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Xie JJ, Ni W, Wei Q, Ma H, Bai G, Shen Y, Wu ZY. New clinical characteristics and novel pathogenic variants of patients with hereditary leukodystrophies. CNS Neurosci Ther 2019; 26:567-575. [PMID: 31885218 PMCID: PMC7163788 DOI: 10.1111/cns.13284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/05/2019] [Accepted: 12/12/2019] [Indexed: 11/28/2022] Open
Abstract
Aim Leukodystrophies are a group of inherited white matter disorders with clinical, genetic, and imaging heterogeneity, which usually pose a diagnostic challenge for physicians. We aimed to identify new clinical characteristics and novel pathogenic variants of hereditary leukodystrophies in this study. Methods Whole exome sequencing (WES) was performed in 28 unrelated patients clinically suspected with leukodystrophies. Leukocytes enzyme activity test, electroencephalogram (EEG), electromyography (EMG), and brain MRI were conducted. Functional analysis was performed, and the pathogenicity of variants was classified according to the American College of Medical Genetics and Genomics (ACMG) standards and guidelines. Results We made definite diagnosis in 8 probands with 12 pathogenic variants and reported new clinical characteristics and imaging features of these patients. Three novel pathogenic variants were identified, including a microdeletion variant c.2654_2654+3del within CSF1R, a nonsense variant c.1321C>T, and a missense variant c.166G>C within GALC. Conclusion Our results have deepened the understanding of clinical, genetic, and imaging heterogeneity of hereditary leukodystrophies, and expanded the spectrum of pathogenic variants and clinical features.
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Affiliation(s)
- Juan-Juan Xie
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Wang Ni
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiao Wei
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Huan Ma
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, China
| | - Ge Bai
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Shen
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi-Ying Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai, China
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2
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Zamani A, Fan H, Luo G. Identification of cellular genes and pathways important for tumorigenicity of hepatocellular carcinoma cell lines by proteomic profiling. Oncotarget 2017; 8:96171-96183. [PMID: 29221196 PMCID: PMC5707090 DOI: 10.18632/oncotarget.21821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 07/18/2017] [Indexed: 12/22/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most commonly diagnosed malignancy of the liver. A more thorough understanding of HCC pathogenesis will provide novel targets for development of cancer drugs to effectively treat HCC. To further this goal, we carried out a proteomic profiling of HCC cell lines Huh-7.4 and Huh-7.5. These two cell lines were derived from subgenomic HCV RNA-replicating Huh-7 cells upon clearance of HCV RNA by antiviral drug treatment. Initially, the tumorigenicity of each cell line was determined and compared in parallel in the same immunedeficient mice. Strikingly, the Huh-7.4 cell line was able to induce tumors, whereas the Huh-7.5 cell line failed to do so, providing unique model systems for identifying cellular genes and pathways important for HCC development and progression. Subsequently, one-dimensional LC-MS/MS proteomic and bioinformatics analyses were performed in the hope of identifying unique cellular genes and pathways responsible for HCC tumorigenicity. Interestingly, a total of 130 cellular genes were found to be significantly up- or downregulated between these two cell lines (r>3 fold, P<0.001). Also, EIF (EIF2&4), mTOR/p70S6K, ERK5, and EGFR signaling pathways were significantly different. Overall, these results provide significant new information to shed light on the underlying biological processes involved in HCC development and progression.
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Affiliation(s)
- Ali Zamani
- Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
- Current address: Department of Pathology and Laboratory Medicine, University of Pennsylvania, School of Medicine, Philadelphia, PA 19104, USA
| | - Huahao Fan
- Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
- Department of Microbiology, Peking University Health Science Center School of Basic Medical Sciences, Beijing, 100191, China
| | - Guangxiang Luo
- Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
- Department of Microbiology, Peking University Health Science Center School of Basic Medical Sciences, Beijing, 100191, China
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3
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Chien KY, Blackburn K, Liu HC, Goshe MB. Proteomic and phosphoproteomic analysis of chicken embryo fibroblasts infected with cell culture-attenuated and vaccine strains of Marek's disease virus. J Proteome Res 2012; 11:5663-77. [PMID: 23106611 DOI: 10.1021/pr300471y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vaccination is an effective strategy to reduce the loss of chickens in the poultry industry caused by Marek's Disease (MD), an avian lymphoproliferative disease. The vaccines currently used are from attenuated serotype 1 Marek's disease virus (MDV) or naturally nononcogenic MDV strains. To prepare for future immunity breaks, functional genomic and proteomic studies have been used to better understand the underlying mechanisms of MDV pathogenicity and the effects induced by the vaccine viruses. In this study, a combined approach of quantitative GeLC-MSE and qualitative ERLIC/IMAC/LC-MS/MS analysis were used to identify abundance changes of proteins and the variations of phosphorylation status resulting from the perturbations due to infection with an attenuated oncogenic virus strain (Md11/75C) and several nononcogenic virus strains (CVI988, FC126 and 301B) in vitro. Using this combined approach, several signal transduction pathways mapped by the identified proteins were found to be altered at both the level of protein abundance and phosphorylation. On the basis of this study, a kinase-dependent pathway to regulate phosphorylation of 4E-BP1 to modulate assembly of the protein translation initiation complex was revealed. The differences of 4E-BP1 phosphorylation patterns as well as the measured abundance changes among several other proteins that regulate host transcriptional and translational activities across the virus strains used in this study provide new insight for future functional and biochemical characterization of specific proteins involved in MDV pathogenesis.
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Affiliation(s)
- Ko-yi Chien
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh North Carolina 27695, United States
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4
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Petrakis S, Raskó T, Russ J, Friedrich RP, Stroedicke M, Riechers SP, Muehlenberg K, Möller A, Reinhardt A, Vinayagam A, Schaefer MH, Boutros M, Tricoire H, Andrade-Navarro MA, Wanker EE. Identification of human proteins that modify misfolding and proteotoxicity of pathogenic ataxin-1. PLoS Genet 2012; 8:e1002897. [PMID: 22916034 PMCID: PMC3420947 DOI: 10.1371/journal.pgen.1002897] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 07/02/2012] [Indexed: 02/06/2023] Open
Abstract
Proteins with long, pathogenic polyglutamine (polyQ) sequences have an enhanced propensity to spontaneously misfold and self-assemble into insoluble protein aggregates. Here, we have identified 21 human proteins that influence polyQ-induced ataxin-1 misfolding and proteotoxicity in cell model systems. By analyzing the protein sequences of these modifiers, we discovered a recurrent presence of coiled-coil (CC) domains in ataxin-1 toxicity enhancers, while such domains were not present in suppressors. This suggests that CC domains contribute to the aggregation- and toxicity-promoting effects of modifiers in mammalian cells. We found that the ataxin-1-interacting protein MED15, computationally predicted to possess an N-terminal CC domain, enhances spontaneous ataxin-1 aggregation in cell-based assays, while no such effect was observed with the truncated protein MED15ΔCC, lacking such a domain. Studies with recombinant proteins confirmed these results and demonstrated that the N-terminal CC domain of MED15 (MED15CC) per se is sufficient to promote spontaneous ataxin-1 aggregation in vitro. Moreover, we observed that a hybrid Pum1 protein harboring the MED15CC domain promotes ataxin-1 aggregation in cell model systems. In strong contrast, wild-type Pum1 lacking a CC domain did not stimulate ataxin-1 polymerization. These results suggest that proteins with CC domains are potent enhancers of polyQ-mediated protein misfolding and aggregation in vitro and in vivo.
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Affiliation(s)
- Spyros Petrakis
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Tamás Raskó
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Jenny Russ
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Ralf P. Friedrich
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Martin Stroedicke
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | | | - Katja Muehlenberg
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Angeli Möller
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Anita Reinhardt
- Unité BFA (EAC 7059), Université Paris Diderot-Paris7/CNRS, Paris, France
| | | | - Martin H. Schaefer
- Computational Biology and Data Mining, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Hervé Tricoire
- Unité BFA (EAC 7059), Université Paris Diderot-Paris7/CNRS, Paris, France
| | | | - Erich E. Wanker
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
- * E-mail:
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5
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Giritharan G, Ilic D, Gormley M, Krtolica A. Human embryonic stem cells derived from embryos at different stages of development share similar transcription profiles. PLoS One 2011; 6:e26570. [PMID: 22039509 PMCID: PMC3198782 DOI: 10.1371/journal.pone.0026570] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 09/29/2011] [Indexed: 11/18/2022] Open
Abstract
We have derived hESC from biopsied blastomeres of cleavage stage embryos under virtually the same conditions we used for the derivation of hESC lines from inner cell mass of blastocyst stage embryos. Blastomere-derived hESC lines exhibited all the standard characteristics of hESC including undifferentiated proliferation, genomic stability, expression of pluripotency markers and the ability to differentiate into the cells of all three germ layers both in vitro and in vivo. To examine whether hESC lines derived from two developmental stages of the embryo differ in gene expression, we have subjected three blastomere-derived hESC lines and two ICM-derived hESC lines grown under identical culture conditions to transcriptome analysis using gene expression arrays. Unlike previously reported comparisons of hESC lines which demonstrated, apart from core hESC-associated pluripotency signature, significant variations in gene expression profiles of different lines, our data show that hESC lines derived and grown under well-controlled defined culture conditions adopt nearly identical gene expression profiles. Moreover, blastomere-derived and ICM-derived hESC exhibited very similar transcriptional profiles independent of the developmental stage of the embryo from which they originated. Furthermore, this profile was evident in very early passages of the cells and did not appear to be affected by extensive passaging. These results suggest that during derivation process cells which give rise to hESC acquire virtually identical stable phenotype and are not affected by the developmental stage of the starting cell population.
