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Kovacs CJ, Antonacci A, Graham A, Jessup F, Rankin W, Brasko B, Maguire F, Washington MA, Kua SC, Burpo FJ, Barnhill JC. Comparing Methods to Genetically Engineer Bacteriophage and Increase Host Range. Mil Med 2024; 189:e1488-e1496. [PMID: 38780999 DOI: 10.1093/milmed/usae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/15/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
INTRODUCTION Antibacterial resistance is an emerging problem in military medicine. Disruptions to the health care systems in war-torn countries that result from ongoing conflict can potentially exacerbate this problem and increase the risk to U.S. forces in the deployed environment. Therefore, novel therapies are needed to mitigate the impact of these potentially devastating infections on military operations. Bacteriophages are viruses that infect and kill bacteria. They can be delivered as therapeutic agents and offer a promising alternative to traditional antibiotic chemotherapy. There are several potential benefits to their use, including high specificity and comparative ease of use in the field setting. However, the process of engineering phages for military medical applications can be a laborious and time-consuming endeavor. This review examines available techniques and compares their efficacy. MATERIALS AND METHODS This review evaluates the scientific literature on the development and application of four methods of bacteriophage genome engineering and their consideration in the context of military applications. Preffered Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed for a systematic review of available literature that met criteria for analysis and inclusion. The research completed for this review article originated from the United States Military Academy's library "Scout" search engine, which compiles results from 254 available databases (including PubMed, Google Scholar, and SciFinder). Particular attention was focused on identifying useful mechanistic insight into the nature of the engineering technique, the ease of use, and the applicability of the technique to countering the problem of antimicrobial resistance in the military setting. RESULTS A total of 52 studies were identified that met inclusion criteria following PRISMA guidelines. The bioengineering techniques analyzed included homologous recombination (12 articles), in vivo recombineering (9 articles), bacteriophage recombineering of electroporated DNA (7 articles), and the CRISPR-Cas system (10 articles). Rates of success and fidelity varied across each platform, and comparative benefits and drawbacks are considered. CONCLUSIONS Each of the phage engineering techniques addressed herein varies in amount of effort and overall success rate. CRISPR-Cas-facilitated modification of phage genomes presents a highly efficient method that does not require a lengthy purification and screening process. It therefore appears to be the method best suited for military medical applications.
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Affiliation(s)
- Christopher J Kovacs
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Alessia Antonacci
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Abigail Graham
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Faye Jessup
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - William Rankin
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Brianna Brasko
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Fiona Maguire
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Michael A Washington
- Department of Clinical Investigation, Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA 30905, USA
| | - Siang C Kua
- Department of Clinical Investigation, Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA 30905, USA
| | - F John Burpo
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Jason C Barnhill
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
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2
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Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
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Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Leal AF, Herreno-Pachón AM, Benincore-Flórez E, Karunathilaka A, Tomatsu S. Current Strategies for Increasing Knock-In Efficiency in CRISPR/Cas9-Based Approaches. Int J Mol Sci 2024; 25:2456. [PMID: 38473704 PMCID: PMC10931195 DOI: 10.3390/ijms25052456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Since its discovery in 2012, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) system has supposed a promising panorama for developing novel and highly precise genome editing-based gene therapy (GT) alternatives, leading to overcoming the challenges associated with classical GT. Classical GT aims to deliver transgenes to the cells via their random integration in the genome or episomal persistence into the nucleus through lentivirus (LV) or adeno-associated virus (AAV), respectively. Although high transgene expression efficiency is achieved by using either LV or AAV, their nature can result in severe side effects in humans. For instance, an LV (NCT03852498)- and AAV9 (NCT05514249)-based GT clinical trials for treating X-linked adrenoleukodystrophy and Duchenne Muscular Dystrophy showed the development of myelodysplastic syndrome and patient's death, respectively. In contrast with classical GT, the CRISPR/Cas9-based genome editing requires the homologous direct repair (HDR) machinery of the cells for inserting the transgene in specific regions of the genome. This sophisticated and well-regulated process is limited in the cell cycle of mammalian cells, and in turn, the nonhomologous end-joining (NHEJ) predominates. Consequently, seeking approaches to increase HDR efficiency over NHEJ is crucial. This manuscript comprehensively reviews the current alternatives for improving the HDR for CRISPR/Cas9-based GTs.
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Affiliation(s)
- Andrés Felipe Leal
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Angelica María Herreno-Pachón
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Eliana Benincore-Flórez
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
| | - Amali Karunathilaka
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shunji Tomatsu
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA 19144, USA
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Nam H, Xie K, Majumdar I, Yang S, Starzyk J, Lee D, Shan R, Li J, Wu H. Engineering Tripartite Gene Editing Machinery for Highly Efficient Non-Viral Targeted Genome Integration. RESEARCH SQUARE 2023:rs.3.rs-3365585. [PMID: 37961210 PMCID: PMC10635301 DOI: 10.21203/rs.3.rs-3365585/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Non-viral DNA donor template has been widely used for targeted genomic integration by homologous recombination (HR). This process has become more efficient with RNA guided endonuclease editor system such as CRISPR/Cas9. Circular single stranded DNA (cssDNA) has been harnessed previously as a genome engineering catalyst (GATALYST) for efficient and safe targeted gene knock-in. Here we developed enGager, a system with enhanced GATALYST associated genome editor, comprising a set of novel genome editors in which the integration efficiency of a circular single-stranded (css) donor DNA is elevated by directly tethering of the cssDNA to a nuclear-localized Cas9 fused with ssDNA binding peptides. Improvements in site-directed genomic integration and expression of a knocked-in DNA encoding GFP were observed at multiple genomic loci in multiple cell lines. The enhancement of integration efficiency, compared to unfused Cas9 editors, ranges from 1.5- to more than 6-fold, with the enhancement most pronounced for transgenes of > 4Kb in length in primary cells. enGager-enhanced genome integration prefers ssDNA donors which, unlike traditional dsDNA donors, are not concatemerized or rearranged prior to and during integration Using an enGager fused to an optimized cssDNA binding peptide, exceptionally efficient, targeted integration of the chimeric antigen receptor (CAR) transgene was achieved in 33% of primary human T cells. Enhanced anti-tumor function of these CAR-T primary cells demonstrated the functional competence of the transgenes. The 'tripartite editors with ssDNA optimized genome engineering' (TESOGENASE™) systems help address the efficacy needs for therapeutic gene modification while avoiding the safety and payload size limitations of viral vectors currently used for CAR-T engineering.
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Affiliation(s)
- Hangu Nam
- Department of Bioengineering, Northeastern University, Boston, MA 02115, United States
| | - Keqiang Xie
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Ishita Majumdar
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Shaobo Yang
- Department of Bioengineering, Northeastern University, Boston, MA 02115, United States
| | - Jakob Starzyk
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Danna Lee
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Richard Shan
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Jiahe Li
- Department of Biomedical Engineering, College of Engineering and School of Medicine, University of Michigan, Ann Arbor, MI 48109, United States
| | - Hao Wu
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
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Richardson RR, Steyert M, Khim SN, Crutcher GW, Brandenburg C, Robertson CD, Romanowski AJ, Inen J, Altas B, Poulopoulos A. Enhancing Precision and Efficiency of Cas9-Mediated Knockin Through Combinatorial Fusions of DNA Repair Proteins. CRISPR J 2023; 6:447-461. [PMID: 37713292 PMCID: PMC10611978 DOI: 10.1089/crispr.2023.0036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/14/2023] [Indexed: 09/17/2023] Open
Abstract
Cas9 targets genomic loci with high specificity. For knockin with double-strand break repair, however, Cas9 often leads to unintended on-target knockout rather than intended edits. This imprecision is a barrier for direct in vivo editing where clonal selection is not feasible. In this study, we demonstrate a high-throughput workflow to comparatively assess on-target efficiency and precision of editing outcomes. Using this workflow, we screened combinations of donor DNA and Cas9 variants, as well as fusions to DNA repair proteins. This yielded novel high-performance double-strand break repair editing agents and combinatorial optimizations, yielding increases in knockin efficiency and precision. Cas9-RC, a novel fusion Cas9 flanked by eRad18 and CtIP[HE], increased knockin performance in vitro and in vivo in the developing mouse brain. Continued comparative assessment of editing efficiency and precision with this framework will further the development of high-performance editing agents for in vivo knockin and future genome therapeutics.
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Affiliation(s)
- Ryan R. Richardson
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marilyn Steyert
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Saovleak N. Khim
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Garrett W. Crutcher
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cheryl Brandenburg
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Colin D. Robertson
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrea J. Romanowski
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey Inen
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Bekir Altas
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Alexandros Poulopoulos
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
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6
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Tabassum T, Pietrogrande G, Healy M, Wolvetang EJ. CRISPR-Cas9 Direct Fusions for Improved Genome Editing via Enhanced Homologous Recombination. Int J Mol Sci 2023; 24:14701. [PMID: 37834150 PMCID: PMC10572186 DOI: 10.3390/ijms241914701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
DNA repair in mammalian cells involves the coordinated action of a range of complex cellular repair machinery. Our understanding of these DNA repair processes has advanced to the extent that they can be leveraged to improve the efficacy and precision of Cas9-assisted genome editing tools. Here, we review how the fusion of CRISPR-Cas9 to functional domains of proteins that directly or indirectly impact the DNA repair process can enhance genome editing. Such studies have allowed the development of diverse technologies that promote efficient gene knock-in for safer genome engineering practices.
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Affiliation(s)
- Tahmina Tabassum
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (T.T.); (G.P.)
| | - Giovanni Pietrogrande
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (T.T.); (G.P.)
| | - Michael Healy
- Institute for Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia;
| | - Ernst J. Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (T.T.); (G.P.)
