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생화학분자생물학회 (Korean Society for Biochemistry and Molecular Biology)
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Mitochondrial genome editing: strategies, challenges, and applications

  • Kayeong Lim (Brain Science Institute, Korea Institute of Science and Technology (KIST))
  • 투고 : 2023.11.10
  • 심사 : 2023.12.21
  • 발행 : 2024.01.31
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초록

Mitochondrial DNA (mtDNA), a multicopy genome found in mitochondria, is crucial for oxidative phosphorylation. Mutations in mtDNA can lead to severe mitochondrial dysfunction in tissues and organs with high energy demand. MtDNA mutations are closely associated with mitochondrial and age-related disease. To better understand the functional role of mtDNA and work toward developing therapeutics, it is essential to advance technology that is capable of manipulating the mitochondrial genome. This review discusses ongoing efforts in mitochondrial genome editing with mtDNA nucleases and base editors, including the tools, delivery strategies, and applications. Future advances in mitochondrial genome editing to address challenges regarding their efficiency and specificity can achieve the promise of therapeutic genome editing.

키워드

과제정보

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (RS-2023-00210965) and the Korea Institute of Science and Technology (KIST) Institutional Program (2E32161). Figures were created with BioRender.com.

참고문헌

  1. Rackham O and Filipovska A (2022) Organization and expression of the mammalian mitochondrial genome. Nat Rev Genet 23, 606-623  https://doi.org/10.1038/s41576-022-00480-x
  2. Gupta R, Kanai M, Durham TJ et al (2023) Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. Nature 620, 839-848  https://doi.org/10.1038/s41586-023-06426-5
  3. Gorman GS, Schaefer AM, Ng Y et al (2015) Prevalence of nuclear and mitochondrial DNA mutations related to adult mitochondrial disease. Ann Neurol 77, 753-759  https://doi.org/10.1002/ana.24362
  4. Anderson S, Bankier AT, Barrell BG et al (1981) Sequence and organization of the human mitochondrial genome. Nature 290, 457-465  https://doi.org/10.1038/290457a0
  5. Chen X, Prosser R, Simonetti S, Sadlock J, Jagiello G and Schon EA (1995) Rearranged mitochondrial genomes are present in human oocytes. Am J Hum Genet 57, 239-247  https://doi.org/10.1002/ajmg.1320570226
  6. Taylor RW and Turnbull DM (2005) Mitochondrial DNA mutations in human disease. Nat Rev Genet 6, 389-402  https://doi.org/10.1038/nrg1606
  7. Kopinski PK, Singh LN, Zhang S, Lott MT and Wallace DC (2021) Mitochondrial DNA variation and cancer. Nat Rev Cancer 21, 431-445  https://doi.org/10.1038/s41568-021-00358-w
  8. Kogelnik AM, Lott MT, Brown MD, Navathe SB and Wallace DC (1996) MITOMAP: a human mitochondrial genome database. Nucleic Acids Res 24, 177-179  https://doi.org/10.1093/nar/24.1.177
  9. He Y, Wu J, Dressman DC et al (2010) Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. Nature 464, 610-614  https://doi.org/10.1038/nature08802
  10. Rossignol R, Faustin B, Rocher C, Malgat M, Mazat JP and Letellier T (2003) Mitochondrial threshold effects. Biochem J 370, 751-762  https://doi.org/10.1042/bj20021594
  11. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA and Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821  https://doi.org/10.1126/science.1225829
  12. Komor AC, Kim YB, Packer MS, Zuris JA and Liu DR (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420-424  https://doi.org/10.1038/nature17946
  13. Gaudelli NM, Komor AC, Rees HA et al (2017) Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551, 464-471  https://doi.org/10.1038/nature24644
  14. Anzalone AV, Randolph PB, Davis JR et al (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149-157  https://doi.org/10.1038/s41586-019-1711-4
  15. Gammage PA, Moraes CT and Minczuk M (2018) Mitochondrial genome engineering: the revolution may not be CRISPR-Ized. Trends Genet 34, 101-110  https://doi.org/10.1016/j.tig.2017.11.001