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Affiliation(s)
| | - Dusko Ilic
- SLL Sciences, StemLifeLine, Inc., San Carlos, California, United States of America
| | - Matthew Gormley
- University of California San Francisco, San Francisco, California, United States of America
| | - Ana Krtolica
- SLL Sciences, StemLifeLine, Inc., San Carlos, California, United States of America
- * E-mail:
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6
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Rosenfeld AB, Racaniello VR. Components of the multifactor complex needed for internal initiation by the IRES of hepatitis C virus in Saccharomyces cerevisiae. RNA Biol 2010; 7:596-605. [PMID: 20935471 DOI: 10.4161/rna.7.5.13096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Interaction between the 40S ribosomal subunit and the IRES of hepatitis C virus (HCV) is thought to be independent of initiation proteins, while joining of the 60S ribosomal subunit, and initiation of translation is dependent upon components of the translation machinery. An established in vivo functional assay for internal initiation mediated by the HCV IRES was used to identify proteins needed for IRES dependent translation in Saccharomyces cerevisiae strains possessing alterations of the translation machinery. Internal initiation dependent upon the HCV IRES was abrogated in strains lacking eIF5B, and reduced in strains with altered eIF3, either lacking the Hcr1p subunit, a component of eIF3 not previously known to interact with HCV RNA, or possessing an amino acid change in the Rpg1p subunit. The HCV RNA-induced conformational change in the 40S subunit might affect positioning of eIF3 and lead to different interactions between the ribosome, eIF3, and the multifactor complex. HCV IRES dependent initiation was unaffected in strains in which the concentration of the initiating tRNA was reduced. Alteration of the δ subunit of eIF2B, which leads to inefficient recycling, or substitution of aspartic acid for serine 51 of eIF2α had no effect on internal initiation. Production of human Pkr inhibited HCV IRES dependent initiation in yeast. The synthesis of Pkr in yeast is known to result in high levels of eIF2α phosphorylation, increased Gcn4p synthesis, and reduced ribosomal protein production. These alterations may explain the effect of Pkr synthesis on HCV IRES dependent initiation in yeast.
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Affiliation(s)
- Amy B Rosenfeld
- Department of Microbiology, Columbia University College of Physicians & Surgeons, New York, NY, USA.
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7
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Fontanes V, Raychaudhuri S, Dasgupta A. A cell-permeable peptide inhibits hepatitis C virus replication by sequestering IRES transacting factors. Virology 2009; 394:82-90. [PMID: 19740508 PMCID: PMC2767405 DOI: 10.1016/j.virol.2009.08.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 05/25/2009] [Accepted: 08/04/2009] [Indexed: 02/05/2023]
Abstract
Hepatitis C virus (HCV) infection frequently leads to chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. There is no effective therapy or vaccine available to HCV-infected patients other than interferon-ribavarin combination, which is effective in a relatively small percentage of infected patients. Our previous results have shown that a synthetic peptide (LAP) corresponding to the N-terminal 18 amino acids of the Lupus autoantigen (La) was a potent inhibitor of HCV IRES-mediated translation. We demonstrate here that LAP efficiently blocks HCV replication of infectious JFH1 virus in cell culture. Our data suggest that LAP forms complexes with IRES-transacting factors (ITAFs) PTB and PCBP2. LAP-mediated inhibition of HCV IRES-mediated translation in vitro could be fully rescued by recombinant PCB and PCBP2. Also transient expression of PTB / PCBP2 combination significantly restores HCV replication in LAP-inhibited cultures. These results suggest that ITAFs could be potential targets to block HCV replication.
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Affiliation(s)
- Vanessa Fontanes
- Department of Microbiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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8
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Jaffrelo L, Chabas S, Reigadas S, Pflieger A, Wychowski C, Rumi J, Ventura M, Toulmé JJ, Staedel C. A functional selection of viral genetic elements in cultured cells to identify hepatitis C virus RNA translation inhibitors. Nucleic Acids Res 2008; 36:e95. [PMID: 18614605 PMCID: PMC2528164 DOI: 10.1093/nar/gkn427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We developed a functional selection system based on randomized genetic elements (GE) to identify potential regulators of hepatitis C virus (HCV) RNA translation, a process initiated by an internal ribosomal entry site (IRES). A retroviral HCV GE library was introduced into HepG2 cells, stably expressing the Herpes simplex virus thymidine kinase (HSV-TK) under the control of the HCV IRES. Cells that expressed transduced GEs inhibiting HSV-TK were selected via their resistance to ganciclovir. Six major GEs were rescued by PCR on the selected cell DNA and identified as HCV elements. We validated our strategy by further studying the activity of one of them, GE4, encoding the 5′ end of the viral NS5A gene. GE4 inhibited HCV IRES-, but not cap-dependent, reporter translation in human hepatic cell lines and inhibited HCV infection at a post-entry step, decreasing by 85% the number of viral RNA copies. This method can be applied to the identification of gene expression regulators.
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9
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Ratra R, Lal SK. Functional genomics as a tool in virus research. Indian J Microbiol 2008; 48:195-201. [PMID: 23100713 PMCID: PMC3450177 DOI: 10.1007/s12088-008-0032-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2008] [Accepted: 05/10/2008] [Indexed: 01/28/2023] Open
Abstract
Genomics is the study of an organism’s entire genome. It started out as a great scientific endeavor in the 1990s which aimed to sequence the complete genomes of certain biological species. However viruses are not new to this field as complete viral genomes have routinely been sequenced since the past thirty years. The ‘genomic era’ has been said to have revolutionized biology. This knowledge of full genomes has created the field of functional genomics in today’s post-genomic era, which, is in most part concerned with the studies on the expression of the organism’s genome under different conditions. This article is an attempt to introduce its readers to the application of functional genomics to address and answer several complex biological issues in virus research.
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Affiliation(s)
- Ruchi Ratra
- Virology Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
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10
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The FUSE binding protein is a cellular factor required for efficient replication of hepatitis C virus. J Virol 2008; 82:5761-73. [PMID: 18400844 DOI: 10.1128/jvi.00064-08] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatitis C virus (HCV) infection is the leading cause of liver cirrhosis and hepatocellular carcinoma and one of the primary indications for liver transplantation. The molecular mechanisms underlying the actions of host factors in HCV replication remain poorly defined. FUSE (far upstream element of the c-myc proto-oncogene) binding protein (FBP) is a cellular factor that we have identified as a binder of HCV 3' nontranslated region (3'NTR). Mapping of the binding site showed that FBP specifically interacts with the poly(U) tract within the poly(U/UC) region of the 3'NTR. Silencing of FBP expression by small interfering RNA in cells carrying HCV subgenomic replicons severely reduced viral replication, while overexpression of FBP significantly enhanced viral replication. We confirmed these observations by an in vitro HCV replication assay in the cell-free replicative lysate, which suggested that there is a direct correlation between the cellular FBP level and HCV replication. FBP immunoprecipitation coprecipitated HCV nonstructural protein 5A (NS5A), indicating that FBP interacts with HCV NS5A, which is known to function as a link between HCV translation and replication. Although FBP is mainly localized in the nucleus, we found that in MH14 cells a significant level of this protein is colocalized with NS5A in the cytosol, a site of HCV replication. While the mechanism of FBP involvement in HCV replication is yet to be delineated, our findings suggest that it may be an important regulatory component that is essential for efficient replication of HCV.
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11
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Watanabe T, Umehara T, Kohara M. Therapeutic application of RNA interference for hepatitis C virus. Adv Drug Deliv Rev 2007; 59:1263-76. [PMID: 17822803 DOI: 10.1016/j.addr.2007.03.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 03/01/2007] [Indexed: 12/23/2022]
Abstract
RNA interference (RNAi) is a sequence-specific post-transcriptional gene silencing by double-stranded RNA. Because the phenomenon is conserved and ubiquitous in mammalian cells, RNAi has considerable therapeutic potential for human pathogenic gene products. Recent studies have demonstrated the clinical potential of logically designed small interfering RNA (siRNA). However, there are still obstacles in using RNAi as an antiviral therapy, particularly for hepatitis C virus (HCV) that displays a high rate of mutation. Furthermore, delivery is also an important obstacle for siRNA based gene therapy. This paper presents the potential applications and the hurdles facing anti-HCV siRNA drugs. The present review provides insight into the feasible therapeutic strategies of siRNA technology, and its potential for silencing genes associated with HCV disease.