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7
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Nam H, Xie K, Majumdar I, Yang S, Starzyk J, Lee D, Shan R, Li J, Wu H. TESOGENASE, An Engineered Nuclease Editor for Enhanced Targeted Genome Integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.553855. [PMID: 37693500 PMCID: PMC10491117 DOI: 10.1101/2023.08.28.553855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Non-viral DNA donor template has been widely used for targeted genomic integration by homologous recombination (HR). This process has become more efficient with RNA guided endonuclease editor system such as CRISPR/Cas9. Circular single stranded DNA (cssDNA) has been harnessed previously as a g enome engineering c atalyst (GATALYST) for efficient and safe targeted gene knock-in. However, the engineering efficiency is bottlenecked by the nucleoplasm trafficking and genomic tethering of cssDNA donor, especially for extra-large transgene integration. Here we developed enGager, en hanced G ATALYST a ssociated g enome e ditor system by fusion of nucleus localization signal (NLS) peptide tagged Cas9 with various single stranded DNA binding protein modules through a GFP reporter Knock-in screening. The enGager system assembles an integrative genome integration machinery by forming tripartite complex for engineered nuclease editors, sgRNA and ssDNA donors, thereby facilitate the nucleus trafficking of DNA donors and increase their active local concentration at the targeted genomic site. When applied for genome integration with cssDNA donor templates to diverse genomic loci in various cell types, these enGagers outperform unfused editors. The enhancement of integration efficiency ranges from 1.5- to more than 6-fold, with the effect being more prominent for > 4Kb transgene knock-in in primary cells. We further demonstrated that enGager mediated enhancement for genome integration is ssDNA, but less dsDNA dependent. Using one of the mini-enGagers, we demonstrated large chimeric antigen receptor (CAR) transgene integration in primary T cells with exceptional efficiency and anti-tumor function. These tripartite e ditors with s sDNA o ptimized g enome en gineering system (TESOGENASE TM ) add a set of novel endonuclease editors into the gene-editing toolbox for potential cell and gene therapeutic development based on ssDNA mediated non-viral genome engineering. Highlight A reporter Knock-in screening establishes enGager system to identify TESOGENASE editor to improving ssDNA mediated genome integrationMini-TESOGENASEs developed by fusing Cas9 nuclease with novel ssDNA binding motifsmRNA mini-TESOGENASEs enhance targeted genome integration via various non-viral delivery approachesEfficient functional CAR-T cell engineering by mini-TESOGENASE.
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8
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Fichter KM, Setayesh T, Malik P. Strategies for precise gene edits in mammalian cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:536-552. [PMID: 37215153 PMCID: PMC10192336 DOI: 10.1016/j.omtn.2023.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
CRISPR-Cas technologies have the potential to revolutionize genetic medicine. However, work is still needed to make this technology clinically efficient for gene correction. A barrier to making precise genetic edits in the human genome is controlling how CRISPR-Cas-induced DNA breaks are repaired by the cell. Since error-prone non-homologous end-joining is often the preferred cellular repair pathway, CRISPR-Cas-induced breaks often result in gene disruption. Homology-directed repair (HDR) makes precise genetic changes and is the clinically desired pathway, but this repair pathway requires a homology donor template and cycling cells. Newer editing strategies, such as base and prime editing, can affect precise repair for relatively small edits without requiring HDR and circumvent cell cycle dependence. However, these technologies have limitations in the extent of genetic editing and require the delivery of bulky cargo. Here, we discuss the pros and cons of precise gene correction using CRISPR-Cas-induced HDR, as well as base and prime editing for repairing small mutations. Finally, we consider emerging new technologies, such as recombination and transposases, which can circumvent both cell cycle and cellular DNA repair dependence for editing the genome.
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Affiliation(s)
- Katye M. Fichter
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Tahereh Setayesh
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Punam Malik
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Hematology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
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9
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Cassidy A, Onal M, Pelletier S. Novel methods for the generation of genetically engineered animal models. Bone 2023; 167:116612. [PMID: 36379415 PMCID: PMC9936561 DOI: 10.1016/j.bone.2022.116612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/15/2022]
Abstract
Genetically modified mouse models have shaped our understanding of biological systems in both physiological and pathological conditions. For decades, mouse genome engineering has relied on transgenesis and spontaneous gene replacement in embryonic stem (ES) cells. While these technologies provided a wealth of knowledge, they remain imprecise and expensive to use. Recent advances in genome editing technologies such as the development of targetable nucleases, the improvement of delivery systems, and the simplification of targeting strategies now allow for the rapid, precise manipulation of the mouse genome. In this review article, we discuss novel methods and targeting strategies for the generation of mouse models for the study of bone and skeletal muscle biology.
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Affiliation(s)
- Annelise Cassidy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Melda Onal
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Stephane Pelletier
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.
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Richardson C, Kelsh RN, J. Richardson R. New advances in CRISPR/Cas-mediated precise gene-editing techniques. Dis Model Mech 2023; 16:dmm049874. [PMID: 36847161 PMCID: PMC10003097 DOI: 10.1242/dmm.049874] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Over the past decade, CRISPR/Cas-based gene editing has become a powerful tool for generating mutations in a variety of model organisms, from Escherichia coli to zebrafish, rodents and large mammals. CRISPR/Cas-based gene editing effectively generates insertions or deletions (indels), which allow for rapid gene disruption. However, a large proportion of human genetic diseases are caused by single-base-pair substitutions, which result in more subtle alterations to protein function, and which require more complex and precise editing to recreate in model systems. Precise genome editing (PGE) methods, however, typically have efficiencies of less than a tenth of those that generate less-specific indels, and so there has been a great deal of effort to improve PGE efficiency. Such optimisations include optimal guide RNA and mutation-bearing donor DNA template design, modulation of DNA repair pathways that underpin how edits result from Cas-induced cuts, and the development of Cas9 fusion proteins that introduce edits via alternative mechanisms. In this Review, we provide an overview of the recent progress in optimising PGE methods and their potential for generating models of human genetic disease.
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Affiliation(s)
- Chris Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Robert N. Kelsh
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Rebecca J. Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
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Mark JKK, Lim CSY, Nordin F, Tye GJ. Expression of mammalian proteins for diagnostics and therapeutics: a review. Mol Biol Rep 2022; 49:10593-10608. [PMID: 35674877 PMCID: PMC9175168 DOI: 10.1007/s11033-022-07651-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/25/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Antibodies have proven to be remarkably successful for biomedical applications. They play important roles in epidemiology and medicine from diagnostics of diseases to therapeutics, treating diseases from incessant chronic diseases such as rheumatology to pandemic outbreaks. With no end in sight for the demand for antibody products, optimizations and new techniques must be expanded to accommodate this. METHODS AND RESULTS This review discusses optimizations and techniques for antibody production through choice of discovery platforms, expression systems, cell culture mediums, and other strategies to increase expression yield. Each system has its own merits and demerits, and the strategy chosen is critical in addressing various biological aspects. CONCLUSIONS There is still insufficient evidence to validate the efficacy of some of these techniques, and further research is needed to consolidate these industrial production systems. There is no doubt that more strategies, systems, and pipelines will contribute to enhance biopharmaceutical production.
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Affiliation(s)
- Jacqueline Kar Kei Mark
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Penang, Minden, Malaysia
| | - Crystale Siew Ying Lim
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, No 1 Jalan Menara Gading, UCSI Heights, Taman Connaught, 56000, Kuala Lumpur, Cheras, Malaysia
| | - Fazlina Nordin
- Tissue Engineering Centre (TEC), Universiti Kebangsaan Malaysia Medical Centre (UKMMC), 56000, Kuala Lumpur, Cheras, Malaysia
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Penang, Minden, Malaysia.
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12
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Bekaert B, Boel A, Cosemans G, De Witte L, Menten B, Heindryckx B. CRISPR/Cas gene editing in the human germline. Semin Cell Dev Biol 2022; 131:93-107. [PMID: 35305903 DOI: 10.1016/j.semcdb.2022.03.012] [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: 11/15/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/14/2022]
Abstract
The ease and efficacy of CRISPR/Cas9 germline gene editing in animal models paved the way to human germline gene editing (HGGE), by which permanent changes can be introduced into the embryo. Distinct genes can be knocked out to examine their function during embryonic development. Alternatively, specific sequences can be introduced which can be applied to correct disease-causing mutations. To date, it has been shown that the success of HGGE is dependent on various experimental parameters and that various hurdles (i.e. loss-of-heterozygosity and mosaicism) need to be overcome before clinical applications should be considered. Due to the shortage of human germline material and the ethical constraints concerning HGGE, alternative models such as stem cells have been evaluated as well, in terms of their predictive value on the genetic outcome for HGGE approaches. This review will give an overview of the state of the art of HGGE in oocytes and embryos, and its accompanying challenges.
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Affiliation(s)
- B Bekaert
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - A Boel
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - G Cosemans
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - L De Witte
- Center for Medical Genetics Ghent, Ghent University, Department of Biomolecular Medicine, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - B Menten
- Center for Medical Genetics Ghent, Ghent University, Department of Biomolecular Medicine, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - B Heindryckx
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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13
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Economos NG, Thapar U, Balasubramanian N, Karras GI, Glazer PM. An ELISA-based platform for rapid identification of structure-dependent nucleic acid-protein interactions detects novel DNA triplex interactors. J Biol Chem 2022; 298:102398. [PMID: 35988651 PMCID: PMC9493393 DOI: 10.1016/j.jbc.2022.102398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 11/21/2022] Open
Abstract
Unusual nucleic acid structures play vital roles as intermediates in many cellular processes and, in the case of peptide nucleic acid (PNA)–mediated triplexes, are leveraged as tools for therapeutic gene editing. However, due to their transient nature, an understanding of the factors that interact with and process dynamic nucleic acid structures remains limited. Here, we developed snapELISA (structure-specific nucleic acid-binding protein ELISA), a rapid high-throughput platform to interrogate and compare up to 2688 parallel nucleic acid structure–protein interactions in vitro. We applied this system to both triplex-forming oligonucleotide–induced DNA triplexes and DNA-bound PNA heterotriplexes to describe the identification of previously known and novel interactors for both structures. For PNA heterotriplex recognition analyses, snapELISA identified factors implicated in nucleotide excision repair (XPA, XPC), single-strand annealing repair (RAD52), and recombination intermediate structure binding (TOP3A, BLM, MUS81). We went on to validate selected factor localization to genome-targeted PNA structures within clinically relevant loci in human cells. Surprisingly, these results demonstrated XRCC5 localization to PNA triplex-forming sites in the genome, suggesting the presence of a double-strand break intermediate. These results describe a powerful comparative approach for identifying structure-specific nucleic acid interactions and expand our understanding of the mechanisms of triplex structure recognition and repair.
