were no subtypes or quasispecies noted in CIMM-HCV.
Collapse
Affiliation(s)
- Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, California, USA
| | - Michael O Alberti
- Department of Biology, California Lutheran University, Thousand Oaks, California, USA
| | - Ravi S Braich
- California Institute of Molecular Medicine, Ventura, California, USA
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Nickolas Chelyapov
- California Institute of Molecular Medicine, Ventura, California, USA
- University of Southern California, Los Angeles, California, USA
| | - David Bayles
- California Institute of Molecular Medicine, Ventura, California, USA
| | | | - S Zaki Salahuddin
- California Institute of Molecular Medicine, Ventura, California, USA
| |
Collapse
|
23
|
Gallegos-Orozco JF, Arenas JI, Vargas HE, Kibler KV, Wilkinson JK, Nowicki M, Radkowski M, Nasseri J, Rakela J, Laskus T. Selection of different 5' untranslated region hepatitis C virus variants during post-transfusion and post-transplantation infection. J Viral Hepat 2006; 13:489-98. [PMID: 16792543 DOI: 10.1111/j.1365-2893.2006.00724.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND Hepatitis C virus (HCV) translation is initiated in a cap-independent manner by an internal ribosome entry site (IRES) located within the 5' untranslated region (5'UTR). Sequence changes in this region could affect translation efficiency and presumably viral replication. AIM To determine translation efficiency of 5'UTR variants developing during post-transfusion hepatitis C in two immunocompetent subjects and in two immunosuppressed liver recipients with recurrent HCV. METHODS Sequential samples were screened for 5'UTR changes by single-strand conformation polymorphism followed by cloning and sequencing whenever band pattern suggested sequence changes. 5'UTR variants were tested for IRES activity using a bicistronic dual luciferase expression plasmid transfected into HepG2 and Huh7 cell-lines. RESULTS In the transfused patients, translation efficiency of 5'UTR variants from early post-transfusion samples was 5.1- to 13.7-fold higher than that of predominant variants found in late follow-up samples. Post-transplant variants in the other two patients had 2.6- to 5.9-fold higher translation efficiency than those present only in pretransplant samples. CONCLUSION In the immunocompetent host there may be selection of low translation efficiency HCV variants over the course of infection. However, in immunosuppressed subjects the opposite seems to be true as low translation efficiency variants are superseded by high translation efficiency variants.
Collapse
Affiliation(s)
- J F Gallegos-Orozco
- Division of Transplantation Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Di Liberto G, Roque-Afonso AM, Kara R, Ducoulombier D, Fallot G, Samuel D, Feray C. Clinical and therapeutic implications of hepatitis C virus compartmentalization. Gastroenterology 2006; 131:76-84. [PMID: 16831592 DOI: 10.1053/j.gastro.2006.04.016] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Accepted: 04/07/2006] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Blood mononuclear cells (BMCs) frequently are infected by hepatitis C virus (HCV) variants that are not found in plasma. The influence of this compartmentalization on the natural and therapeutic outcome of hepatitis C is unknown. METHODS We studied 119 patients with previously untreated chronic HCV infection. Sixty-five of these patients started first-line treatment with pegylated interferon-alfa and ribavirin after enrollment in the study. The internal ribosomal entry site (IRES) of HCV RNA was amplified and compared between plasma and BMCs by means of single-strand conformational polymorphism (SSCP) analysis, line-probe assay, and cloning sequencing. RESULTS The IRES SSCP patterns differed between plasma and BMCs in 54 (48%) of 113 assessable patients. Twenty-seven (24%) of these patients were co-infected by 2 HCV types or subtypes, only 1 of which was detectable in BMCs (n = 25) or in plasma (n = 2). SSCP-defined compartmentalization was more frequent in former drug users than in others (35/56 [60%] vs 19/56 [34%]; P < .01), and less frequent in patients with genotype 1 HCV in plasma (26/73 [24%] vs 28/40 [65%]; P < .01). The only variables that were independently predictive of a sustained virologic response were SSCP-defined compartmentalization (25/31 vs 10/32; P = .0001) and genotype 2 or 3 infection of BMCs (22/31 vs 8/34; P = .002). CONCLUSIONS A significant proportion of patients with hepatitis C are co-infected by 2 or more HCV variants with distinct IRES sequences and distinct cellular tropism. This compartmentalization is a strong independent predictor of treatment efficacy.
