1
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Zhang H, Wang H, An Y, Chen Z. Construction and application of adenoviral vectors. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102027. [PMID: 37808925 PMCID: PMC10556817 DOI: 10.1016/j.omtn.2023.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Adenoviral vectors have been widely used as vaccine candidates or potential vaccine candidates against infectious diseases due to the convenience of genome manipulation, their ability to accommodate large exogenous gene fragments, easy access of obtaining high-titer of virus, and high efficiency of transduction. At the same time, adenoviral vectors have also been used extensively in clinical research for cancer gene therapy and treatment of diseases caused by a single gene defect. However, application of adenovirus also faces a series of challenges such as poor targeting, strong immune response against the vector itself, and they cannot be used repeatedly. It is believed that these problems will be solved gradually with further research and technological development in related fields. Here, we review the construction methods of adenoviral vectors, including "gutless" adenovirus and discuss application of adenoviral vectors as prophylactic vaccines for infectious pathogens and their application prospects as therapeutic vaccines for cancer and other kinds of chronic infectious disease such as human papillomavirus, hepatitis B virus, and hepatitis C virus.
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Affiliation(s)
- Hongbo Zhang
- Department of Basic Research, Ab&B Bio-Tech CO., LTD. JS, Taizhou, Jiangsu, China
| | - Hongdan Wang
- Department of Basic Research, Ab&B Bio-Tech CO., LTD. JS, Taizhou, Jiangsu, China
| | - Youcai An
- Department of Basic Research, Ab&B Bio-Tech CO., LTD. JS, Taizhou, Jiangsu, China
| | - Ze Chen
- Department of Basic Research, Ab&B Bio-Tech CO., LTD. JS, Taizhou, Jiangsu, China
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2
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Li C, Georgakopoulou A, Newby GA, Chen PJ, Everette KA, Paschoudi K, Vlachaki E, Gil S, Anderson AK, Koob T, Huang L, Wang H, Kiem HP, Liu DR, Yannaki E, Lieber A. In vivo HSC prime editing rescues sickle cell disease in a mouse model. Blood 2023; 141:2085-2099. [PMID: 36800642 PMCID: PMC10163316 DOI: 10.1182/blood.2022018252] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/19/2023] Open
Abstract
Sickle cell disease (SCD) is a monogenic disease caused by a nucleotide mutation in the β-globin gene. Current gene therapy studies are mainly focused on lentiviral vector-mediated gene addition or CRISPR/Cas9-mediated fetal globin reactivation, leaving the root cause unfixed. We developed a vectorized prime editing system that can directly repair the SCD mutation in hematopoietic stem cells (HSCs) in vivo in a SCD mouse model (CD46/Townes mice). Our approach involved a single intravenous injection of a nonintegrating, prime editor-expressing viral vector into mobilized CD46/Townes mice and low-dose drug selection in vivo. This procedure resulted in the correction of ∼40% of βS alleles in HSCs. On average, 43% of sickle hemoglobin was replaced by adult hemoglobin, thereby greatly mitigating the SCD phenotypes. Transplantation in secondary recipients demonstrated that long-term repopulating HSCs were edited. Highly efficient target site editing was achieved with minimal generation of insertions and deletions and no detectable off-target editing. Because of its simplicity and portability, our in vivo prime editing approach has the potential for application in resource-poor countries where SCD is prevalent.
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Affiliation(s)
- Chang Li
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Aphrodite Georgakopoulou
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Peter J. Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Kelcee A. Everette
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Kiriaki Paschoudi
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Efthymia Vlachaki
- Hematological Laboratory, Second Department of Internal Medicine, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, Hippokration General Hospital, Thessaloniki, Greece
| | - Sucheol Gil
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Anna K. Anderson
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Theodore Koob
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Lishan Huang
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Hongjie Wang
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Hans-Peter Kiem
- Stem and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Evangelia Yannaki
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
| | - André Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
- Department of Pathology, University of Washington, Seattle, WA
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3
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Kraus C, Sontheimer EJ. Applications of Anti-CRISPR Proteins in Genome Editing and Biotechnology. J Mol Biol 2023; 435:168120. [PMID: 37100169 DOI: 10.1016/j.jmb.2023.168120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
In the ten years since the discovery of the first anti-CRISPR (Acr) proteins, the number of validated Acrs has expanded rapidly, as has our understanding of the diverse mechanisms they employ to suppress natural CRISPR-Cas immunity. Many, though not all, function via direct, specific interaction with Cas protein effectors. The abilities of Acr proteins to modulate the activities and properties of CRISPR-Cas effectors have been exploited for an ever-increasing spectrum of biotechnological uses, most of which involve the establishment of control over genome editing systems. This control can be used to minimize off-target editing, restrict editing based on spatial, temporal, or conditional cues, limit the spread of gene drive systems, and select for genome-edited bacteriophages. Anti-CRISPRs have also been developed to overcome bacterial immunity, facilitate viral vector production, control synthetic gene circuits, and other purposes. The impressive and ever-growing diversity of Acr inhibitory mechanisms will continue to allow the tailored applications of Acrs.
