Efficient mitochondrial A-to-G base editors for the generation of mitochondrial disease models

Liang Chen^#^{1

2

3}, Mengjia Hong^#⁴, Changming Luan^#⁴, Meng Yuan⁴, Yiming Wang⁵, Xinyuan Guo⁴, Yue Fang^{6

7}, Hao Huang⁴, Xiaohua Dong^{5

8}, Hongyi Gao⁴, Dan Zhang⁴, Xi Chen⁹, Dihao Meng⁴, Molin Huang⁴, Zongyi Yi¹⁰, Mingyao Liu^{4

9}, Wensheng Wei^{10

11}, Liangcai Gao⁴, Gaojie Song⁴, Xiaoming Zhou^{6

7}, Dali Li^{12

13

14}

Affiliations

¹ Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China. chenliang@lglab.ac.cn.
² Lingang Laboratory, Shanghai, China. chenliang@lglab.ac.cn.
³ School of Pharmacy, East China Normal University, Shanghai, China. chenliang@lglab.ac.cn.
⁴ Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China.
⁵ Lingang Laboratory, Shanghai, China.
⁶ Key Laboratory of Brain Functional Genomics of Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China.
⁷ New York University-East China Normal University Institute of Brain and Cognitive Science, New York University, Shanghai, Shanghai, China.
⁸ School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
⁹ BRL Medicine, Inc., Shanghai, China.
¹⁰ 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, China.
¹¹ Changping Laboratory, Beijing, China.
¹² Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China. dlli@bio.ecnu.edu.cn.
¹³ School of Pharmacy, East China Normal University, Shanghai, China. dlli@bio.ecnu.edu.cn.
¹⁴ Shanghai Academy of Natural Sciences (SANS), Shanghai, China. dlli@bio.ecnu.edu.cn.

^# Contributed equally.

PMID: 40461783
DOI: 10.1038/s41587-025-02685-x

Efficient mitochondrial A-to-G base editors for the generation of mitochondrial disease models

Liang Chen et al. Nat Biotechnol. 2025.

. 2025 Jun 3.

doi: 10.1038/s41587-025-02685-x. Online ahead of print.

Authors

Affiliations

¹ Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China. chenliang@lglab.ac.cn.
² Lingang Laboratory, Shanghai, China. chenliang@lglab.ac.cn.
³ School of Pharmacy, East China Normal University, Shanghai, China. chenliang@lglab.ac.cn.
⁴ Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China.
⁵ Lingang Laboratory, Shanghai, China.
⁶ Key Laboratory of Brain Functional Genomics of Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, School of Life Sciences, East China Normal University, Shanghai, China.
⁷ New York University-East China Normal University Institute of Brain and Cognitive Science, New York University, Shanghai, Shanghai, China.
⁸ School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
⁹ BRL Medicine, Inc., Shanghai, China.
¹⁰ 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, China.
¹¹ Changping Laboratory, Beijing, China.
¹² Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China. dlli@bio.ecnu.edu.cn.
¹³ School of Pharmacy, East China Normal University, Shanghai, China. dlli@bio.ecnu.edu.cn.
¹⁴ Shanghai Academy of Natural Sciences (SANS), Shanghai, China. dlli@bio.ecnu.edu.cn.

^# Contributed equally.

PMID: 40461783
DOI: 10.1038/s41587-025-02685-x

Abstract

Existing A-to-G base editors for mitochondrial DNA (mtDNA) are limited by low efficiency. We used directed evolution to discover variants of the TadA-8e base editors that have substantially increased activity and expanded targeting compatibility for both nuclear and mitochondrial adenine base editing, especially in previously unfavored sequence contexts. The engineered mtDNA editors (eTd-mtABEs) showed up to 87% editing efficiency in human cells, with greatly reduced DNA and RNA off-target effects. Strand-selective A-to-G editing was enhanced by an average of 3.2-fold with substitution of DddA to DNA nickases in eTd-mtABE backbones compared to mitochondrial ABEs. In rat cells, editing efficiencies of eTd-mtABEs were up to 145-fold higher compared to split DddA transcription activator-like effector-linked deaminase. We also generated rats with sensorineural hearing loss by installing targeted mutations with frequencies of up to 44% through embryonic injection. The developed eTd-mtABEs are efficient and precise mtDNA-engineering tools for basic research and translational studies.

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Conflict of interest statement

Competing interests: The authors have submitted patent applications based on the results reported in this study (L.C., D.L., M.H. and C.L.). The remaining authors declare no competing interests.

References

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Efficient mitochondrial A-to-G base editors for the generation of mitochondrial disease models

Affiliations

Efficient mitochondrial A-to-G base editors for the generation of mitochondrial disease models

Authors

Affiliations

Abstract

Conflict of interest statement

References

Grants and funding

LinkOut - more resources

Full Text Sources