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Affiliation(s)
- Tsunamasa Watanabe
- Department of Microbiology and Cell Biology, The Tokyo Metropolitan Institute of Medical Science, 3-18-22, Honkomagome, Bunkyo-ku, Tokyo 113-8613, Japan
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12
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Randall G, Panis M, Cooper JD, Tellinghuisen TL, Sukhodolets KE, Pfeffer S, Landthaler M, Landgraf P, Kan S, Lindenbach BD, Chien M, Weir DB, Russo JJ, Ju J, Brownstein MJ, Sheridan R, Sander C, Zavolan M, Tuschl T, Rice CM. Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A 2007; 104:12884-9. [PMID: 17616579 PMCID: PMC1937561 DOI: 10.1073/pnas.0704894104] [Citation(s) in RCA: 433] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Indexed: 02/06/2023] Open
Abstract
Recently identified hepatitis C virus (HCV) isolates that are infectious in cell culture provide a genetic system to evaluate the significance of virus-host interactions for HCV replication. We have completed a systematic RNAi screen wherein siRNAs were designed that target 62 host genes encoding proteins that physically interact with HCV RNA or proteins or belong to cellular pathways thought to modulate HCV infection. This includes 10 host proteins that we identify in this study to bind HCV NS5A. siRNAs that target 26 of these host genes alter infectious HCV production >3-fold. Included in this set of 26 were siRNAs that target Dicer, a principal component of the RNAi silencing pathway. Contrary to the hypothesis that RNAi is an antiviral pathway in mammals, as has been reported for subgenomic HCV replicons, siRNAs that target Dicer inhibited HCV replication. Furthermore, siRNAs that target several other components of the RNAi pathway also inhibit HCV replication. MicroRNA profiling of human liver, human hepatoma Huh-7.5 cells, and Huh-7.5 cells that harbor replicating HCV demonstrated that miR-122 is the predominant microRNA in each environment. miR-122 has been previously implicated in positively regulating the replication of HCV genotype 1 replicons. We find that 2'-O-methyl antisense oligonucleotide depletion of miR-122 also inhibits HCV genotype 2a replication and infectious virus production. Our data define 26 host genes that modulate HCV infection and indicate that the requirement for functional RNAi for HCV replication is dominant over any antiviral activity this pathway may exert against HCV.
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Affiliation(s)
- Glenn Randall
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and
- Department of Microbiology, University of Chicago, Chicago, IL 60637
| | - Maryline Panis
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and
| | - Jacob D. Cooper
- Department of Microbiology, University of Chicago, Chicago, IL 60637
| | | | - Karen E. Sukhodolets
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Sebastien Pfeffer
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021
| | - Markus Landthaler
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021
| | - Pablo Landgraf
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021
| | - Sherry Kan
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and
| | - Brett D. Lindenbach
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and
| | | | - David B. Weir
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | | | - Jingyue Ju
- Columbia Genome Center, New York, NY 10032
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | | | - Robert Sheridan
- Computational Biology Center, Memorial Sloan–Kettering Cancer Center, New York, NY 10021; and
| | - Chris Sander
- Computational Biology Center, Memorial Sloan–Kettering Cancer Center, New York, NY 10021; and
| | - Mihaela Zavolan
- Biozentrum, Universität Basel, CH-4056 Basel, Switzerland; and
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and
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13
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Li QX, Tan P, Ke N, Wong-Staal F. Ribozyme technology for cancer gene target identification and validation. Adv Cancer Res 2007; 96:103-43. [PMID: 17161678 DOI: 10.1016/s0065-230x(06)96005-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribozymes are naturally occurring RNAs with catalytic activities including cis- or trans- cleavage of RNA at predefined sequence sites. This activity has been exploited for specific gene inactivation in cells during the last two decades, and ribozymes have been important functional genomics tools, especially in the pre-RNAi era. It has also been broadly applied in drug target identification and validation in pharmaceutical R&D. This chapter covers many application principles and case studies of ribozyme technology in the areas of cancer research. We also described RNAi applications in some of the same studies for comparison. Although RNAi may be more effective than ribozymes in many respects, they are nonetheless built on many of the same principles.
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Affiliation(s)
- Qi-Xiang Li
- Immusol, Inc., San Diego, California 92121, USA
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14
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MacCallum PR, Jack SC, Egan PA, McDermott BT, Elliott RM, Chan SW. Cap-dependent and hepatitis C virus internal ribosome entry site-mediated translation are modulated by phosphorylation of eIF2alpha under oxidative stress. J Gen Virol 2006; 87:3251-3262. [PMID: 17030858 DOI: 10.1099/vir.0.82051-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Chronic hepatitis C is often associated with oxidative stress. Hepatitis C virus (HCV) utilizes an internal ribosome entry site (IRES) element for translation, in contrast to cap-dependent translation of the majority of cellular proteins. To understand how virus translation is modulated under oxidative stress, HCV IRES-mediated translation was compared with cap-dependent translation using a bicistronic reporter construct and hydrogen peroxide (H2O2) as a stress inducer. In H2O2-sensitive HeLa cells, H2O2 repressed translation in a time- and dose-dependent manner, concomitant with the kinetics of eIF2alpha phosphorylation. A phosphomimetic of eIF2alpha, which mimics the structure of the phosphorylated eIF2alpha, was sufficient to repress translation in the absence of H2O2. In H2O2-resistant HepG2 cells, H2O2 activated both HCV IRES-mediated and cap-dependent translation, associated with an increased level of phospho-eIF2alpha. It was postulated that H2O2 might stimulate translation in HepG2 cells via an eIF2alpha-independent mechanism, whereas the simultaneous phosphorylation of eIF2alpha repressed part of the translational activities. Indeed, the translational repression was released in the presence of a non-phosphorylatable mutant, eIF2alpha-SA, resulting in further enhancement of both translational activities after exposure to H2O2. In HuH7 cells, which exhibited an intermediate level of sensitivity towards H2O2, both HCV IRES-mediated and cap-dependent translational activities were upregulated after treatment with various doses of H2O2, but the highest level of induction was achieved with a low level of H2O2, which may represent the physiological level of H2O2. At this level, the HCV IRES-mediated translation was preferentially upregulated compared with cap-dependent translation.
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Affiliation(s)
- Paul R MacCallum
- Faculty of Life Sciences, The University of Manchester, Jackson's Mill, PO Box 88, Sackville Street, Manchester M60 1QD, UK
| | - Samantha C Jack
- Faculty of Life Sciences, The University of Manchester, Jackson's Mill, PO Box 88, Sackville Street, Manchester M60 1QD, UK
| | - Philip A Egan
- Faculty of Life Sciences, The University of Manchester, Jackson's Mill, PO Box 88, Sackville Street, Manchester M60 1QD, UK
| | - Benjamin T McDermott
- Faculty of Life Sciences, The University of Manchester, Jackson's Mill, PO Box 88, Sackville Street, Manchester M60 1QD, UK
| | - Richard M Elliott
- Centre for Biomolecular Sciences, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Shiu-Wan Chan
- Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
- Faculty of Life Sciences, The University of Manchester, Jackson's Mill, PO Box 88, Sackville Street, Manchester M60 1QD, UK
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15
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Yang JP, Fan W, Rogers C, Chatterton JE, Bliesath J, Liu G, Ke N, Wang CY, Rhoades K, Wong-Staal F, Li QX. A novel RNAi library based on partially randomized consensus sequences of nuclear receptors: Identifying the receptors involved in amyloid β degradation. Genomics 2006; 88:282-92. [PMID: 16631344 DOI: 10.1016/j.ygeno.2006.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 03/13/2006] [Accepted: 03/16/2006] [Indexed: 10/24/2022]
Abstract
Combinatorial gene inactivation using an RNAi library is a powerful approach to discovering novel functional genes. However, generation of a comprehensive RNAi library remains technically challenging. In this report, we describe a simple and novel approach to designing gene-family-specific RNAi libraries by targeting conserved motifs using degenerate oligonucleotides. We created an siRNA library in the pHUMU vector using partially randomized sequences targeting the consensus region in the ZnF_C4 signature motif of the nuclear hormone receptors and thus against the entire receptor superfamily. For proof of principle, we adapted a reporter assay to screen this library for receptors that might be involved in reducing amyloid beta peptide accumulation. We modified a previously described luciferase reporter assay to measure the amyloid beta precursor cleavages occurring only between beta- and gamma-secretase cleavage sites, thus excluding the major gamma-secretase activities that could generate neurotoxic Abeta peptides. Our screen using this assay identified siRNA vectors that specifically increase the Abeta40/42 cleavage and pointed to a potential receptor target, ROR-gamma. SiRNAs targeting other regions of ROR-gamma not only confirmed the observed reporter activity but also reduced the level of the toxic Abeta peptides. The results demonstrated a general principle for the creation and application of this RNAi library approach for functional gene discovery within a predefined protein family. The discovered negative effect of ROR-gamma on the degradation of the toxic Abeta peptides may also provide a potential drug target or targetable pathway for intervention of Alzheimer disease.
