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Feng Q, Li Q, Zhou H, Wang Z, Lin C, Jiang Z, Liu T, Wang D. CRISPR technology in human diseases. MedComm (Beijing) 2024; 5:e672. [PMID: 39081515 PMCID: PMC11286548 DOI: 10.1002/mco2.672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Gene editing is a growing gene engineering technique that allows accurate editing of a broad spectrum of gene-regulated diseases to achieve curative treatment and also has the potential to be used as an adjunct to the conventional treatment of diseases. Gene editing technology, mainly based on clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein systems, which is capable of generating genetic modifications in somatic cells, provides a promising new strategy for gene therapy for a wide range of human diseases. Currently, gene editing technology shows great application prospects in a variety of human diseases, not only in therapeutic potential but also in the construction of animal models of human diseases. This paper describes the application of gene editing technology in hematological diseases, solid tumors, immune disorders, ophthalmological diseases, and metabolic diseases; focuses on the therapeutic strategies of gene editing technology in sickle cell disease; provides an overview of the role of gene editing technology in the construction of animal models of human diseases; and discusses the limitations of gene editing technology in the treatment of diseases, which is intended to provide an important reference for the applications of gene editing technology in the human disease.
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Affiliation(s)
- Qiang Feng
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
- Research and Development CentreBaicheng Medical CollegeBaichengChina
| | - Qirong Li
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Hengzong Zhou
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Zhan Wang
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Chao Lin
- School of Grain Science and TechnologyJilin Business and Technology CollegeChangchunChina
| | - Ziping Jiang
- Department of Hand and Foot SurgeryThe First Hospital of Jilin UniversityChangchunChina
| | - Tianjia Liu
- Research and Development CentreBaicheng Medical CollegeBaichengChina
| | - Dongxu Wang
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
- Department of Hand and Foot SurgeryThe First Hospital of Jilin UniversityChangchunChina
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2
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Han Y, Jia Z, Xu K, Li Y, Lu S, Guan L. CRISPR-Cpf1 system and its applications in animal genome editing. Mol Genet Genomics 2024; 299:75. [PMID: 39085660 DOI: 10.1007/s00438-024-02166-x] [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: 11/20/2023] [Accepted: 07/11/2024] [Indexed: 08/02/2024]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein (Cas) system is a gene editing technology guided by RNA endonuclease. The CRISPR-Cas12a (also known as CRISPR-Cpf1) system is extensively utilized in genome editing research due to its accuracy and high efficiency. In this paper, we primarily focus on the application of CRISPR-Cpf1 technology in the construction of disease models and gene therapy. Firstly, the structure and mechanism of the CRISPR-Cas system are introduced. Secondly, the similarities and differences between CRISPR-Cpf1 and CRISPR-Cas9 technologies are compared. Thirdly, the main focus is on the application of the CRISPR-Cpf1 system in cell and animal genome editing. Finally, the challenges faced by CRISPR-Cpf1 technology and corresponding strategies are analyzed. Although CRISPR-Cpf1 technology has certain off-target effects, it can effectively and accurately edit cell and animal genomes, and has significant advantages in the preclinical research.
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Affiliation(s)
- Yawei Han
- College of Tobacco Science and Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, Henan, China
| | - Zisen Jia
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Number 601, Jinsui Road, Xinxiang, 453003, Henan, China
| | - Keli Xu
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Number 601, Jinsui Road, Xinxiang, 453003, Henan, China
| | - Yangyang Li
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Number 601, Jinsui Road, Xinxiang, 453003, Henan, China
| | - Suxiang Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Lihong Guan
- Stem Cells and Biotherapy Engineering Research Center of Henan, National Joint Engineering Laboratory of Stem Cells and Biotherapy, School of Life Science and Technology, Xinxiang Medical University, Number 601, Jinsui Road, Xinxiang, 453003, Henan, China.
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Ruan J, Yu X, Xu H, Cui W, Zhang K, Liu C, Sun W, Huang X, An L, Zhang Y. Suppressor tRNA in gene therapy. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2613-y. [PMID: 38926247 DOI: 10.1007/s11427-024-2613-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/08/2024] [Indexed: 06/28/2024]
Abstract
Suppressor tRNAs are engineered or naturally occurring transfer RNA molecules that have shown promise in gene therapy for diseases caused by nonsense mutations, which result in premature termination codons (PTCs) in coding sequence, leading to truncated, often nonfunctional proteins. Suppressor tRNAs can recognize and pair with these PTCs, allowing the ribosome to continue translation and produce a full-length protein. This review introduces the mechanism and development of suppressor tRNAs, compares suppressor tRNAs with other readthrough therapies, discusses their potential for clinical therapy, limitations, and obstacles. We also summarize the applications of suppressor tRNAs in both in vitro and in vivo, offering new insights into the research and treatment of nonsense mutation diseases.
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Affiliation(s)
- Jingjing Ruan
- The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Liangzhu Laboratory, Hangzhou, 310000, China
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Xiaoxiao Yu
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Huixia Xu
- Department of Thoracic and Cardiovascular Surgery, Huaihe Hospital of Henan University, Henan University, Kaifeng, 475000, China
| | - Wenrui Cui
- Translational Medicine Center, Huaihe Hospital of Henan University, Henan University, Kaifeng, 475000, China
| | - Kaiye Zhang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Chenyang Liu
- Translational Medicine Center, Huaihe Hospital of Henan University, Henan University, Kaifeng, 475000, China
| | - Wenlong Sun
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Xiaodan Huang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Lei An
- Translational Medicine Center, Huaihe Hospital of Henan University, Henan University, Kaifeng, 475000, China.
| | - Yue Zhang
- The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Liangzhu Laboratory, Hangzhou, 310000, China.
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China.
- Translational Medicine Center, Huaihe Hospital of Henan University, Henan University, Kaifeng, 475000, China.
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4
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Jin M, Lin J, Li H, Li Z, Yang D, Wang Y, Yu Y, Shao Z, Chen L, Wang Z, Zhang Y, Zhang X, Wang N, Xu C, Yang H, Chen WJ, Li G. Correction of human nonsense mutation via adenine base editing for Duchenne muscular dystrophy treatment in mouse. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102165. [PMID: 38571746 PMCID: PMC10988125 DOI: 10.1016/j.omtn.2024.102165] [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] [Received: 07/27/2023] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Duchenne muscular dystrophy (DMD) is the most prevalent herediatry disease in men, characterized by dystrophin deficiency, progressive muscle wasting, cardiac insufficiency, and premature mortality, with no effective therapeutic options. Here, we investigated whether adenine base editing can correct pathological nonsense point mutations leading to premature stop codons in the dystrophin gene. We identified 27 causative nonsense mutations in our DMD patient cohort. Treatment with adenine base editor (ABE) could restore dystrophin expression by direct A-to-G editing of pathological nonsense mutations in cardiomyocytes generated from DMD patient-derived induced pluripotent stem cells. We also generated two humanized mouse models of DMD expressing mutation-bearing exons 23 or 30 of human dystrophin gene. Intramuscular administration of ABE, driven by ubiquitous or muscle-specific promoters could correct these nonsense mutations in vivo, albeit with higher efficiency in exon 30, restoring dystrophin expression in skeletal fibers of humanized DMD mice. Moreover, a single systemic delivery of ABE with human single guide RNA (sgRNA) could induce body-wide dystrophin expression and improve muscle function in rotarod tests of humanized DMD mice. These findings demonstrate that ABE with human sgRNAs can confer therapeutic alleviation of DMD in mice, providing a basis for development of adenine base editing therapies in monogenic diseases.
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Affiliation(s)
- Ming Jin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Jiajia Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Haisen Li
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
- School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Zhifang Li
- Lingang Laboratory, Shanghai 200031, China
| | - Dong Yang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Yin Wang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Yuyang Yu
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Zhurui Shao
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Long Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Zhiqiang Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Yu Zhang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Xiumei Zhang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Chunlong Xu
- Lingang Laboratory, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China
| | - Hui Yang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China
| | - Wan-Jin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Guoling Li
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
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Wei J, Liu J, Wang Z, Yang Y, Tian Y, Wang S, Gao BQ, Gao S, Yang L, Tang J, Wang Y. Engineering of a high-fidelity Cas12a nuclease variant capable of allele-specific editing. PLoS Biol 2024; 22:e3002680. [PMID: 38865309 PMCID: PMC11168656 DOI: 10.1371/journal.pbio.3002680] [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: 07/23/2023] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Abstract
CRISPR-Cas12a, often regarded as a precise genome editor, still requires improvements in specificity. In this study, we used a GFP-activation assay to screen 14 new Cas12a nucleases for mammalian genome editing, successfully identifying 9 active ones. Notably, these Cas12a nucleases prefer pyrimidine-rich PAMs. Among these nucleases, we extensively characterized Mb4Cas12a obtained from Moraxella bovis CCUG 2133, which recognizes a YYN PAM (Y = C or T). Our biochemical analysis demonstrates that Mb4Cas12a can cleave double-strand DNA across a wide temperature range. To improve specificity, we constructed a SWISS-MODEL of Mb4Cas12a based on the FnCas12a crystal structure and identified 8 amino acids potentially forming hydrogen bonds at the target DNA-crRNA interface. By replacing these amino acids with alanine to disrupt the hydrogen bond, we tested the influence of each mutation on Mb4Cas12a specificity. Interestingly, the F370A mutation improved specificity with minimal influence on activity. Further study showed that Mb4Cas12a-F370A is capable of discriminating single-nucleotide polymorphisms. These new Cas12a orthologs and high-fidelity variants hold substantial promise for therapeutic applications.
