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Li XH, Lu HZ, Yao JB, Zhang C, Shi TQ, Huang H. Recent advances in the application of CRISPR/Cas-based gene editing technology in Filamentous Fungi. Biotechnol Adv 2025; 81:108561. [PMID: 40086675 DOI: 10.1016/j.biotechadv.2025.108561] [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: 12/05/2024] [Revised: 03/03/2025] [Accepted: 03/07/2025] [Indexed: 03/16/2025]
Abstract
Filamentous fungi are essential industrial microorganisms that can serve as sources of enzymes, organic acids, terpenoids, and other bioactive compounds with significant applications in food, medicine, and agriculture. However, the underdevelopment of gene editing tools limits the full exploitation of filamentous fungi, which still present numerous untapped potential applications. In recent years, the CRISPR/Cas (clustered regularly interspaced short palindromic repeats) system, a versatile genome-editing tool, has advanced significantly and been widely applied in filamentous fungi, showcasing considerable research potential. This review examines the development and mechanisms of genome-editing tools in filamentous fungi, and contrasts the CRISPR/Cas9 and CRISPR/Cpf1 systems. The transformation and delivery strategies of the CRISPR/Cas system in filamentous fungi are also examined. Additionally, recent applications of CRISPR/Cas systems in filamentous fungi are summarized, such as gene disruption, base editing, and gene regulation. Strategies to enhance editing efficiency and reduce off-target effects are also highlighted, with the aim of providing insights for the future construction and optimization of CRISPR/Cas systems in filamentous fungi.
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Affiliation(s)
- Xu-Hong Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, China
| | - Hui-Zhi Lu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, China
| | - Ji-Bao Yao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, China
| | - Chi Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, China.
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, China
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2
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Peña-Gutiérrez I, Olalla-Sastre B, Río P, Rodríguez-Madoz JR. Beyond precision: evaluation of off-target clustered regularly interspaced short palindromic repeats/Cas9-mediated genome editing. Cytotherapy 2025; 27:279-286. [PMID: 39652018 DOI: 10.1016/j.jcyt.2024.10.010] [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: 08/08/2024] [Revised: 10/21/2024] [Accepted: 10/21/2024] [Indexed: 12/16/2024]
Abstract
The gene editing field has advanced rapidly since the development of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system because of its applicability in precisely modifying the genome. Among its multiple applications, the correction of genetic diseases has emerged as a potential curative treatment for many disorders that have eluded a cure to date. Despite its efficiency in achieving therapeutic levels of correction, the unexpected adverse effects of editing due to CRISPR/Cas9 nuclease activity are a major concern when translating these new strategies to the clinic. Multiple in silico tools and empirical methods have been developed to evaluate these off-target edits as well as other adverse alterations of the genome, including rearrangements, not only in ex vivo experiments but also in in vivo experiments. In this review, we summarize the available methods for the assessment of off-target effects of CRISPR/Cas9 systems, highlighting their advantages and limitations. Special attention will be paid to their application in pre-clinical studies and clinical trials, both in the manufacturing product and in the long-term follow-up of patients.
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Affiliation(s)
- Irene Peña-Gutiérrez
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain; Instituto de Investigaciones Sanitarias, Fundación Jiménez Díaz, Madrid, Spain
| | - Beatriz Olalla-Sastre
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain; Instituto de Investigaciones Sanitarias, Fundación Jiménez Díaz, Madrid, Spain
| | - Paula Río
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain; Instituto de Investigaciones Sanitarias, Fundación Jiménez Díaz, Madrid, Spain.
| | - Juan R Rodríguez-Madoz
- Hemato-Oncology Program, Instituto de Investigación Sanitaria de Navarra, Cima Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain.
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3
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Mentani A, Maresca M, Shiriaeva A. Prime Editing: Mechanistic Insights and DNA Repair Modulation. Cells 2025; 14:277. [PMID: 39996750 PMCID: PMC11853414 DOI: 10.3390/cells14040277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 01/15/2025] [Accepted: 01/24/2025] [Indexed: 02/26/2025] Open
Abstract
Prime editing is a genome editing technique that allows precise modifications of cellular DNA without relying on donor DNA templates. Recently, several different prime editor proteins have been published in the literature, relying on single- or double-strand breaks. When prime editing occurs, the DNA undergoes one of several DNA repair pathways, and these processes can be modulated with the use of inhibitors. Firstly, this review provides an overview of several DNA repair mechanisms and their modulation by known inhibitors. In addition, we summarize different published prime editors and provide a comprehensive overview of associated DNA repair mechanisms. Finally, we discuss the delivery and safety aspects of prime editing.
