1
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Celotti M, Derks LLM, van Es J, van Boxtel R, Clevers H, Geurts MH. Protocol to create isogenic disease models from adult stem cell-derived organoids using next-generation CRISPR tools. STAR Protoc 2024; 5:103189. [PMID: 39003744 PMCID: PMC11298932 DOI: 10.1016/j.xpro.2024.103189] [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: 03/29/2024] [Revised: 05/20/2024] [Accepted: 06/20/2024] [Indexed: 07/16/2024] Open
Abstract
Isogenic disease models, such as genetically engineered organoids, provide insight into the impact of genetic variants on organ function. Here, we present a protocol to create isogenic disease models from adult stem cell-derived organoids using next-generation CRISPR tools. We describe steps for single guide RNA (sgRNA) design and cloning, electroporation, and selecting electroporated cells. We then detail procedures for clonal line generation. Next-generation CRISPR tools do not require double-stranded break (DSB) induction for their function, thus simplifying in vitro disease model generation. For complete details on the use and execution of this protocol, please refer to Geurts et al.1,2.
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Affiliation(s)
- Martina Celotti
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands.
| | - Lucca L M Derks
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Johan van Es
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Ruben van Boxtel
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Maarten H Geurts
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands.
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2
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Zhao N, Zhou J, Tao T, Wang Q, Tang J, Li D, Gou S, Guan Z, Olajide JS, Lin J, Wang S, Li X, Zhou J, Gao Z, Wang G. Evolved cytidine and adenine base editors with high precision and minimized off-target activity by a continuous directed evolution system in mammalian cells. Nat Commun 2024; 15:8140. [PMID: 39289397 PMCID: PMC11408606 DOI: 10.1038/s41467-024-52483-3] [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: 12/22/2023] [Accepted: 09/10/2024] [Indexed: 09/19/2024] Open
Abstract
Continuous directed evolution of base editors (BEs) has been successful in bacteria cells, but not yet in mammalian cells. Here, we report the development of a Continuous Directed Evolution system in Mammalian cells (CDEM). CDEM enables the BE evolution in a full-length manner with Cas9 nickase. We harness CDEM to evolve the deaminases of cytosine base editor BE3 and adenine base editors, ABEmax and ABE8e. The evolved cytidine deaminase variants on BE4 architecture show not only narrowed editing windows, but also higher editing purity and low off-target activity without a trade-off in on-targeting activity. The evolved ABEmax and ABE8e variants exhibit narrowed or shifted editing windows to different extents, and lower off-target effects. The results illustrate that CDEM is a simple but powerful approach to continuously evolve BEs without size restriction in the mammalian environment, which is advantageous over continuous directed evolution system in bacteria cells.
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Affiliation(s)
- Na Zhao
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
- Guangzhou JinHua JiYin Technology Co., Ltd., Guangzhou, China
| | - Jian Zhou
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China.
- Department of Laboratory Medicines, The First Affiliated Hospital of Xi'an Medical University, Xi'an, China.
| | - Tianfu Tao
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Qi Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jie Tang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Dengluan Li
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Shixue Gou
- Guangzhou National Laboratory, Guangzhou, China
| | - Zhihong Guan
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Joshua Seun Olajide
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jiejing Lin
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Shuo Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaoping Li
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
| | - Jiankui Zhou
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zongliang Gao
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China.
| | - Gang Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China.
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3
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Li B, Sun C, Li J, Gao C. Targeted genome-modification tools and their advanced applications in crop breeding. Nat Rev Genet 2024; 25:603-622. [PMID: 38658741 DOI: 10.1038/s41576-024-00720-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2024] [Indexed: 04/26/2024]
Abstract
Crop improvement by genome editing involves the targeted alteration of genes to improve plant traits, such as stress tolerance, disease resistance or nutritional content. Techniques for the targeted modification of genomes have evolved from generating random mutations to precise base substitutions, followed by insertions, substitutions and deletions of small DNA fragments, and are finally starting to achieve precision manipulation of large DNA segments. Recent developments in base editing, prime editing and other CRISPR-associated systems have laid a solid technological foundation to enable plant basic research and precise molecular breeding. In this Review, we systematically outline the technological principles underlying precise and targeted genome-modification methods. We also review methods for the delivery of genome-editing reagents in plants and outline emerging crop-breeding strategies based on targeted genome modification. Finally, we consider potential future developments in precise genome-editing technologies, delivery methods and crop-breeding approaches, as well as regulatory policies for genome-editing products.
