101
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Deng Q, Chen Z, Shi L, Lin H. Developmental progress of CRISPR/Cas9 and its therapeutic applications for HIV-1 infection. Rev Med Virol 2018; 28:e1998. [PMID: 30024073 DOI: 10.1002/rmv.1998] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/10/2018] [Accepted: 06/19/2018] [Indexed: 12/14/2022]
Abstract
The CRISPR/Cas9 system has been developed as a powerful tool for targeted gene editing. As a result of technical enhancements in recent years, this technology has become the method of choice for efficiently modifying targeted HIV-1 genome efficiently as part of HIV therapy. CRISPR can be modified to target specific sequences that Cas9 then cuts. In this article, we outline the development of the CRISPR/Cas9 system. We also show how this technology can be used for the prevention and treatment of HIV-1 infection. Optimistically, this technology promises to make a significant impact on the fight against HIV-1 in the future.
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Affiliation(s)
- Qiudi Deng
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Zisheng Chen
- Department of Respiratory Medicine, The sixth affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Lei Shi
- Department of Food Safety and Nutrition Research, Jinan University, Guangzhou, China
| | - Huafeng Lin
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China.,Department of Food Safety and Nutrition Research, Jinan University, Guangzhou, China
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102
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Mahas A, Mahfouz M. Engineering virus resistance via CRISPR-Cas systems. Curr Opin Virol 2018; 32:1-8. [PMID: 30005359 DOI: 10.1016/j.coviro.2018.06.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/25/2018] [Indexed: 12/15/2022]
Abstract
In prokaryotes, CRISPR/Cas adaptive immunity systems target and destroy nucleic acids derived from invading bacteriophages and other foreign genetic elements. In eukaryotes, the native function of these systems has been exploited to combat viruses in mammals and plants. Rewired CRISPR/Cas9 and CRISPR/Cas13 systems have been used to confer resistance against DNA and RNA viruses, respectively. Here, we discuss recent approaches employing CRISPR/Cas systems to combat viruses in eukaryotes, highlight key challenges, and provide future perspectives. Moreover, we discuss the application of CRISPR/Cas systems in genome-wide screens to identify key host factors for virus infection to enhance our understanding of basic virus biology and to identify and study virus-host interactions.
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Affiliation(s)
- Ahmed Mahas
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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103
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Roychoudhury P, De Silva Feelixge H, Reeves D, Mayer BT, Stone D, Schiffer JT, Jerome KR. Viral diversity is an obligate consideration in CRISPR/Cas9 designs for targeting the HIV reservoir. BMC Biol 2018; 16:75. [PMID: 29996827 PMCID: PMC6040082 DOI: 10.1186/s12915-018-0544-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 06/21/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND RNA-guided CRISPR/Cas9 systems can be designed to mutate or excise the integrated HIV genome from latently infected cells and have therefore been proposed as a curative approach for HIV. However, most studies to date have focused on molecular clones with ideal target site recognition and do not account for target site variability observed within and between patients. For clinical success and broad applicability, guide RNA (gRNA) selection must account for circulating strain diversity and incorporate the within-host diversity of HIV. RESULTS We identified a set of gRNAs targeting HIV LTR, gag, and pol using publicly available sequences for these genes and ranked gRNAs according to global conservation across HIV-1 group M and within subtypes A-C. By considering paired and triplet combinations of gRNAs, we found triplet sets of target sites such that at least one of the gRNAs in the set was present in over 98% of all globally available sequences. We then selected 59 gRNAs from our list of highly conserved LTR target sites and evaluated in vitro activity using a loss-of-function LTR-GFP fusion reporter. We achieved efficient GFP knockdown with multiple gRNAs and found clustering of highly active gRNA target sites near the middle of the LTR. Using published deep-sequence data from HIV-infected patients, we found that globally conserved sites also had greater within-host target conservation. Lastly, we developed a mathematical model based on varying distributions of within-host HIV sequence diversity and enzyme efficacy. We used the model to estimate the number of doses required to deplete the latent reservoir and achieve functional cure thresholds. Our modeling results highlight the importance of within-host target site conservation. While increased doses may overcome low target cleavage efficiency, inadequate targeting of rare strains is predicted to lead to rebound upon cART cessation even with many doses. CONCLUSIONS Target site selection must account for global and within host viral genetic diversity. Globally conserved target sites are good starting points for design, but multiplexing is essential for depleting quasispecies and preventing viral load rebound upon therapy cessation.
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Affiliation(s)
| | | | - Daniel Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Bryan T Mayer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
- Department of Medicine, University of Washington, Seattle, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA.
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104
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Mefferd AL, Bogerd HP, Irwan ID, Cullen BR. Insights into the mechanisms underlying the inactivation of HIV-1 proviruses by CRISPR/Cas. Virology 2018; 520:116-126. [PMID: 29857168 PMCID: PMC6100742 DOI: 10.1016/j.virol.2018.05.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022]
Abstract
DNA editing using CRISPR/Cas has emerged as a potential treatment for diseases caused by pathogenic human DNA viruses. One potential target is HIV-1, which replicates via a chromosomally integrated DNA provirus. While CRISPR/Cas can protect T cells from de novo HIV-1 infection, HIV-1 frequently becomes resistant due to mutations in the chosen single guide RNA (sgRNA) target site. To address this problem, we asked whether an sgRNA targeted to a conserved, functionally critical HIV-1 sequence might prevent the selection of escape mutants. We report that two sgRNAs specific for the HIV-1 transactivation response (TAR) element produce opposite results: the TAR2 sgRNA rapidly selects for mutants that retain TAR function, but are no longer inhibited by Cas9, while the TAR1 sgRNA fails to select any replication competent TAR mutants, most probably because it is targeted to a region of TAR that is disrupted by even minor mutations.
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Affiliation(s)
- Adam L Mefferd
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Hal P Bogerd
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ishak D Irwan
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Bryan R Cullen
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
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105
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De Silva Feelixge HS, Stone D, Roychoudhury P, Aubert M, Jerome KR. CRISPR/Cas9 and Genome Editing for Viral Disease-Is Resistance Futile? ACS Infect Dis 2018; 4:871-880. [PMID: 29522311 PMCID: PMC5993632 DOI: 10.1021/acsinfecdis.7b00273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chronic viral infections remain a major public health issue affecting millions of people worldwide. Highly active antiviral treatments have significantly improved prognosis and infection-related morbidity and mortality but have failed to eliminate persistent viral forms. Therefore, new strategies to either eradicate or control these viral reservoirs are paramount to allow patients to stop antiretroviral therapy and realize a cure. Viral genome disruption based on gene editing by programmable endonucleases is one promising curative gene therapy approach. Recent findings on RNA-guided human immunodeficiency virus 1 (HIV-1) genome cleavage by Cas9 and other gene-editing enzymes in latently infected cells have shown high levels of site-specific genome disruption and potent inhibition of virus replication. However, HIV-1 can readily develop resistance to genome editing at a single antiviral target site. Current data suggest that cellular repair associated with DNA double-strand breaks can accelerate the emergence of resistance. On the other hand, a combination antiviral target strategy can exploit the same repair mechanism to functionally cure HIV-1 infection in vitro while avoiding the development of resistance. This perspective summarizes recent findings on the biology of resistance to genome editing and discusses the significance of viral genetic diversity on the application of gene editing strategies toward cure.
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Affiliation(s)
- Harshana S De Silva Feelixge
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, 1959 NE Pacific St, Seattle 98195, WA, USA
| | - Martine Aubert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
- Department of Laboratory Medicine, University of Washington, 1959 NE Pacific St, Seattle 98195, WA, USA
- Department of Microbiology, University of Washington, 1959 NE Pacific St, Seattle 98195, WA, USA
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106
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Wang Q, Liu S, Liu Z, Ke Z, Li C, Yu X, Chen S, Guo D. Genome scale screening identification of SaCas9/gRNAs for targeting HIV-1 provirus and suppression of HIV-1 infection. Virus Res 2018; 250:21-30. [PMID: 29625148 DOI: 10.1016/j.virusres.2018.04.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/02/2018] [Accepted: 04/02/2018] [Indexed: 01/06/2023]
Abstract
The CRISPR/Cas9 gene-editing approach has been widely used in anti-HIV-1 gene therapy research. However, the major challenges facing the therapeutic application of CRISPR/Cas9 are the precise genome cleavage efficacy and efficient delivery of Cas9/gRNA specifically to the HIV-infected cells. Recently, a small size Cas9 from Staphylococcus aureus (SaCas9) has shown promise in genome editing in eukaryotic cells, suggesting a potential usage in blocking HIV-1 infection by targeting the HIV-1 genome. Here, we designed 43 guide RNAs (gRNAs) against the HIV-1 genome, thereby identifying 8 gRNAs that efficiently and specifically disrupt the target DNA by SaCas9. In addition, we found the selected gRNAs induce SaCas9 to disrupt the latent HIV-1 provirus and suppress HIV-1 proviral reactivation in latently infected Jurkat C11 cells. We further confirmed that the dual or triple gRNAs in an all-in-one lentiviral vector could reduce viral production in TZM-bl cells as well as in Jurkat T cells. Moreover, we did not detect any off-target cleavages in the predicted sites, suggesting that through all-in-one lentiviral vector-mediated HIV-1 genome editing, the selected SaCas9/gRNAs can provide an alternative and flexible strategy for anti-HIV gene therapy.