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Affiliation(s)
- Astrid Mentani
- Genome Engineering, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Marcello Maresca
- Genome Engineering, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Anna Shiriaeva
- Genome Engineering, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
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Wang G, Liu X, Wang A, Wen J, Kim P, Song Q, Liu X, Zhou X. CRISPRoffT: comprehensive database of CRISPR/Cas off-targets. Nucleic Acids Res 2025; 53:D914-D924. [PMID: 39526384 PMCID: PMC11701555 DOI: 10.1093/nar/gkae1025] [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: 09/05/2024] [Revised: 10/02/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024] Open
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated protein) programmable nuclease system continues to evolve, with in vivo therapeutic gene editing increasingly applied in clinical settings. However, off-target effects remain a significant challenge, hindering its broader clinical application. To enhance the development of gene-editing therapies and the accuracy of prediction algorithms, we developed CRISPRoffT (https://ccsm.uth.edu/CRISPRoffT/). Users can access a comprehensive repository of off-target regions predicted and validated by a diverse range of technologies across various cell lines, Cas enzyme variants, engineered sgRNAs (single guide RNAs) and CRISPR editing systems. CRISPRoffT integrates results of off-target analysis from 74 studies, encompassing 29 experimental prediction techniques, 368 guide sequences, 226 164 potential guide and off-target pairs and 8840 validated off-targets. CRISPRoffT features off-target data from different CRISPR approaches (knockout, base editing and prime editing) applied under diverse experimental conditions, including 85 different Cas/guide RNA (gRNA) combinations used across 34 different human and mouse cell lines. CRISPRoffT provides results of comparative analyses for individual guide sequences, genes, cell types, techniques and Cas/gRNA combinations under different conditions. CRISPRoffT is a unique resource providing valuable insights that facilitate the safety-driven design of CRISPR-based therapeutics, inform experimental design, advance the development of computational off-target prediction algorithms and guide RNA design algorithms.
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Affiliation(s)
- Grant Wang
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030, USA
| | - Xiaona Liu
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030, USA
| | - Aoqi Wang
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, 2222 Xinchuan Road, Chengdu, Sichuan, 610041, PR China
| | - Jianguo Wen
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030, USA
| | - Qianqian Song
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, 1889 Museum Road, Gainesville, FL, 32611, USA
| | - Xiaona Liu
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030, USA
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Shao C, Liu Q, Xu J, Zhang J, Zhang C, Xin Y, Ye Y, Lin B, Zhang X, Cheng L, Xu X, Xu P. Efficient and in situ correction of hemoglobin Constant Spring mutation by prime editing in human hematopoietic cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102371. [PMID: 39640014 PMCID: PMC11617223 DOI: 10.1016/j.omtn.2024.102371] [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: 02/13/2024] [Accepted: 10/24/2024] [Indexed: 12/07/2024]
Abstract
Hemoglobin Constant Spring (Hb CS) is the most common non-deletional and clinically significant α-thalassemic mutation, and it is caused by an anti-termination mutation at the α2-globin gene stop codon. We developed a prime editing strategy for the creation and correction of Hb CS. We showed that prime editing could efficiently introduce Hb CS mutations in both human erythroblast cell lines (an average frequency of 32%) and primary hematopoietic stem and progenitor cells (HSPCs) from healthy donors (an average frequency of 27%). By targeting the established Hb CS homozygous erythroblasts, we achieved an average frequency of 32% in situ correction without selection. Notably, prime editing corrected the Hb CS mutation to wild type at an average frequency of 21% in HSPCs from three patients with hemoglobin H Constant Spring (HCS). Erythrocytes that differentiated from prime-edited erythroblasts or HSPCs exhibited a significant reduction in the amount of αCS-globin chains. Insertions and deletions on HBA2 locus and Cas9-dependent DNA off-target editing were detected with relatively low frequency after prime editing. Our findings showed that prime editing can successfully correct Hb CS in erythroblasts and patient HSPCs, which provides proof of principle for its therapeutic potential in HCS.