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Affiliation(s)
- Boshu Li
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao Sun
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiayang Li
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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4
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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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5
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Liu L, Zhang Z, Wang C, Yan F, Sun W, Zhou X, Miao W, Zhou H. Developing guanine base editors for G-to-T editing in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1557-1560. [PMID: 38934772 DOI: 10.1111/jipb.13729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Two guanine base editors created using an engineered N-methylpurine DNA glycosylase with CRISPR systems achieved targeted G-to-T editing with 4.94-12.50% efficiency in rice (Oryza sativa). The combined use of the DNA glycosylase and deaminases enabled co-editing of target guanines with adenines or cytosines.
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Affiliation(s)
- Lang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
- Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China
| | - Zhongming Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- School of Plant Protection, Hainan University, Haikou, 570228, China
| | - Chenyang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fang Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenxian Sun
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Weiguo Miao
- School of Plant Protection, Hainan University, Haikou, 570228, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China
- Key Laboratory of Gene Editing Technologies, Ministry of Agricultural and Rural Affairs, Sanya, 572024, China
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6
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Yi Z, Zhang X, Wei X, Li J, Ren J, Zhang X, Zhang Y, Tang H, Chang X, Yu Y, Wei W. Programmable DNA pyrimidine base editing via engineered uracil-DNA glycosylase. Nat Commun 2024; 15:6397. [PMID: 39080265 PMCID: PMC11289083 DOI: 10.1038/s41467-024-50012-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: 03/19/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
DNA base editing technologies predominantly utilize engineered deaminases, limiting their ability to edit thymine and guanine directly. In this study, we successfully achieve base editing of both cytidine and thymine by leveraging the translesion DNA synthesis pathway through the engineering of uracil-DNA glycosylase (UNG). Employing structure-based rational design, exploration of homologous proteins, and mutation screening, we identify a Deinococcus radiodurans UNG mutant capable of effectively editing thymine. When fused with the nickase Cas9, the engineered DrUNG protein facilitates efficient thymine base editing at endogenous sites, achieving editing efficiencies up to 55% without enrichment and exhibiting minimal cellular toxicity. This thymine base editor (TBE) exhibits high editing specificity and significantly restores IDUA enzyme activity in cells derived from patients with Hurler syndrome. TBEs represent efficient, specific, and low-toxicity approaches to base editing with potential applications in treating relevant diseases.
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Affiliation(s)
- Zongyi Yi
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Xiaoxue Zhang
- Changping Laboratory, Beijing, People's Republic of China
| | - Xiaoxu Wei
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, People's Republic of China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Jiayi Li
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, People's Republic of China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Jiwu Ren
- Changping Laboratory, Beijing, People's Republic of China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Xue Zhang
- Changping Laboratory, Beijing, People's Republic of China
| | - Yike Zhang
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, People's Republic of China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Huixian Tang
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, People's Republic of China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Xiwen Chang
- Changping Laboratory, Beijing, People's Republic of China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Ying Yu
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, People's Republic of China.
- Changping Laboratory, Beijing, People's Republic of China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China.
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7
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Wu X, Yang J, Zhang J, Song Y. Gene editing therapy for cardiovascular diseases. MedComm (Beijing) 2024; 5:e639. [PMID: 38974714 PMCID: PMC11224995 DOI: 10.1002/mco2.639] [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: 10/18/2023] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 07/09/2024] Open
Abstract
The development of gene editing tools has been a significant area of research in the life sciences for nearly 30 years. These tools have been widely utilized in disease detection and mechanism research. In the new century, they have shown potential in addressing various scientific challenges and saving lives through gene editing therapies, particularly in combating cardiovascular disease (CVD). The rapid advancement of gene editing therapies has provided optimism for CVD patients. The progress of gene editing therapy for CVDs is a comprehensive reflection of the practical implementation of gene editing technology in both clinical and basic research settings, as well as the steady advancement of research and treatment of CVDs. This article provides an overview of the commonly utilized DNA-targeted gene editing tools developed thus far, with a specific focus on the application of these tools, particularly the clustered regularly interspaced short palindromic repeat/CRISPR-associated genes (Cas) (CRISPR/Cas) system, in CVD gene editing therapy. It also delves into the challenges and limitations of current gene editing therapies, while summarizing ongoing research and clinical trials related to CVD. The aim is to facilitate further exploration by relevant researchers by summarizing the successful applications of gene editing tools in the field of CVD.