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Affiliation(s)
- Qiankun Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, PR China.
| | - Shuai Liu
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, PR China.
| | - Zhepeng Liu
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, PR China.
| | - Zunhui Ke
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, PR China.
| | - Chunmei Li
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, PR China; School of Medicine (Shenzhen), Sun Yat-sen University, Guangzhou 510080, PR China.
| | - Xiao Yu
- Institute of health inspection and testing, Hubei Provincial Center for Disease Control and Prevention, Zhuodaoquan North Road 6, Wuhan 430079, Hubei, PR China.
| | - Shuliang Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, PR China; Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, 1900 Coffey Road, Columbus, OH 43210, USA.
| | - Deyin Guo
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, PR China; School of Medicine (Shenzhen), Sun Yat-sen University, Guangzhou 510080, PR China.
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107
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Liang P, Zhang X, Chen Y, Huang J. Developmental history and application of CRISPR in human disease. J Gene Med 2018. [PMID: 28623876 DOI: 10.1002/jgm.2963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-editing tools are programmable artificial nucleases, mainly including zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeat (CRISPR). By recognizing and cleaving specific DNA sequences, genome-editing tools make it possible to generate site-specific DNA double-strand breaks (DSBs) in the genome. DSBs will then be repaired by either error-prone nonhomologous end joining or high-fidelity homologous recombination mechanisms. Through these two different mechanisms, endogenous genes can be knocked out or precisely repaired/modified. Rapid developments in genome-editing tools, especially CRISPR, have revolutionized human disease models generation, for example, various zebrafish, mouse, rat, pig, monkey and human cell lines have been constructed. Here, we review the developmental history of CRISPR and its application in studies of human diseases. In addition, we also briefly discussed the therapeutic application of CRISPR in the near future.
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Affiliation(s)
- Puping Liang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of G uangdong Province, The Third Affiliated Hospital, Guangzhou Medical University and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiya Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuxi Chen
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Junjiu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of G uangdong Province, The Third Affiliated Hospital, Guangzhou Medical University and School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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108
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Darcis G, Das AT, Berkhout B. Tackling HIV Persistence: Pharmacological versus CRISPR-Based Shock Strategies. Viruses 2018; 10:v10040157. [PMID: 29596334 PMCID: PMC5923451 DOI: 10.3390/v10040157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 02/07/2023] Open
Abstract
Jan Svoboda studied aspects of viral latency, in particular with respect to disease induction by avian RNA tumor viruses, which were later renamed as part of the extended retrovirus family. The course of retroviral pathogenesis is intrinsically linked to their unique property of integrating the DNA copy of the retroviral genome into that of the host cell, thus forming the provirus. Retroviral latency has recently become of major clinical interest to allow a better understanding of why we can effectively block the human immunodeficiency virus type 1 (HIV-1) in infected individuals with antiviral drugs, yet never reach a cure. We will discuss HIV-1 latency and its direct consequence—the formation of long-lasting HIV-1 reservoirs. We next focus on one of the most explored strategies in tackling HIV-1 reservoirs—the “shock and kill” strategy—which describes the broadly explored pharmacological way of kicking the latent provirus, with subsequent killing of the virus-producing cell by the immune system. We furthermore present how the clustered regularly interspaced palindromic repeats (CRISPR) and associated protein (Cas) system can be harnessed to reach the same objective by reactivating HIV-1 gene expression from latency. We will review the benefits and drawbacks of these different cure strategies.
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Affiliation(s)
- Gilles Darcis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
- Infectious Diseases Department, Liège University Hospital, 4000 Liege, Belgium.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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109
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Abstract
Advances in Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated system (CRISPR/Cas9) has dramatically reshaped our ability to edit genomes. The scientific community is using CRISPR/Cas9 for various biotechnological and medical purposes. One of its most important uses is developing potential therapeutic strategies against diseases. CRISPR/Cas9 based approaches have been increasingly applied to the treatment of human diseases like cancer, genetic, immunological and neurological disorders and viral diseases. These strategies using CRISPR/Cas9 are not only therapy oriented but can also be used for disease modeling as well, which in turn can lead to the improved understanding of mechanisms of various infectious and genetic diseases. In addition, CRISPR/Cas9 system can also be used as programmable antibiotics to kill the bacteria sequence specifically and therefore can bypass multidrug resistance. Furthermore, CRISPR/Cas9 based gene drive may also hold the potential to limit the spread of vector borne diseases. This bacterial and archaeal adaptive immune system might be a therapeutic answer to previous incurable diseases, of course rigorous testing is required to corroborate these claims. In this review, we provide an insight about the recent developments using CRISPR/Cas9 against various diseases with respect to disease modeling and treatment, and what future perspectives should be noted while using this technology.
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110
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Liu H, Soyars CL, Li J, Fei Q, He G, Peterson BA, Meyers BC, Nimchuk ZL, Wang X. CRISPR/Cas9-mediated resistance to cauliflower mosaic virus. PLANT DIRECT 2018; 2:e00047. [PMID: 31245713 PMCID: PMC6508564 DOI: 10.1002/pld3.47] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/25/2018] [Accepted: 02/06/2018] [Indexed: 05/03/2023]
Abstract
Viral diseases are a leading cause of worldwide yield losses in crop production. Breeding of resistance genes (R gene) into elite crop cultivars has been the standard and most cost-effective practice. However, R gene-mediated resistance is limited by the available R genes within genetic resources and in many cases, by strain specificity. Therefore, it is important to generate new and broad-spectrum antiviral strategies. The CRISPR-Cas9 (clustered regularly interspaced palindromic repeat, CRISPR-associated) editing system has been employed to confer resistance to human viruses and several plant single-stranded DNA geminiviruses, pointing out the possible application of the CRISPR-Cas9 system for virus control. Here, we demonstrate that strong viral resistance to cauliflower mosaic virus (CaMV), a pararetrovirus with a double-stranded DNA genome, can be achieved through Cas9-mediated multiplex targeting of the viral coat protein sequence. We further show that small interfering RNAs (siRNA) are produced and mostly map to the 3' end of single-guide RNAs (sgRNA), although very low levels of siRNAs map to the spacer region as well. However, these siRNAs are not responsible for the inhibited CaMV infection because there is no resistance if Cas9 is not present. We have also observed edited viruses in systematically infected leaves in some transgenic plants, with short deletions or insertions consistent with Cas9-induced DNA breaks at the sgRNA target sites in coat protein coding sequence. These edited coat proteins, in most cases, led to earlier translation stop and thus, nonfunctional coat proteins. We also recovered wild-type CP sequence in these infected transgenic plants, suggesting these edited viral genomes were packaged by wild-type coat proteins. Our data demonstrate that the CRISPR-Cas9 system can be used for virus control against plant pararetroviruses with further modifications.
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Affiliation(s)
- Haijie Liu
- Department of Plant Pathology, Physiology and Weed ScienceVirginia TechBlacksburgVAUSA
| | - Cara L. Soyars
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Jianhui Li
- Department of Plant Pathology, Physiology and Weed ScienceVirginia TechBlacksburgVAUSA
| | - Qili Fei
- Department of Plant & Soil SciencesDelaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Guijuan He
- Department of Plant Pathology, Physiology and Weed ScienceVirginia TechBlacksburgVAUSA
| | - Brenda A. Peterson
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Blake C. Meyers
- Department of Plant & Soil SciencesDelaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Division of Plant SciencesUniversity of Missouri – ColumbiaColumbiaMOUSA
| | - Zachary L. Nimchuk
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
- Faculty of Health SciencesVirginia TechBlacksburgVAUSA
- Curriculum in Genetics and Molecular BiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Xiaofeng Wang
- Department of Plant Pathology, Physiology and Weed ScienceVirginia TechBlacksburgVAUSA
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111
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Ren L, Peng Z, Ouyang T, Liu X, Chen X, Ye L, Fan J, Ouyang H, Pang D, Bai J. Subculturing cells have no effect on CRISPR/Cas9-mediated cleavage of UL30 gene in pseudorabies virus. Animal Model Exp Med 2018; 1:74-77. [PMID: 30891550 PMCID: PMC6357676 DOI: 10.1002/ame2.12006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/22/2018] [Indexed: 01/15/2023] Open
Abstract
CRISPR/Cas9-mediated genome editing can inhibit virus infection by targeting the conserved regions of the viral genomic DNA. Unexpectedly, we found previously that pseudorabies virus (PRV) could escape from CRISPR/Cas9-mediated inhibition. In order to elucidate whether the escape of PRV from Cas9-mediated inhibition was due to cell deficiencies, such as genetic instability of sgRNA or Cas9 protein, the positive cells were passaged ten times, and PRV infection in the sgRNA-expressing cells was evaluated in the present study. The results showed that subculturing cells has no effect on Cas9-mediated cleavage of PRV. Different passages of PX459-PRV cells can stably express sgRNA to facilitate Cas9/sgRNA cleavage on the UL30 gene of PRV, resulting in a pronounced inhibition of PRV infection. Studies to elucidate the mechanism of PRV escape are currently in progress.