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Affiliation(s)
- Congwen Shao
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Engineering and Technology Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Qing Liu
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Engineering and Technology Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jinchao Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jianxiang Zhang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, Jiangsu 215123, China
| | - Chengpeng Zhang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, Jiangsu 215123, China
| | - Ye Xin
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yuhua Ye
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Engineering and Technology Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Bin Lin
- Guangzhou Jiexu Gene Technology Co. Ltd., Guangzhou, Guangdong 510535, China
| | - Xinhua Zhang
- Department of Hematology, 923rd Hospital of the People’s Liberation Army, Nanning, Guangxi 530021, China
| | - Li Cheng
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, Jiangsu 215123, China
| | - Xiangmin Xu
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Engineering and Technology Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Peng Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, Jiangsu 215123, China
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6
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Merlin JPJ, Abrahamse H. Optimizing CRISPR/Cas9 precision: Mitigating off-target effects for safe integration with photodynamic and stem cell therapies in cancer treatment. Biomed Pharmacother 2024; 180:117516. [PMID: 39332185 DOI: 10.1016/j.biopha.2024.117516] [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: 07/12/2024] [Revised: 09/22/2024] [Accepted: 09/25/2024] [Indexed: 09/29/2024] Open
Abstract
CRISPR/Cas9 precision genome editing has revolutionized cancer treatment by introducing specific alterations to the cancer genome. But the therapeutic potential of CRISPR/Cas9 is limited by off-target effects, which can cause undesired changes to genomic regions and create major safety concerns. The primary emphasis lies in their implications within the realm of cancer photodynamic therapy (PDT), where precision is paramount. PDT is a promising cancer treatment method; nevertheless, its effectiveness is severely limited and readily leads to recurrence due to the therapeutic resistance of cancer stem cells (CSCs). With a focus on targeted genome editing into cancer cells during PDT and stem cell treatment (SCT), the review aims to further the ongoing search for safer and more accurate CRISPR/Cas9-mediated methods. At the core of this exploration are recent advancements and novel techniques that offer promise in mitigating the risks associated with off-target effects. With a focus on cancer PDT and SCT, this review critically assesses the landscape of off-target effects in CRISPR/Cas9 applications, offering a comprehensive knowledge of their nature and prevalence. A key component of the review is the assessment of cutting-edge delivery methods, such as technologies based on nanoparticles (NPs), to optimize the distribution of CRISPR components. Additionally, the study delves into the intricacies of guide RNA design, focusing on advancements that bolster specificity and minimize off-target effects, crucial elements in ensuring the precision required for effective cancer PDT and SCT. By synthesizing insights from various methodologies, including the exploration of innovative genome editing tools and leveraging robust validation methods and bioinformatics tools, the review aspires to chart a course towards more reliable and precise CRISPR-Cas9 applications in cancer PDT and SCT. For safe PDT and SCT integration in cancer therapy, CRISPR/Cas9 precision optimization is essential. Utilizing sophisticated molecular and computational techniques to address off-target effects is crucial to realizing the therapeutic promise of these technologies, which will ultimately lead to the development of individualized and successful cancer treatment strategies. Our long-term goals are to improve precision genome editing for more potent cancer therapy approaches by refining the way CRISPR/Cas9 is integrated with photodynamic and stem cell therapies.
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Affiliation(s)
- J P Jose Merlin
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, South Africa.