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Affiliation(s)
- Jingjing Wei
- Department of Cardiology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Jingtong Liu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Ziwen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuan Yang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Yuwen Tian
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Shengzhou Wang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Bao-Qing Gao
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Molecular Medicine, Children’s Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Li Yang
- Center for Molecular Medicine, Children’s Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Junnan Tang
- Department of Cardiology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongming Wang
- Department of Cardiology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
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Shi H, Li L, Mu S, Gou S, Liu X, Chen F, Chen M, Jin Q, Lai L, Wang K. Exonuclease editor promotes precision of gene editing in mammalian cells. BMC Biol 2024; 22:119. [PMID: 38769511 PMCID: PMC11107001 DOI: 10.1186/s12915-024-01918-w] [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: 04/28/2023] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Many efforts have been made to improve the precision of Cas9-mediated gene editing through increasing knock-in efficiency and decreasing byproducts, which proved to be challenging. RESULTS Here, we have developed a human exonuclease 1-based genome-editing tool, referred to as exonuclease editor. When compared to Cas9, the exonuclease editor gave rise to increased HDR efficiency, reduced NHEJ repair frequency, and significantly elevated HDR/indel ratio. Robust gene editing precision of exonuclease editor was even superior to the fusion of Cas9 with E1B or DN1S, two previously reported precision-enhancing domains. Notably, exonuclease editor inhibited NHEJ at double strand breaks locally rather than globally, reducing indel frequency without compromising genome integrity. The replacement of Cas9 with single-strand DNA break-creating Cas9 nickase further increased the HDR/indel ratio by 453-fold than the original Cas9. In addition, exonuclease editor resulted in high microhomology-mediated end joining efficiency, allowing accurate and flexible deletion of targeted sequences with extended lengths with the aid of paired sgRNAs. Exonuclease editor was further used for correction of DMD patient-derived induced pluripotent stem cells, where 30.0% of colonies were repaired by HDR versus 11.1% in the control. CONCLUSIONS Therefore, the exonuclease editor system provides a versatile and safe genome editing tool with high precision and holds promise for therapeutic gene correction.
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Affiliation(s)
- Hui Shi
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
| | - Lei Li
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangshuang Mu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shixue Gou
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
| | - Xiaoyi Liu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangbing Chen
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Menglong Chen
- Department of Neurology and Stroke Centre, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Qin Jin
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
| | - Liangxue Lai
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
| | - Kepin Wang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
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Laurent M, Geoffroy M, Pavani G, Guiraud S. CRISPR-Based Gene Therapies: From Preclinical to Clinical Treatments. Cells 2024; 13:800. [PMID: 38786024 PMCID: PMC11119143 DOI: 10.3390/cells13100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
In recent years, clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) protein have emerged as a revolutionary gene editing tool to treat inherited disorders affecting different organ systems, such as blood and muscles. Both hematological and neuromuscular genetic disorders benefit from genome editing approaches but face different challenges in their clinical translation. The ability of CRISPR/Cas9 technologies to modify hematopoietic stem cells ex vivo has greatly accelerated the development of genetic therapies for blood disorders. In the last decade, many clinical trials were initiated and are now delivering encouraging results. The recent FDA approval of Casgevy, the first CRISPR/Cas9-based drug for severe sickle cell disease and transfusion-dependent β-thalassemia, represents a significant milestone in the field and highlights the great potential of this technology. Similar preclinical efforts are currently expanding CRISPR therapies to other hematologic disorders such as primary immunodeficiencies. In the neuromuscular field, the versatility of CRISPR/Cas9 has been instrumental for the generation of new cellular and animal models of Duchenne muscular dystrophy (DMD), offering innovative platforms to speed up preclinical development of therapeutic solutions. Several corrective interventions have been proposed to genetically restore dystrophin production using the CRISPR toolbox and have demonstrated promising results in different DMD animal models. Although these advances represent a significant step forward to the clinical translation of CRISPR/Cas9 therapies to DMD, there are still many hurdles to overcome, such as in vivo delivery methods associated with high viral vector doses, together with safety and immunological concerns. Collectively, the results obtained in the hematological and neuromuscular fields emphasize the transformative impact of CRISPR/Cas9 for patients affected by these debilitating conditions. As each field suffers from different and specific challenges, the clinical translation of CRISPR therapies may progress differentially depending on the genetic disorder. Ongoing investigations and clinical trials will address risks and limitations of these therapies, including long-term efficacy, potential genotoxicity, and adverse immune reactions. This review provides insights into the diverse applications of CRISPR-based technologies in both preclinical and clinical settings for monogenic blood disorders and muscular dystrophy and compare advances in both fields while highlighting current trends, difficulties, and challenges to overcome.
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Affiliation(s)
- Marine Laurent
- INTEGRARE, UMR_S951, Genethon, Inserm, Univ Evry, Université Paris-Saclay, 91190 Evry, France
| | | | - Giulia Pavani
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Simon Guiraud
- SQY Therapeutics, 78180 Montigny-le-Bretonneux, France
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8
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Wang Y, Zhai Y, Zhang M, Song C, Zhang Y, Zhang G. Escaping from CRISPR-Cas-mediated knockout: the facts, mechanisms, and applications. Cell Mol Biol Lett 2024; 29:48. [PMID: 38589794 PMCID: PMC11003099 DOI: 10.1186/s11658-024-00565-x] [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: 10/01/2023] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats and associated Cas protein (CRISPR-Cas), a powerful genome editing tool, has revolutionized gene function investigation and exhibits huge potential for clinical applications. CRISPR-Cas-mediated gene knockout has already become a routine method in research laboratories. However, in the last few years, accumulating evidences have demonstrated that genes knocked out by CRISPR-Cas may not be truly silenced. Functional residual proteins could be generated in such knockout organisms to compensate the putative loss of function, termed herein knockout escaping. In line with this, several CRISPR-Cas-mediated knockout screenings have discovered much less abnormal phenotypes than expected. How does knockout escaping happen and how often does it happen have not been systematically reviewed yet. Without knowing this, knockout results could easily be misinterpreted. In this review, we summarize these evidences and propose two main mechanisms allowing knockout escaping. To avoid the confusion caused by knockout escaping, several strategies are discussed as well as their advantages and disadvantages. On the other hand, knockout escaping also provides convenient tools for studying essential genes and treating monogenic disorders such as Duchenne muscular dystrophy, which are discussed in the end.
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Affiliation(s)
- Ying Wang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- School of Public Health, Qingdao University, Qingdao, China
| | - Yujing Zhai
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- School of Public Health, Qingdao University, Qingdao, China
| | - Mingzhe Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Chunlin Song
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yuqing Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Gang Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
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9
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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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10
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Badon IW, Oh Y, Kim HJ, Lee SH. Recent application of CRISPR-Cas12 and OMEGA system for genome editing. Mol Ther 2024; 32:32-43. [PMID: 37952084 PMCID: PMC10787141 DOI: 10.1016/j.ymthe.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
In 2012, it was discovered that precise gene editing could be induced in target DNA using the reprogrammable characteristics of the CRISPR system. Since then, several studies have investigated the potential of the CRISPR system to edit various biological organisms. For the typical CRISPR system obtained from bacteria and archaea, many application studies have been conducted and have spread to various fields. To date, orthologs with various characteristics other than CRISPR-Cas9 have been discovered and are being intensively studied in the field of gene editing. CRISPR-Cas12 and its varied orthologs are representative examples of genome editing tools and have superior properties in terms of in vivo target gene editing compared with Cas9. Recently, TnpB and Fanzor of the OMEGA (obligate mobile element guided activity) system were identified to be the ancestor of CRISPR-Cas12 on the basis of phylogenetic analysis. Notably, the compact sizes of Cas12 and OMEGA endonucleases allow adeno-associated virus (AAV) delivery; hence, they are set to challenge Cas9 for in vivo gene therapy. This review is focused on these RNA-guided reprogrammable endonucleases: their structure, biochemistry, off-target effects, and applications in therapeutic gene editing.
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Affiliation(s)
- Isabel Wen Badon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yeounsun Oh
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ho-Joong Kim
- Department of Chemistry, Chosun University, Gwangju 61452, Republic of Korea.
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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11
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Tyumentseva M, Tyumentsev A, Akimkin V. CRISPR/Cas9 Landscape: Current State and Future Perspectives. Int J Mol Sci 2023; 24:16077. [PMID: 38003266 PMCID: PMC10671331 DOI: 10.3390/ijms242216077] [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: 10/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (A.T.); (V.A.)
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12
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Roberts TC, Wood MJA, Davies KE. Therapeutic approaches for Duchenne muscular dystrophy. Nat Rev Drug Discov 2023; 22:917-934. [PMID: 37652974 DOI: 10.1038/s41573-023-00775-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a monogenic muscle-wasting disorder and a priority candidate for molecular and cellular therapeutics. Although rare, it is the most common inherited myopathy affecting children and so has been the focus of intense research activity. It is caused by mutations that disrupt production of the dystrophin protein, and a plethora of drug development approaches are under way that aim to restore dystrophin function, including exon skipping, stop codon readthrough, gene replacement, cell therapy and gene editing. These efforts have led to the clinical approval of four exon skipping antisense oligonucleotides, one stop codon readthrough drug and one gene therapy product, with other approvals likely soon. Here, we discuss the latest therapeutic strategies that are under development and being deployed to treat DMD. Lessons from these drug development programmes are likely to have a major impact on the DMD field, but also on molecular and cellular medicine more generally. Thus, DMD is a pioneer disease at the forefront of future drug discovery efforts, with these experimental treatments paving the way for therapies using similar mechanisms of action being developed for other genetic diseases.
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Affiliation(s)
- Thomas C Roberts
- Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
- MDUK Oxford Neuromuscular Centre, Oxford, UK.
| | - Matthew J A Wood
- Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
- MDUK Oxford Neuromuscular Centre, Oxford, UK
| | - Kay E Davies
- MDUK Oxford Neuromuscular Centre, Oxford, UK.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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13
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Ding L, Xu X, Wang X, Chen X, Lu Y, Xu J, Peng C. Qualitative and Quantitative Detection of CRISPR-Associated Cas Gene in Gene-Edited Foods. Foods 2023; 12:3681. [PMID: 37835336 PMCID: PMC10572612 DOI: 10.3390/foods12193681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Effective regulation of gene-edited products and resolution of public concerns are the prerequisites for the industrialization of gene-edited crops and their derived foods. CRISPR-associated protein, the core element of the CRISPR system, requires to be regulated. Thus, there is an urgent need to establish qualitative and quantitative detection methods for the Cas gene. In the present study, the primers and probes were designed and screened for Cas12a (Cpf1), which is the most commonly used target site in gene editing; we performed PCR system optimization, determined the optimal primer concentration and annealing temperature, and established qualitative PCR and quantitative PCR (qPCR) assays for detecting Cpf1 in gene editing by specificity and sensitivity tests. In specificity testing, qualitative PCR and qPCR methods could 100% detect samples containing Cpf1 DNA, while the detection rate of other samples without Cpf1 was 0%. In the assay sensitivity test, the limit of detection of qualitative PCR was 0.1% (approximately 44 copies), and the limit of detection of the qPCR method was 14 copies. In the stability test, both the qualitative PCR and qPCR methods were repeated 60 times at their corresponding lowest detection limit concentrations, and the results were positive. Thus, the qualitative and quantitative assays for Cpf1 are specific, sensitive, and stable. The method provides technical support for the effective monitoring of gene-edited products and their derived foods in the future.