Collapse
Affiliation(s)
- Gaëtana Di Liberto
- Institut National de la Santé et de la Recherche Médicale, INSERM, Centre de Recherche Biomedicale Beaujon-Bichat, Faculté de Médecine Xavier Bichat, Paris, France
| | | | | | | | | | | | | |
Collapse
|
25
|
Blackard JT, Kemmer N, Sherman KE. Extrahepatic replication of HCV: insights into clinical manifestations and biological consequences. Hepatology 2006; 44:15-22. [PMID: 16799966 DOI: 10.1002/hep.21283] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An estimated 170 million persons are infected with the hepatitis C virus (HCV) worldwide. While hepatocytes are the major site of infection, a broad clinical spectrum of extrahepatic complications and diseases are associated with chronic HCV infection, highlighting the involvement of HCV in a variety of non-hepatic pathogenic processes. There is a growing body of evidence to suggest that HCV can replicate efficiently in extrahepatic tissues and cell types, including peripheral blood mononuclear cells. Nonetheless, laboratory confirmation of HCV replication in extrahepatic sites is fraught with technical challenges, and in vitro systems to investigate extrahepatic replication of HCV are severely limited. Thus, future studies of extrahepatic replication should combine innovative in vitro assays with a prospective cohort design to maximize our understanding of this important phenomenon to the pathogenesis and treatment response rates of HCV.
Collapse
Affiliation(s)
- Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
| | | | | |
Collapse
|
26
|
Yasmeen A, Hamid S, Granath FN, Lindström H, Elliott RM, Siddiqui AA, Persson MAA. Correlation between translation efficiency and outcome of combination therapy in chronic hepatitis C genotype 3. J Viral Hepat 2006; 13:87-95. [PMID: 16436126 DOI: 10.1111/j.1365-2893.2005.00660.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Combination therapy with interferon-alpha (IFN-alpha) and ribavirin (RBV) in chronic hepatitis C demonstrates the best responses against hepatitis C virus (HCV) of genotype 3. Still, it has proven to be ineffective in 20-30% of patients infected with this genotype. In the present study, we analysed the translation efficiency mediated by the internal ribosome entry site (IRES) region in HCV genotype 3 genomes isolated from sustained responders (SR) and non-responders (NR), assuming that this may influence the outcome of treatment. Pretreatment isolates of genotype 3 from 22 individuals (15 SR, seven NR) were selected for such analyses. The IRES region [nucleotide (nt) 1-407] was cloned into a dual luciferase vector and IRES activity assessed following transfection into various cell lines. Low relative translation efficiency was observed for IRES elements derived from SR patients, whereas those of NR patients showed significantly greater translation efficiency (29.7 +/- 13 vs 69.4 +/- 22; P < 0.01). Subsequently, the effect of IFN-alpha plus RBV on IRES-driven translation in vitro was determined. A greater suppressive effect was observed on IRES activity isolated from seven SR patients, when compared with seven NR patients. In conclusion, IRES efficiency in vitro correlated with treatment response for HCV genotype 3. Further studies are warranted to investigate whether IRES efficiency in vitro, or sequence motifs associated with IRES efficiency, will be worthwhile to explore as prognostic tools for other HCV genotypes in the treatment of chronic HCV infection.
Collapse
Affiliation(s)
- A Yasmeen
- Department of Medicine, Center for Molecular Medicine, and Clinical Epidemiology Unit, Karolinska Hospital, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | | | | | | |
Collapse
|
27
|
Murata T, Hijikata M, Shimotohno K. Enhancement of internal ribosome entry site-mediated translation and replication of hepatitis C virus by PD98059. Virology 2005; 340:105-15. [PMID: 16005928 DOI: 10.1016/j.virol.2005.06.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Revised: 05/11/2005] [Accepted: 06/08/2005] [Indexed: 12/22/2022]
Abstract
Translation initiation of hepatitis C virus (HCV) occurs in an internal ribosome entry site (IRES)-dependent manner. We found that HCV IRES-dependent protein synthesis is enhanced by PD98059, an inhibitor of the extracellular signal-regulated kinase (ERK) signaling pathway, while cellular cap-dependent translation was relatively unaffected by the compound. Treatment of cells with PD98059 allowed for robust HCV replication following cellular incubation with HCV-positive serum. Though the molecular mechanism underlying IRES enhancement remains elusive, PD98059 is a potent accelerator of HCV RNA replication.