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Affiliation(s)
- Nicholas G Economos
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT; Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Upasna Thapar
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nanda Balasubramanian
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT
| | - Georgios I Karras
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX; Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX.
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT; Department of Genetics, Yale University School of Medicine, New Haven, CT.
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14
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Finney M, Romanowski J, Adelman ZN. Strategies to improve homology-based repair outcomes following CRISPR-based gene editing in mosquitoes: lessons in how to keep any repair disruptions local. Virol J 2022; 19:128. [PMID: 35908059 PMCID: PMC9338592 DOI: 10.1186/s12985-022-01859-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
Programmable gene editing systems such as CRISPR-Cas have made mosquito genome engineering more practical and accessible, catalyzing the development of cutting-edge genetic methods of disease vector control. This progress, however, has been limited by the low efficiency of homology-directed repair (HDR)-based sequence integration at DNA double-strand breaks (DSBs) and a lack of understanding about DSB repair in mosquitoes. Innovative efforts to optimize HDR sequence integration by inhibiting non-homologous end joining or promoting HDR have been performed in mammalian systems, however many of these approaches have not been applied to mosquitoes. Here, we review some of the most relevant steps of DNA DSB repair choice and highlight promising approaches that influence this choice to enhance HDR in the context of mosquito gene editing.
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Affiliation(s)
- Micaela Finney
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA
| | - Joseph Romanowski
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA
| | - Zach N Adelman
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA.
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15
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Shams F, Bayat H, Mohammadian O, Mahboudi S, Vahidnezhad H, Soosanabadi M, Rahimpour A. Advance trends in targeting homology-directed repair for accurate gene editing: An inclusive review of small molecules and modified CRISPR-Cas9 systems. BIOIMPACTS 2022; 12:371-391. [PMID: 35975201 PMCID: PMC9376165 DOI: 10.34172/bi.2022.23871] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 11/25/2022]
Abstract
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Introduction: Clustered regularly interspaced short palindromic repeat and its associated protein (CRISPR-Cas)-based technologies generate targeted modifications in host genome by inducing site-specific double-strand breaks (DSBs) that can serve as a substrate for homology-directed repair (HDR) in both in vitro and in vivo models. HDR pathway could enhance incorporation of exogenous DNA templates into the CRISPR-Cas9-mediated DSB site. Owing to low rate of HDR pathway, the efficiency of accurate genome editing is diminished. Enhancing the efficiency of HDR can provide fast, easy, and accurate technologies based on CRISPR-Cas9 technologies.
Methods: The current study presents an overview of attempts conducted on the precise genome editing strategies based on small molecules and modified CRISPR-Cas9 systems.
Results: In order to increase HDR rate in targeted cells, several logical strategies have been introduced such as generating CRISPR effector chimeric proteins, anti-CRISPR proteins, modified Cas9 with donor template, and using validated synthetic or natural small molecules for either inhibiting non-homologous end joining (NHEJ), stimulating HDR, or synchronizing cell cycle. Recently, high-throughput screening methods have been applied for identification of small molecules which along with the CRISPR system can regulate precise genome editing through HDR.
Conclusion: The stimulation of HDR components or inhibiting NHEJ can increase the accuracy of CRISPR-Cas-mediated engineering systems. Generating chimeric programmable endonucleases provide this opportunity to direct DNA template close proximity of CRISPR-Cas-mediated DSB. Small molecules and their derivatives can also proficiently block or activate certain DNA repair pathways and bring up novel perspectives for increasing HDR efficiency, especially in human cells. Further, high throughput screening of small molecule libraries could result in more discoveries of promising chemicals that improve HDR efficiency and CRISPR-Cas9 systems.
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Affiliation(s)
- Forough Shams
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Mohammadian
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mahboudi
- Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Azam Rahimpour
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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16
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Lainšček D, Forstnerič V, Mikolič V, Malenšek Š, Pečan P, Benčina M, Sever M, Podgornik H, Jerala R. Coiled-coil heterodimer-based recruitment of an exonuclease to CRISPR/Cas for enhanced gene editing. Nat Commun 2022; 13:3604. [PMID: 35739111 PMCID: PMC9226073 DOI: 10.1038/s41467-022-31386-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
The CRISPR/Cas system has emerged as a powerful and versatile genome engineering tool, revolutionizing biological and biomedical sciences, where an improvement of efficiency could have a strong impact. Here we present a strategy to enhance gene editing based on the concerted action of Cas9 and an exonuclease. Non-covalent recruitment of exonuclease to Cas9/gRNA complex via genetically encoded coiled-coil based domains, termed CCExo, recruited the exonuclease to the cleavage site and robustly increased gene knock-out due to progressive DNA strand recession at the cleavage site, causing decreased re-ligation of the nonedited DNA. CCExo exhibited increased deletion size and enhanced gene inactivation efficiency in the context of several DNA targets, gRNA selection, Cas variants, tested cell lines and type of delivery. Targeting a sequence-specific oncogenic chromosomal translocation using CCExo in cells of chronic myelogenous leukemia patients and in an animal model led to the reduction or elimination of cancer, establishing it as a highly specific tool for treating CML and potentially other appropriate diseases with genetic etiology.
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Affiliation(s)
- Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana, 1000, Slovenia
| | - Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
| | - Veronika Mikolič
- Department of Hematology, Division of Internal Medicine, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Špela Malenšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Peter Pečan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana, 1000, Slovenia
| | - Matjaž Sever
- Department of Hematology, Division of Internal Medicine, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana, 1000, Slovenia
| | - Helena Podgornik
- Department of Hematology, Division of Internal Medicine, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, 1000, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana, 1000, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia.
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana, 1000, Slovenia.
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17
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Ali A, Xiao W, Babar ME, Bi Y. Double-Stranded Break Repair in Mammalian Cells and Precise Genome Editing. Genes (Basel) 2022; 13:genes13050737. [PMID: 35627122 PMCID: PMC9142082 DOI: 10.3390/genes13050737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, double-strand breaks (DSBs) are repaired predominantly by error-prone non-homologous end joining (NHEJ), but less prevalently by error-free template-dependent homologous recombination (HR). DSB repair pathway selection is the bedrock for genome editing. NHEJ results in random mutations when repairing DSB, while HR induces high-fidelity sequence-specific variations, but with an undesirable low efficiency. In this review, we first discuss the latest insights into the action mode of NHEJ and HR in a panoramic view. We then propose the future direction of genome editing by virtue of these advancements. We suggest that by switching NHEJ to HR, full fidelity genome editing and robust gene knock-in could be enabled. We also envision that RNA molecules could be repurposed by RNA-templated DSB repair to mediate precise genetic editing.
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Affiliation(s)
- Akhtar Ali
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan
| | - Wei Xiao
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
| | - Masroor Ellahi Babar
- The University of Agriculture Dera Ismail Khan, Dera Ismail Khan 29220, Pakistan;
| | - Yanzhen Bi
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Correspondence: ; Tel.: +86-151-0714-8708
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18
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Ou-Yang H, Yang SH, Chen W, Yang SH, Cidem A, Sung LY, Chen CM. Cruciform DNA Structures Act as Legible Templates for Accelerating Homologous Recombination in Transgenic Animals. Int J Mol Sci 2022; 23:3973. [PMID: 35409332 PMCID: PMC9000021 DOI: 10.3390/ijms23073973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
Inverted repeat (IR) DNA sequences compose cruciform structures. Some genetic disorders are the result of genome inversion or translocation by cruciform DNA structures. The present study examined whether exogenous DNA integration into the chromosomes of transgenic animals was related to cruciform DNA structures. Large imperfect cruciform structures were frequently predicted around predestinated transgene integration sites in host genomes of microinjection-based transgenic (Tg) animals (αLA-LPH Tg goat, Akr1A1eGFP/eGFP Tg mouse, and NFκB-Luc Tg mouse) or CRISPR/Cas9 gene-editing (GE) animals (αLA-AP1 GE mouse). Transgene cassettes were imperfectly matched with their predestinated sequences. According to the analyzed data, we proposed a putative model in which the flexible cruciform DNA structures acted as a legible template for DNA integration into linear DNAs or double-strand break (DSB) alleles. To demonstrate this model, artificial inverted repeat knock-in (KI) reporter plasmids were created to analyze the KI rate using the CRISPR/Cas9 system in NIH3T3 cells. Notably, the KI rate of the 5′ homologous arm inverted repeat donor plasmid (5′IR) with the ROSA gRNA group (31.5%) was significantly higher than the knock-in reporter donor plasmid (KIR) with the ROSA gRNA group (21.3%, p < 0.05). However, the KI rate of the 3′ inverted terminal repeat/inverted repeat donor plasmid (3′ITRIR) group was not different from the KIR group (23.0% vs. 22.0%). These results demonstrated that the legibility of the sequence with the cruciform DNA existing in the transgene promoted homologous recombination (HR) with a higher KI rate. Our findings suggest that flexible cruciform DNAs folded by IR sequences improve the legibility and accelerate DNA 3′-overhang integration into the host genome via homologous recombination machinery.