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Affiliation(s)
- Lin Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoli Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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14
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Egorova TV, Polikarpova AV, Vassilieva SG, Dzhenkova MA, Savchenko IM, Velyaev OA, Shmidt AA, Soldatov VO, Pokrovskii MV, Deykin AV, Bardina MV. CRISPR-Cas9 correction in the DMD mouse model is accompanied by upregulation of Dp71f protein. Mol Ther Methods Clin Dev 2023; 30:161-180. [PMID: 37457303 PMCID: PMC10339130 DOI: 10.1016/j.omtm.2023.06.006] [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: 08/10/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a severe hereditary disease caused by a deficiency in the dystrophin protein. The most frequent types of disease-causing mutations in the DMD gene are frameshift deletions of one or more exons. Precision genome editing systems such as CRISPR-Cas9 have shown potential to restore open reading frames in numerous animal studies. Here, we applied an AAV-CRISPR double-cut strategy to correct a mutation in the DMD mouse model with exon 8-34 deletion, encompassing the N-terminal actin-binding domain. We report successful excision of the 100-kb genomic sequence, which includes exons 6 and 7, and partial improvement in cardiorespiratory function. While corrected mRNA was abundant in muscle tissues, only a low level of truncated dystrophin was produced, possibly because of protein instability. Furthermore, CRISPR-Cas9-mediated genome editing upregulated the Dp71f dystrophin isoform on the sarcolemma. Given the previously reported Dp71-associated muscle pathology, our results question the applicability of genome editing strategies for some DMD patients with N-terminal mutations. The safety and efficacy of CRISPR-Cas9 constructs require rigorous investigation in patient-specific animal models.
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Affiliation(s)
- Tatiana V. Egorova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
| | - Anna V. Polikarpova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
| | - Svetlana G. Vassilieva
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Marina A. Dzhenkova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Irina M. Savchenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Oleg A. Velyaev
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna A. Shmidt
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Vladislav O. Soldatov
- Research Institute of Living Systems Pharmacology, Belgorod National Research University, Belgorod 308007, Russia
| | - Mikhail V. Pokrovskii
- Research Institute of Living Systems Pharmacology, Belgorod National Research University, Belgorod 308007, Russia
| | - Alexey V. Deykin
- Marlin Biotech LLC, Sochi 354340, Russia
- Joint Center for Genetic Technologies, Laboratory of Genetic Technologies and Gene Editing for Biomedicine and Veterinary Medicine, Department of Pharmacology and Clinical Pharmacology, Belgorod National Research University, Belgorod 308015, Russia
| | - Maryana V. Bardina
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
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15
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Stirm M, Shashikadze B, Blutke A, Kemter E, Lange A, Stöckl JB, Jaudas F, Laane L, Kurome M, Keßler B, Zakhartchenko V, Bähr A, Klymiuk N, Nagashima H, Walter MC, Wurst W, Kupatt C, Fröhlich T, Wolf E. Systemic deletion of DMD exon 51 rescues clinically severe Duchenne muscular dystrophy in a pig model lacking DMD exon 52. Proc Natl Acad Sci U S A 2023; 120:e2301250120. [PMID: 37428903 PMCID: PMC10629550 DOI: 10.1073/pnas.2301250120] [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: 01/22/2023] [Accepted: 06/10/2023] [Indexed: 07/12/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal X-linked disease caused by mutations in the DMD gene, leading to complete absence of dystrophin and progressive degeneration of skeletal musculature and myocardium. In DMD patients and in a corresponding pig model with a deletion of DMD exon 52 (DMDΔ52), expression of an internally shortened dystrophin can be achieved by skipping of DMD exon 51 to reframe the transcript. To predict the best possible outcome of this strategy, we generated DMDΔ51-52 pigs, additionally representing a model for Becker muscular dystrophy (BMD). DMDΔ51-52 skeletal muscle and myocardium samples stained positive for dystrophin and did not show the characteristic dystrophic alterations observed in DMDΔ52 pigs. Western blot analysis confirmed the presence of dystrophin in the skeletal muscle and myocardium of DMDΔ51-52 pigs and its absence in DMDΔ52 pigs. The proteome profile of skeletal muscle, which showed a large number of abundance alterations in DMDΔ52 vs. wild-type (WT) samples, was normalized in DMDΔ51-52 samples. Cardiac function at age 3.5 mo was significantly reduced in DMDΔ52 pigs (mean left ventricular ejection fraction 58.8% vs. 70.3% in WT) but completely rescued in DMDΔ51-52 pigs (72.3%), in line with normalization of the myocardial proteome profile. Our findings indicate that ubiquitous deletion of DMD exon 51 in DMDΔ52 pigs largely rescues the rapidly progressing, severe muscular dystrophy and the reduced cardiac function of this model. Long-term follow-up studies of DMDΔ51-52 pigs will show if they develop symptoms of the milder BMD.
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Affiliation(s)
- Michael Stirm
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Bachuki Shashikadze
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich81377, Germany
| | - Andreas Blutke
- Institute of Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, Munich80539, Germany
| | - Elisabeth Kemter
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Andreas Lange
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Jan B. Stöckl
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich81377, Germany
| | - Florian Jaudas
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Laeticia Laane
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Mayuko Kurome
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Barbara Keßler
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Valeri Zakhartchenko
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
| | - Andrea Bähr
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar, Technical University Munich, Munich81675, Germany
| | - Nikolai Klymiuk
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar, Technical University Munich, Munich81675, Germany
| | - Hiroshi Nagashima
- Meiji University International Institute for Bio-Resource Research, Kawasaki214-8571, Japan
| | - Maggie C. Walter
- Department of Neurology, Friedrich Baur Institute, LMU Munich, Munich80336, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Munich, Neuherberg85674, Germany
- Chair of Developmental Genetics, TUM School of Life Sciences, Technische Universität München, Freising85354, Germany
| | - Christian Kupatt
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar, Technical University Munich, Munich81675, Germany
- German Center for Cardiovascular Research, Munich Heart Alliance, Munich81675, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich81377, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich81377, Germany
- Center for Innovative Medical Models, Department of Veterinary Sciences, LMU Munich, Oberschleissheim85764, Germany
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich81377, Germany
- Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer, LMU Munich, Munich81377, Germany
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16
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Bez Batti Angulski A, Hosny N, Cohen H, Martin AA, Hahn D, Bauer J, Metzger JM. Duchenne muscular dystrophy: disease mechanism and therapeutic strategies. Front Physiol 2023; 14:1183101. [PMID: 37435300 PMCID: PMC10330733 DOI: 10.3389/fphys.2023.1183101] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/24/2023] [Indexed: 07/13/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe, progressive, and ultimately fatal disease of skeletal muscle wasting, respiratory insufficiency, and cardiomyopathy. The identification of the dystrophin gene as central to DMD pathogenesis has led to the understanding of the muscle membrane and the proteins involved in membrane stability as the focal point of the disease. The lessons learned from decades of research in human genetics, biochemistry, and physiology have culminated in establishing the myriad functionalities of dystrophin in striated muscle biology. Here, we review the pathophysiological basis of DMD and discuss recent progress toward the development of therapeutic strategies for DMD that are currently close to or are in human clinical trials. The first section of the review focuses on DMD and the mechanisms contributing to membrane instability, inflammation, and fibrosis. The second section discusses therapeutic strategies currently used to treat DMD. This includes a focus on outlining the strengths and limitations of approaches directed at correcting the genetic defect through dystrophin gene replacement, modification, repair, and/or a range of dystrophin-independent approaches. The final section highlights the different therapeutic strategies for DMD currently in clinical trials.
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Affiliation(s)
| | | | | | | | | | | | - Joseph M. Metzger
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, United States
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17
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Varghese DS, Oommen D, John A, Ali BR. GRP78/BiP alleviates oxLDL-induced hepatotoxicity in familial hypercholesterolemia caused by missense variants of LDLR in a HepG2 cellular model. Lipids Health Dis 2023; 22:69. [PMID: 37248472 DOI: 10.1186/s12944-023-01835-x] [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: 02/22/2023] [Accepted: 05/13/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND AND AIMS The accumulation of misfolded proteins, encoded by genetic variants of functional genes leads to Endoplasmic Reticulum (ER) stress, which is a critical consequence in human disorders such as familial hypercholesterolemia, cardiovascular and hepatic diseases. In addition to the identification of ER stress as a contributing factor to pathogenicity, extensive studies on the role of oxidized Low-Density Lipoprotein (oxLDL) and its ill effects in expediting cardiovascular diseases and other metabolic comorbidities are well documented. However, the current understanding of its role in hepatic insults needs to be revised. This study elucidates the molecular mechanisms underlying the progression of oxLDL and ER stress-induced cytotoxicity in HepG2. METHODS HepG2 cells stably expressing wild-type Low-Density lipoprotein receptor (WT-LDLR) and missense variants of LDLR that are pathogenically associated with familial hypercholesterolemia were used as the in vitro models. The relative mRNA expression and protein profiles of ER stress sensors, inflammatory and apoptotic markers, together with cytotoxic assays and measurement of mitochondrial membrane potential, were carried out in HepG2 cells treated with 100 µg per ml oxLDL for 24 to 48 h. 1-way or 2-way ANOVA was used for statistical analyses of datasets. RESULTS ER stress responses are elicited along all three arms of the unfolded protein response (UPR), with adverse cytotoxic and inflammatory responses in oxLDL-treated conditions. Interestingly, oxLDL-treated ER-stressed HepG2 cells manifested intriguingly low expression of BiP- the master regulator of ER stress, as observed earlier by various researchers in liver biopsies of Non-Alcoholic Steatohepatitis (NASH) patients. This study shows that overexpression of BiP rescues hepatic cells from cytotoxic and inflammatory mechanisms instigated by ER stress in combination with oxLDL, along the ER and mitochondrial membrane and restores cellular homeostasis. CONCLUSION The data provide interesting leads that identify patients with familial hypercholesterolemia conditions and potentially other Endoplasmic Reticulum Associated Degradation (ERAD) diseases as highly susceptible to developing hepatic insults with molecular signatures like those manifested in Non-Alcoholic Fatty Liver Disease (NAFLD) and NASH. LIMITATIONS AND FUTURE PERSPECTIVES Although the use of HepG2 cells as the model is a major caveat of the study, the findings of this research may be used as the pilot study to expand further investigations in primary hepatocytes or iPSC- derived cellular models.