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Affiliation(s)
- Lin‐zhu Ren
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Zhi‐yuan Peng
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Ting Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Xiao‐hui Liu
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Xin‐rong Chen
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
- The Laboratory Animal CenterThe Academic of Military Medical SciencesBeijingChina
| | - Li Ye
- The Laboratory Animal CenterThe Academic of Military Medical SciencesBeijingChina
| | - Jun‐wen Fan
- The Laboratory Animal CenterThe Academic of Military Medical SciencesBeijingChina
| | - Hong‐sheng Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Da‐xin Pang
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Jie‐ying Bai
- The Laboratory Animal CenterThe Academic of Military Medical SciencesBeijingChina
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112
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Thompson DB, Aboulhouda S, Hysolli E, Smith CJ, Wang S, Castanon O, Church GM. The Future of Multiplexed Eukaryotic Genome Engineering. ACS Chem Biol 2018; 13:313-325. [PMID: 29241002 PMCID: PMC5880278 DOI: 10.1021/acschembio.7b00842] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multiplex genome editing is the simultaneous introduction of multiple distinct modifications to a given genome. Though in its infancy, maturation of this field will facilitate powerful new biomedical research approaches and will enable a host of far-reaching biological engineering applications, including new therapeutic modalities and industrial applications, as well as "genome writing" and de-extinction efforts. In this Perspective, we focus on multiplex editing of large eukaryotic genomes. We describe the current state of multiplexed genome editing, the current limits of our ability to multiplex edits, and provide perspective on the many applications that fully realized multiplex editing technologies would enable in higher eukaryotic genomes. We offer a broad look at future directions, covering emergent CRISPR-based technologies, advances in intracellular delivery, and new DNA assembly approaches that may enable future genome editing on a massively multiplexed scale.
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Affiliation(s)
- David B. Thompson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Soufiane Aboulhouda
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Eriona Hysolli
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Cory J. Smith
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Stan Wang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Oscar Castanon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau, France
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
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113
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Multiplex CRISPR/Cas9 system impairs HCMV replication by excising an essential viral gene. PLoS One 2018; 13:e0192602. [PMID: 29447206 PMCID: PMC5813945 DOI: 10.1371/journal.pone.0192602] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/28/2018] [Indexed: 01/20/2023] Open
Abstract
Anti-HCMV treatments used in immunosuppressed patients reduce viral replication, but resistant viral strains can emerge. Moreover, these drugs do not target latently infected cells. We designed two anti-viral CRISPR/Cas9 strategies to target the UL122/123 gene, a key regulator of lytic replication and reactivation from latency. The singleplex strategy contains one gRNA to target the start codon. The multiplex strategy contains three gRNAs to excise the complete UL122/123 gene. Primary fibroblasts and U-251 MG cells were transduced with lentiviral vectors encoding Cas9 and one or three gRNAs. Both strategies induced mutations in the target gene and a concomitant reduction of immediate early (IE) protein expression in primary fibroblasts. Further detailed analysis in U-251 MG cells showed that the singleplex strategy induced 50% of indels in the viral genome, leading to a reduction in IE protein expression. The multiplex strategy excised the IE gene in 90% of all viral genomes and thus led to the inhibition of IE protein expression. Consequently, viral genome replication and late protein expression were reduced by 90%. Finally, the production of new viral particles was nearly abrogated. In conclusion, the multiplex anti-UL122/123 CRISPR/Cas9 system can target the viral genome efficiently enough to significantly prevent viral replication.
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114
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Halder UC. Bone marrow stem cells to destroy circulating HIV: a hypothetical therapeutic strategy. ACTA ACUST UNITED AC 2018; 25:3. [PMID: 29445623 PMCID: PMC5800069 DOI: 10.1186/s40709-018-0075-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 01/27/2018] [Indexed: 12/19/2022]
Abstract
Human immunodeficiency virus (HIV) still poses enigmatic threats to human life. This virus has mastered in bypassing anti retroviral therapy leading to patients’ death. Circulating viruses are phenomenal for the disease outcome. This hypothesis proposes a therapeutic strategy utilizing receptor-integrated hematopoietic, erythroid and red blood cells. Here, HIV specific receptors trap circulating viruses that enter erythrocyte cytoplasm and form inactive integration complex. This model depicts easy, effective removal of circulating HIV without any adverse effect.
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Affiliation(s)
- Umesh Chandra Halder
- Department of Zoology, Raniganj Girls' College, Searsole, Rajbari, Raniganj, Paschim Barddhaman, West Bengal 713358 India
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115
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Yue H, Zhou X, Cheng M, Xing D. Graphene oxide-mediated Cas9/sgRNA delivery for efficient genome editing. NANOSCALE 2018; 10:1063-1071. [PMID: 29266160 DOI: 10.1039/c7nr07999k] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Direct cellular delivery of CRISPR/Cas9 complexes is of great significance for genome editing and other recently developed applications, such as gene expression regulation and RNA/DNA imaging. Here, we first constructed a graphene oxide (GO)-polyethylene glycol (PEG)-polyethylenimine (PEI) nanocarrier for the delivery of high-molecular-weight Cas9/single-guide RNA (sgRNA) complexes for endocytosis, endosomal escape, nuclear entry, and gene editing. The results demonstrate that the nanocarrier can be used successfully for efficient gene editing in human AGS cells with an efficiency of ∼39%. The results also show that this nanocarrier can protect sgRNA from enzymatic degradation, thus exhibiting extremely high stability, which is critical for future in vivo applications. Thus, this GO-mediated Cas9/sgRNA delivery system has potential as a new approach for biomedical research and targeted gene engineering applications.
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Affiliation(s)
- Huahua Yue
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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116
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Wang G, Zhao N, Berkhout B, Das AT. CRISPR-Cas based antiviral strategies against HIV-1. Virus Res 2018; 244:321-332. [PMID: 28760348 DOI: 10.1016/j.virusres.2017.07.020] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 12/25/2022]
Abstract
In bacteria and archaea, the clustered regularly interspaced short palindromic repeats (CRISPR) and associated proteins (Cas) confer adaptive immunity against exogenous DNA elements. This CRISPR-Cas system has been turned into an effective tool for editing of eukaryotic DNA genomes. Pathogenic viruses that have a double-stranded DNA (dsDNA) genome or that replicate through a dsDNA intermediate can also be targeted with this DNA editing tool. Here, we review how CRISPR-Cas was used in novel therapeutic approaches against the human immunodeficiency virus type-1 (HIV-1), focusing on approaches that aim to permanently inactivate all virus genomes or to prevent viral persistence in latent reservoirs.
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Affiliation(s)
- Gang Wang
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Na Zhao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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117
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Yuen KS, Wang ZM, Wong NHM, Zhang ZQ, Cheng TF, Lui WY, Chan CP, Jin DY. Suppression of Epstein-Barr virus DNA load in latently infected nasopharyngeal carcinoma cells by CRISPR/Cas9. Virus Res 2018; 244:296-303. [PMID: 28456574 DOI: 10.1016/j.virusres.2017.04.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 12/27/2022]
Abstract
Epstein-Barr virus (EBV) infects more than 90% of the world's adult population. Once established, latent infection of nasopharyngeal epithelial cells with EBV is difficult to eradicate and might lead to the development of nasopharyngeal carcinoma (NPC) in a small subset of individuals. In this study we explored the anti-EBV potential of CRISPR/Cas9 targeting of EBV genome in infected NPC cells. We designed gRNAs to target different regions of the EBV genome and transfected them into C666-1 cells. The levels of EBV DNA in transfected cells were decreased by about 50%. The suppressive effect on EBV DNA load lasted for weeks but could not be further enhanced by re-transfection of gRNA. Suppression of EBV by CRISPR/Cas9 did not affect survival of C666-1 cells but sensitized them to chemotherapeutic killing by cisplatin and 5-fluorouracil. Our work provides the proof-of-principle for suppressing EBV DNA load with CRISPR/Cas9 and a potential new strategy to sensitize EBV-infected NPC cells to chemotherapy.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Protein 9
- CRISPR-Cas Systems
- Cell Line, Tumor
- Cell Survival/drug effects
- Cisplatin/pharmacology
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Endonucleases/genetics
- Endonucleases/metabolism
- Epithelial Cells/drug effects
- Epithelial Cells/pathology
- Epithelial Cells/virology
- Fluorouracil/pharmacology
- Gene Editing/methods
- Genome, Viral
- Herpesvirus 4, Human/drug effects
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/growth & development
- Herpesvirus 4, Human/metabolism
- Humans
- Nasopharynx/drug effects
- Nasopharynx/pathology
- Nasopharynx/virology
- Plasmids/chemistry
- Plasmids/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Viral Load/drug effects
- Virus Latency/genetics
- Virus Replication
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Affiliation(s)
- Kit-San Yuen
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Zhong-Min Wang
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Nok-Hei Mickey Wong
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Zhi-Qian Zhang
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Tsz-Fung Cheng
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Wai-Yin Lui
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
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118
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Wei C, Wang F, Liu W, Zhao W, Yang Y, Li K, Xiao L, Shen J. CRISPR/Cas9 targeting of the androgen receptor suppresses the growth of LNCaP human prostate cancer cells. Mol Med Rep 2017; 17:2901-2906. [PMID: 29257308 PMCID: PMC5783506 DOI: 10.3892/mmr.2017.8257] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 11/02/2017] [Indexed: 01/05/2023] Open
Abstract
Androgens have been recognized to be primary causative agents of prostate cancer. Following binding to the androgen receptor (AR), androgens serve important roles in the carcinogenesis of prostate cancers. ARs serve an important role during all stages of prostate cancer, and inhibiting their function may help to slow prostate cancer growth. In the present study, the AR gene was targeted in androgen-positive prostate cancer cells using the clustered regularly interspaced short palindromic repeats-associated protein (CRISPR/Cas) system. A total of three different single-guide RNAs (sgRNAs) were designed according to the three different target sites in the AR gene. The optimal sgRNA with a specific target effect was effectively screened to cleave the AR gene in androgen-positive prostate cancer cell lines, and to suppress the growth of androgen-sensitive prostate cancer in vitro. The AR-sgRNA-guided CRISPR/Cas system was able to disrupt the AR at specific sites and inhibit the growth of androgen-sensitive prostate cancer cells; further studies demonstrated that the decreased cell proliferation was due to cellular apoptosis. The results of the present study suggested that the CRISPR/Cas system may be a useful therapeutic strategy for the treatment of prostate cancer.