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Affiliation(s)
| | - Erik J Sontheimer
- RNA Therapeutics Institute; Program in Molecular Medicine, and; Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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4
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Zakrzewska M, Burmistrz M. Mechanisms regulating the CRISPR-Cas systems. Front Microbiol 2023; 14:1060337. [PMID: 36925473 PMCID: PMC10013973 DOI: 10.3389/fmicb.2023.1060337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/10/2023] [Indexed: 03/08/2023] Open
Abstract
The CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR associated proteins) is a prokaryotic system that enables sequence specific recognition and cleavage of nucleic acids. This is possible due to cooperation between CRISPR array which contains short fragments of DNA called spacers that are complimentary to the targeted nucleic acid and Cas proteins, which take part in processes of: acquisition of new spacers, processing them into their functional form as well as recognition and cleavage of targeted nucleic acids. The primary role of CRISPR-Cas systems is to provide their host with an adaptive and hereditary immunity against exogenous nucleic acids. This system is present in many variants in both Bacteria and Archea. Due to its modular structure, and programmability CRISPR-Cas system become attractive tool for modern molecular biology. Since their discovery and implementation, the CRISPR-Cas systems revolutionized areas of gene editing and regulation of gene expression. Although our knowledge on how CRISPR-Cas systems work has increased rapidly in recent years, there is still little information on how these systems are controlled and how they interact with other cellular mechanisms. Such regulation can be the result of both auto-regulatory mechanisms as well as exogenous proteins of phage origin. Better understanding of these interaction networks would be beneficial for optimization of current and development of new CRISPR-Cas-based tools. In this review we summarize current knowledge on the various molecular mechanisms that affect activity of CRISPR-Cas systems.
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Affiliation(s)
- Marta Zakrzewska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland.,Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michal Burmistrz
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Warsaw, Poland
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5
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Li C, Georgakopoulou A, Newby GA, Everette KA, Nizamis E, Paschoudi K, Vlachaki E, Gil S, Anderson AK, Koob T, Huang L, Wang H, Kiem HP, Liu DR, Yannaki E, Lieber A. In vivo base editing by a single i.v. vector injection for treatment of hemoglobinopathies. JCI Insight 2022; 7:e162939. [PMID: 36006707 PMCID: PMC9675455 DOI: 10.1172/jci.insight.162939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Individuals with β-thalassemia or sickle cell disease and hereditary persistence of fetal hemoglobin (HPFH) possessing 30% fetal hemoglobin (HbF) appear to be symptom free. Here, we used a nonintegrating HDAd5/35++ vector expressing a highly efficient and accurate version of an adenine base editor (ABE8e) to install, in vivo, a -113 A>G HPFH mutation in the γ-globin promoters in healthy CD46/β-YAC mice carrying the human β-globin locus. Our in vivo hematopoietic stem cell (HSC) editing/selection strategy involves only s.c. and i.v. injections and does not require myeloablation and HSC transplantation. In vivo HSC base editing in CD46/β-YAC mice resulted in > 60% -113 A>G conversion, with 30% γ-globin of β-globin expressed in 70% of erythrocytes. Importantly, no off-target editing at sites predicted by CIRCLE-Seq or in silico was detected. Furthermore, no critical alterations in the transcriptome of in vivo edited mice were found by RNA-Seq. In vitro, in HSCs from β-thalassemia and patients with sickle cell disease, transduction with the base editor vector mediated efficient -113 A>G conversion and reactivation of γ-globin expression with subsequent phenotypic correction of erythroid cells. Because our in vivo base editing strategy is safe and technically simple, it has the potential for clinical application in developing countries where hemoglobinopathies are prevalent.