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Affiliation(s)
- Xinyu Wu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious DiseasesKey Laboratory for Zoonosis Research of the Ministry of Educationand College of Veterinary MedicineJilin UniversityChangchunChina
| | - Jie Yang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious DiseasesKey Laboratory for Zoonosis Research of the Ministry of Educationand College of Veterinary MedicineJilin UniversityChangchunChina
| | - Jiayao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious DiseasesKey Laboratory for Zoonosis Research of the Ministry of Educationand College of Veterinary MedicineJilin UniversityChangchunChina
| | - Yuning Song
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious DiseasesKey Laboratory for Zoonosis Research of the Ministry of Educationand College of Veterinary MedicineJilin UniversityChangchunChina
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8
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Liu Y, Kong J, Liu G, Li Z, Xiao Y. Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401797. [PMID: 38728624 PMCID: PMC11267366 DOI: 10.1002/advs.202401797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.
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Affiliation(s)
- Yongfeng Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Mudi Meng Honors CollegeChina Pharmaceutical UniversityNanjing210009China
| | - Jianping Kong
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Gongyu Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Zhaoxing Li
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
| | - Yibei Xiao
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
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9
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Tong H, Wang H, Wang X, Liu N, Li G, Wu D, Li Y, Jin M, Li H, Wei Y, Li T, Yuan Y, Shi L, Yao X, Zhou Y, Yang H. Development of deaminase-free T-to-S base editor and C-to-G base editor by engineered human uracil DNA glycosylase. Nat Commun 2024; 15:4897. [PMID: 38851742 PMCID: PMC11162499 DOI: 10.1038/s41467-024-49343-5] [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: 03/18/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024] Open
Abstract
DNA base editors enable direct editing of adenine (A), cytosine (C), or guanine (G), but there is no base editor for direct thymine (T) editing currently. Here we develop two deaminase-free glycosylase-based base editors for direct T editing (gTBE) and C editing (gCBE) by fusing Cas9 nickase (nCas9) with engineered human uracil DNA glycosylase (UNG) variants. By several rounds of structure-informed rational mutagenesis on UNG in cultured human cells, we obtain gTBE and gCBE with high activity of T-to-S (i.e., T-to-C or T-to-G) and C-to-G conversions, respectively. Furthermore, we conduct parallel comparison of gTBE/gCBE with those recently developed using other protein engineering strategies, and find gTBE/gCBE show the outperformance. Thus, we provide several base editors, gTBEs and gCBEs, with corresponding engineered UNG variants, broadening the targeting scope of base editors.
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Affiliation(s)
- Huawei Tong
- HuidaGene Therapeutics Co., Ltd., Shanghai, China.
| | | | - Xuchen Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Nana Liu
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Guoling Li
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Danni Wu
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Yun Li
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Ming Jin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Hengbin Li
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Yinghui Wei
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- School of Future Technology on Bio-Breeding, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Tong Li
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Yuan Yuan
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Linyu Shi
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Xuan Yao
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Yingsi Zhou
- HuidaGene Therapeutics Co., Ltd., Shanghai, China.
| | - Hui Yang
- HuidaGene Therapeutics Co., Ltd., Shanghai, China.
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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10
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Tian Y, Li X, Xie J, Zheng Z, Shen R, Cao X, Wang M, Dong C, Zhu JK. Targeted G-to-T base editing for generation of novel herbicide-resistance gene alleles in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1048-1051. [PMID: 38578176 DOI: 10.1111/jipb.13657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024]
Abstract
A newly developed rice guanine base editor (OsGTBE) achieves targeted and efficient G-to-T editing (C-to-A in the opposite strand) in rice. Using OsGTBE to edit endogenous herbicide-resistant loci generated several novel alleles conferring herbicide resistance, highlighting its utility in creating valuable germplasm and enhancing genetic diversity..