Collapse
Affiliation(s)
- Takayuki Murata
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | | | | |
Collapse
|
28
|
Roque-Afonso AM, Ducoulombier D, Di Liberto G, Kara R, Gigou M, Dussaix E, Samuel D, Féray C. Compartmentalization of hepatitis C virus genotypes between plasma and peripheral blood mononuclear cells. J Virol 2005; 79:6349-57. [PMID: 15858018 PMCID: PMC1091708 DOI: 10.1128/jvi.79.10.6349-6357.2005] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Differences in hepatitis C virus (HCV) variants of the highly conserved 5' untranslated region (UTR) have been observed between plasma and peripheral blood mononuclear cells (PBMC). The prevalence and the mechanisms of this compartmentalization are unknown. Plasma and PBMC HCV variants were compared by single-strand conformation polymorphism (SSCP) and by cloning or by genotyping with a line probe assay (LiPA) in 116 chronically infected patients, including 44 liver transplant recipients. SSCP patterns differed between compartments in 43/109 analyzable patients (39%). Differences were significantly more frequent in patients with transplants (21/38 [55%] versus 22/71 [31%]; P < 0.01) and in those who acquired HCV through multiple transfusions before 1991 (15/20; 75%) or through drug injection (16/31; 52%) than in those infected through an unknown route (7/29; 24%) or through a single transfusion (5/29; 17%; P < 0.001). Cloning of the 5' UTR, LiPA analysis, and nonstructural region 5B sequencing revealed different genotypes in the two compartments from 10 patients (9%). In nine patients, the genotype detected in PBMC was not detected in plasma and was weak or undetectable in the liver in three cases. This genotypic compartmentalization persisted for years in three patients and after liver transplantation in two. The present study shows that a significant proportion of HCV-infected subjects harbor in their PBMC highly divergent variants which were likely acquired through superinfections.
Collapse
|
29
|
van Leeuwen HC, Reusken CBEM, Roeten M, Dalebout TJ, Riezu-Boj JI, Ruiz J, Spaan WJM. Evolution of naturally occurring 5' non-translated region variants of hepatitis C virus genotype 1b in selectable replicons. J Gen Virol 2004; 85:1859-1866. [PMID: 15218170 DOI: 10.1099/vir.0.79924-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Quasispecies shifts are essential for the development of persistent hepatitis C virus (HCV) infection. Naturally occurring sequence variations in the 5' non-translated region (NTR) of the virus could lead to changes in protein expression levels, reflecting selective forces on the virus. The extreme 5' end of the virus' genome, containing signals essential for replication, is followed by an internal ribosomal entry site (IRES) essential for protein translation as well as replication. The 5' NTR is highly conserved and has a complex RNA secondary structure consisting of several stem-loops. This report analyses the quasispecies distribution of the 5' NTR of an HCV genotype 1b clinical isolate and found a number of sequences differing from the consensus sequence. The consensus sequence, as well as a major variant located in stem-loop IIIa of the IRES, was investigated using self-replicating HCV RNA molecules in human hepatoma cells. The stem-loop IIIa mutation, which is predicted to disrupt the stem structure, showed slightly lower translation efficiency but was severely impaired in the colony formation of selectable HCV replicons. Interestingly, during selection of colonies supporting autonomous replication, mutations emerged that restored the base pairing in the stem-loop. Recloning of these altered IRESs confirmed that these second site revertants were more efficient in colony formation. In conclusion, naturally occurring variants in the HCV 5' NTR can lead to changes in their replication ability. Furthermore, IRES quasispecies evolution was observed in vitro under the selective pressure of the replicon system.