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Affiliation(s)
- Chang Li
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Aphrodite Georgakopoulou
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Chemistry and Chemical Biology and
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Kelcee A. Everette
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Chemistry and Chemical Biology and
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Evangelos Nizamis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Kiriaki Paschoudi
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Efthymia Vlachaki
- Hematological Laboratory, Second Department of Internal Medicine, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, Hippokration General Hospital, Thessaloniki, Greece
| | - Sucheol Gil
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Anna K. Anderson
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Theodore Koob
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Lishan Huang
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Hongjie Wang
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Hans-Peter Kiem
- Stem and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Chemistry and Chemical Biology and
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Evangelia Yannaki
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
| | - André Lieber
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
- Department of Pathology, University of Washington, Seattle, Washington, USA
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6
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Jacobs R, Singh P, Smith T, Arbuthnot P, Maepa MB. Prospects of viral vector-mediated delivery of sequences encoding anti-HBV designer endonucleases. Gene Ther 2022:10.1038/s41434-022-00342-5. [PMID: 35606493 DOI: 10.1038/s41434-022-00342-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/09/2022]
Abstract
Available treatment for chronic hepatitis B virus (HBV) infection offers modest functional curative efficacy. The viral replicative intermediate comprising covalently closed circular DNA (cccDNA) is responsible for persistent chronic HBV infection. Hence, current efforts have focused on developing therapies that disable cccDNA. Employing gene editing tools has emerged as an attractive strategy, with the end goal of establishing permanently inactivated cccDNA. Although anti-HBV designer nucleases are effective in vivo, none has yet progressed to clinical trial. Lack of safe and efficient delivery systems remains the limiting factor. Several vectors may be used to deliver anti-HBV gene editor-encoding sequences, with viral vectors being at the forefront. Despite the challenges associated with packaging large gene editor-encoding sequences into viral vectors, advancement in the field is overcoming such limitations. Translation of viral vector-mediated gene editing against HBV to clinical application is within reach. This review discusses the prospects of delivering HBV targeted designer nucleases using viral vectors.
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Affiliation(s)
- Ridhwaanah Jacobs
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Prashika Singh
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tiffany Smith
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mohube Betty Maepa
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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7
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Cui YR, Wang SJ, Ma T, Yu P, Chen J, Guo T, Meng G, Jiang B, Dong J, Liu J. KPT330 improves Cas9 precision genome- and base-editing by selectively regulating mRNA nuclear export. Commun Biol 2022; 5:237. [PMID: 35301428 PMCID: PMC8931069 DOI: 10.1038/s42003-022-03188-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 02/22/2022] [Indexed: 12/21/2022] Open
Abstract
CRISPR-based genome engineering tools are associated with off-target effects that constitutively active Cas9 protein may instigate. Previous studies have revealed the feasibility of modulating Cas9-based genome- and base-editing tools using protein or small-molecule CRISPR inhibitors. Here we screened a set of small molecule compounds with irreversible warhead, aiming to identifying small-molecule modulators of CRISPR-Cas9. It was found that selective inhibitors of nuclear export (SINEs) could efficiently inhibit the cellular activity of Cas9 in the form of genome-, base- and prime-editing tools. Interestingly, SINEs did not function as direct inhibitors to Cas9, but modulated Cas9 activities by interfering with the nuclear export process of Cas9 mRNA. Thus, to the best of our knowledge, SINEs represent the first reported indirect, irreversible inhibitors of CRISPR-Cas9. Most importantly, an FDA-approved anticancer drug KPT330, along with other examined SINEs, could improve the specificities of CRISPR-Cas9-based genome- and base editing tools in human cells. Our study expands the toolbox of CRISPR modulating elements and provides a feasible approach to improving the specificity of CRISPR-Cas9-based genome engineering tools. The FDA-approved anti-cancer drug, KPT330, can indirectly inhibit Cas9 by interfering with Cas9 mRNA nuclear export and help reduce off-target editing in cells.
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Affiliation(s)
- Yan-Ru Cui
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Shao-Jie Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Tiancheng Ma
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, 200032, Shanghai, China
| | - Peihong Yu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Taijie Guo
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, 200032, Shanghai, China
| | - Genyi Meng
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, 200032, Shanghai, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Jiajia Dong
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, 200032, Shanghai, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. .,Shanghai Clinical Research and Trial Center, 201210, Shanghai, China. .,Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. .,Guangzhou Laboratory, Guangzhou International Bio Island, No. 9 XingDaoHuanBei Road, 510005, Guangzhou, Guangdong, China.