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Affiliation(s)
- Chaogang Wei
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Fengjiao Wang
- Department of Pharmacy, The Affiliated Children's Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Wei Liu
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Wenlu Zhao
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Yi Yang
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Kai Li
- Center of Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Li Xiao
- Center of Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Junkang Shen
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
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119
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Zhao N, Wang G, Das AT, Berkhout B. Combinatorial CRISPR-Cas9 and RNA Interference Attack on HIV-1 DNA and RNA Can Lead to Cross-Resistance. Antimicrob Agents Chemother 2017; 61:e01486-17. [PMID: 28893790 PMCID: PMC5700367 DOI: 10.1128/aac.01486-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/02/2017] [Indexed: 11/20/2022] Open
Abstract
Many potent antiviral drugs have been developed against HIV-1, and their combined action is usually successful in achieving durable virus suppression in infected individuals. This success is based on two effects: additive or even synergistic virus inhibition and an increase in the genetic threshold for development of drug resistance. More recently, several genetic approaches have been developed to attack the HIV-1 genome in a gene therapy setting. We set out to test the combinatorial possibilities for a therapy based on the CRISPR-Cas9 and RNA interference (RNAi) mechanisms that attack the viral DNA and RNA, respectively. When two different sites in the HIV-1 genome were targeted, either with dual CRISPR-Cas9 antivirals or with a combination of CRISPR-Cas9 and RNAi antivirals, we observed additive inhibition, much like what was reported for antiviral drugs. However, when the same or overlapping viral sequence was attacked by the antivirals, rapid escape from a CRISPR-Cas9 antiviral, assisted by the error-prone nonhomologous end joining (NHEJ) DNA repair machinery, accelerated the development of cross-resistance to the other CRISPR-Cas9 or RNAi antiviral. Thus, genetic antiviral approaches can be combined, but overlap should be avoided.
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MESH Headings
- Antiviral Agents/chemistry
- Antiviral Agents/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- CRISPR-Associated Protein 9
- CRISPR-Cas Systems
- Cell Line, Transformed
- DNA, Viral/antagonists & inhibitors
- DNA, Viral/biosynthesis
- DNA, Viral/genetics
- Drug Resistance, Viral/genetics
- Endonucleases/genetics
- Endonucleases/metabolism
- Gene Expression Regulation, Viral
- Genome, Viral
- HIV Core Protein p24/antagonists & inhibitors
- HIV Core Protein p24/biosynthesis
- HIV Core Protein p24/genetics
- HIV-1/genetics
- HIV-1/metabolism
- Humans
- Molecular Targeted Therapy
- RNA Interference
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Viral/antagonists & inhibitors
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- T-Lymphocytes/virology
- Virus Replication
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Affiliation(s)
- Na Zhao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Gang Wang
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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120
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Tang YD, Liu JT, Wang TY, Sun MX, Tian ZJ, Cai XH. CRISPR/Cas9-mediated multiple single guide RNAs potently abrogate pseudorabies virus replication. Arch Virol 2017; 162:3881-3886. [PMID: 28900740 DOI: 10.1007/s00705-017-3553-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 08/02/2017] [Indexed: 01/12/2023]
Abstract
Pseudorabies virus (PRV) is a swine herpesvirus that causes significant morbidity and mortality in swine populations and has caused huge economic losses in the worldwide swine industry. Currently, there is no effective antiviral drug in clinical use for PRV infection; it is also difficult to eliminate PRV from infected swine. In our study, we set out to combat these swine herpesvirus infections by exploiting the CRISPR/Cas9 system. We designed 75 single guide RNAs (sgRNA) by targeting both essential and non-essential genes across the genome of PRV. We applied a firefly luciferase-tagged reporter PRV virus for high-throughput sgRNA screening and found that most of the sgRNAs significantly inhibited PRV replication. More importantly, using a transfection assay, we demonstrated that simultaneous targeting of PRV with multiple sgRNAs completely abolished the production of infectious viruses in cells. These data suggest that CRISPR/Cas9 could be a novel therapeutic agent against PRV in the future.
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Affiliation(s)
- Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 678 HaPing Road, XiangFang, Harbin, 150069, China
| | - Ji-Ting Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 678 HaPing Road, XiangFang, Harbin, 150069, China
| | - Tong-Yun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 678 HaPing Road, XiangFang, Harbin, 150069, China
| | - Ming-Xia Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 678 HaPing Road, XiangFang, Harbin, 150069, China
| | - Zhi-Jun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 678 HaPing Road, XiangFang, Harbin, 150069, China
| | - Xue-Hui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 678 HaPing Road, XiangFang, Harbin, 150069, China.
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121
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Kunze C, Börner K, Kienle E, Orschmann T, Rusha E, Schneider M, Radivojkov-Blagojevic M, Drukker M, Desbordes S, Grimm D, Brack-Werner R. Synthetic AAV/CRISPR vectors for blocking HIV-1 expression in persistently infected astrocytes. Glia 2017; 66:413-427. [PMID: 29119608 DOI: 10.1002/glia.23254] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 10/04/2017] [Accepted: 10/11/2017] [Indexed: 01/08/2023]
Abstract
Astrocytes, the most abundant cells in the mammalian brain, perform key functions and are involved in several neurodegenerative diseases. The human immunodeficiency virus (HIV) can persist in astrocytes, contributing to the HIV burden and neurological dysfunctions in infected individuals. While a comprehensive approach to HIV cure must include the targeting of HIV-1 in astrocytes, dedicated tools for this purpose are still lacking. Here we report a novel Adeno-associated virus-based vector (AAV9P1) with a synthetic surface peptide for transduction of astrocytes. Analysis of AAV9P1 transduction efficiencies with single brain cell populations, including primary human brain cells, as well as human brain organoids demonstrated that AAV9P1 targeted terminally differentiated human astrocytes much more efficiently than neurons. We then investigated whether AAV9P1 can be used to deliver HIV-inhibitory genes to astrocytes. To this end we generated AAV9P1 vectors containing genes for HIV-1 proviral editing by CRISPR/Cas9. Latently HIV-1 infected astrocytes transduced with these vectors showed significantly diminished reactivation of proviruses, compared with untransduced cultures. Sequence analysis identified mutations/deletions in key HIV-1 transcriptional control regions. We conclude that AAV9P1 is a promising tool for gene delivery to astrocytes and may facilitate inactivation/destruction of persisting HIV-1 proviruses in astrocyte reservoirs.
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Affiliation(s)
- Christine Kunze
- Institute of Virology, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | - Kathleen Börner
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg, 69120, Germany.,German Center for Infection Research (DZIF), Partner site Heidelberg, Heidelberg, 69120, Germany
| | - Eike Kienle
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg, 69120, Germany
| | - Tanja Orschmann
- SCADEV, Institute of Developmental Genetics, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | - Ejona Rusha
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | - Martha Schneider
- Institute of Virology, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | | | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | - Sabrina Desbordes
- SCADEV, Institute of Developmental Genetics, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | - Dirk Grimm
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg, 69120, Germany.,German Center for Infection Research (DZIF), Partner site Heidelberg, Heidelberg, 69120, Germany
| | - Ruth Brack-Werner
- Institute of Virology, Helmholtz Center Munich, Neuherberg, 85764, Germany
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122
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Dampier W, Sullivan NT, Chung CH, Mell JC, Nonnemacher MR, Wigdahl B. Designing broad-spectrum anti-HIV-1 gRNAs to target patient-derived variants. Sci Rep 2017; 7:14413. [PMID: 29089503 PMCID: PMC5663707 DOI: 10.1038/s41598-017-12612-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/05/2017] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated protein 9 (Cas9), including specific guide RNAs (gRNAs), can excise integrated human immunodeficiency virus type 1 (HIV-1) provirus from host chromosomes. To date, anti-HIV-1 gRNAs have been designed to account for off-target activity, however, they seldom account for genetic variation in the HIV-1 genome within and between patients, which will be crucial for therapeutic application of this technology. This analysis tests the ability of published anti-HIV-1 gRNAs to cleave publicly available patient-derived HIV-1 sequences to inform gRNA design and provides basic computational tools to researchers in the field.
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Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- School of Biomedical Engineering and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Neil T Sullivan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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123
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Rogers GL, Cannon PM. Gene Therapy Approaches to Human Immunodeficiency Virus and Other Infectious Diseases. Hematol Oncol Clin North Am 2017; 31:883-895. [PMID: 28895854 DOI: 10.1016/j.hoc.2017.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Advances in gene therapy technologies, particularly in gene editing, are suggesting new avenues for the treatment of human immunodeficiency virus and other infectious diseases. This article outlines recent developments in antiviral gene therapies, including those based on the disruption of entry receptors or that target viral genomes using targeted nucleases, such as the CRISPR/Cas9 system. In addition, new ways to express circulating antiviral factors, such as antibodies, and approaches to harness and engineer the immune system to provide an antiviral effect that is not naturally achieved are described.
