Cas12a Base Editors Induce Efficient and Specific Editing with Low DNA Damage Response
Xiao Wang,
Chengfeng Ding,
Wenxia Yu,
Ying Wang,
Siting He,
Bei Yang,
Yi-Chun Xiong,
Jia Wei,
Jifang Li,
Jiayi Liang,
Zongyang Lu,
Wei Zhu,
Jing Wu,
Zhi Zhou,
Xingxu Huang,
Zhen Liu,
Li Yang,
Jia Chen
Affiliations
Xiao Wang
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
Chengfeng Ding
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
Wenxia Yu
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
Ying Wang
CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
Siting He
University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
Bei Yang
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
Yi-Chun Xiong
CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
Jia Wei
CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
Jifang Li
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
Jiayi Liang
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
Zongyang Lu
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
Wei Zhu
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
Jing Wu
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
Zhi Zhou
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
Xingxu Huang
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
Zhen Liu
Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; Corresponding author
Li Yang
CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Corresponding author
Jia Chen
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; Corresponding author
Summary: The advent of base editors (BEs) holds great potential for correcting pathogenic-related point mutations to treat relevant diseases. However, Cas9 nickase (nCas9)-derived BEs lead to DNA double-strand breaks, which can trigger unwanted DNA damage response (DDR). Here, we show that the original version of catalytically dead Cas12a (dCas12a)-conjugated BEs induce a basal level of DNA breaks and minimally activate DDR proteins, including H2AX, ATM, ATR, and p53. By fusing dCas12a with engineered human apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A (APOBEC3A), we further develop the BEACON (base editing induced by human APOBEC3A and Cas12a without DNA break) system to achieve enhanced deamination efficiency and editing specificity. Efficient C-to-T editing is achieved by BEACON in mammalian cells at levels comparable to AncBE4max, with only low levels of DDR and minimal RNA off-target mutations. Importantly, BEACON induces in vivo base editing in mouse embryos, and targeted C-to-T conversions are detected in F0 mice.