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8
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Self-inactivating, all-in-one AAV vectors for precision Cas9 genome editing via homology-directed repair in vivo. Nat Commun 2021; 12:6267. [PMID: 34725353 PMCID: PMC8560862 DOI: 10.1038/s41467-021-26518-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 10/06/2021] [Indexed: 12/26/2022] Open
Abstract
Adeno-associated virus (AAV) vectors are important delivery platforms for therapeutic genome editing but are severely constrained by cargo limits. Simultaneous delivery of multiple vectors can limit dose and efficacy and increase safety risks. Here, we describe single-vector, ~4.8-kb AAV platforms that express Nme2Cas9 and either two sgRNAs for segmental deletions, or a single sgRNA with a homology-directed repair (HDR) template. We also use anti-CRISPR proteins to enable production of vectors that self-inactivate via Nme2Cas9 cleavage. We further introduce a nanopore-based sequencing platform that is designed to profile rAAV genomes and serves as a quality control measure for vector homogeneity. We demonstrate that these platforms can effectively treat two disease models [type I hereditary tyrosinemia (HT-I) and mucopolysaccharidosis type I (MPS-I)] in mice by HDR-based correction of the disease allele. These results will enable the engineering of single-vector AAVs that can achieve diverse therapeutic genome editing outcomes. Long-term expression of Cas9 following precision genome editing in vivo may lead to undesirable consequences. Here we show that a single-vector, self-inactivating AAV system containing Cas9 nuclease, guide, and DNA donor can use homology-directed repair to correct disease mutations in vivo.
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9
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Jia N, Patel DJ. Structure-based functional mechanisms and biotechnology applications of anti-CRISPR proteins. Nat Rev Mol Cell Biol 2021; 22:563-579. [PMID: 34089013 DOI: 10.1038/s41580-021-00371-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2021] [Indexed: 02/03/2023]
Abstract
CRISPR loci and Cas proteins provide adaptive immunity in prokaryotes against invading bacteriophages and plasmids. In response, bacteriophages have evolved a broad spectrum of anti-CRISPR proteins (anti-CRISPRs) to counteract and overcome this immunity pathway. Numerous anti-CRISPRs have been identified to date, which suppress single-subunit Cas effectors (in CRISPR class 2, type II, V and VI systems) and multisubunit Cascade effectors (in CRISPR class 1, type I and III systems). Crystallography and cryo-electron microscopy structural studies of anti-CRISPRs bound to effector complexes, complemented by functional experiments in vitro and in vivo, have identified four major CRISPR-Cas suppression mechanisms: inhibition of CRISPR-Cas complex assembly, blocking of target binding, prevention of target cleavage, and degradation of cyclic oligonucleotide signalling molecules. In this Review, we discuss novel mechanistic insights into anti-CRISPR function that have emerged from X-ray crystallography and cryo-electron microscopy studies, and how these structures in combination with function studies provide valuable tools for the ever-growing CRISPR-Cas biotechnology toolbox, to be used for precise and robust genome editing and other applications.
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Affiliation(s)
- Ning Jia
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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10
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Modell AE, Siriwardena SU, Shoba VM, Li X, Choudhary A. Chemical and optical control of CRISPR-associated nucleases. Curr Opin Chem Biol 2020; 60:113-121. [PMID: 33253976 DOI: 10.1016/j.cbpa.2020.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system of bacteria has furnished programmable nucleases (e.g., Cas9) that are transforming the field of genome editing with applications in basic and biomedical research, biotechnology, and agriculture. However, broader real-world applications of Cas9 require precision control of its activity over dose, time, and space as off-target effects, embryonic mosaicism, chromosomal translocations, and genotoxicity have been observed with elevated and/or prolonged nuclease activity. Here, we review chemical and optical methods for precision control of Cas9's activity.
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Affiliation(s)
- Ashley E Modell
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Sachini U Siriwardena
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Veronika M Shoba
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Xing Li
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA.