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Affiliation(s)
- Geoffrey L Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, HMR 413A, Los Angeles, CA 90033, USA
| | - Paula M Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, HMR 413A, Los Angeles, CA 90033, USA.
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124
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Soppe JA, Lebbink RJ. Antiviral Goes Viral: Harnessing CRISPR/Cas9 to Combat Viruses in Humans. Trends Microbiol 2017; 25:833-850. [PMID: 28522157 DOI: 10.1016/j.tim.2017.04.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/07/2017] [Accepted: 04/19/2017] [Indexed: 12/11/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems are RNA-guided sequence-specific prokaryotic antiviral immune systems. In prokaryotes, small RNA molecules guide Cas effector endonucleases to invading foreign genetic elements in a sequence-dependent manner, resulting in DNA cleavage by the endonuclease upon target binding. A rewired CRISPR/Cas9 system can be used for targeted and precise genome editing in eukaryotic cells. CRISPR/Cas has also been harnessed to target human pathogenic viruses as a potential new antiviral strategy. Here, we review recent CRISPR/Cas9-based approaches to combat specific human viruses in humans and discuss challenges that need to be overcome before CRISPR/Cas9 may be used in the clinic as an antiviral strategy.
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Affiliation(s)
- Jasper Adriaan Soppe
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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125
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Wahid B, Usman S, Ali A, Saleem K, Rafique S, Naz Z, Ahsan Ashfaq H, Idrees M. Therapeutic Strategies of Clustered Regularly Interspaced Palindromic Repeats-Cas Systems for Different Viral Infections. Viral Immunol 2017; 30:552-559. [DOI: 10.1089/vim.2017.0055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Braira Wahid
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sana Usman
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Amjad Ali
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Komal Saleem
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shazia Rafique
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Hafiz Ahsan Ashfaq
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
- Vice Chancellor Hazara University, Mansehra, Pakistan
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126
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Jakobsdottir GM, Iliopoulou M, Nolan R, Alvarez L, Compton AA, Padilla-Parra S. On the Whereabouts of HIV-1 Cellular Entry and Its Fusion Ports. Trends Mol Med 2017; 23:932-944. [PMID: 28899754 DOI: 10.1016/j.molmed.2017.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/12/2017] [Accepted: 08/14/2017] [Indexed: 01/06/2023]
Abstract
HIV-1 disseminates to diverse tissues through different cell types and establishes long-lived reservoirs. The exact cellular compartment where fusion occurs differs depending on the cell type and mode of viral transmission. This implies that HIV-1 may modulate a number of common host cell factors in different cell types. In this review, we evaluate recent advances on the host cell factors that play an important role in HIV-1 entry and fusion. New insights from restriction factors inhibiting virus-cell fusion in vitro may contribute to the development of future therapeutic interventions. Collectively, novel findings underline the need for potent, host-directed therapies that disrupt the earliest stages of the virus life cycle and preclude the emergence of resistant viral variants.
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Affiliation(s)
- G Maria Jakobsdottir
- Wellcome Trust Centre for Human Genetics, Cellular Imaging, University of Oxford, Oxford, UK
| | - Maro Iliopoulou
- Wellcome Trust Centre for Human Genetics, Cellular Imaging, University of Oxford, Oxford, UK
| | - Rory Nolan
- Wellcome Trust Centre for Human Genetics, Cellular Imaging, University of Oxford, Oxford, UK
| | - Luis Alvarez
- Wellcome Trust Centre for Human Genetics, Cellular Imaging, University of Oxford, Oxford, UK
| | - Alex A Compton
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Sergi Padilla-Parra
- Wellcome Trust Centre for Human Genetics, Cellular Imaging, University of Oxford, Oxford, UK; Division of Structural Biology, University of Oxford,The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK.
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Abstract
PURPOSE OF REVIEW Highly active antiretroviral treatment has dramatically improved the prognosis for people living with HIV by preventing AIDS-related morbidity and mortality through profound suppression of viral replication. However, a long-lived viral reservoir persists in latently infected cells that harbor replication-competent HIV genomes. If therapy is discontinued, latently infected memory cells inevitably reactivate and produce infectious virus, resulting in viral rebound. The reservoir is the biggest obstacle to a cure of HIV. RECENT FINDINGS This review summarizes significant advances of the past year in the development of cellular and gene therapies for HIV cure. In particular, we highlight work done on suppression or disruption of HIV coreceptors, vectored delivery of antibodies and antibody-like molecules, T-cell therapies and HIV genome disruption. SUMMARY Several recent advancements in cellular and gene therapies have emerged at the forefront of HIV cure research, potentially having broad implications for the future of HIV treatment.
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128
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Kwarteng A, Ahuno ST, Kwakye-Nuako G. The therapeutic landscape of HIV-1 via genome editing. AIDS Res Ther 2017; 14:32. [PMID: 28705213 PMCID: PMC5513397 DOI: 10.1186/s12981-017-0157-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 05/30/2017] [Indexed: 12/31/2022] Open
Abstract
Current treatment for HIV-1 largely relies on chemotherapy through the administration of antiretroviral drugs. While the search for anti-HIV-1 vaccine remain elusive, the use of highly active antiretroviral therapies (HAART) have been far-reaching and has changed HIV-1 into a manageable chronic infection. There is compelling evidence, including several side-effects of ARTs, suggesting that eradication of HIV-1 cannot depend solely on antiretrovirals. Gene therapy, an expanding treatment strategy, using RNA interference (RNAi) and programmable nucleases such as meganuclease, zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR-Cas9) are transforming the therapeutic landscape of HIV-1. TALENS and ZFNS are structurally similar modular systems, which consist of a FokI endonuclease fused to custom-designed effector proteins but have been largely limited, particularly ZFNs, due to their complexity and cost of protein engineering. However, the newly developed CRISPR-Cas9 system, consists of a single guide RNA (sgRNA), which directs a Cas9 endonuclease to complementary target sites, and serves as a superior alternative to the previous protein-based systems. The techniques have been successfully applied to the development of better HIV-1 models, generation of protective mutations in endogenous/host cells, disruption of HIV-1 genomes and even reactivating latent viruses for better detection and clearance by host immune response. Here, we focus on gene editing-based HIV-1 treatment and research in addition to providing perspectives for refining these techniques.
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Affiliation(s)
- Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), PMB, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Samuel Terkper Ahuno
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), PMB, Kumasi, Ghana
| | - Godwin Kwakye-Nuako
- Department of Biomedical Sciences, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
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129
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White MK, Kaminski R, Young WB, Roehm PC, Khalili K. CRISPR Editing Technology in Biological and Biomedical Investigation. J Cell Biochem 2017; 118:3586-3594. [PMID: 28460414 DOI: 10.1002/jcb.26099] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 01/01/2023]
Abstract
The CRISPR or clustered regularly interspaced short palindromic repeats system is currently the most advanced approach to genome editing and is notable for providing an unprecedented degree of specificity, effectiveness, and versatility in genetic manipulation. CRISPR evolved as a prokaryotic immune system to provide an acquired immunity and resistance to foreign genetic elements such as bacteriophages. It has recently been developed into a tool for the specific targeting of nucleotide sequences within complex eukaryotic genomes for the purpose of genetic manipulation. The power of CRISPR lies in its simplicity and ease of use, its flexibility to be targeted to any given nucleotide sequence by the choice of an easily synthesized guide RNA, and its ready ability to continue to undergo technical improvements. Applications for CRISPR are numerous including creation of novel transgenic cell animals for research, high-throughput screening of gene function, potential clinical gene therapy, and nongene-editing approaches such as modulating gene activity and fluorescent tagging. In this prospect article, we will describe the salient features of the CRISPR system with an emphasis on important drawbacks and considerations with respect to eliminating off-target events and obtaining efficient CRISPR delivery. We will discuss recent technical developments to the system and we will illustrate some of the most recent applications with an emphasis on approaches to eliminate human viruses including HIV-1, JCV and HSV-1 and prospects for the future. J. Cell. Biochem. 118: 3586-3594, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Martyn K White
- Center for Neurovirology and Comprehensive NeuroAIDS Center, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, Pennsylvania, 19140
| | - Rafal Kaminski
- Center for Neurovirology and Comprehensive NeuroAIDS Center, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, Pennsylvania, 19140
| | - Won-Bin Young
- Center for Neurovirology and Comprehensive NeuroAIDS Center, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, Pennsylvania, 19140
| | - Pamela C Roehm
- Center for Neurovirology and Comprehensive NeuroAIDS Center, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, Pennsylvania, 19140
| | - Kamel Khalili
- Center for Neurovirology and Comprehensive NeuroAIDS Center, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, Pennsylvania, 19140
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130
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Schwartz C, Bouchat S, Marban C, Gautier V, Van Lint C, Rohr O, Le Douce V. On the way to find a cure: Purging latent HIV-1 reservoirs. Biochem Pharmacol 2017; 146:10-22. [PMID: 28687465 DOI: 10.1016/j.bcp.2017.07.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/03/2017] [Indexed: 12/29/2022]
Abstract
Introduction of cART in 1996 has drastically increased the life expectancy of people living with HIV-1. However, this treatment has not allowed cure as cessation of cART is associated with a rapid viral rebound. The main barrier to the eradication of the virus is related to the persistence of latent HIV reservoirs. Evidence is now accumulating that purging the HIV-1 reservoir might lead to a cure or a remission. The most studied strategy is the so called "shock and kill" therapy. This strategy is based on reactivation of dormant viruses from the latently-infected reservoirs (the shock) followed by the eradication of the reservoirs (the kill). This review focuses mainly on the recent advances made in the "shock and kill" therapy. We believe that a cure or a remission will come from combinatorial approaches i.e. combination of drugs to reactivate the dormant virus from all the reservoirs including the one located in sanctuaries, and combination of strategies boosting the immune system. Alternative strategies based on cell and gene therapy or based in inducing deep latency, which are evoked in this review reinforce the idea that at least a remission is attainable.
