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Ren CY, Liu YS, He YS, Zhang LP, Rao JH, Rao Y, Chen JH. Engineered CBEs based on Macaca fascicularis A3A with improved properties for precise genome editing. Cell Rep 2024; 43:113878. [PMID: 38431844 DOI: 10.1016/j.celrep.2024.113878] [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: 06/27/2023] [Revised: 11/20/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
Cytidine deaminase defines the properties of cytosine base editors (CBEs) for C-to-T conversion. Replacing the cytidine deaminase rat APOBEC1 (rA1) in CBEs with a human APOBEC3A (hA3A) improves CBE properties. However, the potential CBE application of macaque A3A orthologs remains undetermined. Our current study develops and evaluates engineered CBEs based on Macaca fascicularis A3A (mA3A). Here, we demonstrate that BE4-mA3A and its RNA-editing-derived variants exhibit improved CBE properties, except for DNA off-target activity, compared to BE3-rA1 and BE4-rA1. Unexpectedly, deleting Ser-Val-Arg (SVR) in BE4-mA3A dramatically reduces DNA and RNA off-target activities and improves editing accuracy, with on-target efficiency unaffected. In contrast, a chimeric BE4-hA3A-SVR+ shows editing efficiency increased by about 50%, with other properties unaffected. Our findings demonstrate that mA3A-based CBEs could provide prototype options with advantages over rA1- and hA3A-based CBEs for further optimization, highlighting the importance of the SVR motif in defining CBE intrinsic properties.
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Affiliation(s)
- Chun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan-Shan Liu
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China
| | - Yu-Shan He
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Lin-Pei Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jun-Hua Rao
- Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Xinshijie Eye Hospital, Wuxi, China.
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Hinch R, Donnelly P, Hinch AG. Meiotic DNA breaks drive multifaceted mutagenesis in the human germ line. Science 2023; 382:eadh2531. [PMID: 38033082 PMCID: PMC7615360 DOI: 10.1126/science.adh2531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/29/2023] [Indexed: 12/02/2023]
Abstract
Meiotic recombination commences with hundreds of programmed DNA breaks; however, the degree to which they are accurately repaired remains poorly understood. We report that meiotic break repair is eightfold more mutagenic for single-base substitutions than was previously understood, leading to de novo mutation in one in four sperm and one in 12 eggs. Its impact on indels and structural variants is even higher, with 100- to 1300-fold increases in rates per break. We uncovered new mutational signatures and footprints relative to break sites, which implicate unexpected biochemical processes and error-prone DNA repair mechanisms, including translesion synthesis and end joining in meiotic break repair. We provide evidence that these mechanisms drive mutagenesis in human germ lines and lead to disruption of hundreds of genes genome wide.
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Affiliation(s)
- Robert Hinch
- Big Data Institute, University of Oxford; Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford; Oxford, UK
- Genomics plc; Oxford, UK
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Dudley JP. APOBECs: Our fickle friends? PLoS Pathog 2023; 19:e1011364. [PMID: 37200235 DOI: 10.1371/journal.ppat.1011364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Affiliation(s)
- Jaquelin P Dudley
- Department of Molecular Biosciences and LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America
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Costiniuk CT, Ahmad A. Potential HIV/ART-mediated germline mutations causing congenital inborn errors of immunity in children born to HIV+ couples: an alarming spectre. AIDS 2022; 36:2215-2216. [PMID: 36382438 DOI: 10.1097/qad.0000000000003391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Cecilia T Costiniuk
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre, Montreal
| | - Ali Ahmad
- CHU Sainte-Justine Research Center/University of Montreal, Quebec, Canada
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