Collapse
Affiliation(s)
- Hans C van Leeuwen
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Chantal B E M Reusken
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Marko Roeten
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Tim J Dalebout
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Jose Ignacio Riezu-Boj
- Division of Hepatology and Gene Therapy, Clínica Universitaria/Department of Medicine, Fundación para la Investigación Medica Aplicada (FIMA), University of Navarra, Pamplona, Spain
| | - Juan Ruiz
- Division of Hepatology and Gene Therapy, Clínica Universitaria/Department of Medicine, Fundación para la Investigación Medica Aplicada (FIMA), University of Navarra, Pamplona, Spain
| | - Willy J M Spaan
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| |
Collapse
|
30
|
Forton DM, Karayiannis P, Mahmud N, Taylor-Robinson SD, Thomas HC. Identification of unique hepatitis C virus quasispecies in the central nervous system and comparative analysis of internal translational efficiency of brain, liver, and serum variants. J Virol 2004; 78:5170-83. [PMID: 15113899 PMCID: PMC400349 DOI: 10.1128/jvi.78.10.5170-5183.2004] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Reports of cerebral dysfunction in chronic hepatitis C virus (HCV) infection have led to the suggestion that HCV may infect the central nervous system (CNS). We used reverse transcription-PCR, cloning, and sequencing to define quasispecies for the HCV internal ribosomal entry site (IRES) and hypervariable region 1 (HVR1) in autopsy-derived brain, liver, lymph node, and serum samples. There was evidence of tissue compartmentalization of sequences in the brain in two patients, with between 24 and 55% of brain-derived IRES sequences absent from the serum, and significant phylogenetic and phenetic clustering of the brain and lymph node HVR1 sequences. The IRES initiates cap-independent translation of the viral polyprotein. Two unique brain-derived IRES mutations (C(204)-->A and G(243)-->A), which have previously been associated with lymphoid replication and altered translational efficiency in cell culture, were found in one patient. We used a dicistronic reporter vector to test whether brain-derived variants showed altered IRES-mediated translational efficiency, which might favor CNS infection. The translational efficiencies of the brain-derived IRES sequences were generally reduced compared to those of the master serum and liver sequences in rabbit reticulocyte cell lysates and two human cell lines, HuH7 (liver) and CHME3 (microglial). The C(204)-->A and G(243)-->A mutations showed preserved translational efficiency in HuH7 cells but reduced efficiency in CHME3 cells. Our data provide evidence that the CNS is a site of HCV replication, consistent with the recent demonstration of negative-strand HCV RNA in brain, and suggest that IRES polymorphisms may be important as a viral strategy of reduced translation to favor latency in the CNS.
Collapse
Affiliation(s)
- Daniel M Forton
- Hepatology Section, Division of Medicine, Faculty of Medicine, Imperial College London, 10th Floor, QEQM Building, St. Mary's Hospital, South Wharf Road, London W2 1NY, United Kingdom.
| | | | | | | | | |
Collapse
|
31
|
Thelu MA, Drouet E, Hilleret MN, Zarski JP. Lack of clinical significance of variability in the internal ribosome entry site of hepatitis C virus. J Med Virol 2004; 72:396-405. [PMID: 14748063 DOI: 10.1002/jmv.20021] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The extreme 5'-proximal sequence of the hepatitis C virus (HCV) genome including the 5' non-coding region (5'NCR) of 341 nucleotide long and the first 30 nucleotides of the core region is highly conserved among different HCV genotypes. It contains a segment termed Internal Ribosome Entry Site (IRES) that regulates the cap-independent translation of HCV-RNA to polyprotein. Sequence variability in this region has important implications for structural organisation and function of the IRES element and could correlate with HCV RNA concentration or response to antiviral therapy. Fourteen patients (seven women, seven men) with chronic hepatitis C were separated into two groups according to their response to antiviral therapy. Seven of these were sustained responders to treatment by Interferon alpha 2b and Ribavirin and seven were non-responders. After cloning-sequencing, the IRES (nt 21 to 374) appears to be structurally highly conserved. However some variability was found between the different isolates obtained: 209 substitutions with a median of four variants/patients. Comparison of the number of variants present in the viral population of the sustained responders and non-responders patients do not show any difference. Positioning of the mutations on the predicted IRES secondary structure showed that the distribution of the mutations and their apparition frequency were different between the two groups. The translation initiator AUG-4 codon, located in the stem-loop IV, is never modified. Variations observed in the IRES are not a parameter of response to antiviral therapy, but the integrity of this region is a necessary condition to maintain its activity.
Collapse
Affiliation(s)
- Marie-Ange Thelu
- Département d'Hépato-Gastroentérologie, Hôpital Albert Michallon, Grenoble, France.
| | | | | | | |
Collapse
|
32
|
Ducoulombier D, Roque-Afonso AM, Di Liberto G, Penin F, Kara R, Richard Y, Dussaix E, Féray C. Frequent compartmentalization of hepatitis C virus variants in circulating B cells and monocytes. Hepatology 2004; 39:817-25. [PMID: 14999702 DOI: 10.1002/hep.20087] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Differences in the composition of the hepatitis C virus (HCV) quasispecies between plasma and blood mononuclear cells (BMC) strongly suggest that BMCs support viral replication. We examined the frequency of such compartmentalization, the cell types involved, the constraints exerted on the different variants, and the role of immunoglobulin-complexed variants. We screened the hypervariable region (HVR1) of HCV isolates from 14 HBsAg- and HIV-seronegative patients with chronic HCV infection. HCV RNA was amplified and cloned from plasma, the immunoglobulin G (IgG)-bound fraction, and total and sorted BMCs (CD19+, CD8+, CD4+, and CD14+ cells). Compartmentalization was estimated using a matrix correlation test. The ratio of nonsynonymous/synonymous substitutions (d(N)/d(S) ratio) was calculated for each compartment. HCV RNA was detected in 3/3 BMC, 11/11 CD19+, 10/11 CD14+, 4/11 CD8+ and 0/11 CD4+ cell samples. HVR1 sequences were significantly different between plasma and at least one cellular compartment in all nine cases analyzed, and between B cells (CD19+) and monocytes (CD14+) in all five available cases. IgG-bound variants were distinct from cellular variants. D(N)/d(S) ratios were similar (n = 3) or lower (n = 6) in cellular compartments compared with plasma and the IgG-bound fraction. In conclusion, HCV compartmentalization is a common phenomenon. B cells and monocytes harbor HCV variants showing a low rate of nonsynonymous mutations, a feature that might contribute to the persistence of HCV infection.