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Affiliation(s)
- Christian Schwartz
- University of Strasbourg, EA7292, DHPI, Institute of Parasitology and Tropical Pathology, Strasbourg, France; University of Strasbourg, IUT Louis Pasteur, Schiltigheim, France.
| | - Sophie Bouchat
- Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), 12 rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Céline Marban
- University of Strasbourg, Inserm UMR 1121 Faculté de Chirurgie Dentaire Pavillon Leriche 1, place de l'Hôpital Strasbourg, France
| | - Virginie Gautier
- UCD, Centre for Research in Infectious Diseases (CRID), School of Medicine University College Dublin, Belfield, Dublin 4, Ireland
| | - Carine Van Lint
- Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), 12 rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Olivier Rohr
- University of Strasbourg, EA7292, DHPI, Institute of Parasitology and Tropical Pathology, Strasbourg, France; University of Strasbourg, IUT Louis Pasteur, Schiltigheim, France
| | - Valentin Le Douce
- UCD, Centre for Research in Infectious Diseases (CRID), School of Medicine University College Dublin, Belfield, Dublin 4, Ireland
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131
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Singh V, Gohil N, Ramírez García R, Braddick D, Fofié CK. Recent Advances in CRISPR-Cas9 Genome Editing Technology for Biological and Biomedical Investigations. J Cell Biochem 2017; 119:81-94. [PMID: 28544016 DOI: 10.1002/jcb.26165] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 02/06/2023]
Abstract
The Type II CRISPR-Cas9 system is a simple, efficient, and versatile tool for targeted genome editing in a wide range of organisms and cell types. It continues to gain more scientific interest and has established itself as an extremely powerful technology within our synthetic biology toolkit. It works upon a targeted site and generates a double strand breaks that become repaired by either the NHEJ or the HDR pathway, modifying or permanently replacing the genomic target sequences of interest. These can include viral targets, single-mutation genetic diseases, and multiple-site corrections for wide scale disease states, offering the potential to manage and cure some of mankind's most persistent biomedical menaces. Here, we present the developing progress and future potential of CRISPR-Cas9 in biological and biomedical investigations, toward numerous therapeutic, biomedical, and biotechnological applications, as well as some of the challenges within. J. Cell. Biochem. 119: 81-94, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Vijai Singh
- Department of Microbiology, Synthetic Biology Laboratory, School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar 382007, India
| | - Nisarg Gohil
- Department of Microbiology, Synthetic Biology Laboratory, School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar 382007, India
| | - Robert Ramírez García
- Department of Microbiology, Synthetic Biology Laboratory, School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar 382007, India
| | | | - Christian Kuete Fofié
- Department of Microbiology, Synthetic Biology Laboratory, School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar 382007, India.,Faculty of Science, Laboratory of Animal Physiology and Phytopharmacology, University of Dschang, Dschang, Cameroon
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132
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Current application of CRISPR/Cas9 gene-editing technique to eradication of HIV/AIDS. Gene Ther 2017; 24:377-384. [PMID: 28471431 DOI: 10.1038/gt.2017.35] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 01/25/2017] [Accepted: 02/01/2017] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) remains a major health hazard despite significant advances in prevention and treatment of HIV infection. The major reason for the persistence of HIV/AIDS is the inability of existing treatments to clear or eradicate the multiple HIV reservoirs that exist in the human body. To suppress the virus replication and rebound, HIV/AIDS patients must take life-long antiviral medications. The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system is an emerging gene-editing technique with the potential to eliminate or disrupt HIV-integrated genomes or HIV-infected cells from multiple HIV reservoirs, which could result in the complete cure of HIV/AIDS. Encouraging progress has already been reported for the application of the CRISPR/Cas9 technique to HIV/AIDS treatment and prevention, both in vitro in human patient cells and in vivo in animal model experiments. In this review, we will summarize the most recent progress in the application of the CRISPR/Cas9 gene-editing technique to HIV/AIDS therapy and elimination. Future directions and trends of such applications are also discussed.
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133
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Zhang H, McCarty N. CRISPR Editing in Biological and Biomedical Investigation. J Cell Biochem 2017; 118:4152-4162. [PMID: 28467679 PMCID: PMC7166568 DOI: 10.1002/jcb.26111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 05/02/2017] [Indexed: 12/27/2022]
Abstract
The revolutionary technology for genome editing known as the clustered regularly interspaced short palindromic repeat (CRISPR)‐CRISPR‐associated protein 9 (Cas9) system has sparked advancements in biological and biomedical research. The scientific breakthrough of the development of CRISPR‐Cas9 technology has allowed us to recapitulate human diseases by generating animal models of interest ranging from zebrafish to non‐human primates. The CRISPR‐Cas9 system can also be used to delineate the mechanisms underlying the development of human disorders and to precisely correct disease‐causing mutations. Repurposing this technology enables wider applications in transcriptome and epigenome manipulation and holds promise to reach the clinic. In this review, we highlight the latest advances of the CRISPR‐Cas9 system in different platforms and discuss the hurdles and challenges this technology is facing. J. Cell. Biochem. 118: 4152–4162, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Han Zhang
- Center for Stem Cell and Regenerative Disease, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas-Health Science Center at Houston, Houston, Texas, 77030
| | - Nami McCarty
- Center for Stem Cell and Regenerative Disease, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas-Health Science Center at Houston, Houston, Texas, 77030
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134
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Yin C, Zhang T, Qu X, Zhang Y, Putatunda R, Xiao X, Li F, Xiao W, Zhao H, Dai S, Qin X, Mo X, Young WB, Khalili K, Hu W. In Vivo Excision of HIV-1 Provirus by saCas9 and Multiplex Single-Guide RNAs in Animal Models. Mol Ther 2017; 25:1168-1186. [PMID: 28366764 PMCID: PMC5417847 DOI: 10.1016/j.ymthe.2017.03.012] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 02/05/2023] Open
Abstract
CRISPR-associated protein 9 (Cas9)-mediated genome editing provides a promising cure for HIV-1/AIDS; however, gene delivery efficiency in vivo remains an obstacle to overcome. Here, we demonstrate the feasibility and efficiency of excising the HIV-1 provirus in three different animal models using an all-in-one adeno-associated virus (AAV) vector to deliver multiplex single-guide RNAs (sgRNAs) plus Staphylococcus aureus Cas9 (saCas9). The quadruplex sgRNAs/saCas9 vector outperformed the duplex vector in excising the integrated HIV-1 genome in cultured neural stem/progenitor cells from HIV-1 Tg26 transgenic mice. Intravenously injected quadruplex sgRNAs/saCas9 AAV-DJ/8 excised HIV-1 proviral DNA and significantly reduced viral RNA expression in several organs/tissues of Tg26 mice. In EcoHIV acutely infected mice, intravenously injected quadruplex sgRNAs/saCas9 AAV-DJ/8 reduced systemic EcoHIV infection, as determined by live bioluminescence imaging. Additionally, this quadruplex vector induced efficient proviral excision, as determined by PCR genotyping in the liver, lungs, brain, and spleen. Finally, in humanized bone marrow/liver/thymus (BLT) mice with chronic HIV-1 infection, successful proviral excision was detected by PCR genotyping in the spleen, lungs, heart, colon, and brain after a single intravenous injection of quadruplex sgRNAs/saCas9 AAV-DJ/8. In conclusion, in vivo excision of HIV-1 proviral DNA by sgRNAs/saCas9 in solid tissues/organs can be achieved via AAV delivery, a significant step toward human clinical trials.
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MESH Headings
- Animals
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- Dependovirus/genetics
- Dependovirus/metabolism
- Disease Models, Animal
- Endonucleases/genetics
- Endonucleases/metabolism
- Gene Editing/methods
- Genetic Therapy/methods
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Genome, Viral
- HIV Infections/pathology
- HIV Infections/therapy
- HIV Infections/virology
- HIV Long Terminal Repeat
- HIV-1/genetics
- HIV-1/metabolism
- Humans
- Mice
- Mice, Transgenic
- Oligonucleotides/genetics
- Oligonucleotides/metabolism
- Proviruses/genetics
- Proviruses/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Staphylococcus aureus/chemistry
- Staphylococcus aureus/enzymology
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
- pol Gene Products, Human Immunodeficiency Virus/genetics
- pol Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Chaoran Yin
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Ting Zhang
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Xiying Qu
- Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Yonggang Zhang
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Raj Putatunda
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Xiao Xiao
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Fang Li
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Weidong Xiao
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Huaqing Zhao
- Department of Clinical Science, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Shen Dai
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Xuebin Qin
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Won-Bin Young
- Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA.
| | - Wenhui Hu
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA.