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Affiliation(s)
- Jian-Ping Yang
- Immusol, Inc., 10790 Roselle Street, San Diego, CA 92121, USA
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16
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Harris D, Zhang Z, Chaubey B, Pandey VN. Identification of cellular factors associated with the 3'-nontranslated region of the hepatitis C virus genome. Mol Cell Proteomics 2006; 5:1006-18. [PMID: 16500930 DOI: 10.1074/mcp.m500429-mcp200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Chronic infection by hepatitis C virus (HCV) is the leading cause of severe hepatitis that often develops into liver cirrhosis and hepatocellular carcinoma. The molecular mechanisms underlying HCV replication and pathogenesis are poorly understood. Similarly, the role(s) of host factors in the replication of HCV remains largely undefined. Based on our knowledge of other RNA viruses, it is likely that a number of cellular factors may be involved in facilitating HCV replication. It has been demonstrated that elements within the 3'-nontranslated region (3'-NTR) of the (+) strand HCV genome are essential for initiation of (-) strand synthesis. The RNA signals within the highly conserved 3'-NTR may be the site for recruiting cellular factors that mediate virus replication/pathogenesis. However, the identities of putative cellular factors interacting with these RNA signals remain unknown. In this report, we demonstrate that an RNA affinity capture system developed in our laboratory used in conjunction with LC/MS/MS allowed us to positively identify more than 70 cellular proteins that interact with the 3'-NTR (+) of HCV. Binding of these cellular proteins was not competed out by a 10-fold excess of nonspecific competitor RNA. With few exceptions, all of the identified cellular proteins are RNA-binding proteins whose reported cellular functions provide unique insights into host cell-virus interactions and possible mechanisms influencing HCV replication and HCV-associated pathogenesis. Small interfering RNA-mediated silencing of selected 3'-NTR-binding proteins in an HCV replicon cell line reduced replicon RNA to undetectable levels, suggesting important roles for these cellular factors in HCV replication.
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Affiliation(s)
- Dylan Harris
- Department of Biochemistry and Molecular Biology and Centre for the Study of Emerging and Re-emerging Pathogens, University of Medicine and Dentistry of New Jersey--New Jersey Medical School, Newark, New Jersey 07103, USA
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17
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Matsumoto S, Akashi H, Taira K. Screening and determination of gene function using randomized ribozyme and siRNA libraries. Handb Exp Pharmacol 2006:197-221. [PMID: 16594617 DOI: 10.1007/3-540-27262-3_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Rapid progress in the sequencing of the genomes of model organisms, such as the mouse, rat, nematode, fly, and Arabidopsis, as well as the human genome, has provided abundant sequence information, but functions of long stretches of these genomes remain to be determined. RNA-based technologies hold promise as tools that allow us to identify the specific functions of portions of these genomes. In particular, catalytic RNAs, known also as ribozymes, can be engineered for optimization of their activities in the intracellular environment. The introduction of a library of active ribozymes into cells, with subsequent screening for phenotypic changes, can be used for the rapid identification ofa gene function. Ribozyme technology complements another RNA-based tool for the determination of gene function, which is based on libraries of small interfering RNAs (siRNAs).
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Affiliation(s)
- S Matsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, 113-8656 Tokyo, Japan
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18
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Abstract
The development of new treatment strategies for the therapy of hepatitis C is an unmet need. There has already been an enormous improvement in the therapy of chronic hepatitis C since the early 1990s, but the sustained virologic response rates are still unsatisfactory for certain patient groups. Novel therapeutic strategies, especially for the difficult-to-treat patients, are currently being tested. This review discusses the latest achievements in the treatment of chronic heptatis C.
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Affiliation(s)
- Markus Cornberg
- Kompentenznetz Hepatitis, Medizinische Hochschule Hannover, Departments of Gastroenterology, Hepatology and Endocrinology, Carl-Neuberg Str. 1, D-30625 Hannover, Germany
| | - Michael P Manns
- Kompentenznetz Hepatitis, Medizinische Hochschule Hannover, Departments of Gastroenterology, Hepatology and Endocrinology, Carl-Neuberg Str. 1, D-30625 Hannover, Germany
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19
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Ito M, Kawano K, Miyagishi M, Taira K. Genome-wide application of RNAi to the discovery of potential drug targets. FEBS Lett 2005; 579:5988-95. [PMID: 16153642 DOI: 10.1016/j.febslet.2005.08.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 08/05/2005] [Accepted: 08/11/2005] [Indexed: 12/23/2022]
Abstract
Progress is being made in the development of RNA interference-based (RNAi-based) strategies for the control of gene expression. It has been demonstrated that small interfering RNAs (siRNAs) can silence the expression of target genes in a sequence-specific manner in mammalian cells. Various groups, including our own, have developed systems for vector-mediated specific RNAi. Vector-based siRNA- (or shRNA) expression libraries directed against the entire human genome and siRNA libraries based on chemically synthesized oligonucleotides now allow the rapid identification of functional genes and potential drug targets. Use of such libraries will enhance our understanding of numerous biological phenomena and contribute to the rational design of drugs against heritable, infectious and malignant diseases.
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Affiliation(s)
- Masanori Ito
- Gene Function Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 4, 1-1-1 Higashi, Tsukuba Science City 305-8562, Japan
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20
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Vlassov AV, Koval OA, Johnston BH, Kazakov SA. ROLL: a method of preparation of gene-specific oligonucleotide libraries. Oligonucleotides 2005; 14:210-20. [PMID: 15625916 DOI: 10.1089/oli.2004.14.210] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The selection of nucleic acid sequences capable of specifically and efficiently hybridizing to target sequences is crucial to the success of many applications, including microarrays, PCR and other amplification procedures, antisense inhibition, ribozyme-mediated cleavage, and RNA interference (RNAi). Methods of selection using nucleotide sequence libraries have several advantages over rational approaches using defined sequences. However, the high complexity of completely random (degenerate) libraries and their high toxicity in cell-based assays make their use in many applications impractical. Gene-specific oligonucleotide libraries, which contain all possible sequences of a certain length occurring within a given gene, have much lower complexity and, thus, can significantly simplify and accelerate sequence screening. Here, we describe a new method for the preparation of gene-specific libraries using the ligation of randomized oligonucleotide probes hybridized adjacently on target polynucleotide templates followed by PCR amplification. We call this method random oligonucleotide ligated libraries (ROLL).
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21
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Abstract
Catalytic RNAs, also known as ribozymes, can be engineered to optimize their activities in the intracellular environment. The introduction of a library of active ribozymes into cells, and the subsequent screening for phenotypic changes, allows the rapid identification of gene function. For the determination of gene function, ribozyme technology complements another RNA-based tool that is based on libraries of small interfering RNAs.
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Affiliation(s)
- Hideo Akashi
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan
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22
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Suyama E, Kawasaki H, Wadhwa R, Taira K. Cell migration and metastasis as targets of small RNA-based molecular genetic analyses. J Muscle Res Cell Motil 2005; 25:303-8. [PMID: 15548858 DOI: 10.1007/s10974-004-4343-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Metastatic tumor cells can migrate from one place to another in the body. This involves their adherence to host cell layers and subsequent transcellular movements by a complex process, molecular basis of which are yet to be clarified. Elucidation of genes functionally involved in metastasis may lead to deeper understanding of the mechanism of cell migration, and identification and designing of metastasis-modulating strategies for cancer therapeutics. We review here cell migration in tumor metastasis and the use of small RNA-based approaches to identify functional genes. We then describe our promising novel approach that uses randomized ribozyme libraries for identification of genes involved in cell migration, a consistent feature of metastatic cells.
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Affiliation(s)
- Eigo Suyama
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
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23
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Seyhan AA, Vlassov AV, Ilves H, Egry L, Kaspar RL, Kazakov SA, Johnston BH. Complete, gene-specific siRNA libraries: production and expression in mammalian cells. RNA (NEW YORK, N.Y.) 2005; 11:837-46. [PMID: 15840823 PMCID: PMC1370768 DOI: 10.1261/rna.7285805] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Accepted: 02/08/2005] [Indexed: 05/24/2023]
Abstract
Short interfering RNAs (siRNAs) are widely used to silence the expression of specific genes. Current practice for designing effective siRNAs is to use algorithms based on sequence-efficacy correlations; however, there are many highly effective sequences that these algorithms do not anticipate. To ensure that the best siRNAs are identified, all possible gene-specific siRNA sequences of appropriate lengths should be screened in cell culture. Synthesizing and testing all such sequences individually is costly. A potentially much easier alternative is to prepare a mixture of all these sequences (a gene-specific library), express them in cells, select cells having the desired phenotype, and identify the siRNA contained within the selected cells. Here we describe two new methods for preparing and expressing such libraries. The first uses cloned Dicer or RNase III to digest gene-specific RNA duplexes to siRNAs, which are then converted to the corresponding DNA sequences by attaching RNA primers and performing reverse transcription-PCR. The second method involves partial DNase I digestion of gene-specific DNA, purification of a 20-30-bp fraction, and amplification by attaching DNA adapters followed by PCR. DNA libraries specific for TNF-alpha, DsRed, and part of the hepatitis C virus genome, generated by methods, were inserted into siRNA expression vectors between convergent human U6 and H1 promoters. Randomly selected clones from each library together with vectors expressing the corresponding target genes were cotransfected into 293FT cells and assayed for target gene inhibition. About 10%-20% of siRNAs represented in these libraries show significant inhibition of their target genes. Most of these inhibitory sequences are not predicted by existing algorithms.