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Affiliation(s)
- Huan Ou-Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Shiao-Hsuan Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Reproductive Medicine Center, Department of Gynecology, Changhua Christian Hospital, Changhua 515, Taiwan
| | - Wei Chen
- Division of Pulmonary and Critical Care Medicine, Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
| | - Shang-Hsun Yang
- Department of Physiology, National Cheng Kung University, Tainan 701, Taiwan;
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Abdulkadir Cidem
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum 25250, Turkey
| | - Li-Ying Sung
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Chuan-Mu Chen
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Rong-Hsing Translational Medicine Research Center, Taichung Veterans General Hospital, Taichung 407, Taiwan
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19
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Feng S, Wang Z, Li A, Xie X, Liu J, Li S, Li Y, Wang B, Hu L, Yang L, Guo T. Strategies for High-Efficiency Mutation Using the CRISPR/Cas System. Front Cell Dev Biol 2022; 9:803252. [PMID: 35198566 PMCID: PMC8860194 DOI: 10.3389/fcell.2021.803252] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/22/2021] [Indexed: 12/15/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated systems have revolutionized traditional gene-editing tools and are a significant tool for ameliorating gene defects. Characterized by high target specificity, extraordinary efficiency, and cost-effectiveness, CRISPR/Cas systems have displayed tremendous potential for genetic manipulation in almost any organism and cell type. Despite their numerous advantages, however, CRISPR/Cas systems have some inherent limitations, such as off-target effects, unsatisfactory efficiency of delivery, and unwanted adverse effects, thereby resulting in a desire to explore approaches to address these issues. Strategies for improving the efficiency of CRISPR/Cas-induced mutations, such as reducing off-target effects, improving the design and modification of sgRNA, optimizing the editing time and the temperature, choice of delivery system, and enrichment of sgRNA, are comprehensively described in this review. Additionally, several newly emerging approaches, including the use of Cas variants, anti-CRISPR proteins, and mutant enrichment, are discussed in detail. Furthermore, the authors provide a deep analysis of the current challenges in the utilization of CRISPR/Cas systems and the future applications of CRISPR/Cas systems in various scenarios. This review not only serves as a reference for improving the maturity of CRISPR/Cas systems but also supplies practical guidance for expanding the applicability of this technology.
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Affiliation(s)
- Shuying Feng
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zilong Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Aifang Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xin Xie
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Junjie Liu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Shuxuan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yalan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Baiyan Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lina Hu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lianhe Yang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Tao Guo
- Department of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
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20
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Sun W, Liu H, Yin W, Qiao J, Zhao X, Liu Y. Strategies for Enhancing the Homology-directed Repair Efficiency of CRISPR-Cas Systems. CRISPR J 2022; 5:7-18. [PMID: 35076280 DOI: 10.1089/crispr.2021.0039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The CRISPR-Cas nuclease has emerged as a powerful genome-editing tool in recent years. The CRISPR-Cas system induces double-strand breaks that can be repaired via the non-homologous end joining or homology-directed repair (HDR) pathway. Compared to non-homologous end joining, HDR can be used for the treatment of incurable monogenetic diseases. Therefore, remarkable efforts have been dedicated to enhancing the efficacy of HDR. In this review, we summarize the currently used strategies for enhancing the HDR efficiency of CRISPR-Cas systems based on three factors: (1) regulation of the key factors in the DNA repair pathways, (2) modulation of the components in the CRISPR machinery, and (3) alteration of the intracellular environment around double-strand breaks. Representative cases and potential solutions for further improving HDR efficiency are also discussed, facilitating the development of new CRISPR technologies to achieve highly precise genetic manipulation in the future.
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Affiliation(s)
- Wenli Sun
- School of Life Science and Technology, Wuhan Polytechnic University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China
| | - Hui Liu
- Department of Hematology, Renmin Hospital of Wuhan University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China
| | - Wenhao Yin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China
| | - Jie Qiao
- School of Life Science and Technology, Wuhan Polytechnic University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China
| | - Xueke Zhao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Henan, People's Republic of China; and Ltd., Hubei, People's Republic of China
| | - Yi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China.,BravoVax Co., Ltd., Hubei, People's Republic of China
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21
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Yoshimatsu S, Nakajima M, Qian E, Sanosaka T, Sato T, Okano H. Homologous Recombination-Enhancing Factors Identified by Comparative Transcriptomic Analyses of Pluripotent Stem Cell of Human and Common Marmoset. Cells 2022; 11:cells11030360. [PMID: 35159172 PMCID: PMC8834151 DOI: 10.3390/cells11030360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/12/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
A previous study assessing the efficiency of the genome editing technology CRISPR-Cas9 for knock-in gene targeting in common marmoset (marmoset; Callithrix jacchus) embryonic stem cells (ESCs) unexpectedly identified innately enhanced homologous recombination activity in marmoset ESCs. Here, we compared gene expression in marmoset and human pluripotent stem cells using transcriptomic and quantitative PCR analyses and found that five HR-related genes (BRCA1, BRCA2, RAD51C, RAD51D, and RAD51) were upregulated in marmoset cells. A total of four of these upregulated genes enhanced HR efficiency with CRISPR-Cas9 in human pluripotent stem cells. Thus, the present study provides a novel insight into species-specific mechanisms for the choice of DNA repair pathways.
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Affiliation(s)
- Sho Yoshimatsu
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan; (S.Y.); (M.N.); (E.Q.); (T.S.); (T.S.)
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Saitama 351-0198, Japan
| | - Mayutaka Nakajima
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan; (S.Y.); (M.N.); (E.Q.); (T.S.); (T.S.)
| | - Emi Qian
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan; (S.Y.); (M.N.); (E.Q.); (T.S.); (T.S.)
| | - Tsukasa Sanosaka
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan; (S.Y.); (M.N.); (E.Q.); (T.S.); (T.S.)
| | - Tsukika Sato
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan; (S.Y.); (M.N.); (E.Q.); (T.S.); (T.S.)
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan; (S.Y.); (M.N.); (E.Q.); (T.S.); (T.S.)
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Saitama 351-0198, Japan
- Correspondence:
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22
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Movahedi A, Wei H, Zhou X, Fountain JC, Chen ZH, Mu Z, Sun W, Zhang J, Li D, Guo B, Varshney RK, Yang L, Zhuge Q. Precise exogenous insertion and sequence replacements in poplar by simultaneous HDR overexpression and NHEJ suppression using CRISPR-Cas9. HORTICULTURE RESEARCH 2022; 9:uhac154. [PMID: 36133672 PMCID: PMC9478684 DOI: 10.1093/hr/uhac154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 07/22/2022] [Accepted: 06/27/2022] [Indexed: 05/21/2023]
Abstract
CRISPR-mediated genome editing has become a powerful tool for the genetic modification of biological traits. However, developing an efficient, site-specific, gene knock-in system based on homology-directed DNA repair (HDR) remains a significant challenge in plants, especially in woody species like poplar. Here, we show that simultaneous inhibition of non-homologous end joining (NHEJ) recombination cofactor XRCC4 and overexpression of HDR enhancer factors CtIP and MRE11 can improve HDR efficiency for gene knock-in. Using this approach, the BleoR gene was integrated onto the 3' end of the MKK2 MAP kinase gene to generate a BleoR-MKK2 fusion protein. Based on fully edited nucleotides evaluated by TaqMan real-time PCR, the HDR-mediated knock-in efficiency was up to 48% when using XRCC4 silencing incorporated with a combination of CtIP and MRE11 overexpression compared with no HDR enhancement or NHEJ silencing. Furthermore, this combination of HDR enhancer overexpression and NHEJ repression also increased genome targeting efficiency and gave 7-fold fewer CRISPR-induced insertions and deletions (InDels), resulting in no functional effects on MKK2-based salt stress responses in poplar. Therefore, this approach may be useful not only in poplar and plants or crops but also in mammals for improving CRISPR-mediated gene knock-in efficiency.
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Affiliation(s)
| | - Hui Wei
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | | | | | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Zhiying Mu
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Weibo Sun
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Jiaxin Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Dawei Li
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Baozhu Guo
- USDA-ARS, Crop Genetics and Breeding Research Unit, Tifton, GA 31793, USA
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23
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Reint G, Li Z, Labun K, Keskitalo S, Soppa I, Mamia K, Tolo E, Szymanska M, Meza-Zepeda LA, Lorenz S, Cieslar-Pobuda A, Hu X, Bordin DL, Staerk J, Valen E, Schmierer B, Varjosalo M, Taipale J, Haapaniemi E. Rapid genome editing by CRISPR-Cas9-POLD3 fusion. eLife 2021; 10:75415. [PMID: 34898428 PMCID: PMC8747517 DOI: 10.7554/elife.75415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022] Open
Abstract
Precision CRISPR gene editing relies on the cellular homology-directed DNA repair (HDR) to introduce custom DNA sequences to target sites. The HDR editing efficiency varies between cell types and genomic sites, and the sources of this variation are incompletely understood. Here, we have studied the effect of 450 DNA repair protein-Cas9 fusions on CRISPR genome editing outcomes. We find the majority of fusions to improve precision genome editing only modestly in a locus- and cell-type specific manner. We identify Cas9-POLD3 fusion that enhances editing by speeding up the initiation of DNA repair. We conclude that while DNA repair protein fusions to Cas9 can improve HDR CRISPR editing, most need to be optimized to the cell type and genomic site, highlighting the diversity of factors contributing to locus-specific genome editing outcomes.