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135
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De Silva Feelixge HS, Jerome KR. Excision of Latent HIV-1 from Infected Cells In Vivo: An Important Step Forward. Mol Ther 2017; 25:1062-1064. [PMID: 28462817 DOI: 10.1016/j.ymthe.2017.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Laboratory Medicine, University of Washington, Seattle, WA 98105, USA.
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136
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Abstract
PURPOSE OF REVIEW Alternative approaches to conventional drug-based cancer treatments have seen T cell therapies deployed more widely over the last decade. This is largely due to their ability to target and kill specific cell types based on receptor recognition. Introduction of recombinant T cell receptors (TCRs) using viral vectors and HLA-independent T cell therapies using chimeric antigen receptors (CARs) are discussed. This article reviews the tools used for genome editing, with particular emphasis on the applications of site-specific DNA nuclease mediated editing for T cell therapies. RECENT FINDINGS Genetic engineering of T cells using TCRs and CARs with redirected antigen-targeting specificity has resulted in clinical success of several immunotherapies. In conjunction, the application of genome editing technologies has resulted in the generation of HLA-independent universal T cells for allogeneic transplantation, improved T cell sustainability through knockout of the checkpoint inhibitor, programmed cell death protein-1 (PD-1), and has shown efficacy as an antiviral therapy through direct targeting of viral genomic sequences and entry receptors. SUMMARY The combined use of engineered antigen-targeting moieties and innovative genome editing technologies have recently shown success in a small number of clinical trials targeting HIV and hematological malignancies and are now being incorporated into existing strategies for other immunotherapies.
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Affiliation(s)
- Juliette M. K. M. Delhove
- Molecular Immunology Unit, UCL Great Ormond Street Institute of Child Health, University College London (UCL), 30 Guilford Street, London, WC1N 1EH UK
| | - Waseem Qasim
- Molecular Immunology Unit, UCL Great Ormond Street Institute of Child Health, University College London (UCL), 30 Guilford Street, London, WC1N 1EH UK
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137
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Dlamini Z, Hull R. Can the HIV-1 splicing machinery be targeted for drug discovery? HIV AIDS-RESEARCH AND PALLIATIVE CARE 2017; 9:63-75. [PMID: 28331370 PMCID: PMC5354533 DOI: 10.2147/hiv.s120576] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
HIV-1 is able to express multiple protein types and isoforms from a single 9 kb mRNA transcript. These proteins are also expressed at particular stages of viral development, and this is achieved through the control of alternative splicing and the export of these transcripts from the nucleus. The nuclear export is controlled by the HIV protein Rev being required to transport incompletely spliced and partially spliced mRNA from the nucleus where they are normally retained. This implies a close relationship between the control of alternate splicing and the nuclear export of mRNA in the control of HIV-1 viral proliferation. This review discusses both the processes. The specificity and regulation of splicing in HIV-1 is controlled by the use of specific splice sites as well as exonic splicing enhancer and exonic splicing silencer sequences. The use of these silencer and enhancer sequences is dependent on the serine arginine family of proteins as well as the heterogeneous nuclear ribonucleoprotein family of proteins that bind to these sequences and increase or decrease splicing. Since alternative splicing is such a critical factor in viral development, it presents itself as a promising drug target. This review aims to discuss the inhibition of splicing, which would stall viral development, as an anti-HIV therapeutic strategy. In this review, the most recent knowledge of splicing in human immunodeficiency viral development and the latest therapeutic strategies targeting human immunodeficiency viral splicing are discussed.
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Affiliation(s)
- Zodwa Dlamini
- Research, Innovation & Engagements Portfolio, Mangosuthu University of Technology, Durban, South Africa
| | - Rodney Hull
- Research, Innovation & Engagements Portfolio, Mangosuthu University of Technology, Durban, South Africa
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138
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Song F, Stieger K. Optimizing the DNA Donor Template for Homology-Directed Repair of Double-Strand Breaks. MOLECULAR THERAPY. NUCLEIC ACIDS 2017. [PMID: 28624224 PMCID: PMC5363683 DOI: 10.1016/j.omtn.2017.02.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated proteins) technology enables rapid and precise genome editing at any desired genomic position in almost all cells and organisms. In this study, we analyzed the impact of different repair templates on the frequency of homology-directed repair (HDR) and non-homologous end joining (NHEJ). We used a stable HEK293 cell line expressing the traffic light reporter (TLR-3) system to quantify HDR and NHEJ events following transfection with Cas9, eight different guide RNAs, and a 1,000 bp donor template generated either as circular plasmid, as linearized plasmid with long 3′ or 5′ backbone overhang, or as PCR product. The sequence to be corrected was either centrally located (RS55), with a shorter 5′ homologous region (RS37), or with a shorter 3′ homologous region (RS73). Guide RNAs targeting the transcriptionally active strand (T5, T7) showed significantly higher NHEJ frequencies compared with guide RNAs targeting the transcriptionally inactive strand. HDR activity was highest when using the linearized plasmid with the short 5′ backbone overhang and the RS37 design. The results demonstrate the importance of the design of the guide RNA and template DNA on the frequency of DNA repair events and, ultimately, on the outcome of treatment approaches using HDR.
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Affiliation(s)
- Fei Song
- Department of Ophthalmology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University Giessen, 35392 Giessen, Germany.
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139
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Novel AIDS therapies based on gene editing. Cell Mol Life Sci 2017; 74:2439-2450. [PMID: 28210784 DOI: 10.1007/s00018-017-2479-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 01/20/2017] [Accepted: 01/30/2017] [Indexed: 01/03/2023]
Abstract
HIV/AIDS remains a major public health issue. In 2014, it was estimated that 36.9 million people are living with HIV worldwide, including 2.6 million children. Since the advent of combination antiretroviral therapy (cART), in the 1990s, treatment has been so successful that in many parts of the world, HIV has become a chronic condition in which progression to AIDS has become increasingly rare. However, while people with HIV can expect to live a normal life span with cART, lifelong medication is required and cardiovascular, renal, liver, and neurologic diseases are still possible, which continues to prompt research for a cure for HIV. Infected reservoir cells, such as CD4+ T cells and myeloid cells, allow persistence of HIV as an integrated DNA provirus and serve as a potential source for the re-emergence of virus. Attempts to eradicate HIV from these cells have focused mainly on the so-called "shock and kill" approach, where cellular reactivation is induced so as to trigger the purging of virus-producing cells by cytolysis or immune attack. This approach has several limitations and its usefulness in clinical applications remains to be assessed. Recent advances in gene-editing technology have allowed the use of this approach for inactivating integrated proviral DNA in the genome of latently infected cells or knocking out HIV receptors. Here, we review this strategy and its potential to eliminate the latent HIV reservoir resulting in a sterile cure of AIDS.
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Lebbink RJ, de Jong DCM, Wolters F, Kruse EM, van Ham PM, Wiertz EJHJ, Nijhuis M. A combinational CRISPR/Cas9 gene-editing approach can halt HIV replication and prevent viral escape. Sci Rep 2017; 7:41968. [PMID: 28176813 PMCID: PMC5296774 DOI: 10.1038/srep41968] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/30/2016] [Indexed: 01/05/2023] Open
Abstract
HIV presents one of the highest evolutionary rates ever detected and combination antiretroviral therapy is needed to overcome the plasticity of the virus population and control viral replication. Conventional treatments lack the ability to clear the latent reservoir, which remains the major obstacle towards a cure. Novel strategies, such as CRISPR/Cas9 gRNA-based genome-editing, can permanently disrupt the HIV genome. However, HIV genome-editing may accelerate viral escape, questioning the feasibility of the approach. Here, we demonstrate that CRISPR/Cas9 targeting of single HIV loci, only partially inhibits HIV replication and facilitates rapid viral escape at the target site. A combinatorial approach of two strong gRNAs targeting different regions of the HIV genome can completely abrogate viral replication and prevent viral escape. Our data shows that the accelerating effect of gene-editing on viral escape can be overcome and as such gene-editing may provide a future alternative for control of HIV-infection.