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Affiliation(s)
- Attila A Seyhan
- SomaGenics, Inc., 2161 Delaware Ave., Santa Cruz, CA 95060, USA
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24
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Lu H, Li W, Noble WS, Payan D, Anderson DC. Riboproteomics of the hepatitis C virus internal ribosomal entry site. J Proteome Res 2005; 3:949-57. [PMID: 15473682 DOI: 10.1021/pr0499592] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hepatitis C virus (HCV) protein translation is mediated by a cis-acting RNA, an internal ribosomal entry site (IRES), located in the 5' nontranslated region of the viral RNA. To examine proteins bound to the IRES, which could include proteins important for its function as well as potential drug targets, we used shotgun peptide sequencing to identify proteins in quadruplicate protein affinity extracts of lysed Huh7 cells, obtained using a biotinylated IRES. Twenty-six proteins bound the HCV IRES but not a reversed complementary sequence RNA or vector RNA controls. These included five ribosomal subunits, nine eukaryotic initiation factor 3 subunits, and novel interacting proteins such as the cytoskeletal-related proteins actin, FHOS (formin homologue overexpressed in spleen) and MIP-T3 (microtubule interacting protein that associates with TRAF3). Other novel HCV IRES-binding proteins included UNR (upstream of N-ras), UNR-interacting protein, and the RNA-binding proteins PAI-1 (plasminogen activator inhibitor-1) mRNA binding protein and Ewing sarcoma breakpoint 1 region protein EWS. A large set of additional proteins bound both the HCV IRES and a reversed complementary IRES sequence control, including the known HCV interactors PTB (polypyrimidine tract binding protein), the La autoantigen, and nucleolin. The discovery of these novel HCV IRES-binding proteins suggests links between IRES biology and the cytoskeleton, signal transduction, and other cellular functions.
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Affiliation(s)
- Henry Lu
- Rigel, Inc., South San Francisco, California 94066, USA
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25
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Honda M, Shimazaki T, Kaneko S. La protein is a potent regulator of replication of hepatitis C virus in patients with chronic hepatitis C through internal ribosomal entry site-directed translation. Gastroenterology 2005; 128:449-62. [PMID: 15685555 DOI: 10.1053/j.gastro.2004.11.064] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Translation of hepatitis C virus is an essential step of viral replication and is mediated by an internal ribosome entry site. We previously reported that the hepatitis C virus internal ribosome entry site is most active during the synthetic (S) or mitotic (M) phases and lowest during quiescent (G 0 ) phase. Here, we investigated host factors responsible for the regulation of the hepatitis C virus internal ribosome entry site. METHODS We synchronized the cell-cycle progression and evaluated gene-expression dynamics of host factors and kinetics of hepatitis C virus internal ribosome entry site activity in cells at various points during the cell cycle by using a complementary DNA microarray. We also validated the significance of identified host factors on hepatitis C virus replication in vivo. RESULTS Hepatitis C virus internal ribosome entry site activity correlated with a gene cluster induced in the S and G 2 /M phases. It is interesting to note that most initiation factors known to bind or interact with the hepatitis C virus internal ribosome entry site [poly(rC)-binding protein 2, polypyrimidine tract binding protein, eukaryotic initiation factor 3, eukaryotic initiation factor 2gamma, eukaryotic initiation factor 2beta, La protein, and heterogenous nuclear ribonucleoprotein L] were induced during the S and G 2 /M phases. Expression of La protein, polypyrimidine tract binding protein, and eukaryotic initiation factor 3 (p116, p170) were predominantly repressed in G 0 phase and induced in S and G 2 /M phases. Suppression or overexpression of La protein and polypyrimidine tract binding protein in RCF-26 significantly changed hepatitis C virus internal ribosome entry site activity. In the livers of patients with chronic hepatitis C, expression of La protein was significantly increased and correlated with the amount of hepatitis C virus RNA. CONCLUSIONS Hepatitis C virus uses host factors induced during cell division but not during quiescence for replication. Of these, La protein is a potent regulator and enhances hepatitis C virus replication in regenerating hepatocytes in patients with chronic hepatitis C.
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Affiliation(s)
- Masao Honda
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
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26
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Sano M, Kato Y, Taira K. Functional gene-discovery systems based on libraries of hammerhead and hairpin ribozymes and short hairpin RNAs. MOLECULAR BIOSYSTEMS 2005; 1:27-35. [PMID: 16880960 DOI: 10.1039/b503235k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abundant information about the nucleotide sequence of the human genome has become readily available and it is now necessary to develop methods for the identification of genes that are involved in important cellular, developmental and disease-related processes. Identification methods based on the activities of hammerhead and hairpin ribozymes and of short hairpin RNAs (shRNAs), whose target specificities are coupled with loss-of-function phenotypes, have received increasing attention as possible tools for the rapid identification of key genes involved in such processes. We describe here recent advances that have been made with libraries of ribozymes and shRNAs and compare the advantages of the different types of library. The use of such libraries has already revealed new details of several important physiological phenomena.
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Affiliation(s)
- Masayuki Sano
- Gene Function Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Science City, Japan
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27
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Otto GA, Puglisi JD. The pathway of HCV IRES-mediated translation initiation. Cell 2004; 119:369-80. [PMID: 15507208 DOI: 10.1016/j.cell.2004.09.038] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2004] [Revised: 09/02/2004] [Accepted: 09/10/2004] [Indexed: 01/11/2023]
Abstract
The HCV internal ribosome entry site (IRES) directly regulates the assembly of translation initiation complexes on viral mRNA by a sequential pathway that is distinct from canonical eukaryotic initiation. The HCV IRES can form a binary complex with an eIF-free 40S ribosomal subunit. Next, a 48S-like complex assembles at the AUG initiation codon upon association of eIF3 and ternary complex. 80S complex formation is rate limiting and follows the GTP-dependent association of the 60S subunit. Efficient assembly of the 48S-like and 80S complexes on the IRES mRNA is dependent upon maintenance of the highly conserved HCV IRES structure. This revised model of HCV IRES translation initiation provides a context to understand the function of different HCV IRES domains during translation initiation.
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Affiliation(s)
- Geoff A Otto
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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28
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Waninger S, Kuhen K, Hu X, Chatterton JE, Wong-Staal F, Tang H. Identification of cellular cofactors for human immunodeficiency virus replication via a ribozyme-based genomics approach. J Virol 2004; 78:12829-37. [PMID: 15542635 PMCID: PMC524980 DOI: 10.1128/jvi.78.23.12829-12837.2004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Ribozymes are small, catalytic RNA molecules that can be engineered to down-regulate gene expression by cleaving specific mRNA. Here we report the selection of hairpin ribozymes that inhibit human immunodeficiency virus (HIV) replication from a combinatorial ribozyme library. We identified a total of 17 effective ribozymes, each capable of inhibiting HIV infection of human CD4(+) cells. These ribozymes target diverse steps of the viral replication cycle, ranging from entry to transcription. One ribozyme suppressed HIV integration and transcription by inhibiting the expression of the Ku80 subunit of the DNA-activated protein kinase. Another ribozyme specifically inhibited long terminal repeat transactivation, while two additional ones blocked a step that can be bypassed by vesicular stomatitis virus G-protein pseudotyping. The function of Ku80 in HIV replication and its mechanism of action were further confirmed using short interfering RNA. Identification of the gene targets of these and other selected ribozymes may reveal novel therapeutic targets for combating HIV infection.
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Affiliation(s)
- Shani Waninger
- Department of Biological Sciences, Biology Unit 1, Florida State University, Tallahassee, FL 32306-4370, USA
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29
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Wadhwa R, Yaguchi T, Kaur K, Suyama E, Kawasaki H, Taira K, Kaul SC. Use of a Randomized Hybrid Ribozyme Library for Identification of Genes Involved in Muscle Differentiation. J Biol Chem 2004; 279:51622-9. [PMID: 15448151 DOI: 10.1074/jbc.m407428200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have employed the hybrid hammerhead ribozyme-based gene discovery system for identification of genes functionally involved in muscle differentiation using in vitro myoblast differentiation assay. The major muscle regulatory genes (MyoD1, Mylk, myosin, myogenin, and Myf5) were identified endorsing the validity of this method. Other gene targets included tumor suppressors and cell cycle regulators (p19ARF and p21WAF1), FGFR-4, fibronectin, Prkg2, Pdk4, fem, and six novel proteins. Functional involvement of three of the identified targets in myoblast differentiation was confirmed by their specific knockdown using ribozymes and siRNA. Besides demonstrating a simple and an effective method of isolation of gene functions involved in muscle differentiation, we report for the first time that overexpression of Fem, a member of the sex-determining family of proteins, caused accelerated myotube formation, and its targeting deferred myoblast differentiation. This functional gene screening is not only helpful in understanding the molecular pathways of muscle differentiation but also to design molecular strategies for myopathologic therapies.