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Affiliation(s)
- Ganna Reint
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Zhuokun Li
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Kornel Labun
- Department of Informatics, Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Salla Keskitalo
- Centre for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Inkeri Soppa
- Centre for Molecular Medicine, University of Oslo, Oslo, Finland
| | - Katariina Mamia
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Eero Tolo
- Faculty of Social Sciences, University of Helsinki, Oslo, Finland
| | | | - Leonardo A Meza-Zepeda
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Xian Hu
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Diana L Bordin
- Department of Clinical Molecular Biology, Akershus University Hospital, Oslo, Norway
| | - Judith Staerk
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Eivind Valen
- Center for Biotechnology, University of Bergen, Bergen, Norway
| | - Bernhard Schmierer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Markku Varjosalo
- Centre for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Emma Haapaniemi
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
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24
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Wimmer T, Bonthu D, Moeschl V, Kleekamp P, Thiel C, Lytvynchuk L, Ellinwood M, Stieger K. A Bioluminescence Resonance Energy Transfer-Based Reporter System: Characterization and Applications. CRISPR J 2021; 4:884-895. [PMID: 34847743 DOI: 10.1089/crispr.2021.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genome editing strategies and DNA repair research need powerful analytical tools. We generated a bioluminescence resonance energy transfer (BRET)-based reporter for the quantification of indel frequencies induced by DNA repair. The BRET reporter, expressed as a single molecule, consists of a mutated Renilla reniformis luciferase domain and a GFP2 domain separated by a shuttle-cloning box for the integration of any given endonuclease target sequence. The luciferase activity acts both as energy donor and as the internal standard, while the loss of GFP2 fluorescence acts as a reporter for the out-of-frame sequence alterations that result from the DNA repair via the non-homologous end joining/microhomology-mediated end joining DNA repair pathways of the endonuclease-mediated DNA double-strand break. This results in a decrease of the fluorescence/luminescence ratio. Employing this reporter in different experimental scenarios, using different cell lines and diseases targeted, we quantified the influence of both protein knockdown of DNA repair pathways as well as guide RNA mismatches on CRISPR-mediated nuclease activity and subsequent repair based on mutagenic repair on the reporter. In conclusion, we demonstrated this BRET-based reporter to be a robust and sensitive analytical tool for assessment of variety of different genome editing-based approaches.
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Affiliation(s)
- Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Dileep Bonthu
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Vincent Moeschl
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Philip Kleekamp
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christian Thiel
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Lyubomyr Lytvynchuk
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | | | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
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25
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van Essen M, Riepsaame J, Jacob J. CRISPR-Cas Gene Perturbation and Editing in Human Induced Pluripotent Stem Cells. CRISPR J 2021; 4:634-655. [PMID: 34582693 DOI: 10.1089/crispr.2021.0063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Directing the fates of human pluripotent stem cells (hPSC) to generate a multitude of differentiated cell types allows the study of the genetic regulation of human development and disease. The translational potential of hPSC is maximized by exploiting CRISPR to silence or activate genes with spatial and temporal precision permanently or reversibly. Here, we summarize the increasingly refined and diverse CRISPR toolkit for the latter forms of gene perturbation in hPSC and their downstream applications. We discuss newer methods to install edits efficiently with single nucleotide resolution and describe pooled CRISPR screens as a powerful means of unbiased discovery of genes associated with a phenotype of interest. Last, we discuss the potential of these combined technologies in the treatment of hitherto intractable human diseases and the challenges to their implementation in the clinic.
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Affiliation(s)
- Max van Essen
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom; and University of Oxford, Oxford, United Kingdom
| | - Joey Riepsaame
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - John Jacob
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom; and University of Oxford, Oxford, United Kingdom
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26
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Koniali L, Lederer CW, Kleanthous M. Therapy Development by Genome Editing of Hematopoietic Stem Cells. Cells 2021; 10:1492. [PMID: 34198536 PMCID: PMC8231983 DOI: 10.3390/cells10061492] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Accessibility of hematopoietic stem cells (HSCs) for the manipulation and repopulation of the blood and immune systems has placed them at the forefront of cell and gene therapy development. Recent advances in genome-editing tools, in particular for clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) and CRISPR/Cas-derived editing systems, have transformed the gene therapy landscape. Their versatility and the ability to edit genomic sequences and facilitate gene disruption, correction or insertion, have broadened the spectrum of potential gene therapy targets and accelerated the development of potential curative therapies for many rare diseases treatable by transplantation or modification of HSCs. Ongoing developments seek to address efficiency and precision of HSC modification, tolerability of treatment and the distribution and affordability of corresponding therapies. Here, we give an overview of recent progress in the field of HSC genome editing as treatment for inherited disorders and summarize the most significant findings from corresponding preclinical and clinical studies. With emphasis on HSC-based therapies, we also discuss technical hurdles that need to be overcome en route to clinical translation of genome editing and indicate advances that may facilitate routine application beyond the most common disorders.
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Affiliation(s)
- Lola Koniali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (L.K.); (M.K.)
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (L.K.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (L.K.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
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27
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Wilde JJ, Aida T, Del Rosario RCH, Kaiser T, Qi P, Wienisch M, Zhang Q, Colvin S, Feng G. Efficient embryonic homozygous gene conversion via RAD51-enhanced interhomolog repair. Cell 2021; 184:3267-3280.e18. [PMID: 34043941 PMCID: PMC8240950 DOI: 10.1016/j.cell.2021.04.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 03/03/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Searching for factors to improve knockin efficiency for therapeutic applications, biotechnology, and generation of non-human primate models of disease, we found that the strand exchange protein RAD51 can significantly increase Cas9-mediated homozygous knockin in mouse embryos through an interhomolog repair (IHR) mechanism. IHR is a hallmark of meiosis but only occurs at low frequencies in somatic cells, and its occurrence in zygotes is controversial. Using multiple approaches, we provide evidence for an endogenous IHR mechanism in the early embryo that can be enhanced by RAD51. This process can be harnessed to generate homozygotes from wild-type zygotes using exogenous donors and to convert heterozygous alleles into homozygous alleles without exogenous templates. Furthermore, we identify additional IHR-promoting factors and describe features of IHR events. Together, our findings show conclusive evidence for IHR in mouse embryos and describe an efficient method for enhanced gene conversion.
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Affiliation(s)
- Jonathan J Wilde
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
| | - Tomomi Aida
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Ricardo C H Del Rosario
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias Kaiser
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Peimin Qi
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Martin Wienisch
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Qiangge Zhang
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Steven Colvin
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Guoping Feng
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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28
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Čermák T. Sequence modification on demand: search and replace tools for precise gene editing in plants. Transgenic Res 2021; 30:353-379. [PMID: 34086167 DOI: 10.1007/s11248-021-00253-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/05/2021] [Indexed: 12/26/2022]
Abstract
Until recently, our ability to generate allelic diversity in plants was limited to introduction of variants from domesticated and wild species by breeding via uncontrolled recombination or the use of chemical and physical mutagens-processes that are lengthy and costly or lack specificity, respectively. Gene editing provides a faster and more precise way to create new variation, although its application in plants has been dominated by the creation of short insertion and deletion mutations leading to loss of gene function, mostly due to the dependence of editing outcomes on DNA repair pathway choices intrinsic to higher eukaryotes. Other types of edits such as point mutations and precise and pre-designed targeted sequence insertions have rarely been implemented, despite providing means to modulate the expression of target genes or to engineer the function and stability of their protein products. Several advancements have been developed in recent years to facilitate custom editing by regulation of repair pathway choices or by taking advantage of alternative types of DNA repair. We have seen the advent of novel gene editing tools that are independent of DNA double-strand break repair, and methods completely independent of host DNA repair processes are being increasingly explored. With the aim to provide a comprehensive review of the state-of-the-art methodology for allele replacement in plants, I discuss the adoption of these improvements for plant genome engineering.
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29
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Wang C, Cheng JKW, Zhang Q, Hughes NW, Xia Q, Winslow MM, Cong L. Microbial single-strand annealing proteins enable CRISPR gene-editing tools with improved knock-in efficiencies and reduced off-target effects. Nucleic Acids Res 2021; 49:e36. [PMID: 33619540 PMCID: PMC8034634 DOI: 10.1093/nar/gkaa1264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 12/15/2022] Open
Abstract
Several existing technologies enable short genomic alterations including generating indels and short nucleotide variants, however, engineering more significant genomic changes is more challenging due to reduced efficiency and precision. Here, we developed RecT Editor via Designer-Cas9-Initiated Targeting (REDIT), which leverages phage single-stranded DNA-annealing proteins (SSAP) RecT for mammalian genome engineering. Relative to Cas9-mediated homology-directed repair (HDR), REDIT yielded up to a 5-fold increase of efficiency to insert kilobase-scale exogenous sequences at defined genomic regions. We validated our REDIT approach using different formats and lengths of knock-in templates. We further demonstrated that REDIT tools using Cas9 nickase have efficient gene-editing activities and reduced off-target errors, measured using a combination of targeted sequencing, genome-wide indel, and insertion mapping assays. Our experiments inhibiting repair enzyme activities suggested that REDIT has the potential to overcome limitations of endogenous DNA repair steps. Finally, our REDIT method is applicable across cell types including human stem cells, and is generalizable to different Cas9 enzymes.
