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Chen X, Chen M, Zhu Y, Sun H, Wang Y, Xie Y, Ji L, Wang C, Hu Z, Guo X, Xu Z, Zhang J, Yang S, Liang D, Shen B. Correction of a homoplasmic mitochondrial tRNA mutation in patient-derived iPSCs via a mitochondrial base editor. Commun Biol 2023; 6:1116. [PMID: 37923818 PMCID: PMC10624837 DOI: 10.1038/s42003-023-05500-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023] Open
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.
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Affiliation(s)
- Xiaoxu Chen
- 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
| | - Mingyue Chen
- 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
| | - Yuqing Zhu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China
| | - Haifeng Sun
- 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
| | - Yue Wang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
| | - Yuan Xie
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China
| | - Lianfu Ji
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Cheng Wang
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China.
| | - Jun Zhang
- 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.
| | - Shiwei Yang
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China.
| | - Dong Liang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China.
| | - Bin Shen
- 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.
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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Sun H, Wang Z, Shen L, Feng Y, Han L, Qian X, Meng R, Ji K, Liang D, Zhou F, Lou X, Zhang J, Shen B. Developing mitochondrial base editors with diverse context compatibility and high fidelity via saturated spacer library. Nat Commun 2023; 14:6625. [PMID: 37857619 PMCID: PMC10587121 DOI: 10.1038/s41467-023-42359-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
DddA-derived cytosine base editors (DdCBEs) greatly facilitated the basic and therapeutic research of mitochondrial DNA mutation diseases. Here we devise a saturated spacer library and successfully identify seven DddA homologs by performing high-throughput sequencing based screen. DddAs of Streptomyces sp. BK438 and Lachnospiraceae bacterium sunii NSJ-8 display high deaminase activity with a strong GC context preference, and DddA of Ruminococcus sp. AF17-6 is highly compatible to AC context. We also find that different split sites result in wide divergence on off-target activity and context preference of DdCBEs derived from these DddA homologs. Additionally, we demonstrate the orthogonality between DddA and DddIA, and successfully minimize the nuclear off-target editing by co-expressing corresponding nuclear-localized DddIA. The current study presents a comprehensive and unbiased strategy for screening and characterizing dsDNA cytidine deaminases, and expands the toolbox for mtDNA editing, providing additional insights for optimizing dsDNA base editors.
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Affiliation(s)
- Haifeng Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Zhaojun Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Limini Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Yeling Feng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Lu Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Xuezhen Qian
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Runde Meng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Kangming Ji
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Dong Liang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China
| | - Fei Zhou
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Xin Lou
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311100, China.
| | - Jun Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China.
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China.
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