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Affiliation(s)
- Renu Wadhwa
- Gene Function Research Center, National Institute of Advanced Industrial Science & Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
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30
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Deocaris CC, Kaul SC, Taira K, Wadhwa R. Emerging Technologies: Trendy RNA Tools for Aging Research. J Gerontol A Biol Sci Med Sci 2004; 59:771-83. [PMID: 15345725 DOI: 10.1093/gerona/59.8.b771] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aging is an inevitable biological phenomenon. Attempts to understand its mechanisms and, consequently, to therapeutically decelerate or even reverse the process are limited by its daunting complexity. Rapid and robust functional genomic tools suited to a wide array of experimental model systems are needed to dissect the interplay of individual genes during aging. In this article, we review principles that transcend the view of RNA, from a molecule merely mediating the flow of genetic information, into a unique molecular tool. In the form of catalytic molecular scissors (ribozymes), antibody-like antagonists (aptamers) and gene silencers (interfering RNAs, RNAi) can be effectively used to dissect biofunctions conserved throughout the evolution. In this review, application of recent RNA tools in aging research is discussed.
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Affiliation(s)
- Custer C Deocaris
- Gene Function Research Center, National Institute of Advanced Industrial Science & Technology (AIST), 1-1-1 Higashi, Tsukuba Science City 305-8562, Japan
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31
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Suyama E, Wadhwa R, Kaur K, Miyagishi M, Kaul SC, Kawasaki H, Taira K. Identification of metastasis-related genes in a mouse model using a library of randomized ribozymes. J Biol Chem 2004; 279:38083-6. [PMID: 15247279 DOI: 10.1074/jbc.c400313200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Libraries of randomized ribozymes have considerable potential as tools for the identification of functional genes critically involved in a biological phenotype of interest in vitro. We have used a ribozyme library in an in vivo mouse model to identify genes related to metastasis. We injected weakly metastatic melanoma cells that had been treated with the library intravenously into mice. We then isolated ribozymes that accelerated metastasis from pulmonary tumors that had developed from metastasizing cells. As candidates for metastasis-related genes that were targets of the isolated ribozymes, we identified five unknown and three known genes: stromal interaction molecule 1 (STIM1), polymerase gamma2 accessory subunit (Polg2), and cytochrome P450, family 2, subfamily d, polypeptide 22 (Cyp2d22). Repression of four of these by small interfering RNAs indeed resulted in the accelerated mobility of cells in in vitro scratch-wound assay. The further characterization of these candidate genes would provide clues to the complex mechanism(s) of metastasis.
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Affiliation(s)
- Eigo Suyama
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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32
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Miyagishi M, Matsumoto S, Taira K. Generation of an shRNAi expression library against the whole human transcripts. Virus Res 2004; 102:117-24. [PMID: 15068887 DOI: 10.1016/j.virusres.2004.01.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
RNA interference is a phenomenon in which expression of an individual gene can be specifically silenced by introducing a double-stranded RNA, homologous to the gene, and is receiving attention as a powerful tool for reverse genetics in the post-genome era. Throughout our current research to generate an siRNA expression library for the whole human genome, we face many technical difficulties. We present here the strategies for overcoming some of the difficulties, including the development of genetically stable and highly active siRNA expression vectors, the selection procedure of the favorable target sites, and the efficient and low cost procedure for constructing an siRNA expression library. Furthermore, we demonstrate that the screening using the constructed siRNA-expression library indeed works, by evaluating siRNA-expression library against apoptosis-related genes.
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Affiliation(s)
- Makoto Miyagishi
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Japan
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33
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Dasgupta A, Das S, Izumi R, Venkatesan A, Barat B. Targeting internal ribosome entry site (IRES)-mediated translation to block hepatitis C and other RNA viruses. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09533.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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34
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Montel V, Kleeman J, Agarwal D, Spinella D, Kawai K, Tarin D. Altered metastatic behavior of human breast cancer cells after experimental manipulation of matrix metalloproteinase 8 gene expression. Cancer Res 2004; 64:1687-94. [PMID: 14996728 DOI: 10.1158/0008-5472.can-03-2047] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Previous work in our laboratory led to the cloning, from the same parent tumor cell line (MDA-MB-435), of two human breast cancer cell lines (M-4A4 and NM-2C5) with opposite metastatic phenotypes. Additional investigations revealed that the nonmetastatic cell line NM-2C5 overexpressed the neutrophil collagenase, matrix metalloproteinase (MMP)-8, relative to its partner. Because other studies have implicated the MMP family in promoting tumor metastasis, we investigated the apparently paradoxical expression of MMP-8 in these cell lines. By genetic engineering, we inverted its relative levels of expression in the two partners and studied the effects on the behavior of the tumors that they generated in athymic mice. Knock-down of expression in NM-2C5 cells by transduction with a sequence encoding a specific ribozyme and overexpression of MMP-8 in M-4A4 cells by retroviral transduction both strikingly changed metastatic performance in opposite directions, indicating that this gene plays a role in the regulation of tumor metastasis.
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Affiliation(s)
- Valerie Montel
- Department of Pathology, University of California, San Diego Cancer Center, La Jolla, California 92093, USA
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Ray PS, Das S. Inhibition of hepatitis C virus IRES-mediated translation by small RNAs analogous to stem-loop structures of the 5'-untranslated region. Nucleic Acids Res 2004; 32:1678-87. [PMID: 15020704 PMCID: PMC390326 DOI: 10.1093/nar/gkh328] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Translation of the hepatitis C virus (HCV) RNA is mediated by the interaction of ribosomes and cellular proteins with an internal ribosome entry site (IRES) located within the 5'-untranslated region (5'-UTR). We have investigated whether small RNA molecules corresponding to the different stem-loop (SL) domains of the HCV IRES, when introduced in trans, can bind to the cellular proteins and antagonize their binding to the viral IRES, thereby inhibiting HCV IRES-mediated translation. We have found that a RNA molecule corresponding to SL III could efficiently inhibit HCV IRES-mediated translation in a dose-dependent manner without affecting cap-dependent translation. The SL III RNA was found to bind to most of the cellular proteins which interacted with the HCV 5'-UTR. A smaller RNA corresponding to SL e+f of domain III also strongly and selectively inhibited HCV IRES-mediated translation. This RNA molecule interacted with the ribosomal S5 protein and prevented the recruitment of the 40S ribosomal subunit. This study reveals valuable insights into the role of the SL structures of the HCV IRES in mediating ribosome entry. Finally, these results provide a basis for developing anti-HCV therapy using small RNA molecules mimicking the SL structures of the 5'-UTR to specifically block viral RNA translation.
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Affiliation(s)
- Partho Sarothi Ray
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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Abstract
RNAs, besides bridging genetic information to proteins, the major determinants of bio-structures and functions, serve as active regulators of gene expression. Initiated nearly 20 years ago with ribozymes (the small RNAs with catalytic activity providing fine tuning of gene expression and function, used as molecular scissors and tools for gene discovery), an era of more complex and coordinated gene regulation by small RNAs, siRNA, and miRNA has recently started. Simple nucleotide complementarity results in highly ordered and regulated events, such as assembly of RNA and proteins, resulting in gene silencing either by mRNA degradation or suppression of translation. This article reviews our contributions to the understanding of structure, the function of small RNAs, their use in biotechnology, and the understanding of phenotypes such as apoptosis, metastasis, and differentiation.