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Affiliation(s)
- Divya Saro Varghese
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Deepu Oommen
- Present Address: Indian Institute of Science, C V Raman Road, 560012, Bangalore, India
| | - Anne John
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
- Zayed Centre for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.
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18
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Yang X, Zhang B. A review on CRISPR/Cas: a versatile tool for cancer screening, diagnosis, and clinic treatment. Funct Integr Genomics 2023; 23:182. [PMID: 37231285 DOI: 10.1007/s10142-023-01117-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
Cancer is one of the leading causes of death worldwide and it has the trend of increase incidence. However, in the past decades, as quickly developed new technologies and modified old techniques for cancer screening, diagnosis, and treatment, the cancer-caused mortality rates dropped quickly, and the survival times of cancer patients are enhanced. However, the current death rate is still about 50% and the survival patients always suffer from the side effect of current cancer treatments. Recently developed Nobel Prize-winning CRISPR/Cas technology provides new hope on cancer screening, early diagnosis, and clinic treatment as well as new drug development. Currently, four major CRISPR/Cas9-derived genome editors, CRISPR/Cas9 nucleotide sequence editor, CRISPR/Cas base editor (BE), CRISPR prime editor (PE), and CRISPR interference (CRISPRi) (including both CRISPRa and CRISPRr), were well developed and used to various research and applications, including cancer biology study and cancer screening, diagnosis, and treatment. Additionally, CRISPR/Cas12 and CRISPR/Cas13 genome editors were also widely used in cancer-related basic and applied research as well as treatment. Cancer-associated SNPs and genetic mutations as well as both oncogenes and tumor suppressor genes are perfect targets for CRISPR/Cas-based gene therapy for cancer treatment. CRISPR/Cas is also employed to modify and generate new Chimeric antigen receptor (CAR) T-cells for improving its safety, efficiency, and longer-time last for treating various cancers. Currently, there are many clinic trails of CRISPR-based gene therapy for cancer treatments. Although all CRISPR/Cas-derived genome and epigenome tools are promising methods for cancer biology study and treatment, the efficiency and long term-safety are still the major concerns for CRISPR-based gene therapy. Developing new CRISPR/Cas delivery methods and reducing the potential side effects, including off-target impacts, will enhance CRISPR/Cas application in cancer-related research, diagnosis, and therapeutical treatment.
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Affiliation(s)
- Xianguang Yang
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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19
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Eisen B, Binah O. Modeling Duchenne Muscular Dystrophy Cardiomyopathy with Patients' Induced Pluripotent Stem-Cell-Derived Cardiomyocytes. Int J Mol Sci 2023; 24:ijms24108657. [PMID: 37240001 DOI: 10.3390/ijms24108657] [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: 04/20/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle degenerative disease caused by mutations in the dystrophin gene, resulting in death by the end of the third decade of life at the latest. A key aspect of the DMD clinical phenotype is dilated cardiomyopathy, affecting virtually all patients by the end of the second decade of life. Furthermore, despite respiratory complications still being the leading cause of death, with advancements in medical care in recent years, cardiac involvement has become an increasing cause of mortality. Over the years, extensive research has been conducted using different DMD animal models, including the mdx mouse. While these models present certain important similarities to human DMD patients, they also have some differences which pose a challenge to researchers. The development of somatic cell reprograming technology has enabled generation of human induced pluripotent stem cells (hiPSCs) which can be differentiated into different cell types. This technology provides a potentially endless pool of human cells for research. Furthermore, hiPSCs can be generated from patients, thus providing patient-specific cells and enabling research tailored to different mutations. DMD cardiac involvement has been shown in animal models to include changes in gene expression of different proteins, abnormal cellular Ca2+ handling, and other aberrations. To gain a better understanding of the disease mechanisms, it is imperative to validate these findings in human cells. Furthermore, with the recent advancements in gene-editing technology, hiPSCs provide a valuable platform for research and development of new therapies including the possibility of regenerative medicine. In this article, we review the DMD cardiac-related research performed so far using human hiPSCs-derived cardiomyocytes (hiPSC-CMs) carrying DMD mutations.
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Affiliation(s)
- Binyamin Eisen
- Cardiac Research Laboratory, Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Ofer Binah
- Cardiac Research Laboratory, Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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20
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Yu D. An overview of recent US-approved gene therapies for Duchenne muscular dystrophy and their respective clinical development programs. DRUGS & THERAPY PERSPECTIVES 2023. [DOI: 10.1007/s40267-023-00986-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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21
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Yang Y, Wang D, Lü P, Ma S, Chen K. Research progress on nucleic acid detection and genome editing of CRISPR/Cas12 system. Mol Biol Rep 2023; 50:3723-3738. [PMID: 36648696 PMCID: PMC9843688 DOI: 10.1007/s11033-023-08240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023]
Abstract
PURPOSE This work characterizes the applications of CRISPR/Cas12 system, including nucleic acid detection, animal, plant and microbial genome editing. METHODS The literature on CRISPR/Cas12 system was collected and reviewed. RESULTS CRISPR/Cas system is an acquired immune system derived from bacteria and archaea, which has become the most popular technology around the world because of its outstanding contribution in genome editing. Type V CRISPR/Cas systems are distinguished by a single RNA-guided RuvC nuclease domain with single effector molecule. Cas12a, the first reported type V CRISPR/Cas system, targets double-stranded DNA (dsDNA) adjacent to PAM sequences and trans-cleaves single-stranded DNA (ssDNA). We present the applications of CRISPR/Cas12 system for nucleic acid detection and genome editing in animals, plants and microorganisms. Furthermore, this review also summarizes the applications of other Cas12 proteins, such as Cas12b, Cas12c, Cas12d, and so on, which further widen the application prospects of CRISPR/Cas12 system. CONCLUSIONS Knowledge of the applications of CRISPR/Cas12 system is necessary for improving the understanding of the functional diversity of CRISPR/Cas12 system and also provides significant references for further research and utilization of CRISPR/Cas12 in other new fields.
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Affiliation(s)
- Yanhua Yang
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China.
| | - Dandan Wang
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
| | - Shangshang Ma
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
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22
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Padmaswari MH, Agrawal S, Jia MS, Ivy A, Maxenberger DA, Burcham LA, Nelson CE. Delivery challenges for CRISPR-Cas9 genome editing for Duchenne muscular dystrophy. BIOPHYSICS REVIEWS 2023; 4:011307. [PMID: 36864908 PMCID: PMC9969352 DOI: 10.1063/5.0131452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Duchene muscular dystrophy (DMD) is an X-linked neuromuscular disorder that affects about one in every 5000 live male births. DMD is caused by mutations in the gene that codes for dystrophin, which is required for muscle membrane stabilization. The loss of functional dystrophin causes muscle degradation that leads to weakness, loss of ambulation, cardiac and respiratory complications, and eventually, premature death. Therapies to treat DMD have advanced in the past decade, with treatments in clinical trials and four exon-skipping drugs receiving conditional Food and Drug Administration approval. However, to date, no treatment has provided long-term correction. Gene editing has emerged as a promising approach to treating DMD. There is a wide range of tools, including meganucleases, zinc finger nucleases, transcription activator-like effector nucleases, and, most notably, RNA-guided enzymes from the bacterial adaptive immune system clustered regularly interspaced short palindromic repeats (CRISPR). Although challenges in using CRISPR for gene therapy in humans still abound, including safety and efficiency of delivery, the future for CRISPR gene editing for DMD is promising. This review will summarize the progress in CRISPR gene editing for DMD including key summaries of current approaches, delivery methodologies, and the challenges that gene editing still faces as well as prospective solutions.
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Affiliation(s)
| | - Shilpi Agrawal
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Mary S. Jia
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Allie Ivy
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Daniel A. Maxenberger
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Landon A. Burcham
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, USA
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23
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An update on CRISPR-Cas12 as a versatile tool in genome editing. Mol Biol Rep 2023; 50:2865-2881. [PMID: 36641494 DOI: 10.1007/s11033-023-08239-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/03/2023] [Indexed: 01/16/2023]
Abstract
Gene editing techniques, which help in modification of any DNA sequence at ease, have revolutionized the world of Genetic engineering. Although there are other gene-editing techniques, CRISPR has emerged as the chief and most preferred tool due to its simplicity and capacity to execute effective gene editing in a wide range of organisms. Although Cas9 has widely been employed for genetic modification over the years, Cas12 systems have lately emerged as a viable option. This review primarily focuses on assessing Cas12-mediated mutagenesis and elucidating the editing efficacy of both Cpf1 (Cas12a) and C2c1 (Cas12b) systems in microbes, plants, and other species. Also, we reviewed several genetic alterations that have been performed with these Cas12 systems to improve editing efficiency. Furthermore, the experimental benefits and applications of Cas12 systems are highlighted in this study.
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24
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Phan HTL, Kim K, Lee H, Seong JK. Progress in and Prospects of Genome Editing Tools for Human Disease Model Development and Therapeutic Applications. Genes (Basel) 2023; 14:483. [PMID: 36833410 PMCID: PMC9957140 DOI: 10.3390/genes14020483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Programmable nucleases, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas, are widely accepted because of their diversity and enormous potential for targeted genomic modifications in eukaryotes and other animals. Moreover, rapid advances in genome editing tools have accelerated the ability to produce various genetically modified animal models for studying human diseases. Given the advances in gene editing tools, these animal models are gradually evolving toward mimicking human diseases through the introduction of human pathogenic mutations in their genome rather than the conventional gene knockout. In the present review, we summarize the current progress in and discuss the prospects for developing mouse models of human diseases and their therapeutic applications based on advances in the study of programmable nucleases.
