Correction of a Homoplasmic Mitochondrial TRNA Mutation in Patient-derived IPSCs Via a Mitochondrial Base Editor

Overview

Journal Commun Biol

Specialty Biology

Date 2023 Nov 4

PMID 37923818

Authors

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

Affiliations

Soon will be listed here.

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.

Citing Articles

Engineered mitochondria in diseases: mechanisms, strategies, and applications.

Li M, Wu L, Si H, Wu Y, Liu Y, Zeng Y Signal Transduct Target Ther. 2025; 10(1):71.

PMID: 40025039 PMC: 11873319. DOI: 10.1038/s41392-024-02081-y.

References

Bi C, Wang L, Fan Y, Yuan B, Ramos-Mandujano G, Zhang Y . Single-cell individual full-length mtDNA sequencing by iMiGseq uncovers unexpected heteroplasmy shifts in mtDNA editing. Nucleic Acids Res. 2023; 51(8):e48. PMC: 10164560. DOI: 10.1093/nar/gkad208. View

Bacman S, Kauppila J, Pereira C, Nissanka N, Miranda M, Pinto M . MitoTALEN reduces mutant mtDNA load and restores tRNA levels in a mouse model of heteroplasmic mtDNA mutation. Nat Med. 2018; 24(11):1696-1700. PMC: 6942693. DOI: 10.1038/s41591-018-0166-8. View

Lee S, Lee H, Baek G, Kim J . Precision mitochondrial DNA editing with high-fidelity DddA-derived base editors. Nat Biotechnol. 2022; 41(3):378-386. PMC: 10017512. DOI: 10.1038/s41587-022-01486-w. View

Yu-Wai-Man P, Newman N, Carelli V, Moster M, Biousse V, Sadun A . Bilateral visual improvement with unilateral gene therapy injection for Leber hereditary optic neuropathy. Sci Transl Med. 2020; 12(573). DOI: 10.1126/scitranslmed.aaz7423. View

Yi Z, Zhang X, Tang W, Yu Y, Wei X, Zhang X . Strand-selective base editing of human mitochondrial DNA using mitoBEs. Nat Biotechnol. 2023; 42(3):498-509. PMC: 10940147. DOI: 10.1038/s41587-023-01791-y. View

Chen X, Liang D, Guo J, Zhang J, Sun H, Zhang X . DdCBE-mediated mitochondrial base editing in human 3PN embryos. Cell Discov. 2022; 8(1):8. PMC: 8803914. DOI: 10.1038/s41421-021-00358-y. View

McCormick E, Muraresku C, Falk M . Mitochondrial Genomics: A complex field now coming of age. Curr Genet Med Rep. 2018; 6(2):52-61. PMC: 6205240. DOI: 10.1007/s40142-018-0137-x. View

Robinson B . Lactic acidemia and mitochondrial disease. Mol Genet Metab. 2006; 89(1-2):3-13. DOI: 10.1016/j.ymgme.2006.05.015. View

Qi X, Chen X, Guo J, Zhang X, Sun H, Wang J . Precision modeling of mitochondrial disease in rats via DdCBE-mediated mtDNA editing. Cell Discov. 2021; 7(1):95. PMC: 8523528. DOI: 10.1038/s41421-021-00325-7. View

10.

Pompei M, Pompei F . Overcoming bioethical, legal, and hereditary barriers to mitochondrial replacement therapy in the USA. J Assist Reprod Genet. 2018; 36(3):383-393. PMC: 6439114. DOI: 10.1007/s10815-018-1370-7. View

11.

Boominathan A, Vanhoozer S, Basisty N, Powers K, Crampton A, Wang X . Stable nuclear expression of ATP8 and ATP6 genes rescues a mtDNA Complex V null mutant. Nucleic Acids Res. 2016; 44(19):9342-9357. PMC: 5100594. DOI: 10.1093/nar/gkw756. View

12.

Stern H . Lactic acidosis in paediatrics: clinical and laboratory evaluation. Ann Clin Biochem. 1994; 31 ( Pt 5):410-9. DOI: 10.1177/000456329403100502. View

13.

Artika I . Allotopic expression of mitochondrial genes: Basic strategy and progress. Genes Dis. 2020; 7(4):578-584. PMC: 7729113. DOI: 10.1016/j.gendis.2019.08.001. View

14.

Mok B, de Moraes M, Zeng J, Bosch D, Kotrys A, Raguram A . A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature. 2020; 583(7817):631-637. PMC: 7381381. DOI: 10.1038/s41586-020-2477-4. View

15.

Lei Z, Meng H, Liu L, Zhao H, Rao X, Yan Y . Mitochondrial base editor induces substantial nuclear off-target mutations. Nature. 2022; 606(7915):804-811. DOI: 10.1038/s41586-022-04836-5. View

16.

Reddy P, Ocampo A, Suzuki K, Luo J, Bacman S, Williams S . Selective elimination of mitochondrial mutations in the germline by genome editing. Cell. 2015; 161(3):459-469. PMC: 4505837. DOI: 10.1016/j.cell.2015.03.051. View

17.

Hashimoto M, Bacman S, Peralta S, Falk M, Chomyn A, Chan D . MitoTALEN: A General Approach to Reduce Mutant mtDNA Loads and Restore Oxidative Phosphorylation Function in Mitochondrial Diseases. Mol Ther. 2015; 23(10):1592-9. PMC: 4817924. DOI: 10.1038/mt.2015.126. View

18.

Hirano M, Emmanuele V, Quinzii C . Emerging therapies for mitochondrial diseases. Essays Biochem. 2018; 62(3):467-481. PMC: 6104515. DOI: 10.1042/EBC20170114. View

19.

Rius R, Cowley M, Riley L, Puttick C, Thorburn D, Christodoulou J . Biparental inheritance of mitochondrial DNA in humans is not a common phenomenon. Genet Med. 2019; 21(12):2823-2826. DOI: 10.1038/s41436-019-0568-0. View

20.

Anderson S, Bankier A, Barrell B, de Bruijn M, Coulson A, Drouin J . Sequence and organization of the human mitochondrial genome. Nature. 1981; 290(5806):457-65. DOI: 10.1038/290457a0. View