| | - Heidi Abrahamse
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, South Africa
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Jin Y, Wu Y, Reuben A, Zhu L, Gay CM, Wu Q, Zhou X, Mo H, Zheng Q, Ren J, Fang Z, Peng T, Wang N, Ma L, Fan Y, Song H, Zhang J, Chen M. Single-cell and spatial proteo-transcriptomic profiling reveals immune infiltration heterogeneity associated with neuroendocrine features in small cell lung cancer. Cell Discov 2024; 10:93. [PMID: 39231924 PMCID: PMC11375181 DOI: 10.1038/s41421-024-00703-x] [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: 09/27/2023] [Accepted: 06/23/2024] [Indexed: 09/06/2024] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive pulmonary neuroendocrine malignancy featured by cold tumor immune microenvironment (TIME), limited benefit from immunotherapy, and poor survival. The spatial heterogeneity of TIME significantly associated with anti-tumor immunity has not been systemically studied in SCLC. We performed ultra-high-plex Digital Spatial Profiling on 132 tissue microarray cores from 44 treatment-naive limited-stage SCLC tumors. Incorporating single-cell RNA-sequencing data from a local cohort and published SCLC data, we established a spatial proteo-transcriptomic landscape covering over 18,000 genes and 60 key immuno-oncology proteins that participate in signaling pathways affecting tumorigenesis, immune regulation, and cancer metabolism across 3 pathologically defined spatial compartments (pan-CK-positive tumor nest; CD45/CD3-positive tumor stroma; para-tumor). Our study depicted the spatial transcriptomic and proteomic TIME architecture of SCLC, indicating clear intra-tumor heterogeneity dictated via canonical neuroendocrine subtyping markers; revealed the enrichment of innate immune cells and functionally impaired B cells in tumor nest and suggested potentially important immunoregulatory roles of monocytes/macrophages. We identified RE1 silencing factor (REST) as a potential biomarker for SCLC associated with low neuroendocrine features, more active anti-tumor immunity, and prolonged survival.
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Affiliation(s)
- Ying Jin
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, China
| | - Yuefeng Wu
- The MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Department of Cardiovascular Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE), School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Liang Zhu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Carl M Gay
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qingzhe Wu
- The MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xintong Zhou
- The MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haomin Mo
- The MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qi Zheng
- Department of Cardiovascular Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Junyu Ren
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhaoyuan Fang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE), School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Teng Peng
- Department of Cardiovascular Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Nan Wang
- Cosmos Wisdom Biotech Co. Ltd., Hangzhou, Zhejiang, China
| | - Liang Ma
- Department of Cardiovascular Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yun Fan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Hai Song
- The MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
- Center for Oncology Medicine, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, China.
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ming Chen
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
- United Laboratory of Frontier Radiotherapy Technology of Sun Yat-sen University & Chinese Academy of Sciences Ion Medical Technology Co., Ltd, Guangzhou, Guangdong, China.
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8
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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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9
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Macarrón Palacios A, Korus P, Wilkens BGC, Heshmatpour N, Patnaik SR. Revolutionizing in vivo therapy with CRISPR/Cas genome editing: breakthroughs, opportunities and challenges. Front Genome Ed 2024; 6:1342193. [PMID: 38362491 PMCID: PMC10867117 DOI: 10.3389/fgeed.2024.1342193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/11/2024] [Indexed: 02/17/2024] Open
Abstract
Genome editing using the CRISPR/Cas system has revolutionized the field of genetic engineering, offering unprecedented opportunities for therapeutic applications in vivo. Despite the numerous ongoing clinical trials focusing on ex vivo genome editing, recent studies emphasize the therapeutic promise of in vivo gene editing using CRISPR/Cas technology. However, it is worth noting that the complete attainment of the inherent capabilities of in vivo therapy in humans is yet to be accomplished. Before the full realization of in vivo therapeutic potential, it is crucial to achieve enhanced specificity in selectively targeting defective cells while minimizing harm to healthy cells. This review examines emerging studies, focusing on CRISPR/Cas-based pre-clinical and clinical trials for innovative therapeutic approaches for a wide range of diseases. Furthermore, we emphasize targeting cancer-specific sequences target in genes associated with tumors, shedding light on the diverse strategies employed in cancer treatment. We highlight the various challenges associated with in vivo CRISPR/Cas-based cancer therapy and explore their prospective clinical translatability and the strategies employed to overcome these obstacles.