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Affiliation(s)
- Yifu Tian
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Xinbo Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Jiyong Xie
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zai Zheng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Rundong Shen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Xuesong Cao
- Institute of Advanced Biotechnology, and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Mugui Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Chao Dong
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Jian-Kang Zhu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Institute of Advanced Biotechnology, and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
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11
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Eghbalsaied S, Lawler C, Petersen B, Hajiyev RA, Bischoff SR, Frankenberg S. CRISPR/Cas9-mediated base editors and their prospects for mitochondrial genome engineering. Gene Ther 2024; 31:209-223. [PMID: 38177342 DOI: 10.1038/s41434-023-00434-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024]
Abstract
Base editors are a type of double-stranded break (DSB)-free gene editing technology that has opened up new possibilities for precise manipulation of mitochondrial DNA (mtDNA). This includes cytosine and adenosine base editors and more recently guanosine base editors. Because of having low off-target and indel rates, there is a growing interest in developing and evolving this research field. Here, we provide a detailed update on DNA base editors. While base editing has widely been used for nuclear genome engineering, the growing interest in applying this technology to mitochondrial DNA has been faced with several challenges. While Cas9 protein has been shown to enter mitochondria, use of smaller Cas proteins, such as Cas12a, has higher import efficiency. However, sgRNA transfer into mitochondria is the most challenging step. sgRNA structure and ratio of Cas protein to sgRNA are both important factors for efficient sgRNA entry into mitochondria. In conclusion, while there are still several challenges to be addressed, ongoing research in this field holds the potential for new treatments and therapies for mitochondrial disorders.
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Affiliation(s)
- Shahin Eghbalsaied
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
- Department of Animal Science, Isfahan Branch, Islamic Azad University (IAU), Isfahan, Iran.
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Göttingen, Germany.
| | - Clancy Lawler
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Björn Petersen
- Department of Biotechnology, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute (FLI), Mariensee, Germany
- eGenesis, 2706 HWY E, 53572, Mount Horeb, WI, USA
| | - Raul A Hajiyev
- Department of Genome Engineering, NovoHelix, Miami, FL, USA
- Department of Computer Science, Kent State University, Kent, OH, USA
| | - Steve R Bischoff
- Department of Genome Engineering, NovoHelix, Miami, FL, USA
- Foundry for Genome Engineering & Reproductive Medicine (FGERM), Miami, FL, USA
| | - Stephen Frankenberg
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
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12
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Gawlitt S, Collins SP, Yu Y, Blackman SA, Barquist L, Beisel CL. Expanding the flexibility of base editing for high-throughput genetic screens in bacteria. Nucleic Acids Res 2024; 52:4079-4097. [PMID: 38499498 DOI: 10.1093/nar/gkae174] [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: 07/12/2023] [Revised: 02/07/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide screens have become powerful tools for elucidating genotype-to-phenotype relationships in bacteria. Of the varying techniques to achieve knockout and knockdown, CRISPR base editors are emerging as promising options. However, the limited number of available, efficient target sites hampers their use for high-throughput screening. Here, we make multiple advances to enable flexible base editing as part of high-throughput genetic screening in bacteria. We first co-opt the Streptococcus canis Cas9 that exhibits more flexible protospacer-adjacent motif recognition than the traditional Streptococcus pyogenes Cas9. We then expand beyond introducing premature stop codons by mutating start codons. Next, we derive guide design rules by applying machine learning to an essentiality screen conducted in Escherichia coli. Finally, we rescue poorly edited sites by combining base editing with Cas9-induced cleavage of unedited cells, thereby enriching for intended edits. The efficiency of this dual system was validated through a conditional essentiality screen based on growth in minimal media. Overall, expanding the scope of genome-wide knockout screens with base editors could further facilitate the investigation of new gene functions and interactions in bacteria.
