Correction of a homoplasmic mitochondrial tRNA mutation in patient-derived iPSCs via a mitochondrial base editor

Xiaoxu Chen; Mingyue Chen; Yuqing Zhu; Haifeng Sun; Yue Wang; Yuan Xie; Lianfu Ji; Cheng Wang; Zhibin Hu; Xuejiang Guo; Zhengfeng Xu; Jun Zhang; Shiwei Yang; Dong Liang; Bin Shen

doi:10.1038/s42003-023-05500-y

Correction of a homoplasmic mitochondrial tRNA mutation in patient-derived iPSCs via a mitochondrial base editor

Commun Biol. 2023 Nov 3;6(1):1116. doi: 10.1038/s42003-023-05500-y.

Authors

Xiaoxu Chen^#¹, Mingyue Chen^#¹, Yuqing Zhu^#², Haifeng Sun^#¹, Yue Wang^#³, Yuan Xie⁴, Lianfu Ji⁵, Cheng Wang⁴, Zhibin Hu⁶, Xuejiang Guo³, Zhengfeng Xu⁷, Jun Zhang⁸, Shiwei Yang⁹, Dong Liang¹⁰, Bin Shen^{11

12}

Affiliations

¹ State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Gusu School, Nanjing Medical University, Nanjing, 211166, China.
² Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China.
³ State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China.
⁴ Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China.
⁵ Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China.
⁶ Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
⁷ Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China. zhengfeng_xu_nj@163.com.
⁸ State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Gusu School, Nanjing Medical University, Nanjing, 211166, China. zhang_jun@njmu.edu.cn.
⁹ Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China. jrdoctoryang@163.com.
¹⁰ Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China. liangdong@njmu.edu.cn.
¹¹ State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Gusu School, Nanjing Medical University, Nanjing, 211166, China. binshen@njmu.edu.cn.
¹² Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China. binshen@njmu.edu.cn.

^# Contributed equally.

Abstract

Pathogenic mutations in mitochondrial DNA cause severe and often lethal multi-system symptoms in primary mitochondrial defects. However, effective therapies for these defects are still lacking. Strategies such as employing mitochondrially targeted restriction enzymes or programmable nucleases to shift the ratio of heteroplasmic mutations and allotopic expression of mitochondrial protein-coding genes have limitations in treating mitochondrial homoplasmic mutations, especially in non-coding genes. Here, we conduct a proof of concept study applying a screened DdCBE pair to correct the homoplasmic m.A4300G mutation in induced pluripotent stem cells derived from a patient with hypertrophic cardiomyopathy. We achieve efficient G4300A correction with limited off-target editing, and successfully restore mitochondrial function in corrected induced pluripotent stem cell clones. Our study demonstrates the feasibility of using DdCBE to treat primary mitochondrial defects caused by homoplasmic pathogenic mitochondrial DNA mutations.