51
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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: 192] [Impact Index Per Article: 27.4] [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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52
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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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53
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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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54
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Exploring the potential of genome editing CRISPR-Cas9 technology. Gene 2017; 599:1-18. [DOI: 10.1016/j.gene.2016.11.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/18/2016] [Accepted: 11/06/2016] [Indexed: 12/26/2022]
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55
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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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56
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Kaminski R, Chen Y, Salkind J, Bella R, Young WB, Ferrante P, Karn J, Malcolm T, Hu W, Khalili K. Negative Feedback Regulation of HIV-1 by Gene Editing Strategy. Sci Rep 2016; 6:31527. [PMID: 27528385 PMCID: PMC4985742 DOI: 10.1038/srep31527] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/20/2016] [Indexed: 12/21/2022] Open
Abstract
The CRISPR/Cas9 gene editing method is comprised of the guide RNA (gRNA) to target a specific DNA sequence for cleavage and the Cas9 endonuclease for introducing breaks in the double-stranded DNA identified by the gRNA. Co-expression of both a multiplex of HIV-1-specific gRNAs and Cas9 in cells results in the modification and/or excision of the segment of viral DNA, leading to replication-defective virus. In this study, we have personalized the activity of CRISPR/Cas9 by placing the gene encoding Cas9 under the control of a minimal promoter of HIV-1 that is activated by the HIV-1 Tat protein. We demonstrate that functional activation of CRISPR/Cas9 by Tat during the course of viral infection excises the designated segment of the integrated viral DNA and consequently suppresses viral expression. This strategy was also used in a latently infected CD4+ T-cell model after treatment with a variety of HIV-1 stimulating agents including PMA and TSA. Controlled expression of Cas9 by Tat offers a new strategy for safe implementation of the Cas9 technology for ablation of HIV-1 at a very early stage of HIV-1 replication during the course of the acute phase of infection and the reactivation of silent proviral DNA in latently infected cells.
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Affiliation(s)
- Rafal Kaminski
- Department of Neuroscience Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, 7th Floor Philadelphia, PA 19140, USA
| | - Yilan Chen
- Department of Neuroscience Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, 7th Floor Philadelphia, PA 19140, USA
| | - Julian Salkind
- Department of Neuroscience Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, 7th Floor Philadelphia, PA 19140, USA
| | - Ramona Bella
- Department of Neuroscience Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, 7th Floor Philadelphia, PA 19140, USA
| | - Won-Bin Young
- Department of Radiology University of Pittsburgh School of Medicine Pittsburgh, PA 15219, USA
| | - Pasquale Ferrante
- Department of Neuroscience Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, 7th Floor Philadelphia, PA 19140, USA.,Microbiology and Clinical Microbiology, Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Thomas Malcolm
- Excision Biotherapeutics, Inc., 3624 Market Street, #514, Philadelphia, PA 19104, USA
| | - Wenhui Hu
- Department of Neuroscience Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, 7th Floor Philadelphia, PA 19140, USA
| | - Kamel Khalili
- Department of Neuroscience Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, 7th Floor Philadelphia, PA 19140, USA
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57
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Liang C, Wainberg MA, Das AT, Berkhout B. CRISPR/Cas9: a double-edged sword when used to combat HIV infection. Retrovirology 2016; 13:37. [PMID: 27230886 PMCID: PMC4882869 DOI: 10.1186/s12977-016-0270-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023] Open
Affiliation(s)
- Chen Liang
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC, H3T1E2, Canada. .,Departments of Medicine, Microbiology and Immunology, McGill University, Montreal, QC, H3A 2B4, Canada.
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC, H3T1E2, Canada.,Departments of Medicine, Microbiology and Immunology, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 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, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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