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Affiliation(s)
- Hiroaki Kawasaki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Zhang J, Yamada O, Sakamoto T, Yoshida H, Iwai T, Matsushita Y, Shimamura H, Araki H, Shimotohno K. Down-regulation of viral replication by adenoviral-mediated expression of siRNA against cellular cofactors for hepatitis C virus. Virology 2004; 320:135-43. [PMID: 15003869 DOI: 10.1016/j.virol.2003.11.023] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Revised: 11/17/2003] [Accepted: 11/18/2003] [Indexed: 02/07/2023]
Abstract
Small interfering RNA (siRNA) is currently being evaluated not only as a powerful tool for functional genomics, but also as a potentially promising therapeutic agent for cancer and infectious diseases. Inhibitory effect of siRNA on viral replication has been demonstrated in multiple pathogenic viruses. However, because of the high sequence specificity of siRNA-mediated RNA degradation, antiviral efficacy of siRNA directed to viral genome will be largely limited by emergence of escape variants resistant to siRNA due to high mutation rates of virus, especially RNA viruses such as poliovirus and hepatitis C virus (HCV). To investigate the therapeutic feasibility of siRNAs specific for the putative cellular cofactors for HCV, we constructed adenovirus vectors expressing siRNAs against La, polypyrimidine tract-binding protein (PTB), subunit gamma of human eukaryotic initiation factors 2B (eIF2Bgamma), and human VAMP-associated protein of 33 kDa (hVAP-33). Adenoviral-mediated expression of siRNAs markedly diminished expression of the endogenous genes, and silencing of La, PTB, and hVAP-33 by siRNAs substantially blocked HCV replication in Huh-7 cells. Thus, our studies demonstrate the feasibility and potential of adenoviral-delivered siRNAs specific for cellular cofactors in combating HCV infection, which can be used either alone or in combination with siRNA against viral genome to prevent the escape of mutant variants and provide additive or synergistic anti-HCV effects.
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Affiliation(s)
- Jing Zhang
- Research and Development Center, FUSO Pharmaceutical Industries, LTD, Joto-ku, Osaka 536-8523, Japan.
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Onuki R, Bando Y, Suyama E, Katayama T, Kawasaki H, Baba T, Tohyama M, Taira K. An RNA-dependent protein kinase is involved in tunicamycin-induced apoptosis and Alzheimer's disease. EMBO J 2004; 23:959-68. [PMID: 14765129 PMCID: PMC380987 DOI: 10.1038/sj.emboj.7600049] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2002] [Accepted: 11/18/2003] [Indexed: 01/14/2023] Open
Abstract
Various types of stress, such as disruption of calcium homeostasis, inhibition of protein glycosylation and reduction of disulfide bonds, result in accumulation of misfolded proteins in the endoplasmic reticulum (ER). The initial cellular response involves removal of such proteins by the ER, but excessive and/or long-term stress results in apoptosis. In this study, we used a randomized ribozyme library and ER stress-mediated apoptosis (tunicamycin-induced apoptosis) in SK-N-SH human neuroblastoma cells as a selective phenotype to identify factors involved in this process. We identified a double-stranded RNA-dependent protein kinase (PKR) as one of the participants in this process. The level of nuclear PKR was elevated, but the level of cytoplasmic PKR barely changed in tunicamycin-treated SK-N-SH cells. Furthermore, tunicamycin also raised levels of phosphorylated PKR in the nucleus. We also detected the accumulation of phosphorylated PKR in the nuclei of autopsied brain tissues in Alzheimer's disease. Thus, PKR might play a role in ER stress-induced apoptosis and in Alzheimer's disease.
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Affiliation(s)
- Reiko Onuki
- Gene Function Research Center, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba Science City, Japan
- Department of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba Science City, Japan
| | - Yoshio Bando
- Department of Anatomy I, Asahikawa Medical College, Midorigaoka-higashi, Asahikawa, Hokkaido, Japan
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Yamada-oka, Suita, Osaka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology, Saitama, Japan
| | - Eigo Suyama
- Gene Function Research Center, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba Science City, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Tokyo, Japan
- Genomics Institute of the NovarTis Reserch Foundation, San Diego, CA, USA
| | - Taiichi Katayama
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Yamada-oka, Suita, Osaka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology, Saitama, Japan
- Center for Research in Neurodigenerative Diseases, Toronto, Ontario, Canada
| | - Hiroaki Kawasaki
- Gene Function Research Center, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba Science City, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Tokyo, Japan
| | - Tadashi Baba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba Science City, Japan
| | - Masaya Tohyama
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Yamada-oka, Suita, Osaka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology, Saitama, Japan
| | - Kazunari Taira
- Gene Function Research Center, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba Science City, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Tokyo, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. Tel.: +81 3 5841 8828 or +81 29 861 3015; Fax: +81 3 5841 8828 or +81 29 861 3019; E-mail:
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Kan QC, Yu ZJ, Lei YC, Hao LJ, Yang DL. Lethiferous effects of a recombinant vector carrying thymidine kinase suicide gene on 2.2.15 cells via a self-modulating mechanism. World J Gastroenterol 2003; 9:2216-20. [PMID: 14562381 PMCID: PMC4656466 DOI: 10.3748/wjg.v9.i10.2216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To determine the lethiferous effects of a recombinant vector carrying thymidine kinase (TK) suicide gene on 2.2.15 cells and the possible self-modulating mechanism.
METHODS: A self-modulated expressive plasmid pcDNA3-SCITK was constructed by inserting the fragments carrying hepatitis B virus antisense-S (HBV-anti-S) gene, hepatitis C virus core (HCV-C) gene, internal ribosome entry site (IRES) element of HCV and TK gene into the eukaryotic vector pcDNA3, in which the expression of TK suicide gene was controlled by the HBV S gene transcription. 2.2.15 cells that carry the full HBV genome and stably express series of HBV antigen were transfected with pcDNA3-SCITK or vector pcDNA3-SCI which was used as the mock plasmid. The HepG2 cells transfected with pcDNA3-SCITK were functioned as the negative control. All the transfected cells were incubated in DMEM medium supplemented with 10 μg/mL. of ganciclovir (GCV). The HBsAg levels in the supernatant of cell culture were detected by ELISA on the 1st, 3rd and 6th day post-transfection. Meanwhile, the morphology of tranfected cells was recorded by the photograph and the survival cell ratio was assessed by the trypan blue exclusion test on the 6th day post-transfection.
RESULTS: The structural accuracy of pcDNA3-SCITK was confirmed by restriction endonuclease digestion, PCR with specific primers and DNA sequencing. The HBsAg levels in the supernatant of transfected 2.2.15 cell culture were significantly decreased on the 6th day post-transfection as compared with that of the mock control (P < 0.05). The lethiferous effect of pcDNA3-SCITK expression on 2.2.15 cells was initially noted on the 3rd day after transfection and aggravated on the 6th day post transfection, in which the majority of transfected 2.2.15 cells were observed shrunken, round in shape and even dead. With assessment by the trypan blue exclusion test, the survival cell ratio on the 6th day post transfection was 95% in the negative control and only 11% in the experimental group.
CONCLUSION: The results indicate that suicide gene expression of pcDNA3-SCITK can only respond to HBV-S gene transcription, which may be potentially useful in the treatment of HBV infection and its related liver malignancies.
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Affiliation(s)
- Quan-Cheng Kan
- Division of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
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Kan QC, Yu ZJ, Lei YC, Yang DL, Hao LJ. Construction of the vector that harbors self-restricted system for hepatitis B virus clearance in gene therapy. Shijie Huaren Xiaohua Zazhi 2003; 11:1515-1519. [DOI: 10.11569/wcjd.v11.i10.1515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To construct the vector that harbors self-restricted system for clearing hepatitis B virus, eliminating infected hepatic cells and inhibiting hepatitis B recurrence in gene therapy.
METHODS After amplifying hepatitis C virus (HCV) internal ribosome entry sites (IRES) by reverse-transcription PCR (RT-PCR), the products were cloned into pcDNA3. A biscistronic vector was obtained. A part of sequence in HBV anti-surface gene and part of sequence in HCV core gene were cloned into the vector before IRES site in turn and thymidine kinase (TK) was also cloned into it following the IRES site. After determination by PCR and sequencing, we acquired the vector containing HBV anti-S, HCV-C gene, HCV IRES and thymidine kinase gene, which was named the vector pcDNA3-SCITK. The vectors were separately transfected into HepG2 cells and 2.2.15 cells and all the media contained ganciclovir.
RESULTS The novel vector was transfected into 2.2.15 and hepG2 cells, the expressed protein could destroy the former, but had no effect on HepG2 cells if all the media contained ganciclovir. Apoptosis cells in the former accounted for 15 per cent of all cells by fluorescence (FACS) detection. There was obvious difference between the two types of cells (the later was only 6 per cent).
CONCLUSION The function of genes that pcDNA3-SCITK carried with self-restricted system could be ego-controlled, and it might be used as gene therapy vector for HBV clearance if taking HBV S gene as target gene and TK gene as objective gene.
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Affiliation(s)
- Quan-Cheng Kan
- Department of Clinical Immunology, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Zu-Jiang Yu
- Department of Infectious Disease, the First Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Yan-Chang Lei
- Department of Clinical Immunology, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Dong-Liang Yang
- Department of Clinical Immunology, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Lian-Jie Hao
- Department of Clinical Immunology, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
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Park KS, Lee DK, Lee H, Lee Y, Jang YS, Kim YH, Yang HY, Lee SI, Seol W, Kim JS, Lee SI. Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors. Nat Biotechnol 2003; 21:1208-14. [PMID: 12960965 DOI: 10.1038/nbt868] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2003] [Accepted: 07/01/2003] [Indexed: 11/09/2022]
Abstract
We have developed a method in which randomized libraries of zinc finger-containing artificial transcription factors are used to induce phenotypic variations in yeast and mammalian cells. By linking multiple zinc-finger domains together, we constructed more than 100,000 zinc-finger proteins with diverse DNA-binding specificities and fused each of them to either a transcription activation or repression domain. The resulting transcriptional regulatory proteins were expressed individually in cells, and the transfected cells were screened for various phenotypic changes, such as drug resistance, thermotolerance or osmotolerance in yeast, and differentiation in mammalian cells. Genes associated with the selected phenotypes were also identified. Our results show that randomized libraries of artificial transcription factors are useful tools for functional genomics and phenotypic engineering.