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Affiliation(s)
- Hong Thi Lam Phan
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
- Laboratory of Developmental Biology and Genomics, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology, BIO-MAX/N-Bio Institute, Seoul National University, Seoul 08826, Republic of Korea
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25
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Dhuriya YK, Naik AA. CRISPR: a tool with potential for genomic reprogramming in neurological disorders. Mol Biol Rep 2023; 50:1845-1856. [PMID: 36507966 DOI: 10.1007/s11033-022-08136-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
The intricate neural circuitry of the brain necessitates precise and synchronized transcriptional programs. Any disturbance during embryonic or adult development, whether caused by genetic or environmental factors, may result in refractory and recurrent neurological disorders. Inadequate knowledge of the pathogenic mechanisms underlying neurological disorders is the primary obstacle to the development of effective treatments, necessitating the development of alternative therapeutic approaches to identify rational molecular targets. Recently, with the evolution of CRISPR-Cas9 technology, an engineered RNA system provides precise and highly effective correction or silencing of disease-causing mutations by modulating expression and thereby avoiding the limitations of the RNA interference strategy. This article discusses the CRISPR-Cas9 technology, its mechanisms, and the limitations of the new technology. We provide a glimpse of how the far-reaching implications of CRISPR can open new avenues for the development of tools to combat neurological disorders, as well as a review of recent attempts by neuroscientists to launch therapeutic correction.
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Affiliation(s)
| | - Aijaz A Naik
- National Institute of Mental Health (NIMH), Bethesda, USA.
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26
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Khan S, Sallard E. Current and Prospective Applications of CRISPR-Cas12a in Pluricellular Organisms. Mol Biotechnol 2023; 65:196-205. [PMID: 35939208 PMCID: PMC9841005 DOI: 10.1007/s12033-022-00538-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/15/2022] [Indexed: 01/19/2023]
Abstract
CRISPR-Cas systems play a critical role in the prokaryotic adaptive immunity against mobile genetic elements, such as phages and foreign plasmids. In the last decade, Cas9 has been established as a powerful and versatile gene editing tool. In its wake, the novel RNA-guided endonuclease system CRISPR-Cas12a is transforming biological research due to its unique properties, such as its high specificity or its ability to target T-rich motifs, to induce staggered double-strand breaks and to process RNA arrays. Meanwhile, there is an increasing need for efficient and safe gene activation, repression or editing in pluricellular organisms for crop improvement, gene therapy, research model development, and other goals. In this article, we review CRISPR-Cas12a applications in pluricellular organisms and discuss how the challenges characteristic of these complex models, such as vectorization or temperature variations in ectothermic species, can be overcome.
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Affiliation(s)
- Shaheen Khan
- Department of Molecular Biotechnology and Bioinformatics, Università degli Studi di Milano, Milan, Italy ,Division of Neuroscience, Department of Pharmacology & Toxicology, Vita-Salute San Raffaele University and Hospital, Milan, Italy
| | - Erwan Sallard
- Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Institute for Virology and Microbiology, Witten/Herdecke University, 58453 Witten, Germany
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27
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Enabling Precision Medicine with CRISPR-Cas Genome Editing Technology: A Translational Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:315-339. [DOI: 10.1007/978-981-19-5642-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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28
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Hanson B, Stenler S, Ahlskog N, Chwalenia K, Svrzikapa N, Coenen-Stass AM, Weinberg MS, Wood MJ, Roberts TC. Non-uniform dystrophin re-expression after CRISPR-mediated exon excision in the dystrophin/utrophin double-knockout mouse model of DMD. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 30:379-397. [PMID: 36420212 PMCID: PMC9664411 DOI: 10.1016/j.omtn.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Duchenne muscular dystrophy (DMD) is the most prevalent inherited myopathy affecting children, caused by genetic loss of the gene encoding the dystrophin protein. Here we have investigated the use of the Staphylococcus aureus CRISPR-Cas9 system and a double-cut strategy, delivered using a pair of adeno-associated virus serotype 9 (AAV9) vectors, for dystrophin restoration in the severely affected dystrophin/utrophin double-knockout (dKO) mouse. Single guide RNAs were designed to excise Dmd exon 23, with flanking intronic regions repaired by non-homologous end joining. Exon 23 deletion was confirmed at the DNA level by PCR and Sanger sequencing, and at the RNA level by RT-qPCR. Restoration of dystrophin protein expression was demonstrated by western blot and immunofluorescence staining in mice treated via either intraperitoneal or intravenous routes of delivery. Dystrophin restoration was most effective in the diaphragm, where a maximum of 5.7% of wild-type dystrophin expression was observed. CRISPR treatment was insufficient to extend lifespan in the dKO mouse, and dystrophin was expressed in a within-fiber patchy manner in skeletal muscle tissues. Further analysis revealed a plethora of non-productive DNA repair events, including AAV genome integration at the CRISPR cut sites. This study highlights potential challenges for the successful development of CRISPR therapies in the context of DMD.
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Affiliation(s)
- Britt Hanson
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Sofia Stenler
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Nina Ahlskog
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- Institute of Developmental and Regenerative Medicine, University of Oxford, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Headington, Oxford OX3 7TY, UK
| | - Katarzyna Chwalenia
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- Institute of Developmental and Regenerative Medicine, University of Oxford, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Headington, Oxford OX3 7TY, UK
| | - Nenad Svrzikapa
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- Institute of Developmental and Regenerative Medicine, University of Oxford, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Headington, Oxford OX3 7TY, UK
- Wave Life Sciences Ltd., Cambridge, MA 02138, USA
| | - Anna M.L. Coenen-Stass
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Marc S. Weinberg
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, WITS 2050, South Africa
- Asklepios BioPharmaceutical, Inc., Research Triangle Park, NC 27709, USA
| | - Matthew J.A. Wood
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- Institute of Developmental and Regenerative Medicine, University of Oxford, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Headington, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, South Parks Road, Oxford OX1 3QX, UK
| | - Thomas C. Roberts
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- Institute of Developmental and Regenerative Medicine, University of Oxford, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Headington, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, South Parks Road, Oxford OX1 3QX, UK
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29
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Wang P, Li H, Zhu M, Han RY, Guo S, Han R. Correction of DMD in human iPSC-derived cardiomyocytes by base-editing-induced exon skipping. Mol Ther Methods Clin Dev 2022; 28:40-50. [PMID: 36588820 PMCID: PMC9792405 DOI: 10.1016/j.omtm.2022.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene. Previously, we showed that adenine base editing (ABE) can efficiently correct a nonsense point mutation in a DMD mouse model. Here, we explored the feasibility of base-editing-mediated exon skipping as a therapeutic strategy for DMD using cardiomyocytes derived from human induced pluripotent stem cells (hiPSCs). We first generated a DMD hiPSC line with a large deletion spanning exon 48 through 54 (ΔE48-54) using CRISPR-Cas9 gene editing. Dystrophin expression was disrupted in DMD hiPSC-derived cardiomyocytes (iCMs) as examined by RT-PCR, western blot, and immunofluorescence staining. Transfection of ABE and a guide RNA (gRNA) targeting the splice acceptor led to efficient conversion of AG to GG (35.9% ± 5.7%) and enabled exon 55 skipping. Complete AG to GG conversion in a single clone restored dystrophin expression (42.5% ± 11% of wild type [WT]) in DMD iCMs. Moreover, we designed gRNAs to target the splice sites of exons 6, 7, 8, 43, 44, 46, and 53 in the mutational hotspots and demonstrated their efficiency to induce exon skipping in iCMs. These results highlight the great promise of ABE-mediated exon skipping as a promising therapeutic approach for DMD.
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Affiliation(s)
- Peipei Wang
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Haiwen Li
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Mandi Zhu
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Rena Y. Han
- Olentangy Liberty High School, Powell, OH 43065, USA
| | - Shuliang Guo
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Renzhi Han
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA,Corresponding author Renzhi Han, PhD, Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA.
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30
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Qiu HY, Ji RJ, Zhang Y. Current advances of CRISPR-Cas technology in cell therapy. CELL INSIGHT 2022; 1:100067. [PMID: 37193354 PMCID: PMC10120314 DOI: 10.1016/j.cellin.2022.100067] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 05/18/2023]
Abstract
CRISPR-Cas is a versatile genome editing technology that has been broadly applied in both basic research and translation medicine. Ever since its discovery, the bacterial derived endonucleases have been engineered to a collection of robust genome-editing tools for introducing frameshift mutations or base conversions at site-specific loci. Since the initiation of first-in-human trial in 2016, CRISPR-Cas has been tested in 57 cell therapy trials, 38 of which focusing on engineered CAR-T cells and TCR-T cells for cancer malignancies, 15 trials of engineered hematopoietic stem cells treating hemoglobinopathies, leukemia and AIDS, and 4 trials of engineered iPSCs for diabetes and cancer. Here, we aim to review the recent breakthroughs of CRISPR technology and highlight their applications in cell therapy.
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Affiliation(s)
- Hou-Yuan Qiu
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Rui-Jin Ji
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Ying Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
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31
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Nishiyama T, Zhang Y, Cui M, Li H, Sanchez-Ortiz E, McAnally JR, Tan W, Kim J, Chen K, Xu L, Bassel-Duby R, Olson EN. Precise genomic editing of pathogenic mutations in RBM20 rescues dilated cardiomyopathy. Sci Transl Med 2022; 14:eade1633. [PMID: 36417486 PMCID: PMC10088465 DOI: 10.1126/scitranslmed.ade1633] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Mutations in RNA binding motif protein 20 (RBM20) are a common cause of familial dilated cardiomyopathy (DCM). Many RBM20 mutations cluster within an arginine/serine-rich (RS-rich) domain, which mediates nuclear localization. These mutations induce RBM20 mis-localization to form aberrant ribonucleoprotein (RNP) granules in the cytoplasm of cardiomyocytes and abnormal alternative splicing of cardiac genes, contributing to DCM. We used adenine base editing (ABE) and prime editing (PE) to correct pathogenic p.R634Q and p.R636S mutations in the RS-rich domain in human isogenic induced pluripotent stem cell (iPSC)-derived cardiomyocytes. Using ABE to correct RBM20R634Q human iPSCs, we achieved 92% efficiency of A-to-G editing, which normalized alternative splicing of cardiac genes, restored nuclear localization of RBM20, and eliminated RNP granule formation. In addition, we developed a PE strategy to correct the RBM20R636S mutation in iPSCs and observed A-to-C editing at 40% efficiency. To evaluate the potential of ABE for DCM treatment, we also created Rbm20R636Q mutant mice. Homozygous (R636Q/R636Q) mice developed severe cardiac dysfunction, heart failure, and premature death. Systemic delivery of ABE components containing ABEmax-VRQR-SpCas9 and single-guide RNA by adeno-associated virus serotype 9 in these mice restored cardiac function as assessed by echocardiography and extended life span. As seen by RNA sequencing analysis, ABE correction rescued the cardiac transcriptional profile of treated R636Q/R636Q mice, compared to the abnormal gene expression seen in untreated mice. These findings demonstrate the potential of precise correction of genetic mutations as a promising therapeutic approach for DCM.