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Affiliation(s)
- Robert Jan Lebbink
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dorien C. M. de Jong
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Femke Wolters
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elisabeth M. Kruse
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Petra M. van Ham
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emmanuel J. H. J. Wiertz
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Monique Nijhuis
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Utrecht, The Netherlands
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141
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Menéndez-Arias L, Sebastián-Martín A, Álvarez M. Viral reverse transcriptases. Virus Res 2016; 234:153-176. [PMID: 28043823 DOI: 10.1016/j.virusres.2016.12.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/19/2016] [Accepted: 12/24/2016] [Indexed: 12/11/2022]
Abstract
Reverse transcriptases (RTs) play a major role in the replication of Retroviridae, Metaviridae, Pseudoviridae, Hepadnaviridae and Caulimoviridae. RTs are enzymes that are able to synthesize DNA using RNA or DNA as templates (DNA polymerase activity), and degrade RNA when forming RNA/DNA hybrids (ribonuclease H activity). In retroviruses and LTR retrotransposons (Metaviridae and Pseudoviridae), the coordinated action of both enzymatic activities converts single-stranded RNA into a double-stranded DNA that is flanked by identical sequences known as long terminal repeats (LTRs). RTs of retroviruses and LTR retrotransposons are active as monomers (e.g. murine leukemia virus RT), homodimers (e.g. Ty3 RT) or heterodimers (e.g. human immunodeficiency virus type 1 (HIV-1) RT). RTs lack proofreading activity and display high intrinsic error rates. Besides, high recombination rates observed in retroviruses are promoted by poor processivity that causes template switching, a hallmark of reverse transcription. HIV-1 RT inhibitors acting on its polymerase activity constitute the backbone of current antiretroviral therapies, although novel drugs, including ribonuclease H inhibitors, are still necessary to fight HIV infections. In Hepadnaviridae and Caulimoviridae, reverse transcription leads to the formation of nicked circular DNAs that will be converted into episomal DNA in the host cell nucleus. Structural and biochemical information on their polymerases is limited, although several drugs inhibiting HIV-1 RT are known to be effective against the human hepatitis B virus polymerase. In this review, we summarize current knowledge on reverse transcription in the five virus families and discuss available biochemical and structural information on RTs, including their biosynthesis, enzymatic activities, and potential inhibition.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Alba Sebastián-Martín
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mar Álvarez
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
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142
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Wang G, Zhao N, Berkhout B, Das AT. A Combinatorial CRISPR-Cas9 Attack on HIV-1 DNA Extinguishes All Infectious Provirus in Infected T Cell Cultures. Cell Rep 2016; 17:2819-2826. [PMID: 27974196 DOI: 10.1016/j.celrep.2016.11.057] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/07/2016] [Accepted: 11/18/2016] [Indexed: 01/24/2023] Open
Abstract
Current drug therapies effectively suppress HIV-1 replication but do not inactivate the provirus that persists in latent reservoirs. Recent studies have found that the guide RNA (gRNA)-directed CRISPR/Cas9 system can be used for sequence-specific attack on this proviral DNA. Although potent inhibition of virus replication was reported, HIV-1 can escape from a single antiviral gRNA by mutation of the target sequence. Here, we demonstrate that combinations of two antiviral gRNAs delay viral escape, and identify two gRNA combinations that durably block virus replication. When viral escape is prevented, repeated Cas9 cleavage leads to saturation of major mutations in the conserved target sequences that encode critical proteins. This hypermutation coincides with the loss of replication-competent virus as scored in sensitive co-cultures with unprotected cells, demonstrating complete virus inactivation. These results provide a proof-of-principle that HIV-1-infected cells can be functionally cured by dual-gRNA CRISPR/Cas9 treatment.
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Affiliation(s)
- Gang Wang
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Na Zhao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.
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143
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Abstract
To complete its life cycle, HIV-1 enters the nucleus of the host cell as reverse-transcribed viral DNA. The nucleus is a complex environment, in which chromatin is organized to support different structural and functional aspects of cell physiology. As such, it represents a challenge for an incoming viral genome, which needs to be integrated into cellular DNA to ensure productive infection. Integration of the viral genome into host DNA depends on the enzymatic activity of HIV-1 integrase and involves different cellular factors that influence the selection of integration sites. The selection of integration site has functional consequences for viral transcription, which usually follows the integration event. However, in resting CD4+ T cells, the viral genome can be silenced for long periods of time, which leads to the generation of a latent reservoir of quiescent integrated HIV-1 DNA. Integration represents the only nuclear event in the viral life cycle that can be pharmacologically targeted with current therapies, and the aspects that connect HIV-1 nuclear entry to HIV-1 integration and viral transcription are only beginning to be elucidated.
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Abstract
Despite significant advances in HIV drug treatment regimens, which grant near-normal life expectancies to infected individuals who have good virological control, HIV infection itself remains incurable. In recent years, novel gene- and cell-based therapies have gained increasing attention due to their potential to provide a functional or even sterilizing cure for HIV infection with a one-shot treatment. A functional cure would keep the infection in check and prevent progression to AIDS, while a sterilizing cure would eradicate all HIV viruses from the patient. Genome editing is the most precise form of gene therapy, able to achieve permanent genetic disruption, modification, or insertion at a predesignated genetic locus. The most well-studied candidate for anti-HIV genome editing is CCR5, an essential coreceptor for the majority of HIV strains, and the lack of which confers HIV resistance in naturally occurring homozygous individuals. Genetic disruption of CCR5 to treat HIV has undergone clinical testing, with seven completed or ongoing trials in T cells and hematopoietic stem and progenitor cells, and has shown promising safety and potential efficacy profiles. Here we summarize clinical findings of CCR5 editing for HIV therapy, as well as other genome editing-based approaches under pre-clinical development. The anticipated development of more sophisticated genome editing technologies should continue to benefit HIV cure efforts.
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Affiliation(s)
- Cathy X Wang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California , Los Angeles, California
| | - Paula M Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California , Los Angeles, California
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145
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Jerome KR. Disruption or Excision of Provirus as an Approach to HIV Cure. AIDS Patient Care STDS 2016; 30:551-555. [PMID: 27855263 DOI: 10.1089/apc.2016.0232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
An effective approach to HIV cure will almost certainly require a combination of strategies, including some means of reducing the latent HIV reservoir. Because the integrated HIV provirus represents the major source of viral persistence and reactivation, one attractive approach is the direct targeting of provirus for disruption or excision using targeted endonucleases, such as CRISPR/Cas9, zinc finger nucleases, TAL effector nucleases, or meganucleases (homing endonucleases). This article highlights some of the challenges for successful endonuclease therapy for HIV, including optimization of enzyme activity and specificity, the possible emergence of viral resistance, and most importantly, efficient in vivo delivery of the enzymes to a sufficient portion of the latent reservoir.
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Affiliation(s)
- Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, Washington
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146
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White MK, Hu W, Khalili K. Gene Editing Approaches against Viral Infections and Strategy to Prevent Occurrence of Viral Escape. PLoS Pathog 2016; 12:e1005953. [PMID: 27930735 PMCID: PMC5145235 DOI: 10.1371/journal.ppat.1005953] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Martyn K. White
- Department of Neuroscience, Center for Neurovirology and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, United States of America
| | - Wenhui Hu
- Department of Neuroscience, Center for Neurovirology and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, United States of America
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, United States of America
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147
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Attacking HIV-1 RNA versus DNA by sequence-specific approaches: RNAi versus CRISPR-Cas. Biochem Soc Trans 2016; 44:1355-1365. [DOI: 10.1042/bst20160060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 06/09/2016] [Accepted: 06/21/2016] [Indexed: 01/02/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection can be effectively controlled by potent antiviral drugs, but this never results in a cure. The patient should therefore take these drugs for the rest of his/her life, which can cause drug-resistance and adverse effects. Therefore, more durable therapeutic strategies should be considered, such as a stable gene therapy to protect the target T cells against HIV-1 infection. The development of potent therapeutic regimens based on the RNA interference (RNAi) and clustered regularly interspaced short palindromic repeats (CRISPR-Cas) mechanisms will be described, which can be delivered by lentiviral vectors. These mechanisms attack different forms of the viral genome, the RNA and DNA, respectively, but both mechanisms act in a strictly sequence-specific manner. Early RNAi experiments demonstrated profound virus inhibition, but also indicated that viral escape is possible. Such therapy failure can be prevented by the design of a combinatorial RNAi attack on the virus and this gene therapy is currently being tested in a preclinical humanized mouse model. Recent CRISPR-Cas studies also document robust virus inhibition, but suggest a novel viral escape route that is induced by the cellular nonhomologous end joining DNA repair pathway, which is activated by CRISPR-Cas-induced DNA breaks. We will compare these two approaches for durable HIV-1 suppression and discuss the respective advantages and disadvantages. The potential for future clinical applications will be described.
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148
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Buchholz F, Hauber J. Antiviral therapy of persistent viral infection using genome editing. Curr Opin Virol 2016; 20:85-91. [PMID: 27723558 DOI: 10.1016/j.coviro.2016.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/23/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023]
Abstract
Chronic viral infections are often incurable because current antiviral strategies do not target chromosomally integrated or non-replicating episomal viral genomes. The rapid development of technologies for genome editing may possibly soon allow for therapeutic targeting of viral genomes and, hence, for development of curative strategies for persistent viral infection. However, detailed investigation of different antiviral genome editing approaches recently revealed various undesired effects. In particular, the problem of frequent and swift development of resistant viruses has to be thoroughly analysed before genome editing approaches become an established option for antiviral treatment.
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Affiliation(s)
- Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Am Tatzberg 47/49, D-01307 Dresden, Germany
| | - Joachim Hauber
- Heinrich Pette Institute - Leibniz Institute for Experimental Virology, Martinistrasse 52, D-20251 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg, Germany.
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149
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Mann J, Pasternak AO, Chahroudi A, Singh JA, Ross AL. The latest science from the IAS Towards an HIV Cure Symposium: 16-17 July 2016, Durban, South Africa. J Virus Erad 2016; 2:235-241. [PMID: 27781107 PMCID: PMC5075352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Jaclyn Mann
- HIV Pathogenesis Programme,
University of KwaZulu-Natal,
Durban,
South Africa
| | - Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology,
Academic Medical Center of the University of Amsterdam,
the Netherlands
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine,
Atlanta,
Georgia,
USA
| | | | - Anna Laura Ross
- International and Scientific Relations, ANRS,
Paris,
France,Corresponding author: Anna Laura Ross,
International and Scientific Relations, ANRS,
101 rue de Tolbiac,
75013Paris,
France
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