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Affiliation(s)
- Sandra Gawlitt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Scott P Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Samuel A Blackman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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13
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He Y, Zhou X, Chang C, Chen G, Liu W, Li G, Fan X, Sun M, Miao C, Huang Q, Ma Y, Yuan F, Chang X. Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing. Mol Cell 2024; 84:1257-1270.e6. [PMID: 38377993 DOI: 10.1016/j.molcel.2024.01.021] [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: 10/02/2023] [Revised: 12/20/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
Current base editors (BEs) use DNA deaminases, including cytidine deaminase in cytidine BE (CBE) or adenine deaminase in adenine BE (ABE), to facilitate transition nucleotide substitutions. Combining CBE or ABE with glycosylase enzymes can induce limited transversion mutations. Nonetheless, a critical demand remains for BEs capable of generating alternative mutation types, such as T>G corrections. In this study, we leveraged pre-trained protein language models to optimize a uracil-N-glycosylase (UNG) variant with altered specificity for thymines (eTDG). Notably, after two rounds of testing fewer than 50 top-ranking variants, more than 50% exhibited over 1.5-fold enhancement in enzymatic activities. When eTDG was fused with nCas9, it induced programmable T-to-S (G/C) substitutions and corrected db/db diabetic mutation in mice (up to 55%). Our findings not only establish orthogonal strategies for developing novel BEs but also demonstrate the capacities of protein language models for optimizing enzymes without extensive task-specific training data.
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Affiliation(s)
- Yan He
- Fudan University, 220 Handan Road, Shanghai 200433, China; School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Xibin Zhou
- School of Engineering, Westlake University, Hangzhou, Zhejiang 310014, China
| | - Chong Chang
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Ge Chen
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Weikuan Liu
- Fudan University, 220 Handan Road, Shanghai 200433, China; School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Geng Li
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Xiaoqi Fan
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Mingsun Sun
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Chensi Miao
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Qianyue Huang
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Yunqing Ma
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Fajie Yuan
- School of Engineering, Westlake University, Hangzhou, Zhejiang 310014, China.
| | - Xing Chang
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.
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14
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Xu F, Zheng C, Xu W, Zhang S, Liu S, Chen X, Yao K. Breaking genetic shackles: The advance of base editing in genetic disorder treatment. Front Pharmacol 2024; 15:1364135. [PMID: 38510648 PMCID: PMC10953296 DOI: 10.3389/fphar.2024.1364135] [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: 01/01/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The rapid evolution of gene editing technology has markedly improved the outlook for treating genetic diseases. Base editing, recognized as an exceptionally precise genetic modification tool, is emerging as a focus in the realm of genetic disease therapy. We provide a comprehensive overview of the fundamental principles and delivery methods of cytosine base editors (CBE), adenine base editors (ABE), and RNA base editors, with a particular focus on their applications and recent research advances in the treatment of genetic diseases. We have also explored the potential challenges faced by base editing technology in treatment, including aspects such as targeting specificity, safety, and efficacy, and have enumerated a series of possible solutions to propel the clinical translation of base editing technology. In conclusion, this article not only underscores the present state of base editing technology but also envisions its tremendous potential in the future, providing a novel perspective on the treatment of genetic diseases. It underscores the vast potential of base editing technology in the realm of genetic medicine, providing support for the progression of gene medicine and the development of innovative approaches to genetic disease therapy.
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Affiliation(s)
- Fang Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Caiyan Zheng
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Weihui Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shiyao Zhang
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shanshan Liu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiaopeng Chen
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Kai Yao
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
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15
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Sun Y, Chen Q, Cheng Y, Wang X, Deng Z, Zhou F, Sun Y. Design and Engineering of Light-Induced Base Editors Facilitating Genome Editing with Enhanced Fidelity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305311. [PMID: 38039441 PMCID: PMC10837352 DOI: 10.1002/advs.202305311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/27/2023] [Indexed: 12/03/2023]
Abstract
Base editors, which enable targeted locus nucleotide conversion in genomic DNA without double-stranded breaks, have been engineered as powerful tools for biotechnological and clinical applications. However, the application of base editors is limited by their off-target effects. Continuously expressed deaminases used for gene editing may lead to unwanted base alterations at unpredictable genomic locations. In the present study, blue-light-activated base editors (BLBEs) are engineered based on the distinct photoswitches magnets that can switch from a monomer to dimerization state in response to blue light. By fusing the N- and C-termini of split DNA deaminases with photoswitches Magnets, efficient A-to-G and C-to-T base editing is achieved in response to blue light in prokaryotic and eukaryotic cells. Furthermore, the results showed that BLBEs can realize precise blue light-induced gene editing across broad genomic loci with low off-target activity at the DNA- and RNA-level. Collectively, these findings suggest that the optogenetic utilization of base editing and optical base editors may provide powerful tools to promote the development of optogenetic genome engineering.