Collapse
Affiliation(s)
- Delphine Ducoulombier
- Equipe Propre de l'Institut National de la Santé et de la Recherche Médicale (INSERM 99-41), Unité 481, Faculté de médecine X Bichat, 16 rue Huchard, Paris, France
| | | | | | | | | | | | | | | |
Collapse
|
33
|
McKnight KL, Sandefur S, Phipps KM, Heinz BA. An adenine-to-guanine nucleotide change in the IRES SL-IV domain of picornavirus/hepatitis C chimeric viruses leads to a nonviable phenotype. Virology 2003; 317:345-58. [PMID: 14698672 DOI: 10.1016/j.virol.2003.08.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The inability for the internal ribosomal entry site (IRES) of hepatitis C virus (HCV) to be readily studied in the context of viral replication has been circumvented by constructing chimeras such as with poliovirus (PV), in which translation of the genome polyprotein is under control of the HCV IRES. During our attempts to configure the PV/HCV chimera for our drug discovery efforts, we discovered that an adenine- (A) to-guanine (G) change at nt 350 in domain IV of the HCV IRES resulted in a nonviable phenotype. Similarly, a mengovirus (MV)/HCV chimera using the same configuration with a G at nt 350 (G-350) was found to be nonviable. In contrast, a bovine viral diarrhea virus (BVDV)/HCV chimera remained viable with G-350 in the HCV IRES insert. Second-site, resuscitating mutations were identified from the G-350 PV/HCV and MV/HCV viruses after blind passaging. For both viruses, the resuscitating mutations involved destabilization of domain IV in the HCV IRES. The nonviability of G-350 in the picornavirus/HCV chimeric background might be linked to translation efficiency as indicated by analyses with dual reporter and PV/HCV replicon constructs.
Collapse
Affiliation(s)
- Kevin L McKnight
- Eli Lilly and Company, Lilly Research Laboratories, LCC, Indianapolis, IN 46225, USA.
| | | | | | | |
Collapse
|
34
|
Imbert I, Dimitrova M, Kien F, Kieny MP, Schuster C. Hepatitis C virus IRES efficiency is unaffected by the genomic RNA 3'NTR even in the presence of viral structural or non-structural proteins. J Gen Virol 2003; 84:1549-1557. [PMID: 12771425 DOI: 10.1099/vir.0.18907-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) translation is mediated by an IRES structure. Instead of a poly(A) tail, the 3' end of the genome contains a tripartite 3'NTR composed of a non-conserved region, a polypyrimidine tract and a highly conserved stretch of 98 nt, termed the 3'X region. Using a set of bicistronic recombinant DNA constructs expressing two reporter genes separated by the HCV IRES, it was determined whether the HCV 3'NTR sequence, in the presence or absence of HCV proteins, played a role in the efficiency of HCV IRES-dependent translation ex vivo. Bicistronic expression cassettes were transfected into hepatic and non-hepatic cell lines. These results show that neither the entire 3'NTR nor the 3'X sequence alters IRES-dependent translation efficiency, whatever the cell line tested. A potential effect of the 3'NTR on IRES-dependent translation in the presence of HCV proteins was investigated further. Neither non-structural nor structural HCV proteins had any effect on the efficiency of IRES in this system. In addition, in order to mimic HCV genome organization, monocistronic expression cassettes containing the IRES and a Core-DsRed fusion gene were constructed with or without the 3'NTR. In this context, no effect of the 3'NTR on IRES translation efficiency was observed, even in the presence of HCV proteins. These data demonstrate that HCV translation is not modulated by the viral genomic 3'NTR sequence, even in the presence of HCV structural or non-structural proteins.