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Affiliation(s)
- Takahiko Nishiyama
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Miao Cui
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hui Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Efrain Sanchez-Ortiz
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John R McAnally
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wei Tan
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenian Chen
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Xu
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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32
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Development of an in vivo cleavable donor plasmid for targeted transgene integration by CRISPR-Cas9 and CRISPR-Cas12a. Sci Rep 2022; 12:17775. [PMID: 36272994 PMCID: PMC9588054 DOI: 10.1038/s41598-022-22639-6] [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: 06/09/2022] [Accepted: 10/18/2022] [Indexed: 01/19/2023] Open
Abstract
The CRISPR-Cas system is widely used for genome editing of cultured cells and organisms. The discovery of a new single RNA-guided endonuclease, CRISPR-Cas12a, in addition to the conventional CRISPR-Cas9 has broadened the number of editable target sites on the genome. Here, we developed an in vivo cleavable donor plasmid for precise targeted knock-in of external DNA by both Cas9 and Cas12a. This plasmid, named pCriMGET_9-12a (plasmid of synthetic CRISPR-coded RNA target sequence-equipped donor plasmid-mediated gene targeting via Cas9 and Cas12a), comprises the protospacer-adjacent motif sequences of Cas9 and Cas12a at the side of an off-target free synthetic CRISPR-coded RNA target sequence and a multiple cloning site for donor cassette insertion. pCriMGET_9-12a generates a linearized donor cassette in vivo by both CRISPR-Cas9 and CRISPR-Cas12a, which resulted in increased knock-in efficiency in culture cells. This method also achieved > 25% targeted knock-in of long external DNA (> 4 kb) in mice by both CRISPR-Cas9 and CRISPR-Cas12a. The pCriMGET_9-12a system expands the genomic target space for transgene knock-in and provides a versatile, low-cost, and high-performance CRISPR genome editing tool.
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33
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Li R, Wang Q, She K, Lu F, Yang Y. CRISPR/Cas systems usher in a new era of disease treatment and diagnosis. MOLECULAR BIOMEDICINE 2022; 3:31. [PMID: 36239875 PMCID: PMC9560888 DOI: 10.1186/s43556-022-00095-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022] Open
Abstract
The discovery and development of the CRISPR/Cas system is a milestone in precise medicine. CRISPR/Cas nucleases, base-editing (BE) and prime-editing (PE) are three genome editing technologies derived from CRISPR/Cas. In recent years, CRISPR-based genome editing technologies have created immense therapeutic potential with safe and efficient viral or non-viral delivery systems. Significant progress has been made in applying genome editing strategies to modify T cells and hematopoietic stem cells (HSCs) ex vivo and to treat a wide variety of diseases and disorders in vivo. Nevertheless, the clinical translation of this unique technology still faces many challenges, especially targeting, safety and delivery issues, which require further improvement and optimization. In addition, with the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), CRISPR-based molecular diagnosis has attracted extensive attention. Growing from the specific set of molecular biological discoveries to several active clinical trials, CRISPR/Cas systems offer the opportunity to create a cost-effective, portable and point-of-care diagnosis through nucleic acid screening of diseases. In this review, we describe the development, mechanisms and delivery systems of CRISPR-based genome editing and focus on clinical and preclinical studies of therapeutic CRISPR genome editing in disease treatment as well as its application prospects in therapeutics and molecular detection.
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Affiliation(s)
- Ruiting Li
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China
| | - Qin Wang
- grid.412723.10000 0004 0604 889XSchool of Pharmacy, Southwest Minzu University, Chengdu, 610225 Sichuan China
| | - Kaiqin She
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Fang Lu
- grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yang Yang
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
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34
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Comprehensive assessment of miniature CRISPR-Cas12f nucleases for gene disruption. Nat Commun 2022; 13:5623. [PMID: 36153319 PMCID: PMC9509373 DOI: 10.1038/s41467-022-33346-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/14/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractBecause of their small size, the recently developed CRISPR-Cas12f nucleases can be effectively packaged into adeno-associated viruses for gene therapy. However, a systematic evaluation of the editing outcomes of CRISPR-Cas12f is lacking. In this study, we apply a high-throughput sequencing method to comprehensively assess the editing efficiency, specificity, and safety of four Cas12f proteins in parallel with that of Cas9 and two Cas12a proteins at multiple genomic sites. Cas12f nucleases achieve robust cleavage at most of the tested sites and mainly produce deletional fragments. In contrast, Cas9 and Cas12a show relatively higher editing efficiency at the vast majority of the tested sites. However, the off-target hotspots identified in the Cas9- and Cas12a-edited cells are negligibly detected in the Cas12f-edited cells. Moreover, compared to Cas9 and Cas12a nucleases, Cas12f nucleases reduce the levels of chromosomal translocations, large deletions, and integrated vectors by 2- to 3-fold. Therefore, our findings confirm the editing capacity of Cas12f and reveal the ability of this nuclease family to preserve genome integrity during genome editing.
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35
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CRISPR-Based Therapeutic Gene Editing for Duchenne Muscular Dystrophy: Advances, Challenges and Perspectives. Cells 2022; 11:cells11192964. [PMID: 36230926 PMCID: PMC9564082 DOI: 10.3390/cells11192964] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/19/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe neuromuscular disease arising from loss-of-function mutations in the dystrophin gene and characterized by progressive muscle degeneration, respiratory insufficiency, cardiac failure, and premature death by the age of thirty. Albeit DMD is one of the most common types of fatal genetic diseases, there is no curative treatment for this devastating disorder. In recent years, gene editing via the clustered regularly interspaced short palindromic repeats (CRISPR) system has paved a new path toward correcting pathological mutations at the genetic source, thus enabling the permanent restoration of dystrophin expression and function throughout the musculature. To date, the therapeutic benefits of CRISPR genome-editing systems have been successfully demonstrated in human cells, rodents, canines, and piglets with diverse DMD mutations. Nevertheless, there remain some nonignorable challenges to be solved before the clinical application of CRISPR-based gene therapy. Herein, we provide an overview of therapeutic CRISPR genome-editing systems, summarize recent advancements in their applications in DMD contexts, and discuss several potential obstacles lying ahead of clinical translation.
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36
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A humanized knockin mouse model of Duchenne muscular dystrophy and its correction by CRISPR-Cas9 therapeutic gene editing. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:525-537. [PMID: 36035749 PMCID: PMC9398917 DOI: 10.1016/j.omtn.2022.07.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/20/2022] [Indexed: 01/01/2023]
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37
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La-Rostami F, Wax N, Druschka M, Adams E, Albert C, Fischer M. In Vitro CRISPR-Cpf1 Assay for Differentiation of Fine and Bulk Cocoa ( Theobroma cacao L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8819-8826. [PMID: 35786882 DOI: 10.1021/acs.jafc.2c02537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cocoa cultivation is dominated by the clone "Colleción Castro Naranjal 51" (CCN-51). In contrast, CCN-51 is the expensive and aromatic fine cocoa "Arriba Nacional" from Ecuador. The differences in the overall quality of the beans and in the prices show that it is necessary to develop a rapid and accurate method to distinguish these varieties and prevent food fraud. To this end, we used a CRISPR-Cpf1 assay suitable for AT-rich targets such as the chloroplast genome (cpGenome). SNPs in cocoa plastid genomes were selected to replace the canonical PAM sequence of Cpf1 (5'-TTTV-3'). We developed two assay systems to digest both Arriba and CCN-51. The results were tested qualitatively by agarose gel electrophoresis and quantitatively by capillary gel electrophoresis. Using the assay described here, we were able to reliably detect admixtures of 5% CCN-51 (P < 0.01) and 10% Arriba (P < 0.05). The application to processed cocoa products was also successful.
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Affiliation(s)
- Farshad La-Rostami
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Nils Wax
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Michael Druschka
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Elena Adams
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Chenyang Albert
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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38
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Ferreira P, Choupina AB. CRISPR/Cas9 a simple, inexpensive and effective technique for gene editing. Mol Biol Rep 2022; 49:7079-7086. [PMID: 35716290 PMCID: PMC9206401 DOI: 10.1007/s11033-022-07442-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/26/2021] [Accepted: 04/01/2022] [Indexed: 11/27/2022]
Abstract
In recent years, the number of tools and techniques that enable genetic material to be added, removed or altered at specific locations in the genome has increased significantly. The objective is to know the structure of genomes, the function of genes and improve gene therapy.In this work we intend to explain the functioning of the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) and the advantages that this technique may have compared to previously developed techniques, such as RNA interference (RNAi), Zinc Finger Nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) in gene and genome editing.We will start with the story of the discovery, then its biological function in the adaptive immune system of bacteria against bacteriophage attack, and ending with a description of the mechanism of action and its use in gene editing. We will also discuss other Cas enzymes with great potential for use in genome editing as an alternative to Cas9.CRISPR/Cas9 is a simple, inexpensive, and effective technique for gene editing with multiple applications from the development of functional genomics and epigenetics. This technique will, in the near future, have great applications in the development of cell models for use in medical and pharmaceutical processes, in targeted therapy, and improvement of agricultural and environmental species.
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Affiliation(s)
- Patrick Ferreira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Altino Branco Choupina
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal.