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Affiliation(s)
- Chengkun Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason K W Cheng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhe Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas W Hughes
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Qiong Xia
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Monte M Winslow
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Le Cong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA, USA
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30
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Li Z, Marcel N, Devkota S, Auradkar A, Hedrick SM, Gantz VM, Bier E. CopyCatchers are versatile active genetic elements that detect and quantify inter-homolog somatic gene conversion. Nat Commun 2021; 12:2625. [PMID: 33976171 PMCID: PMC8113449 DOI: 10.1038/s41467-021-22927-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/01/2021] [Indexed: 11/08/2022] Open
Abstract
CRISPR-based active genetic elements, or gene-drives, copied via homology-directed repair (HDR) in the germline, are transmitted to progeny at super-Mendelian frequencies. Active genetic elements also can generate widespread somatic mutations, but the genetic basis for such phenotypes remains uncertain. It is generally assumed that such somatic mutations are generated by non-homologous end-joining (NHEJ), the predominant double stranded break repair pathway active in somatic cells. Here, we develop CopyCatcher systems in Drosophila to detect and quantify somatic gene conversion (SGC) events. CopyCatchers inserted into two independent genetic loci reveal unexpectedly high rates of SGC in the Drosophila eye and thoracic epidermis. Focused RNAi-based genetic screens identify several unanticipated loci altering SGC efficiency, one of which (c-MYC), when downregulated, promotes SGC mediated by both plasmid and homologous chromosome-templates in human HEK293T cells. Collectively, these studies suggest that CopyCatchers can serve as effective discovery platforms to inform potential gene therapy strategies.
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Affiliation(s)
- Zhiqian Li
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Nimi Marcel
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Stephen M Hedrick
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA, USA.
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31
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Chenouard V, Remy S, Tesson L, Ménoret S, Ouisse LH, Cherifi Y, Anegon I. Advances in Genome Editing and Application to the Generation of Genetically Modified Rat Models. Front Genet 2021; 12:615491. [PMID: 33959146 PMCID: PMC8093876 DOI: 10.3389/fgene.2021.615491] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
The rat has been extensively used as a small animal model. Many genetically engineered rat models have emerged in the last two decades, and the advent of gene-specific nucleases has accelerated their generation in recent years. This review covers the techniques and advances used to generate genetically engineered rat lines and their application to the development of rat models more broadly, such as conditional knockouts and reporter gene strains. In addition, genome-editing techniques that remain to be explored in the rat are discussed. The review also focuses more particularly on two areas in which extensive work has been done: human genetic diseases and immune system analysis. Models are thoroughly described in these two areas and highlight the competitive advantages of rat models over available corresponding mouse versions. The objective of this review is to provide a comprehensive description of the advantages and potential of rat models for addressing specific scientific questions and to characterize the best genome-engineering tools for developing new projects.
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Affiliation(s)
- Vanessa Chenouard
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
- genOway, Lyon, France
| | - Séverine Remy
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Laurent Tesson
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Séverine Ménoret
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
- CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, Nantes Université, Nantes, France
| | - Laure-Hélène Ouisse
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | | | - Ignacio Anegon
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
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32
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Reuven N, Adler J, Myers N, Shaul Y. CRISPR Co-Editing Strategy for Scarless Homology-Directed Genome Editing. Int J Mol Sci 2021; 22:3741. [PMID: 33916763 PMCID: PMC8038335 DOI: 10.3390/ijms22073741] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/23/2021] [Accepted: 03/26/2021] [Indexed: 12/27/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 has revolutionized genome editing by providing a simple and robust means to cleave specific genomic sequences. However, introducing templated changes at the targeted site usually requires homology-directed repair (HDR), active in only a small subset of cells in culture. To enrich for HDR-dependent edited cells, we employed a co-editing strategy, editing a gene of interest (GOI) concomitantly with rescuing an endogenous pre-made temperature-sensitive (ts) mutation. By using the repair of the ts mutation as a selectable marker, the selection is "scarless" since editing restores the wild-type (wt) sequence. As proof of principle, we used HEK293 and HeLa cells with a ts mutation in the essential TAF1 gene. CRISPR co-editing of TAF1ts and a GOI resulted in up to 90% of the temperature-resistant cells bearing the desired mutation in the GOI. We used this system to insert large cassettes encoded by plasmid donors and smaller changes encoded by single-stranded oligonucleotide donors (ssODN). Of note, among the genes we edited was the introduction of a T35A mutation in the proteasome subunit PSMB6, which eliminates its caspase-like activity. The edited cells showed a specific reduction in this activity, demonstrating this system's utility in generating cell lines with biologically relevant mutations in endogenous genes. This approach offers a rapid, efficient, and scarless method for selecting genome-edited cells requiring HDR.
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Affiliation(s)
- Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; (J.A.); (N.M.)
| | | | | | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; (J.A.); (N.M.)
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33
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Hackley CR. A Novel Set of Cas9 Fusion Proteins to Stimulate Homologous Recombination: Cas9-HRs. CRISPR J 2021; 4:253-263. [PMID: 33876961 DOI: 10.1089/crispr.2020.0034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
CRISPR- Cas9 has revolutionized genetic engineering. However, the inability to control double-strand break (DSB) repair has severely limited both therapeutic and academic applications. Many attempts have been made to control DSB repair choice. However, particularly in the case of larger edits, none have been able to bypass the rate-limiting step of homologous recombination (HR): long-range 5' end resection. Here, we describe a novel set of Cas9 fusions, Cas9-HRs, designed to bypass the rate-limiting step of HR repair by simultaneously coupling initial and long-range end resection. Here, we demonstrate that Cas9-HRs can increase the rate of homology directed repair (HDR) by 2- to 2.5-fold and decrease p53 mediated cellular toxicity by two- to fourfold compared to Cas9 and are functional in multiple mammalian cell lines with minimal apparent editing site bias. These properties should make Cas9-HRs an attractive option for applications demanding increased HDR rates for long inserts and/or reduced p53 pathway activation.
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34
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Tatiossian KJ, Clark RDE, Huang C, Thornton ME, Grubbs BH, Cannon PM. Rational Selection of CRISPR-Cas9 Guide RNAs for Homology-Directed Genome Editing. Mol Ther 2021; 29:1057-1069. [PMID: 33160457 PMCID: PMC7934447 DOI: 10.1016/j.ymthe.2020.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 09/27/2020] [Accepted: 10/08/2020] [Indexed: 01/27/2023] Open
Abstract
Homology-directed repair (HDR) of a DNA break allows copying of genetic material from an exogenous DNA template and is frequently exploited in CRISPR-Cas9 genome editing. However, HDR is in competition with other DNA repair pathways, including non-homologous end joining (NHEJ) and microhomology-mediated end joining (MMEJ), and the efficiency of HDR outcomes is not predictable. Consequently, to optimize HDR editing, panels of CRISPR-Cas9 guide RNAs (gRNAs) and matched homology templates must be evaluated. We report here that CRISPR-Cas9 indel signatures can instead be used to identify gRNAs that maximize HDR outcomes. Specifically, we show that the frequency of deletions resulting from MMEJ repair, characterized as deletions greater than or equal to 3 bp, better predicts HDR frequency than consideration of total indel frequency. We further demonstrate that tools that predict gRNA indel signatures can be repurposed to identify gRNAs to promote HDR. Finally, by comparing indels generated by S. aureus and S. pyogenes Cas9 targeted to the same site, we add to the growing body of data that the targeted DNA sequence is a major factor governing genome editing outcomes.
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Affiliation(s)
- Kristina J Tatiossian
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Robert D E Clark
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Chun Huang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Matthew E Thornton
- Department of Obstetrics and Gynecology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Brendan H Grubbs
- Department of Obstetrics and Gynecology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Paula M Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
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35
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Advances and Obstacles in Homology-Mediated Gene Editing of Hematopoietic Stem Cells. J Clin Med 2021; 10:jcm10030513. [PMID: 33535527 PMCID: PMC7867106 DOI: 10.3390/jcm10030513] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
Homology-directed gene editing of hematopoietic stem and progenitor cells (HSPCs) is a promising strategy for the treatment of inherited blood disorders, obviating many of the limitations associated with viral vector-mediated gene therapies. The use of CRISPR/Cas9 or other programmable nucleases and improved methods of homology template delivery have enabled precise ex vivo gene editing. These transformative advances have also highlighted technical challenges to achieve high-efficiency gene editing in HSPCs for therapeutic applications. In this review, we discuss recent pre-clinical investigations utilizing homology-mediated gene editing in HSPCs and highlight various strategies to improve editing efficiency in these cells.
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36
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Ocular delivery of CRISPR/Cas genome editing components for treatment of eye diseases. Adv Drug Deliv Rev 2021; 168:181-195. [PMID: 32603815 DOI: 10.1016/j.addr.2020.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/02/2020] [Accepted: 06/12/2020] [Indexed: 12/26/2022]
Abstract
A variety of inherited or multifactorial ocular diseases call for novel treatment paradigms. The newly developed genome editing technology, CRISPR, has shown great promise in treating these diseases, but delivery of the CRISPR/Cas components to target ocular tissues and cells requires appropriate use of vectors and routes of administration to ensure safety, efficacy and specificity. Although adeno-associated viral (AAV) vectors are thus far the most commonly used tool for ocular gene delivery, sustained expression of CRISPR/Cas components may cause immune reactions and an increased risk of off-target editing. In this review, we summarize the ocular administration routes and discuss the advantages and disadvantages of viral and non-viral vectors for delivery of CRISPR/Cas components to the eye. We review the existing studies of CRISPR/Cas genome editing for ocular diseases and discuss the major challenges of the technology in ocular applications. We also discuss the most recently developed CRISPR tools such as base editing and prime editing which may be used for future ocular applications.