Collapse
Affiliation(s)
- Isabelle Imbert
- INSERM U544, Institut de Virologie, 3 rue Koeberlé, 67000 Strasbourg, France
| | - Maria Dimitrova
- INSERM U544, Institut de Virologie, 3 rue Koeberlé, 67000 Strasbourg, France
| | - François Kien
- INSERM U544, Institut de Virologie, 3 rue Koeberlé, 67000 Strasbourg, France
| | - Marie Paule Kieny
- INSERM U544, Institut de Virologie, 3 rue Koeberlé, 67000 Strasbourg, France
| | - Catherine Schuster
- INSERM U544, Institut de Virologie, 3 rue Koeberlé, 67000 Strasbourg, France
| |
Collapse
|
35
|
Malet I, Belnard M, Agut H, Cahour A. From RNA to quasispecies: a DNA polymerase with proofreading activity is highly recommended for accurate assessment of viral diversity. J Virol Methods 2003; 109:161-70. [PMID: 12711059 DOI: 10.1016/s0166-0934(03)00067-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
RNA viruses are characterized by their high rates of genetic variation. Their genetic diversity is generally studied by reverse transcription (RT) followed by polymerase chain reaction (PCR) amplification and nucleotide (nt) sequence determination. The misinterpretation of viral diversity due to copy errors introduced by the enzymes used in this two-step protocol has not yet been assessed systematically. In order to investigate the impact of such errors, we sought to bypass the intrinsic viral heterogeneity by starting from a homogeneous cDNA template. With this in mind, the hepatitis C virus (HCV) 5' non-coding region (5'NCR) was amplified either by PCR starting from a homopolymeric cDNA template or by RT-PCR starting from the in vitro RNA transcript derived from the same original cDNA template. Amplicons were cloned and the 17-20 individual clones were sequenced in each assay. Different quasispecies patterns were obtained with various commercially available DNA polymerases, resulting in different computed error rates. The non-proofreading Taq DNA polymerase provided the highest error rate which was seven times higher than that obtained with the most reliable of the proofreading polymerases tested. We, therefore, emphasize that the misleading interpretation of the observed heterogeneity for a given viral sample could be due to ignorance of the fidelity of the polymerase used for viral genome amplification, and thus that proofreading DNA polymerases should be preferred for the investigation of natural genetic diversity of RNA viruses.
Collapse
Affiliation(s)
- Isabelle Malet
- Laboratoire de Virologie, C.E.R.V.I., UPRES EA 2387, Groupe Hôpital Pitié-Salpêtrière, 83 Bd de l'hôpital, 75651 Paris Cedex 13, France
| | | | | | | |
Collapse
|
36
|
Laporte J, Bain C, Maurel P, Inchauspe G, Agut H, Cahour A. Differential distribution and internal translation efficiency of hepatitis C virus quasispecies present in dendritic and liver cells. Blood 2003; 101:52-7. [PMID: 12393733 DOI: 10.1182/blood-2002-03-0818] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C virus (HCV) is predominantly a hepatotropic virus. Nonetheless, there is mounting evidence that hematopoietic cells may support HCV replication. The HCV 5' untranslated region (5'UTR), responsible for initiation of viral translation, via an internal ribosome entry site (IRES), has been previously described to contain specific nucleotide substitutions when cultured in infected lymphoid cells. Our purpose was to establish whether the 5'UTR polymorphism of quasispecies from 3 cell compartments (liver, peripheral blood mononuclear cells [PBMG], and monocyte-derived dendritic cells [DCs]) of a patient chronically infected with HCV1b affects the corresponding translational efficiencies and thus the capacity for replication. The 5'UTR polymorphism was characterized by identification of changes at 3 crucial sites as compared with the reference nucleotide (nt) sequence: a G insertion between positions 19 and 20, a C>A substitution at position 204 and a G>A substitution at position 243. The quasispecies detected in DCs was unique and differed from those present in the liver, suggesting a particular tropism of HCV quasispecies for DCs. Moreover, its translational activity was significantly impaired when compared with those from liver and PBMCs in different cell lines. This impairment was thoroughly confirmed in primary cultures of both human hepatocytes and monocyte-derived DCs. Taken together, our data lend support both to a specific location and impaired replication of HCV quasispecies in DCs, which could be related to viral persistence and perturbation of DC function in chronically infected patients.