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39
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Torriano S, Baulier E, Garcia Diaz A, Corneo B, Farber DB. CRISPR-AsCas12a Efficiently Corrects a GPR143 Intronic Mutation in Induced Pluripotent Stem Cells from an Ocular Albinism Patient. CRISPR J 2022; 5:457-471. [PMID: 35686978 PMCID: PMC9233509 DOI: 10.1089/crispr.2021.0110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Mutations in the GPR143 gene cause X-linked ocular albinism type 1 (OA1), a disease that severely impairs vision. We recently generated induced pluripotent stem cells (iPSCs) from skin fibroblasts of an OA1 patient carrying a point mutation in intron 7 of GPR143. This mutation activates a new splice site causing the incorporation of a pseudoexon. In this study, we present a high-performance CRISPR-Cas ribonucleoprotein strategy to permanently correct the GPR143 mutation in these patient-derived iPSCs. Interestingly, the two single-guide RNAs available for SpCas9 did not allow the cleavage of the target region. In contrast, the cleavage achieved with the CRISPR-AsCas12a system promoted homology-directed repair at a high rate. The CRISPR-AsCas12a-mediated correction did not alter iPSC pluripotency or genetic stability, nor did it result in off-target events. Moreover, we highlight that the disruption of the pathological splice site caused by CRISPR-AsCas12a-mediated insertions/deletions also rescued the normal splicing of GPR143 and its expression level.
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Affiliation(s)
- Simona Torriano
- Department of Ophthalmology, UCLA School of Medicine, Jules Stein Eye Institute, Los Angeles, California, USA
| | - Edouard Baulier
- Department of Ophthalmology, UCLA School of Medicine, Jules Stein Eye Institute, Los Angeles, California, USA
| | - Alejandro Garcia Diaz
- Stem Cell Core, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, New York, USA
| | - Barbara Corneo
- Stem Cell Core, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, New York, USA
| | - Debora B Farber
- Department of Ophthalmology, UCLA School of Medicine, Jules Stein Eye Institute, Los Angeles, California, USA.,Molecular Biology Institute and UCLA, Los Angeles, California, USA.,Brain Research Institute, UCLA, Los Angeles, California, USA
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40
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Paul B, Chaubet L, Verver DE, Montoya G. Mechanics of CRISPR-Cas12a and engineered variants on λ-DNA. Nucleic Acids Res 2022; 50:5208-5225. [PMID: 34951457 PMCID: PMC9122593 DOI: 10.1093/nar/gkab1272] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Cas12a is an RNA-guided endonuclease that is emerging as a powerful genome-editing tool. Here, we selected a target site on bacteriophage λ-DNA and used optical tweezers combined with fluorescence to provide mechanistic insight into wild type Cas12a and three engineered variants, where the specific dsDNA and the unspecific ssDNA cleavage are dissociated (M1 and M2) and a third one which nicks the target DNA (M3). At low forces wtCas12a and the variants display two main off-target binding sites, while on stretched dsDNA at higher forces numerous binding events appear driven by the mechanical distortion of the DNA and partial matches to the crRNA. The multiple binding events onto dsDNA at high tension do not lead to cleavage, which is observed on the target site at low forces when the DNA is flexible. In addition, activity assays also show that the preferential off-target sites for this crRNA are not cleaved by wtCas12a, indicating that λ-DNA is only severed at the target site. Our single molecule data indicate that the Cas12a scaffold presents singular mechanical properties, which could be used to generate new endonucleases with biomedical and biotechnological applications.
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Affiliation(s)
- Bijoya Paul
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Loïc Chaubet
- LUMICKS, Pilotenstraat 41, 1059 CH, Amsterdam, The Netherlands
| | | | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
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41
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Happi Mbakam C, Lamothe G, Tremblay G, Tremblay JP. CRISPR-Cas9 Gene Therapy for Duchenne Muscular Dystrophy. Neurotherapeutics 2022; 19:931-941. [PMID: 35165856 PMCID: PMC9294086 DOI: 10.1007/s13311-022-01197-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 12/26/2022] Open
Abstract
Discovery of the CRISPR-Cas (clustered regularly interspaced short palindromic repeat, CRISPR-associated) system a decade ago has opened new possibilities in the field of precision medicine. CRISPR-Cas was initially identified in bacteria and archaea to play a protective role against foreign genetic elements during viral infections. The application of this technique for the correction of different mutations found in the Duchenne muscular dystrophy (DMD) gene led to the development of several potential therapeutic approaches for DMD patients. The mutations responsible for Duchenne muscular dystrophy mainly include exon deletions (70% of patients) and point mutations (about 30% of patients). The CRISPR-Cas 9 technology is becoming increasingly precise and is acquiring diverse functions through novel innovations such as base editing and prime editing. However, questions remain about its translation to the clinic. Current research addressing off-target editing, efficient muscle-specific delivery, immune response to nucleases, and vector challenges may eventually lead to the clinical use of the CRISPR-Cas9 technology. In this review, we present recent CRISPR-Cas9 strategies to restore dystrophin expression in vitro and in animal models of DMD.
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Affiliation(s)
- Cedric Happi Mbakam
- CHU de Québec Research Center - Laval University, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada
| | - Gabriel Lamothe
- CHU de Québec Research Center - Laval University, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada
| | - Guillaume Tremblay
- CHU de Québec Research Center - Laval University, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada
| | - Jacques P Tremblay
- CHU de Québec Research Center - Laval University, Québec, Canada.
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada.
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42
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Banas K, Modarai S, Rivera-Torres N, Yoo BC, Bialk PA, Barrett C, Batish M, Kmiec EB. Exon skipping induced by CRISPR-directed gene editing regulates the response to chemotherapy in non-small cell lung carcinoma cells. Gene Ther 2022; 29:357-367. [PMID: 35314779 PMCID: PMC9203268 DOI: 10.1038/s41434-022-00324-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 01/26/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022]
Abstract
We have been developing CRISPR-directed gene editing as an augmentative therapy for the treatment of non-small cell lung carcinoma (NSCLC) by genetic disruption of Nuclear Factor Erythroid 2-Related Factor 2 (NRF2). NRF2 promotes tumor cell survival in response to therapeutic intervention and thus its disablement should restore or enhance effective drug action. Here, we report how NRF2 disruption leads to collateral damage in the form of CRISPR-mediated exon skipping. Heterogeneous populations of transcripts and truncated proteins produce a variable response to chemotherapy, dependent on which functional domain is missing. We identify and characterize predicted and unpredicted transcript populations and discover that several types of transcripts arise through exon skipping; wherein one or two NRF2 exons are missing. In one specific case, the presence or absence of a single nucleotide determines whether an exon is skipped or not by reorganizing Exonic Splicing Enhancers (ESEs). We isolate and characterize the diversity of clones induced by CRISPR activity in a NSCLC tumor cell population, a critical and often overlooked genetic byproduct of this exciting technology. Finally, gRNAs must be designed with care to avoid altering gene expression patterns that can account for variable responses to solid tumor therapy.
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Affiliation(s)
- Kelly Banas
- Gene Editing Institute, ChristianaCare, Newark, DE, USA
| | | | | | | | - Pawel A Bialk
- Gene Editing Institute, ChristianaCare, Newark, DE, USA
| | - Connor Barrett
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, USA
| | - Eric B Kmiec
- Gene Editing Institute, ChristianaCare, Newark, DE, USA.
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43
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Erkut E, Yokota T. CRISPR Therapeutics for Duchenne Muscular Dystrophy. Int J Mol Sci 2022; 23:1832. [PMID: 35163754 PMCID: PMC8836469 DOI: 10.3390/ijms23031832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 02/04/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked recessive neuromuscular disorder with a prevalence of approximately 1 in 3500-5000 males. DMD manifests as childhood-onset muscle degeneration, followed by loss of ambulation, cardiomyopathy, and death in early adulthood due to a lack of functional dystrophin protein. Out-of-frame mutations in the dystrophin gene are the most common underlying cause of DMD. Gene editing via the clustered regularly interspaced short palindromic repeats (CRISPR) system is a promising therapeutic for DMD, as it can permanently correct DMD mutations and thus restore the reading frame, allowing for the production of functional dystrophin. The specific mechanism of gene editing can vary based on a variety of factors such as the number of cuts generated by CRISPR, the presence of an exogenous DNA template, or the current cell cycle stage. CRISPR-mediated gene editing for DMD has been tested both in vitro and in vivo, with many of these studies discussed herein. Additionally, novel modifications to the CRISPR system such as base or prime editors allow for more precise gene editing. Despite recent advances, limitations remain including delivery efficiency, off-target mutagenesis, and long-term maintenance of dystrophin. Further studies focusing on safety and accuracy of the CRISPR system are necessary prior to clinical translation.
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Affiliation(s)
- Esra Erkut
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, 8613-114 Street, Edmonton, AB T6G 2H7, Canada;
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, 8613-114 Street, Edmonton, AB T6G 2H7, Canada;
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, 8613-114 Street, Edmonton, AB T6G 2H7, Canada
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44
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Bremner SB, Mandrycky CJ, Leonard A, Padgett RM, Levinson AR, Rehn ES, Pioner JM, Sniadecki NJ, Mack DL. Full-length dystrophin deficiency leads to contractile and calcium transient defects in human engineered heart tissues. J Tissue Eng 2022; 13:20417314221119628. [PMID: 36003954 PMCID: PMC9393922 DOI: 10.1177/20417314221119628] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022] Open
Abstract
Cardiomyopathy is currently the leading cause of death for patients with Duchenne muscular dystrophy (DMD), a severe neuromuscular disorder affecting young boys. Animal models have provided insight into the mechanisms by which dystrophin protein deficiency causes cardiomyopathy, but there remains a need to develop human models of DMD to validate pathogenic mechanisms and identify therapeutic targets. Here, we have developed human engineered heart tissues (EHTs) from CRISPR-edited, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) expressing a truncated dystrophin protein lacking part of the actin-binding domain. The 3D EHT platform enables direct measurement of contractile force, simultaneous monitoring of Ca2+ transients, and assessment of myofibril structure. Dystrophin-mutant EHTs produced less contractile force as well as delayed kinetics of force generation and relaxation, as compared to isogenic controls. Contractile dysfunction was accompanied by reduced sarcomere length, increased resting cytosolic Ca2+ levels, delayed Ca2+ release and reuptake, and increased beat rate irregularity. Transcriptomic analysis revealed clear differences between dystrophin-deficient and control EHTs, including downregulation of genes related to Ca2+ homeostasis and extracellular matrix organization, and upregulation of genes related to regulation of membrane potential, cardiac muscle development, and heart contraction. These findings indicate that the EHT platform provides the cues necessary to expose the clinically-relevant, functional phenotype of force production as well as mechanistic insights into the role of Ca2+ handling and transcriptomic dysregulation in dystrophic cardiac function, ultimately providing a powerful platform for further studies in disease modeling and drug discovery.