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Affiliation(s)
- Yangning Sun
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
| | - Qi Chen
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
| | - Yanbing Cheng
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
| | - Xi Wang
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
| | - Zixin Deng
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
| | - Fuling Zhou
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Yuhui Sun
- Department of HematologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)Wuhan UniversityWuhan430071China
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16
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Chen Y, Luo X, Kang R, Cui K, Ou J, Zhang X, Liang P. Current therapies for osteoarthritis and prospects of CRISPR-based genome, epigenome, and RNA editing in osteoarthritis treatment. J Genet Genomics 2024; 51:159-183. [PMID: 37516348 DOI: 10.1016/j.jgg.2023.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
Abstract
Osteoarthritis (OA) is one of the most common degenerative joint diseases worldwide, causing pain, disability, and decreased quality of life. The balance between regeneration and inflammation-induced degradation results in multiple etiologies and complex pathogenesis of OA. Currently, there is a lack of effective therapeutic strategies for OA treatment. With the development of CRISPR-based genome, epigenome, and RNA editing tools, OA treatment has been improved by targeting genetic risk factors, activating chondrogenic elements, and modulating inflammatory regulators. Supported by cell therapy and in vivo delivery vectors, genome, epigenome, and RNA editing tools may provide a promising approach for personalized OA therapy. This review summarizes CRISPR-based genome, epigenome, and RNA editing tools that can be applied to the treatment of OA and provides insights into the development of CRISPR-based therapeutics for OA treatment. Moreover, in-depth evaluations of the efficacy and safety of these tools in human OA treatment are needed.
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Affiliation(s)
- Yuxi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xiao Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Rui Kang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Kaixin Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jianping Ou
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Xiya Zhang
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China.
| | - Puping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
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17
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Ye L, Zhao D, Li J, Wang Y, Li B, Yang Y, Hou X, Wang H, Wei Z, Liu X, Li Y, Li S, Liu Y, Zhang X, Bi C. Glycosylase-based base editors for efficient T-to-G and C-to-G editing in mammalian cells. Nat Biotechnol 2024:10.1038/s41587-023-02050-w. [PMID: 38168994 DOI: 10.1038/s41587-023-02050-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 10/27/2023] [Indexed: 01/05/2024]
Abstract
Base editors show promise for treating human genetic diseases, but most current systems use deaminases, which cause off-target effects and are limited in editing type. In this study, we constructed deaminase-free base editors for cytosine (DAF-CBE) and thymine (DAF-TBE), which contain only a cytosine-DNA or a thymine-DNA glycosylase (CDG/TDG) variant, respectively, tethered to a Cas9 nickase. Multiple rounds of mutagenesis by directed evolution in Escherichia coli generated two variants with enhanced base-converting activity-CDG-nCas9 and TDG-nCas9-with efficiencies of up to 58.7% for C-to-A and 54.3% for T-to-A. DAF-BEs achieve C-to-G/T-to-G editing in mammalian cells with minimal Cas9-dependent and Cas9-independent off-target effects as well as minimal RNA off-target effects. Additional engineering resulted in DAF-CBE2/DAF-TBE2, which exhibit altered editing windows from the 5' end to the middle of the protospacer and increased C-to-G/T-to-G editing efficiency of 3.5-fold and 1.2-fold, respectively. Compared to prime editing or CGBEs, DAF-BEs expand conversion types of base editors with similar efficiencies, smaller sizes and lower off-target effects.