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11
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Boucher P, Cui X, Curiel DT. Adenoviral vectors for in vivo delivery of CRISPR-Cas gene editors. J Control Release 2020; 327:788-800. [PMID: 32891680 PMCID: PMC8091654 DOI: 10.1016/j.jconrel.2020.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022]
Abstract
Harnessing the bacterial clustered regularly interspaced short palindromic repeats (CRISPR) system for genome editing in eukaryotes has revolutionized basic biomedical research and translational sciences. The ability to create targeted alterations of the genome through this easy to design system has presented unprecedented opportunities to treat inherited disorders and other diseases such as cancer through gene therapy. A major hurdle is the lack of an efficient and safe in vivo delivery system, limiting most of the current gene therapy efforts to ex vivo editing of extracted cells. Here we discuss the unique features of adenoviral vectors that enable tissue specific and efficient delivery of the CRISPR-Cas machinery for in vivo genome editing.
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Affiliation(s)
- Paul Boucher
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in Saint Louis, St. Louis, MO 63130, USA; Division of Cancer Biology, Department of Radiation Oncology, School of Medicine, Washington University in Saint Louis, St. Louis, MO 63110, USA
| | - Xiaoxia Cui
- Genome Engineering & iPSC Center, Department of Genetics, School of Medicine, Washington University in Saint Louis, St. Louis, MO 63110, USA
| | - David T Curiel
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in Saint Louis, St. Louis, MO 63130, USA; Division of Cancer Biology, Department of Radiation Oncology, School of Medicine, Washington University in Saint Louis, St. Louis, MO 63110, USA; Biologic Therapeutics Center, Department of Radiation Oncology, School of Medicine, Washington University in Saint Louis, St. Louis, MO 63110, USA.
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12
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Davidson AR, Lu WT, Stanley SY, Wang J, Mejdani M, Trost CN, Hicks BT, Lee J, Sontheimer EJ. Anti-CRISPRs: Protein Inhibitors of CRISPR-Cas Systems. Annu Rev Biochem 2020; 89:309-332. [PMID: 32186918 PMCID: PMC9718424 DOI: 10.1146/annurev-biochem-011420-111224] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) together with their accompanying cas (CRISPR-associated) genes are found frequently in bacteria and archaea, serving to defend against invading foreign DNA, such as viral genomes. CRISPR-Cas systems provide a uniquely powerful defense because they can adapt to newly encountered genomes. The adaptive ability of these systems has been exploited, leading to their development as highly effective tools for genome editing. The widespread use of CRISPR-Cas systems has driven a need for methods to control their activity. This review focuses on anti-CRISPRs (Acrs), proteins produced by viruses and other mobile genetic elements that can potently inhibit CRISPR-Cas systems. Discovered in 2013, there are now 54 distinct families of these proteins described, and the functional mechanisms of more than a dozen have been characterized in molecular detail. The investigation of Acrs is leading to a variety of practical applications and is providing exciting new insight into the biology of CRISPR-Cas systems.
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Affiliation(s)
- Alan R Davidson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Wang-Ting Lu
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Sabrina Y Stanley
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
| | - Jingrui Wang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
| | - Marios Mejdani
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Chantel N Trost
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
| | - Brian T Hicks
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Jooyoung Lee
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; ,
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; ,
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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13
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Oncolytic Adenoviruses: Strategies for Improved Targeting and Specificity. Cancers (Basel) 2020; 12:cancers12061504. [PMID: 32526919 PMCID: PMC7352392 DOI: 10.3390/cancers12061504] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer is a major health problem. Most of the treatments exhibit systemic toxicity, as they are not targeted or specific to cancerous cells and tumors. Adenoviruses are very promising gene delivery vectors and have immense potential to deliver targeted therapy. Here, we review a wide range of strategies that have been tried, tested, and demonstrated to enhance the specificity of oncolytic viruses towards specific cancer cells. A combination of these strategies and other conventional therapies may be more effective than any of those strategies alone.