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Affiliation(s)
- Samantha B Bremner
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Christian J Mandrycky
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Andrea Leonard
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
| | - Ruby M Padgett
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
| | - Alan R Levinson
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Ethan S Rehn
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - J Manuel Pioner
- Department of Biology, University of Florence, Florence, Italy
| | - Nathan J Sniadecki
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - David L Mack
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Rehabilitation Medicine, University of Washington, Seattle, WA, USA
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45
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Johnston JR, McNally EM. Genetic correction strategies for Duchenne Muscular Dystrophy and their impact on the heart. PROGRESS IN PEDIATRIC CARDIOLOGY 2021; 63. [PMID: 34898968 DOI: 10.1016/j.ppedcard.2021.101460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Background Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder with early childhood onset characterized by profound loss of muscle strength and associated cardiomyopathy. DMD affects is most often caused by deletions involving single or multiple exons that disrupt the open reading frame of the DMD gene. Mutations causing loss or premature truncation of dystrophin result in dystrophin protein deficiency, which renders the plasma membrane of skeletal myofibers and cardiomyocytes weakened. Aim of Review Genetic correction is in use to treat DMD, since several drugs have been already approved which partially restore dystrophin production through the use of antisense oligonucleotides. There are multiple ongoing clinical trials to evaluate the efficacy of treating DMD with micro-dystrophins delivered by adeno-associated viruses. Future approaches entail gene editing to target the single copy of the DMD gene on the X-chromosome. The primary, near-term goal is restoration of skeletal muscle dystrophin, and for some of these treatments, the efficacy in the heart is not fully known. Here, we discuss the anticipated cardiac outcomes of dystrophin-targeted therapies, and how this information informs genomic medicine for cardiomyopathies, especially in childhood. Key Scientific Concepts of Review Many genetic treatment strategies are being implemented to treat DMD. Since most preclinical testing has focused on skeletal muscle, there is a gap in knowledge about the expected effects of these approaches on cardiac genetic correction and cardiomyopathy progression in DMD. Additional study is needed.
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Affiliation(s)
- Jamie R Johnston
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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Wang X, Dong K, Kong D, Zhou Y, Yin J, Cai F, Wang M, Ye H. A far-red light-inducible CRISPR-Cas12a platform for remote-controlled genome editing and gene activation. SCIENCE ADVANCES 2021; 7:eabh2358. [PMID: 34890237 PMCID: PMC8664267 DOI: 10.1126/sciadv.abh2358] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The CRISPR-Cas12a has been harnessed as a powerful tool for manipulating targeted gene expression. The possibility to manipulate the activity of CRISPR-Cas12a with a more precise spatiotemporal resolution and deep tissue permeability will enable targeted genome engineering and deepen our understanding of the gene functions underlying complex cellular behaviors. However, currently available inducible CRISPR-Cas12a systems are limited by diffusion, cytotoxicity, and poor tissue permeability. Here, we developed a far-red light (FRL)–inducible CRISPR-Cas12a (FICA) system that can robustly induce gene editing in mammalian cells, and an FRL-inducible CRISPR-dCas12a (FIdCA) system based on the protein-tagging system SUperNova (SunTag) that can be used for gene activation under light-emitting diode–based FRL. Moreover, we show that the FIdCA system can be deployed to activate target genes in mouse livers. These results demonstrate that these systems developed here provide robust and efficient platforms for programmable genome manipulation in a noninvasive and spatiotemporal fashion.
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Affiliation(s)
- Xinyi Wang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Kaili Dong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Deqiang Kong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yang Zhou
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jianli Yin
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Fengfeng Cai
- Department of Breast Surgery, Yangpu Hospital, School of Medicine, Tongji University, 450 Tengyue Road, Shanghai 200090, China
| | - Meiyan Wang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
- Corresponding author. (M.W.); (H.Y.)
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
- Corresponding author. (M.W.); (H.Y.)
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Javaid N, Choi S. CRISPR/Cas System and Factors Affecting Its Precision and Efficiency. Front Cell Dev Biol 2021; 9:761709. [PMID: 34901007 PMCID: PMC8652214 DOI: 10.3389/fcell.2021.761709] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
The diverse applications of genetically modified cells and organisms require more precise and efficient genome-editing tool such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas). The CRISPR/Cas system was originally discovered in bacteria as a part of adaptive-immune system with multiple types. Its engineered versions involve multiple host DNA-repair pathways in order to perform genome editing in host cells. However, it is still challenging to get maximum genome-editing efficiency with fewer or no off-targets. Here, we focused on factors affecting the genome-editing efficiency and precision of CRISPR/Cas system along with its defense-mechanism, orthologues, and applications.
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Affiliation(s)
- Nasir Javaid
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University Campus Plaza, Suwon, South Korea
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Luthra R, Kaur S, Bhandari K. Applications of CRISPR as a potential therapeutic. Life Sci 2021; 284:119908. [PMID: 34453943 DOI: 10.1016/j.lfs.2021.119908] [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: 06/19/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 02/06/2023]
Abstract
Genetic disorders and congenital abnormalities are present in 2-5% of births all over the world and can cause up to 50% of all early childhood deaths. The establishment of sophisticated and controlled techniques for customizing DNA manipulation is significant for the therapeutic role in such disorders and further research on them. One such technique is CRISPR that is significant towards optimizing genome editing and therapies, metabolic fluxes as well as artificial genetic systems. CRISPR-Cas9 is a molecular appliance that is applied in the areas of genetic and protein engineering. The CRISPR-CAS system is an integral element of prokaryotic adaptive immunity that allows prokaryotic cells to identify and kill any foreign DNA. The Gene editing property of CRISPR finds various applications like diagnostics and therapeutics in cancer, neurodegenerative disorders, genetic diseases, blindness, etc. This review discusses applications of CRISPR as a therapeutic in various disorders including several genetic diseases (including sickle cell anemia, blindness, thalassemia, cystic fibrosis, hereditary tyrosinemia type I, duchenne muscular dystrophy, mitochondrial disorders), Cancer, Huntington's disease and viral infections (like HIV, COVID, etc.) along with the prospects concerning them. CRISPR-based therapy is also being researched and defined for COVID-19. The related mechanism of CRISPR has been discussed alongside highlighting challenges involved in therapeutic applications of CRISPR.
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Affiliation(s)
- Ritika Luthra
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Simran Kaur
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Kriti Bhandari
- Department of Biotechnology, Delhi Technological University, Delhi, India.
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Dilip Kumar S, Aashabharathi M, KarthigaDevi G, Subbaiya R, Saravanan M. Insights of CRISPR-Cas systems in stem cells: progress in regenerative medicine. Mol Biol Rep 2021; 49:657-673. [PMID: 34687393 DOI: 10.1007/s11033-021-06832-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/24/2021] [Indexed: 12/16/2022]
Abstract
Regenerative medicine, a therapeutic approach using stem cells, aims to rejuvenate and restore the normalized function of the cells, tissues, and organs that are injured, malfunctioning, and afflicted. This influential technology reaches its zenith when it is integrated with the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) technology of genome editing. This tool acts as a programmable restriction enzyme system, which targets DNA as well as RNA and gets redeployed for the customization of DNA/RNA sequences. The dynamic behaviour of nuclear manipulation and transcriptional regulation by CRISPR-Cas technology renders it with numerous employment in the field of biologics and research. Here, the possible impact of the commonly practiced CRISPR-Cas systems in regenerative medicines is being reviewed. Primarily, the discussion of the working mechanism of this system and the fate of stem cells will be scrutinized. A detailed description of the CRISPR based regenerative therapeutic approaches for a horde of diseases like genetic disorders, neural diseases, and blood-related diseases is elucidated.
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Affiliation(s)
- Shanmugam Dilip Kumar
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur, Chennai, Tamil Nadu, 602 117, India
| | - Manimaran Aashabharathi
- Department of Biotechnology, Sree Sastha Institute of Engineering and Technology, Chembarambakkam, Chennai, Tamil Nadu, 600 123, India
| | - Guruviah KarthigaDevi
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur, Chennai, Tamil Nadu, 602 117, India
| | - Ramasamy Subbaiya
- Department of Biological Sciences, School of Mathematics and Natural Sciences, The Copperbelt University, Riverside, Jambo Drive, P.O Box. 21692, Kitwe, Zambia
| | - Muthupandian Saravanan
- AMR and Nanomedicine Laboratory, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, Tamil Nadu, 600 077, India.
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Vicente MM, Chaves-Ferreira M, Jorge JMP, Proença JT, Barreto VM. The Off-Targets of Clustered Regularly Interspaced Short Palindromic Repeats Gene Editing. Front Cell Dev Biol 2021; 9:718466. [PMID: 34604217 PMCID: PMC8484971 DOI: 10.3389/fcell.2021.718466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/09/2021] [Indexed: 12/26/2022] Open
Abstract
The repurposing of the CRISPR/Cas bacterial defense system against bacteriophages as simple and flexible molecular tools has revolutionized the field of gene editing. These tools are now widely used in basic research and clinical trials involving human somatic cells. However, a global moratorium on all clinical uses of human germline editing has been proposed because the technology still lacks the required efficacy and safety. Here we focus on the approaches developed since 2013 to decrease the frequency of unwanted mutations (the off-targets) during CRISPR-based gene editing.
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Affiliation(s)
- Manuel M Vicente
- DNA Breaks Group, NOVA Medical School (NMS), Centro de Estudos de Doenças Crónicas (CEDOC), NOVA University of Lisbon, Lisbon, Portugal
| | - Miguel Chaves-Ferreira
- DNA Breaks Group, NOVA Medical School (NMS), Centro de Estudos de Doenças Crónicas (CEDOC), NOVA University of Lisbon, Lisbon, Portugal
| | - João M P Jorge
- DNA Breaks Group, NOVA Medical School (NMS), Centro de Estudos de Doenças Crónicas (CEDOC), NOVA University of Lisbon, Lisbon, Portugal
| | - João T Proença
- DNA Breaks Group, NOVA Medical School (NMS), Centro de Estudos de Doenças Crónicas (CEDOC), NOVA University of Lisbon, Lisbon, Portugal
| | - Vasco M Barreto
- DNA Breaks Group, NOVA Medical School (NMS), Centro de Estudos de Doenças Crónicas (CEDOC), NOVA University of Lisbon, Lisbon, Portugal
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