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10
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Lee Y, Oh Y, Lee SH. Recent advances in genome engineering by CRISPR technology. BMB Rep 2024; 57:12-18. [PMID: 38053294 PMCID: PMC10828434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/19/2023] [Accepted: 09/27/2023] [Indexed: 12/07/2023] Open
Abstract
Due to the development of CRISPR technology, the era of effective editing of target genes has arrived. However, the offtarget problem that occurs when recognizing target DNA due to the inherent nature of CRISPR components remains the biggest task to be overcome in the future. In this review, the principle of inducing such unintended off-target editing is analyzed from the structural aspect of CRISPR, and the methodology that has been developed to reduce off-target editing until now is summarized. [BMB Reports 2024; 57(1): 12-18].
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Affiliation(s)
- Youngsik Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Yeounsun Oh
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
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11
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Brooks DL, Whittaker MN, Qu P, Musunuru K, Ahrens-Nicklas RC, Wang X. Efficient in vivo prime editing corrects the most frequent phenylketonuria variant, associated with high unmet medical need. Am J Hum Genet 2023; 110:2003-2014. [PMID: 37924808 PMCID: PMC10716342 DOI: 10.1016/j.ajhg.2023.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 11/06/2023] Open
Abstract
The c.1222C>T (p.Arg408Trp) variant in the phenylalanine hydroxylase gene (PAH) is the most frequent cause of phenylketonuria (PKU), the most common inborn error of metabolism. This autosomal-recessive disorder is characterized by accumulation of blood phenylalanine (Phe) to neurotoxic levels. Using real-world data, we observed that despite dietary and medical interventions, most PKU individuals harboring at least one c.1222C>T variant experience chronic, severe Phe elevations and do not comply with Phe monitoring guidelines. Motivated by these findings, we generated an edited c.1222C>T hepatocyte cell line and humanized c.1222C>T mouse models, with which we demonstrated efficient in vitro and in vivo correction of the variant with prime editing. Delivery via adeno-associated viral (AAV) vectors reproducibly achieved complete normalization of blood Phe levels in PKU mice, with up to 52% whole-liver corrective PAH editing. These studies validate a strategy involving prime editing as a potential treatment for a large proportion of individuals with PKU.
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Affiliation(s)
- Dominique L Brooks
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Madelynn N Whittaker
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ping Qu
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kiran Musunuru
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Rebecca C Ahrens-Nicklas
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Metabolic Disease Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiao Wang
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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12
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Petrova IO, Smirnikhina SA. The Development, Optimization and Future of Prime Editing. Int J Mol Sci 2023; 24:17045. [PMID: 38069367 PMCID: PMC10707272 DOI: 10.3390/ijms242317045] [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: 10/23/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Prime editing is a rapidly developing method of CRISPR/Cas-based genome editing. The increasing number of novel PE applications and improved versions demands constant analysis and evaluation. The present review covers the mechanism of prime editing, the optimization of the method and the possible next step in the evolution of CRISPR/Cas9-associated genome editing. The basic components of a prime editing system are a prime editor fusion protein, consisting of nickase and reverse transcriptase, and prime editing guide RNA, consisting of a protospacer, scaffold, primer binding site and reverse transcription template. Some prime editing systems include other parts, such as additional RNA molecules. All of these components were optimized to achieve better efficiency for different target organisms and/or compactization for viral delivery. Insights into prime editing mechanisms allowed us to increase the efficiency by recruiting mismatch repair inhibitors. However, the next step in prime editing evolution requires the incorporation of new mechanisms. Prime editors combined with integrases allow us to combine the precision of prime editing with the target insertion of large, several-kilobase-long DNA fragments.
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Affiliation(s)
- Irina O. Petrova
- Laboratory of Genome Editing, Research Center for Medical Genetics, Moskvorechye 1, 115478 Moscow, Russia
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13
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Jang G, Kweon J, Kim Y. CRISPR prime editing for unconstrained correction of oncogenic KRAS variants. Commun Biol 2023; 6:681. [PMID: 37391511 PMCID: PMC10313713 DOI: 10.1038/s42003-023-05052-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/16/2023] [Indexed: 07/02/2023] Open
Abstract
KRAS is the most commonly mutated RAS family gene and is a primary cause of the occurrence of several types of cancer. However, KRAS mutations have several unique and diverse molecular identities, making it difficult to find specific treatments. Here, we developed universal pegRNAs which can correct all types of G12 and G13 oncogenic KRAS mutations with CRISPR-mediated prime editors (PEs). The universal pegRNA successfully corrected 12 types of KRAS mutations, accounting for 94% of all known KRAS mutations, by up to 54.8% correction frequency in HEK293T/17 cells. We also applied the universal pegRNA to correct endogenous KRAS mutations in human cancer cells and found that G13D KRAS mutation was successfully corrected to wild-type KRAS sequences with up to 40.6% correction frequency without indel mutations. We propose prime editing with the universal pegRNA as a 'one-to-many' potential therapeutic strategy for KRAS oncogene variants.