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Affiliation(s)
- Lijun Ye
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Yiran Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Bo Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yuanzhao Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xueting Hou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Huibin Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhandong Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaoqi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yaqiu Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yajing Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- University of Chinese Academy of Sciences, Beijing, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- University of Chinese Academy of Sciences, Beijing, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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18
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Kim JS, Chen J. Base editing of organellar DNA with programmable deaminases. Nat Rev Mol Cell Biol 2024; 25:34-45. [PMID: 37794167 DOI: 10.1038/s41580-023-00663-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 10/06/2023]
Abstract
Mitochondria and chloroplasts are organelles that include their own genomes, which encode key genes for ATP production and carbon dioxide fixation, respectively. Mutations in mitochondrial DNA can cause diverse genetic disorders and are also linked to ageing and age-related diseases, including cancer. Targeted editing of organellar DNA should be useful for studying organellar genes and developing novel therapeutics, but it has been hindered by lack of efficient tools in living cells. Recently, CRISPR-free, protein-only base editors, such as double-stranded DNA deaminase toxin A-derived cytosine base editors (DdCBEs) and adenine base editors (ABEs), have been developed, which enable targeted organellar DNA editing in human cell lines, animals and plants. In this Review, we present programmable deaminases developed for base editing of organellar DNA in vitro and discuss mitochondrial DNA editing in animals, and plastid genome (plastome) editing in plants. We also discuss precision and efficiency limitations of these tools and propose improvements for therapeutic, agricultural and environmental applications.
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Affiliation(s)
- Jin-Soo Kim
- NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI) and Department of Biochemistry, National University of Singapore, Singapore, Singapore.
- Edgene, Seoul, South Korea.
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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19
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Fu Y, He X, Gao XD, Li F, Ge S, Yang Z, Fan X. Prime editing: current advances and therapeutic opportunities in human diseases. Sci Bull (Beijing) 2023; 68:3278-3291. [PMID: 37973465 DOI: 10.1016/j.scib.2023.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/06/2023] [Accepted: 10/28/2023] [Indexed: 11/19/2023]
Abstract
Gene editing ushers in a new era of disease treatment since many genetic diseases are caused by base-pair mutations in genomic DNA. With the rapid development of genome editing technology, novel editing tools such as base editing and prime editing (PE) have attracted public attention, heralding a great leap forward in this field. PE, in particular, is characterized by no need for double-strand breaks (DSBs) or homology sequence templates with variable application scenarios, including point mutations as well as insertions or deletions. With higher editing efficiency and fewer byproducts than traditional editing tools, PE holds great promise as a therapeutic strategy for human diseases. Subsequently, a growing demand for the standard construction of PE system has spawned numerous easy-to-access internet resources and tools for personalized prime editing guide RNA (pegRNA) design and off-target site prediction. In this review, we mainly introduce the innovation and evolutionary strategy of PE systems and the auxiliary tools for PE design and analysis. Additionally, its application and future potential in the clinical field have been summarized and envisaged.
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Affiliation(s)
- Yidian Fu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Xiaoyu He
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge MA 02138, USA
| | - Fang Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China.
| | - Zhi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China.
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Vu BN, Vu TV, Yoo JY, Nguyen NT, Ko KS, Kim JY, Lee KO. CRISPR-Cas-mediated unfolded protein response control for enhancing plant stress resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1271368. [PMID: 37908833 PMCID: PMC10613997 DOI: 10.3389/fpls.2023.1271368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
Plants consistently encounter environmental stresses that negatively affect their growth and development. To mitigate these challenges, plants have developed a range of adaptive strategies, including the unfolded protein response (UPR), which enables them to manage endoplasmic reticulum (ER) stress resulting from various adverse conditions. The CRISPR-Cas system has emerged as a powerful tool for plant biotechnology, with the potential to improve plant tolerance and resistance to biotic and abiotic stresses, as well as enhance crop productivity and quality by targeting specific genes, including those related to the UPR. This review highlights recent advancements in UPR signaling pathways and CRISPR-Cas technology, with a particular focus on the use of CRISPR-Cas in studying plant UPR. We also explore prospective applications of CRISPR-Cas in engineering UPR-related genes for crop improvement. The integration of CRISPR-Cas technology into plant biotechnology holds the promise to revolutionize agriculture by producing crops with enhanced resistance to environmental stresses, increased productivity, and improved quality traits.
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Affiliation(s)
- Bich Ngoc Vu
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea
| | - Tien Van Vu
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Jae Yong Yoo
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Ngan Thi Nguyen
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea
| | - Ki Seong Ko
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Jae-Yean Kim
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea
- Nulla Bio Inc., Jinju, Republic of Korea
| | - Kyun Oh Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea
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