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37
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Hayashi H, Kubo Y, Izumida M, Matsuyama T. Efficient viral delivery of Cas9 into human safe harbor. Sci Rep 2020; 10:21474. [PMID: 33293588 PMCID: PMC7722726 DOI: 10.1038/s41598-020-78450-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Gene editing using CRISPR/Cas9 is a promising method to cure many human genetic diseases. We have developed an efficient system to deliver Cas9 into the adeno-associated virus integration site 1 (AAVS1) locus, known as a safe harbor, using lentivirus and AAV viral vectors, as a step toward future in vivo transduction. First, we introduced Cas9v1 (derived from Streptococcus pyogenes) at random into the genome using a lentiviral vector. Cas9v1 activity was used when the N-terminal 1.9 kb, and C-terminal 2.3 kb fragments of another Cas9v2 (human codon-optimized) were employed sequentially with specific single-guide RNAs (sgRNAs) and homology donors carried by AAV vectors into the AAVS1 locus. Then, Cas9v1 was removed from the genome by another AAV vector containing sgRNA targeting the long terminal repeat of the lentivirus vector. The reconstituted Cas9v2 in the AAVS1 locus was functional and gene editing was efficient.
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Affiliation(s)
- Hideki Hayashi
- Medical University Research Administrator, Nagasaki University School of Medicine, Nagasaki, Japan.
| | - Yoshinao Kubo
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Mai Izumida
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Toshifumi Matsuyama
- Department of Pathology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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Ma L, Ruan J, Song J, Wen L, Yang D, Zhao J, Xia X, Chen YE, Zhang J, Xu J. MiCas9 increases large size gene knock-in rates and reduces undesirable on-target and off-target indel edits. Nat Commun 2020; 11:6082. [PMID: 33247137 PMCID: PMC7695827 DOI: 10.1038/s41467-020-19842-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/29/2020] [Indexed: 01/09/2023] Open
Abstract
Gene editing nuclease represented by Cas9 efficiently generates DNA double strand breaks at the target locus, followed by repair through either the error-prone non-homologous end joining or the homology directed repair pathways. To improve Cas9's homology directed repair capacity, here we report the development of miCas9 by fusing a minimal motif consisting of thirty-six amino acids to spCas9. MiCas9 binds RAD51 through this fusion motif and enriches RAD51 at the target locus. In comparison to spCas9, miCas9 enhances double-stranded DNA mediated large size gene knock-in rates, systematically reduces off-target insertion and deletion events, maintains or increases single-stranded oligodeoxynucleotides mediated precise gene editing rates, and effectively reduces on-target insertion and deletion rates in knock-in applications. Furthermore, we demonstrate that this fusion motif can work as a "plug and play" module, compatible and synergistic with other Cas9 variants. MiCas9 and the minimal fusion motif may find broad applications in gene editing research and therapeutics.
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Affiliation(s)
- Linyuan Ma
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Jinxue Ruan
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Luan Wen
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Dongshan Yang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Jiangyang Zhao
- Research & Development, ATGC Inc., 100 E Lancaster Avenue, LIMR Building Lab129, Wynnewood, PA, 19096, USA
| | - Xiaofeng Xia
- Research & Development, ATGC Inc., 100 E Lancaster Avenue, LIMR Building Lab129, Wynnewood, PA, 19096, USA
| | - Y Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA.
| | - Jifeng Zhang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA.
| | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA.
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Shin SW, Lee JS. CHO Cell Line Development and Engineering via Site-specific Integration: Challenges and Opportunities. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0093-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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40
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Zhang QS, Tiyaboonchai A, Nygaard S, Baradar K, Major A, Balaji N, Grompe M. Induced Liver Regeneration Enhances CRISPR/Cas9-Mediated Gene Repair in Tyrosinemia Type 1. Hum Gene Ther 2020; 32:294-301. [PMID: 32729326 DOI: 10.1089/hum.2020.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The efficiency of gene repair by homologous recombination in the liver is enhanced by CRISP/Cas9 incision near the mutation. In this study, we explored interventions designed to further enhance in vivo hepatocyte gene repair in a model of hereditary tyrosinemia. A two-AAV system was employed: one virus carried a Staphylococcus pyogenes Cas9 (SpCas9) expression cassette and the other harbored a U6 promoter-driven sgRNA and a fragment of fumarylacetoacetate hydrolase (Fah) genomic DNA as the homologous recombination donor. In neonatal mice, a gene correction frequency of ∼10.8% of hepatocytes was achieved. The efficiency in adult mice was significantly lower at ∼1.6%. To determine whether hepatocyte replication could enhance the targeting frequency, cell division was induced with thyroid hormone T3. This more than doubled the gene correction efficiency to 3.5% (p < 0.005). To determine whether SpCas9 delivery was rate limiting, the gene repair AAV was administered to SpCas9 transgenic mice. However, this did not significantly enhance gene repair. Finally, we tested whether the Fanconi anemia (FA) DNA repair pathway was important in hepatocyte gene repair. Gene correction frequencies were significantly lower in neonatal mice lacking the FA complementation group A (Fanca) gene. Taken together, we conclude that pharmacological induction of hepatocyte replication along with manipulation of DNA repair pathways could be a useful strategy for enhancing in vivo gene correction.
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Affiliation(s)
- Qing-Shuo Zhang
- Department of Pediatrics, Oregon Stem Cell Center, Oregon Health and Science University, Portland, Oregon, USA
| | - Amita Tiyaboonchai
- Department of Pediatrics, Oregon Stem Cell Center, Oregon Health and Science University, Portland, Oregon, USA
| | - Sean Nygaard
- Department of Pediatrics, Oregon Stem Cell Center, Oregon Health and Science University, Portland, Oregon, USA
| | - Kevin Baradar
- Department of Pediatrics, Oregon Stem Cell Center, Oregon Health and Science University, Portland, Oregon, USA
| | - Angela Major
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Niveditha Balaji
- Department of Pediatrics, Oregon Stem Cell Center, Oregon Health and Science University, Portland, Oregon, USA
| | - Markus Grompe
- Department of Pediatrics, Oregon Stem Cell Center, Oregon Health and Science University, Portland, Oregon, USA
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41
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Yang H, Ren S, Yu S, Pan H, Li T, Ge S, Zhang J, Xia N. Methods Favoring Homology-Directed Repair Choice in Response to CRISPR/Cas9 Induced-Double Strand Breaks. Int J Mol Sci 2020; 21:E6461. [PMID: 32899704 PMCID: PMC7555059 DOI: 10.3390/ijms21186461] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 12/15/2022] Open
Abstract
Precise gene editing is-or will soon be-in clinical use for several diseases, and more applications are under development. The programmable nuclease Cas9, directed by a single-guide RNA (sgRNA), can introduce double-strand breaks (DSBs) in target sites of genomic DNA, which constitutes the initial step of gene editing using this novel technology. In mammals, two pathways dominate the repair of the DSBs-nonhomologous end joining (NHEJ) and homology-directed repair (HDR)-and the outcome of gene editing mainly depends on the choice between these two repair pathways. Although HDR is attractive for its high fidelity, the choice of repair pathway is biased in a biological context. Mammalian cells preferentially employ NHEJ over HDR through several mechanisms: NHEJ is active throughout the cell cycle, whereas HDR is restricted to S/G2 phases; NHEJ is faster than HDR; and NHEJ suppresses the HDR process. This suggests that definitive control of outcome of the programmed DNA lesioning could be achieved through manipulating the choice of cellular repair pathway. In this review, we summarize the DSB repair pathways, the mechanisms involved in choice selection based on DNA resection, and make progress in the research investigating strategies that favor Cas9-mediated HDR based on the manipulation of repair pathway choice to increase the frequency of HDR in mammalian cells. The remaining problems in improving HDR efficiency are also discussed. This review should facilitate the development of CRISPR/Cas9 technology to achieve more precise gene editing.
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Affiliation(s)
| | | | | | | | - Tingdong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Collaborative Innovation Centers of Biological Products, School of Public Health, Xiamen University, Xiamen 361102, China; (H.Y.); (S.R.); (S.Y.); (H.P.); (J.Z.); (N.X.)
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Collaborative Innovation Centers of Biological Products, School of Public Health, Xiamen University, Xiamen 361102, China; (H.Y.); (S.R.); (S.Y.); (H.P.); (J.Z.); (N.X.)
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42
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Modulation of DNA double-strand break repair as a strategy to improve precise genome editing. Oncogene 2020; 39:6393-6405. [PMID: 32884115 DOI: 10.1038/s41388-020-01445-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/07/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
In the present day, it is possible to incorporate targeted mutations or replace a gene using genome editing techniques such as customisable CRISPR/Cas9 system. Although induction of DNA double-strand breaks (DSBs) by genome editing tools can be repaired by both non-homologous end joining (NHEJ) and homologous recombination (HR), the skewness of the former pathway in human and other mammals normally result in imprecise repair. Scientists working at the crossroads of DNA repair and genome editing have devised new strategies for using a specific pathway to their advantage. Refinement in the efficiency of precise gene editing was witnessed upon downregulation of NHEJ by knockdown or using small molecule inhibitors on one hand, and upregulation of HR proteins and addition of HR stimulators, other hand. The exploitation of cell cycle phase differences together with appropriate donor DNA length/sequence and small molecules has provided further improvement in precise genome editing. The present article reviews the mechanisms of improving the efficiency of precise genome editing in several model organisms and in clinics.
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43
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Howard SM, Ceppi I, Anand R, Geiger R, Cejka P. The internal region of CtIP negatively regulates DNA end resection. Nucleic Acids Res 2020; 48:5485-5498. [PMID: 32347940 PMCID: PMC7261161 DOI: 10.1093/nar/gkaa273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 04/05/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022] Open
Abstract
DNA double-strand breaks are repaired by end-joining or homologous recombination. A key-committing step of recombination is DNA end resection. In resection, phosphorylated CtIP first promotes the endonuclease of MRE11-RAD50-NBS1 (MRN). Subsequently, CtIP also stimulates the WRN/BLM-DNA2 pathway, coordinating thus both short and long-range resection. The structure of CtIP differs from its orthologues in yeast, as it contains a large internal unstructured region. Here, we conducted a domain analysis of CtIP to define the function of the internal region in DNA end resection. We found that residues 350-600 were entirely dispensable for resection in vitro. A mutant lacking these residues was unexpectedly more efficient than full-length CtIP in DNA end resection and homologous recombination in vivo, and consequently conferred resistance to lesions induced by the topoisomerase poison camptothecin, which require high MRN-CtIP-dependent resection activity for repair. This suggested that the internal CtIP region, further mapped to residues 550-600, may mediate a negative regulatory function to prevent over resection in vivo. The CtIP internal deletion mutant exhibited sensitivity to other DNA-damaging drugs, showing that upregulated resection may be instead toxic under different conditions. These experiments together identify a region within the central CtIP domain that negatively regulates DNA end resection.