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Affiliation(s)
- Kyung-Soon Park
- ToolGen, Inc., 461-6 Jeonmin-Dong, Yuseong-Gu, Daejeon, 305-390, South Korea
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Miyagishi M, Taira K. Strategies for Generation of an siRNA Expression Library Directed Against the Human Genome. Oligonucleotides 2003; 13:325-33. [PMID: 15000823 DOI: 10.1089/154545703322617005] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
RNA interference (RNAi) is a phenomenon whereby expression of an individual gene is specifically silenced by the introduction of a double-stranded RNA (dsRNA) whose sequence is homologous to that of the gene in question. The generation of a small interfering RNA (siRNA) expression library directed against the entire human genome is a project that requires solutions to many difficult technical problems. We present here some strategies for solving some of these problems, including the development of genetically stable and highly active siRNA expression vectors, a procedure for selection of favorable target sites, and an efficient and inexpensive procedure for constructing an siRNA expression library.
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Affiliation(s)
- Makoto Miyagishi
- Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
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44
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Nelson LD, Suyama E, Kawasaki H, Tair K. Use of random ribozyme libraries for the rapid screening of apoptosis- and metastasis-related genes. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1477-3627(03)02369-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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45
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Vyas J, Elia A, Clemens MJ. Inhibition of the protein kinase PKR by the internal ribosome entry site of hepatitis C virus genomic RNA. RNA (NEW YORK, N.Y.) 2003; 9:858-870. [PMID: 12810919 PMCID: PMC1370452 DOI: 10.1261/rna.5330503] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2003] [Accepted: 04/10/2003] [Indexed: 05/24/2023]
Abstract
Translation of the hepatitis C genome is mediated by internal ribosome entry on the structurally complex 5' untranslated region of the large viral RNA. Initiation of protein synthesis by this mechanism is independent of the cap-binding factor eIF4E, but activity of the initiator Met-tRNA(f)-binding factor eIF2 is still required. HCV protein synthesis is thus potentially sensitive to the inhibition of eIF2 activity that can result from the phosphorylation of the latter by the interferon-inducible, double-stranded RNA-activated protein kinase PKR. Two virally encoded proteins, NS5A and E2, have been shown to reduce this inhibitory effect of PKR by impairing the activation of the kinase. Here we present evidence for a third viral strategy for PKR inhibition. A region of the viral RNA comprising part of the internal ribosome entry site (IRES) is able to bind to PKR in competition with double-stranded RNA and can prevent autophosphorylation and activation of the kinase in vitro. The HCV IRES itself has no PKR-activating ability. Consistent with these findings, cotransfection experiments employing a bicistronic reporter construct and wild-type PKR indicate that expression of the protein kinase is less inhibitory towards HCV IRES-driven protein synthesis than towards cap-dependent protein synthesis. These data suggest a dual function for the viral IRES, with both a structural role in promoting initiation complex formation and a regulatory role in preventing inhibition of initiation by PKR.
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Affiliation(s)
- Jashmin Vyas
- Translational Control Group, Department of Basic Medical Sciences, St. George's Hospital Medical School, London SW17 0RE, UK
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46
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Kieft JS, Grech A, Adams P, Doudna JA. Mechanisms of internal ribosome entry in translation initiation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:277-83. [PMID: 12762029 DOI: 10.1101/sqb.2001.66.277] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- J S Kieft
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06511, USA
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Suyama E, Kawasaki H, Nakajima M, Taira K. Identification of genes involved in cell invasion by using a library of randomized hybrid ribozymes. Proc Natl Acad Sci U S A 2003; 100:5616-21. [PMID: 12719525 PMCID: PMC156250 DOI: 10.1073/pnas.1035850100] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Libraries of RNA helicase-coupled randomized ribozymes are a powerful tool for the identification of functional genes. We have demonstrated the usefulness of this functional gene-discovery system by identifying genes involved in tumor invasion, a process that is an essential feature of tumor metastasis: the spread of cancer cells from the original tumor to other sites in the body that imposes serious problems in the prognosis and treatment of cancer. Using a filter-based invasion assay in vitro, we isolated ribozymes that enhanced the invasive properties of NIH 3T3 fibroblasts. Sequence analysis of selected clones and a database search revealed that genes such as the gene for Gem GTPase and uncharacterized genes that resemble genes for myosin phosphatase and protein-tyrosine-phosphatase are involved in cell invasion. Our system for gene identification by using ribozymes and the functional analysis of target genes should help to clarify the complex mechanisms of invasion and metastasis and might provide information that is relevant to cancer therapy.
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Affiliation(s)
- Eigo Suyama
- Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, Hongo, Tokyo 113-8656, Japan
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Puerta-Fernández E, Romero-López C, Barroso-delJesus A, Berzal-Herranz A. Ribozymes: recent advances in the development of RNA tools. FEMS Microbiol Rev 2003; 27:75-97. [PMID: 12697343 DOI: 10.1016/s0168-6445(03)00020-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The discovery 20 years ago that some RNA molecules, called ribozymes, are able to catalyze chemical reactions was a breakthrough in biology. Over the last two decades numerous natural RNA motifs endowed with catalytic activity have been described. They all fit within a few well-defined types that respond to a specific RNA structure. The prototype catalytic domain of each one has been engineered to generate trans-acting ribozymes that catalyze the site-specific cleavage of other RNA molecules. On the 20th anniversary of ribozyme discovery we briefly summarize the main features of the different natural catalytic RNAs. We also describe progress towards developing strategies to ensure an efficient ribozyme-based technology, dedicating special attention to the ones aimed to achieve a new generation of therapeutic agents.
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Affiliation(s)
- Elena Puerta-Fernández
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Ventanilla 11, 18001 Granada, Spain
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Abstract
Hepatitis C virus (HCV) is an emerging virus of medical importance. A majority of HCV infections become chronic and lead to chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. HCV usually induces robust immune responses, but it frequently escapes the immune defense to establish persistent infection. The fact that HCV exists as an evolving quasispecies plays an important role in the selection of escape mutants. Furthermore, several viral proteins interfere with cellular functions, in particular, those involved in the immune response of the host. Several HCV proteins also modulate cell signalling through interaction with different effectors involved in cell proliferation and apoptosis, or in the interferon-signalling pathway. In addition, HCV infects immune cells such as B and T cells, and thus affects their normal functions. These various strategies used by HCV to counter the immune response of the host are reviewed here. A better understanding of these mechanisms would help design new therapeutic targets.
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Affiliation(s)
- Nicole Pavio
- Department of Molecular Microbiology, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
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Luo G, Xin S, Cai Z. Role of the 5'-proximal stem-loop structure of the 5' untranslated region in replication and translation of hepatitis C virus RNA. J Virol 2003; 77:3312-8. [PMID: 12584356 PMCID: PMC149781 DOI: 10.1128/jvi.77.5.3312-3318.2003] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequences of the untranslated regions at the 5' and 3' ends (5'UTR and 3'UTR) of the hepatitis C virus (HCV) RNA genome are highly conserved and contain cis-acting RNA elements for HCV RNA replication. The HCV 5'UTR consists of two distinct RNA elements, a short 5'-proximal stem-loop RNA element (nucleotides 1 to 43) and a longer element of internal ribosome entry site. To determine the sequence and structural requirements of the 5'-proximal stem-loop RNA element in HCV RNA replication and translation, a mutagenesis analysis was preformed by nucleotide deletions and substitutions. Effects of mutations in the 5'-proximal stem-loop RNA element on HCV RNA replication were determined by using a cell-based HCV replicon replication system. Deletion of the first 20 nucleotides from the 5' end resulted in elimination of cell colony formation. Likewise, disruption of the 5'-proximal stem-loop by nucleotide substitutions abolished the ability of HCV RNA to induce cell colony formation. However, restoration of the 5'-proximal stem-loop by compensatory mutations with different nucleotides rescued the ability of the subgenomic HCV RNA to replicate in Huh7 cells. In addition, deletion and nucleotide substitutions of the 5'-proximal stem-loop structure, including the restored stem-loop by compensatory mutations, all resulted in reduction of translation by two- to fivefold, suggesting that the 5'-proximal stem-loop RNA element also modulates HCV RNA translation. These findings demonstrate that the 5'-proximal stem-loop of the HCV RNA is a cis-acting RNA element that regulates HCV RNA replication and translation.
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Affiliation(s)
- Guangxiang Luo
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky 40536, USA.
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