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14
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Marino ND, Pinilla-Redondo R, Csörgő B, Bondy-Denomy J. Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies. Nat Methods 2020; 17:471-479. [DOI: 10.1038/s41592-020-0771-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/05/2020] [Indexed: 12/20/2022]
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15
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Cui YR, Wang SJ, Chen J, Li J, Chen W, Wang S, Meng B, Zhu W, Zhang Z, Yang B, Jiang B, Yang G, Ma P, Liu J. Allosteric inhibition of CRISPR-Cas9 by bacteriophage-derived peptides. Genome Biol 2020; 21:51. [PMID: 32102684 PMCID: PMC7045643 DOI: 10.1186/s13059-020-01956-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/10/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND CRISPR-Cas9 has been developed as a therapeutic agent for various infectious and genetic diseases. In many clinically relevant applications, constitutively active CRISPR-Cas9 is delivered into human cells without a temporal control system. Excessive and prolonged expression of CRISPR-Cas9 can lead to elevated off-target cleavage. The need for modulating CRISPR-Cas9 activity over time and dose has created the demand of developing CRISPR-Cas off switches. Protein and small molecule-based CRISPR-Cas inhibitors have been reported in previous studies. RESULTS We report the discovery of Cas9-inhibiting peptides from inoviridae bacteriophages. These peptides, derived from the periplasmic domain of phage major coat protein G8P (G8PPD), can inhibit the in vitro activity of Streptococcus pyogenes Cas9 (SpCas9) proteins in an allosteric manner. Importantly, the inhibitory activity of G8PPD on SpCas9 is dependent on the order of guide RNA addition. Ectopic expression of full-length G8P (G8PFL) or G8PPD in human cells can inactivate the genome-editing activity of SpyCas9 with minimum alterations of the mutation patterns. Furthermore, unlike the anti-CRISPR protein AcrII4A that completely abolishes the cellular activity of CRISPR-Cas9, G8P co-transfection can reduce the off-target activity of co-transfected SpCas9 while retaining its on-target activity. CONCLUSION G8Ps discovered in the current study represent the first anti-CRISPR peptides that can allosterically inactivate CRISPR-Cas9. This finding may provide insights into developing next-generation CRISPR-Cas inhibitors for precision genome engineering.
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Affiliation(s)
- Yan-Ru Cui
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shao-Jie Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhang Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bing Meng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Wei Zhu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Zhuhong Zhang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 264005, Yantai, Shandong, People's Republic of China
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
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Palmer DJ, Turner DL, Ng P. A Single "All-in-One" Helper-Dependent Adenovirus to Deliver Donor DNA and CRISPR/Cas9 for Efficient Homology-Directed Repair. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:441-447. [PMID: 32154329 PMCID: PMC7058846 DOI: 10.1016/j.omtm.2020.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/28/2020] [Indexed: 11/19/2022]
Abstract
In this study, we developed a single helper-dependent adenovirus (HDAd) to deliver all of the components (donor DNA, CRISPR-associated protein 9 [Cas9], and guide RNA [gRNA]) needed to achieve high-efficiency gene targeting and homology-directed repair in transduced cells. We show that these "all-in-one" HDAds are up to 117-fold more efficient at gene targeting than donor HDAds that do not express CRISPR/Cas9 in human induced pluripotent stem cells (iPSCs). The vast majority (>90%) of targeted recombinants had only one allele targeted, and this was accompanied by high-frequency indel formation in the non-targeted allele at the site of Cas9 cleavage. These indels varied in size and nature, and included large deletions of ∼8 kb. The remaining minority of recombinants had both alleles targeted (so-called bi-allelic targeting). These all-in-one HDAds represent an important platform for accomplishing and expanding the utility of homology-directed repair, especially for difficult-to-transfect cells and for in vivo applications.
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Affiliation(s)
- Donna J. Palmer
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Dustin L. Turner
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Philip Ng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Corresponding author: Philip Ng, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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Li C, Lieber A. Adenovirus vectors in hematopoietic stem cell genome editing. FEBS Lett 2019; 593:3623-3648. [PMID: 31705806 PMCID: PMC10473235 DOI: 10.1002/1873-3468.13668] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/23/2019] [Accepted: 10/27/2019] [Indexed: 12/13/2022]
Abstract
Genome editing of hematopoietic stem cells (HSCs) represents a therapeutic option for a number of hematological genetic diseases, as HSCs have the potential for self-renewal and differentiation into all blood cell lineages. This review presents advances of genome editing in HSCs utilizing adenovirus vectors as delivery vehicles. We focus on capsid-modified, helper-dependent adenovirus vectors that are devoid of all viral genes and therefore exhibit an improved safety profile. We discuss HSC genome engineering for several inherited disorders and infectious diseases including hemoglobinopathies, Fanconi anemia, hemophilia, and HIV-1 infection by ex vivo and in vivo editing in transgenic mice, nonhuman primates, as well as in human CD34+ cells. Mechanisms of therapeutic gene transfer including episomal expression of designer nucleases and base editors, transposase-mediated random integration, and targeted homology-directed repair triggered integration into selected genomic safe harbor loci are also reviewed.
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Affiliation(s)
- Chang Li
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - André Lieber
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
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