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Affiliation(s)
- Sean Michael Howard
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland
| | - Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Roger Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland
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44
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Reginato G, Cejka P. The MRE11 complex: A versatile toolkit for the repair of broken DNA. DNA Repair (Amst) 2020; 91-92:102869. [PMID: 32480356 DOI: 10.1016/j.dnarep.2020.102869] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022]
Abstract
When DNA breaks, the ends need to be stabilized and processed to facilitate subsequent repair, which can occur by either direct but error-prone end-joining with another broken DNA molecule or a more accurate homology-directed repair by the recombination machinery. At the same time, the presence of broken DNA triggers a signaling cascade that regulates the repair events and cellular progression through the cell cycle. The MRE11 nuclease, together with RAD50 and NBS1 forms a complex termed MRN that participates in all these processes. Although MRE11 was first identified more than 20 years ago, deep insights into its mechanism of action and regulation are much more recent. Here we review how MRE11 functions within MRN, and how the complex is further regulated by CtIP and its phosphorylation in a cell cycle dependent manner. We describe how RAD50, NBS1 and CtIP convert MRE11, exhibiting per se a 3'→5' exonuclease activity, into an ensemble that instead degrades primarily the 5'-terminated strand by endonucleolytic cleavage at DNA break sites to generate 3' overhangs, as required for the initiation of homologous recombination. The unique mechanism of DNA end resection by MRN-CtIP makes it a very flexible toolkit to process DNA breaks with a variety of secondary structures and protein blocks. Such a block can also be the Ku heterodimer, and emerging evidence suggests that MRN-CtIP may often need to remove Ku from DNA ends before initiating homologous recombination. Misregulation of DNA break repair results in mutations and chromosome rearrangements that can drive cancer development. Therefore, a detailed understanding of the underlying processes is highly relevant for human health.
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Affiliation(s)
- Giordano Reginato
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
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45
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Maurissen TL, Woltjen K. Synergistic gene editing in human iPS cells via cell cycle and DNA repair modulation. Nat Commun 2020; 11:2876. [PMID: 32513994 PMCID: PMC7280248 DOI: 10.1038/s41467-020-16643-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/13/2020] [Indexed: 01/08/2023] Open
Abstract
Precise gene editing aims at generating single-nucleotide modifications to correct or model human disease. However, precision editing with nucleases such as CRIPSR-Cas9 has seen limited success due to poor efficiency and limited practicality. Here, we establish a fluorescent DNA repair assay in human induced pluripotent stem (iPS) cells to visualize and quantify the frequency of DNA repair outcomes during monoallelic and biallelic targeting. We found that modulating both DNA repair and cell cycle phase via defined culture conditions and small molecules synergistically enhanced the frequency of homology-directed repair (HDR). Notably, targeting in homozygous reporter cells results in high levels of editing with a vast majority of biallelic HDR outcomes. We then leverage efficient biallelic HDR with mixed ssODN repair templates to generate heterozygous mutations. Synergistic gene editing represents an effective strategy to generate precise genetic modifications in human iPS cells. Precision editing with CRISPR-Cas9 often suffers from poor efficiency. Here the authors identify culture conditions and small molecules that synergize to promote homology-directed repair (HDR) in induced pluripotent stem (iPS) cells.
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Affiliation(s)
- Thomas L Maurissen
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.,Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan.
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46
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Improving Precise CRISPR Genome Editing by Small Molecules: Is there a Magic Potion? Cells 2020; 9:cells9051318. [PMID: 32466303 PMCID: PMC7291049 DOI: 10.3390/cells9051318] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/01/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) genome editing has become a standard method in molecular biology, for the establishment of genetically modified cellular and animal models, for the identification and validation of drug targets in animals, and is heavily tested for use in gene therapy of humans. While the efficiency of CRISPR mediated gene targeting is much higher than of classical targeted mutagenesis, the efficiency of CRISPR genome editing to introduce defined changes into the genome is still low. Overcoming this problem will have a great impact on the use of CRISPR genome editing in academic and industrial research and the clinic. This review will present efforts to achieve this goal by small molecules, which modify the DNA repair mechanisms to facilitate the precise alteration of the genome.
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47
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Pasquini G, Cora V, Swiersy A, Achberger K, Antkowiak L, Müller B, Wimmer T, Fraschka SAK, Casadei N, Ueffing M, Liebau S, Stieger K, Busskamp V. Using Transcriptomic Analysis to Assess Double-Strand Break Repair Activity: Towards Precise in vivo Genome Editing. Int J Mol Sci 2020; 21:E1380. [PMID: 32085662 PMCID: PMC7073035 DOI: 10.3390/ijms21041380] [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: 01/23/2020] [Revised: 02/13/2020] [Accepted: 02/15/2020] [Indexed: 12/17/2022] Open
Abstract
Mutations in more than 200 retina-specific genes have been associated with inherited retinal diseases. Genome editing represents a promising emerging field in the treatment of monogenic disorders, as it aims to correct disease-causing mutations within the genome. Genome editing relies on highly specific endonucleases and the capacity of the cells to repair double-strand breaks (DSBs). As DSB pathways are cell-cycle dependent, their activity in postmitotic retinal neurons, with a focus on photoreceptors, needs to be assessed in order to develop therapeutic in vivo genome editing. Three DSB-repair pathways are found in mammalian cells: Non-homologous end joining (NHEJ); microhomology-mediated end joining (MMEJ); and homology-directed repair (HDR). While NHEJ can be used to knock out mutant alleles in dominant disorders, HDR and MMEJ are better suited for precise genome editing, or for replacing entire mutation hotspots in genomic regions. Here, we analyzed transcriptomic in vivo and in vitro data and revealed that HDR is indeed downregulated in postmitotic neurons, whereas MMEJ and NHEJ are active. Using single-cell RNA sequencing analysis, we characterized the dynamics of DSB repair pathways in the transition from dividing cells to postmitotic retinal cells. Time-course bulk RNA-seq data confirmed DSB repair gene expression in both in vivo and in vitro samples. Transcriptomic DSB repair pathway profiles are very similar in adult human, macaque, and mouse retinas, but not in ground squirrel retinas. Moreover, human-induced pluripotent stem-cell-derived neurons and retinal organoids can serve as well suited in vitro testbeds for developing genomic engineering approaches in photoreceptors. Our study provides additional support for designing precise in vivo genome-editing approaches via MMEJ, which is active in mature photoreceptors.
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Affiliation(s)
- Giovanni Pasquini
- Center for Regenerative Therapies (CRTD), Technical University Dresden, 01307 Dresden, Germany
| | - Virginia Cora
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Anka Swiersy
- Center for Regenerative Therapies (CRTD), Technical University Dresden, 01307 Dresden, Germany
| | - Kevin Achberger
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Lena Antkowiak
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Brigitte Müller
- Department of Ophthalmology, Justus-Liebig-University, 35392 Giessen, Germany
| | - Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University, 35392 Giessen, Germany
| | - Sabine Anne-Kristin Fraschka
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- DFG NGS Competence Center Tübingen, 72076 Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- DFG NGS Competence Center Tübingen, 72076 Tübingen, Germany
| | - Marius Ueffing
- Department of Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Liebau
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University, 35392 Giessen, Germany
| | - Volker Busskamp
- Center for Regenerative Therapies (CRTD), Technical University Dresden, 01307 Dresden, Germany
- Universitäts-Augenklinik Bonn, University of Bonn, Dept. of Ophthalmology, 53127 Bonn, Germany
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Reuven N, Adler J, Broennimann K, Myers N, Shaul Y. Recruitment of DNA Repair MRN Complex by Intrinsically Disordered Protein Domain Fused to Cas9 Improves Efficiency of CRISPR-Mediated Genome Editing. Biomolecules 2019; 9:E584. [PMID: 31597252 PMCID: PMC6843829 DOI: 10.3390/biom9100584] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 is a powerful tool for genome editing in cells and organisms. Nevertheless, introducing directed templated changes by homology-directed repair (HDR) requires the cellular DNA repair machinery, such as the MRN complex (Mre11/Rad50/Nbs1). To improve the process, we tailored chimeric constructs of Cas9, in which SpCas9 was fused at its N- or C-terminus to a 126aa intrinsically disordered domain from HSV-1 alkaline nuclease (UL12) that recruits the MRN complex. The chimeric Cas9 constructs were two times more efficient in homology-directed editing of endogenous loci in tissue culture cells. This effect was dependent upon the MRN-recruiting activity of the domain and required lower amounts of the chimeric Cas9 in comparison with unmodified Cas9. The new constructs improved the yield of edited cells when making endogenous point mutations or inserting small tags encoded by oligonucleotide donor DNA (ssODN), and also with larger insertions encoded by plasmid DNA donor templates. Improved editing was achieved with both transfected plasmid-encoded Cas9 constructs as well as recombinant Cas9 protein transfected as ribonucleoprotein complexes. Our strategy was highly efficient in restoring a genetic defect in a cell line, exemplifying the possible implementation of our strategy in gene therapy. These constructs provide a simple approach to improve directed editing.
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Affiliation(s)
- Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Julia Adler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Karin Broennimann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Nadav Myers
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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