Collapse
Affiliation(s)
- Julien Laporte
- Laboratoire de virologie, C.E.R.VI., UPRES EA 2387, Hôpital Pitié-Salpêtrière, Paris, France
| | | | | | | | | | | |
Collapse
|
37
|
Jones LR, Zandomeni R, Weber EL. Quasispecies in the 5' untranslated genomic region of bovine viral diarrhoea virus from a single individual. J Gen Virol 2002; 83:2161-2168. [PMID: 12185269 DOI: 10.1099/0022-1317-83-9-2161] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The variability of the 5' untranslated genomic region (5'UTR) of bovine viral diarrhoea virus (BVDV) RNA obtained from a single individual was analysed. Lung, kidney and spleen tissues from a naturally infected foetus were used as the source of viral RNA. A fragment of 288 bases of the internal ribosome entry site from the BVDV 5'UTR was amplified by RT-PCR using a proofreading DNA polymerase. PCR products were cloned into pGem and, subsequently, transformed into Escherichia coli. The single-strand conformational polymorphisms of 158 lung-derived clones were analysed; a total of 11 banding patterns was observed. DNAs corresponding to all patterns were sequenced. Of the randomly selected clones, 11 and 10 clones derived from the kidney and spleen, respectively, were also sequenced. All sequences presented differences ranging from 1 to 6 nt substitutions. Analysis of the secondary structure of the variant sequences and comparisons to variant nucleotide sites from the 5'UTR of several BVDV isolates showed that the observed changes were almost free of randomness. Clustering and phylogenetic analyses suggested the existence of low-kinetic variants. BVDV quasispecies may be involved in establishing persistent infections by means of eluding maternal antibodies. The methods described here may be adapted easily both to analyse large numbers of samples from other genomic regions and for the study of BVDV quasispecies evolution in other systems.
Collapse
Affiliation(s)
- Leandro Roberto Jones
- Instituto de Virología, CICVyA, INTA-Castelar, CC77 (1708) Morón, Buenos Aires, Argentina1
| | - Rubén Zandomeni
- Consejo Nacional de Investigaciones Científicas, Argentina3
- Instituto de Microbiología y Zoología Agrícola, CICVyA, INTA-Castelar, CC77 (1708) Morón, Buenos Aires, Argentina2
| | - E Laura Weber
- Consejo Nacional de Investigaciones Científicas, Argentina3
- Instituto de Virología, CICVyA, INTA-Castelar, CC77 (1708) Morón, Buenos Aires, Argentina1
| |
Collapse
|
38
|
Soler M, Pellerin M, Malnou CE, Dhumeaux D, Kean KM, Pawlotsky JM. Quasispecies heterogeneity and constraints on the evolution of the 5' noncoding region of hepatitis C virus (HCV): relationship with HCV resistance to interferon-alpha therapy. Virology 2002; 298:160-73. [PMID: 12093183 DOI: 10.1006/viro.2002.1494] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hepatitis C virus (HCV) polyprotein translation depends on direct internal entry of the 40S ribosomal subunit mediated by an internal ribosome entry segment (IRES) located in the 5' noncoding (5'NC) region of the viral genome. HCV is genetically heterogeneous and is characterized by the existence of a quasispecies distribution of the virus population within a single infected individual. Cloning and sequencing strategies were used to characterize 5'NC quasispecies genetically. Similar to coding regions, the HCV 5'NC region was distributed as a quasispecies, but it appeared to be subjected to stronger conservatory constraints than other regions of the HCV genome, probably due to the need for structural (and functional) conservation of the IRES. Indeed, most of the quasispecies substitutions were in unpaired regions of the IRES or clustered such that base-pairing was maintained, whereas only 21% were expected to result in a loss of base-pairing. Quasispecies-related structural changes could be predicted in the core cruciform of IRES domain III composed of the RNA helices which extend from the four-way junction JIIIabc, mostly in minor variants, but sometimes in major ones. The results presented here suggest the simultaneous presence in infected patients of a mixture of genetically distinct but closely related IRES sequences that may have different structures. No significant genetic changes of 5'NC quasispecies were observed after interferon-alpha treatment, except in patients with mixed genotype infection who cleared one of the infecting strains during therapy, suggesting that the quasispecies distribution of IRES sequences does not play a role in HCV resistance to interferon-alpha therapy. In contrast, the overall quasispecies distribution of HCV genomes (including IRES sequences) might participate in regulation of hepatic and extrahepatic HCV replication.