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Affiliation(s)
- Gayoung Jang
- Department of Cell and Genetic Engineering, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jiyeon Kweon
- Department of Cell and Genetic Engineering, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yongsub Kim
- Department of Cell and Genetic Engineering, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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14
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Liang SQ, Liu P, Ponnienselvan K, Suresh S, Chen Z, Kramme C, Chatterjee P, Zhu LJ, Sontheimer EJ, Xue W, Wolfe SA. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nat Methods 2023; 20:898-907. [PMID: 37156841 PMCID: PMC11708963 DOI: 10.1038/s41592-023-01859-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 03/17/2023] [Indexed: 05/10/2023]
Abstract
Prime editors have a broad range of potential research and clinical applications. However, methods to delineate their genome-wide editing activities have generally relied on indirect genome-wide editing assessments or the computational prediction of near-cognate sequences. Here we describe a genome-wide approach for the identification of potential prime editor off-target sites, which we call PE-tag. This method relies on the attachment or insertion of an amplification tag at sites of prime editor activity to allow their identification. PE-tag enables genome-wide profiling of off-target sites in vitro using extracted genomic DNA, in mammalian cell lines and in the adult mouse liver. PE-tag components can be delivered in a variety of formats for off-target site detection. Our studies are consistent with the high specificity previously described for prime editor systems, but we find that off-target editing rates are influenced by prime editing guide RNA design. PE-tag represents an accessible, rapid and sensitive approach for the genome-wide identification of prime editor activity and the evaluation of prime editor safety.
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Affiliation(s)
- Shun-Qing Liang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Karthikeyan Ponnienselvan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Sneha Suresh
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Pranam Chatterjee
- Wyss Institute, Harvard Medical School, Boston, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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15
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Naeem M, Alkhnbashi OS. Current Bioinformatics Tools to Optimize CRISPR/Cas9 Experiments to Reduce Off-Target Effects. Int J Mol Sci 2023; 24:ijms24076261. [PMID: 37047235 PMCID: PMC10094584 DOI: 10.3390/ijms24076261] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
The CRISPR-Cas system has evolved into a cutting-edge technology that has transformed the field of biological sciences through precise genetic manipulation. CRISPR/Cas9 nuclease is evolving into a revolutionizing method to edit any gene of any species with desirable outcomes. The swift advancement of CRISPR-Cas technology is reflected in an ever-expanding ecosystem of bioinformatics tools designed to make CRISPR/Cas9 experiments easier. To assist researchers with efficient guide RNA designs with fewer off-target effects, nuclease target site selection, and experimental validation, bioinformaticians have built and developed a comprehensive set of tools. In this article, we will review the various computational tools available for the assessment of off-target effects, as well as the quantification of nuclease activity and specificity, including web-based search tools and experimental methods, and we will describe how these tools can be optimized for gene knock-out (KO) and gene knock-in (KI) for model organisms. We also discuss future directions in precision genome editing and its applications, as well as challenges in target selection, particularly in predicting off-target effects.
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16
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Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun 2023; 14:212. [PMID: 36639728 PMCID: PMC9838544 DOI: 10.1038/s41467-023-35886-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas gene editing has revolutionized experimental molecular biology over the past decade and holds great promise for the treatment of human genetic diseases. Here we review the development of CRISPR-Cas9/Cas12/Cas13 nucleases, DNA base editors, prime editors, and RNA base editors, focusing on the assessment and improvement of their editing precision and safety, pushing the limit of editing specificity and efficiency. We summarize the capabilities and limitations of each CRISPR tool from DNA editing to RNA editing, and highlight the opportunities for future improvements and applications in basic research, as well as the therapeutic and clinical considerations for their use in patients.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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