Collapse
Affiliation(s)
- Muriel Soler
- Department of Virology (EA 3489), Université Paris XII, Créteil, France
| | | | | | | | | | | |
Collapse
|
39
|
Walewski JL, Gutierrez JA, Branch-Elliman W, Stump DD, Keller TR, Rodriguez A, Benson G, Branch AD. Mutation Master: profiles of substitutions in hepatitis C virus RNA of the core, alternate reading frame, and NS2 coding regions. RNA (NEW YORK, N.Y.) 2002; 8:557-571. [PMID: 12022223 PMCID: PMC1370277 DOI: 10.1017/s1355838202029023] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The RNA genome of the hepatitis C virus (HCV) undergoes rapid evolutionary change. Efforts to control this virus would benefit from the advent of facile methods to identify characteristic features of HCV RNA and proteins, and to condense the vast amount of mutational data into a readily interpretable form. Many HCV sequences are available in GenBank. To facilitate analysis, consensus sequences were constructed to eliminate the overrepresentation of certain genotypes, such as genotype 1, and a novel package of sequence analysis tools was developed. Mutation Master generates profiles of point mutations in a population of sequences and produces a set of visual displays and tables indicating the number, frequency, and character of substitutions. It can be used to analyze hundreds of sequences at a time. When applied to 255 HCV core protein sequences, Mutation Master identified variable domains and a series of mutations meriting further investigation. It flagged position 4, for example, where 90% or more of all sequences in genotypes 1, 2, 4, and 5, have N4, whereas those in genotypes 3, 6, 7, 8, 9, and 10 have L4. This pattern is noteworthy: L (hydrophobic) to N (polar) substitutions are generally rare, and genotypes 1, 2, 4, and 5 do not form a recognized super family of sequences. Thus, the L4N substitution probably arose independently several times. Moreover, not one member of genotypes 1, 2, 4, or 5 has L4 and not one member of genotypes 3, 6, 7, 8, 9, or 10 has N4. This nonoverlapping pattern suggests that coordinated changes at position 4 and a second site are required to yield a viable virus. The package generated a table of genotype-specific substitutions whose future analysis may help to identify interacting amino acids. Three substitutions were present in 100% of genotype 2 members and absent from all others: A68D, R74K, and R114H. Finally, this study revealed thatARFP, a novel protein encoded in an overlapping reading frame, is as conserved as conventional HCV proteins, a result supporting a role for ARFP in the viral life cycle. Whereas most conventional programs for phylogenetic analysis of sequences provide information about overall relatedness of genes or genomes, this program highlights and profiles point mutations. This is important because determinants of pathogenicity and drug susceptibility are likely to result from changes at only one or two key nucleotides or amino acid sites, and would not be detected by the type of pairwise comparisons that have usually been performed on HCV to date. This study is the first application of Mutation Master, which is now available upon request (http://tandem.biomath.mssm.edu/mutationmaster.html).
Collapse
Affiliation(s)
- José L Walewski
- Department of Medicine, Division of Liver and Diseases, Mount Sinai School of Medicine, New York, New York 10029, USA
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Martínez-Salas E, Ramos R, Lafuente E, López de Quinto S. Functional interactions in internal translation initiation directed by viral and cellular IRES elements. J Gen Virol 2001; 82:973-984. [PMID: 11297672 DOI: 10.1099/0022-1317-82-5-973] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Encarnación Martínez-Salas
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain1
| | - Ricardo Ramos
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain1
| | - Esther Lafuente
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain1
| | - Sonia López de Quinto
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain1
| |
Collapse
|
41
|
Abstract
Picornaviruses are small animal viruses with positive-strand genomic RNA, which is translated using cap-independent internal translation initiation. The key role in this is played by ciselements of the 5"-untranslated region (5"-UTR) and, in particular, by the internal ribosome entry site (IRES). The function of translational ciselements requires both canonical translation initiation factors (eIFs) and additional IRES trans-acting factors (ITAFs). All known ITAFs are cell RNA-binding proteins which play a variety of functions in noninfected cells. Specific features of translational ciselements substantially affect the phenotype and, in particular, tissue tropism and pathogenic properties of picornaviruses. It is clear that, in some cases, the molecular mechanism involved is a change in interactions between viral ciselements and ITAFs. The properties and tissue distribution of ITAFs may determine the biological properties of other viruses that also use the IRES-dependent translation initiation. Since this mechanism is also involved in translation of several cell mRNAs, ITAF may contribute to the regulation of the most important aspects of the living activity in noninfected cells.
Collapse
Affiliation(s)
- V. I. Agol
- Chumakov Institute of Poliomyelitis and Virus Encephalites, Russian Academy of Medical Sciences, and, Moscow State University, Moscow, Russia
| |
Collapse
|