  16. Fontana GA and Gahlon HL (2020) Mechanisms of replication and repair in mitochondrial DNA deletion formation. Nucleic Acids Res 48, 11244-11258  https://doi.org/10.1093/nar/gkaa804
  17. Silva-Pinheiro P and Minczuk M (2022) The potential of mitochondrial genome engineering. Nat Rev Genet 23, 199-214  https://doi.org/10.1038/s41576-021-00432-x
  18. Peeva V, Blei D, Trombly G et al (2018) Linear mitochondrial DNA is rapidly degraded by components of the replication machinery. Nat Commun 9, 1727 
  19. Krokan HE and Bjoras M (2013) Base excision repair. Cold Spring Harb Perspect Biol 5, a012583 
  20. Omura T (1998) Mitochondria-targeting sequence, a multi-role sorting sequence recognized at all steps of protein import into mitochondria. J Biochem 123, 1010-1016  https://doi.org/10.1093/oxfordjournals.jbchem.a022036
  21. Gammage PA, Rorbach J, Vincent AI, Rebar EJ and Minczuk M (2014) Mitochondrially targeted ZFNs for selective degradation of pathogenic mitochondrial genomes bearing large-scale deletions or point mutations. EMBO Mol Med 6, 458-466  https://doi.org/10.1002/emmm.201303672
  22. Gammage PA, Gaude E, Van Haute L et al (2016) Near-complete elimination of mutant mtDNA by iterative or dynamic dose-controlled treatment with mtZFNs. Nucleic Acids Res 44, 7804-7816  https://doi.org/10.1093/nar/gkw676
  23. Gammage PA, Viscomi C, Simard ML et al (2018) Genome editing in mitochondria corrects a pathogenic mtDNA mutation in vivo. Nat Med 24, 1691-1695  https://doi.org/10.1038/s41591-018-0165-9
  24. Reddy P, Ocampo A, Suzuki K et al (2015) Selective elimination of mitochondrial mutations in the germline by genome editing. Cell 161, 459-469  https://doi.org/10.1016/j.cell.2015.03.051
  25. Bacman SR, Williams SL, Pinto M, Peralta S and Moraes CT (2013) Specific elimination of mutant mitochondrial genomes in patient-derived cells by mitoTALENs. Nat Med 19, 1111-1113  https://doi.org/10.1038/nm.3261
  26. Hashimoto M, Bacman SR, Peralta S et al (2015) MitoTALEN: a general approach to reduce mutant mtDNA loads and restore oxidative phosphorylation function in mitochondrial diseases. Mol Ther 23, 1592-1599  https://doi.org/10.1038/mt.2015.126
  27. Bacman SR, Kauppila JHK, Pereira CV et al (2018) MitoTALEN reduces mutant mtDNA load and restores tRNA(Ala) levels in a mouse model of heteroplasmic mtDNA mutation. Nat Med 24, 1696-1700  https://doi.org/10.1038/s41591-018-0166-8
  28. Yang Y, Wu H, Kang X et al (2018) Targeted elimination of mutant mitochondrial DNA in MELAS-iPSCs by mitoTALENs. Protein Cell 9, 283-297  https://doi.org/10.1007/s13238-017-0499-y
  29. Yahata N, Boda H and Hata R (2021) Elimination of mutant mtDNA by an optimized mpTALEN restores differentiation capacities of heteroplasmic MELAS-iPSCs. Mol Ther Methods Clin Dev 20, 54-68  https://doi.org/10.1016/j.omtm.2020.10.017
  30. Srivastava S and Moraes CT (2001) Manipulating mitochondrial DNA heteroplasmy by a mitochondrially targeted restriction endonuclease. Hum Mol Genet 10, 3093-3099  https://doi.org/10.1093/hmg/10.26.3093
  31. Bayona-Bafaluy MP, Blits B, Battersby BJ, Shoubridge EA and Moraes CT (2005) Rapid directional shift of mitochondrial DNA heteroplasmy in animal tissues by a mitochondrially targeted restriction endonuclease. Proc Natl Acad Sci U S A 102, 14392-14397  https://doi.org/10.1073/pnas.0502896102
  32. Bacman SR, Williams SL, Duan D and Moraes CT (2012) Manipulation of mtDNA heteroplasmy in all striated muscles of newborn mice by AAV9-mediated delivery of a mitochondria-targeted restriction endonuclease. Gene Ther 19, 1101-1106  https://doi.org/10.1038/gt.2011.196
  33. Tanaka M, Borgeld HJ, Zhang J et al (2002) Gene therapy for mitochondrial disease by delivering restriction endonuclease SmaI into mitochondria. J Biomed Sci 9, 534-541  https://doi.org/10.1159/000064726
  34. Alexeyev MF, Venediktova N, Pastukh V, Shokolenko I, Bonilla G and Wilson GL (2008) Selective elimination of mutant mitochondrial genomes as therapeutic strategy for the treatment of NARP and MILS syndromes. Gene Ther 15, 516-523  https://doi.org/10.1038/gt.2008.11
  35. Pereira CV, Bacman SR, Arguello T et al (2018) mitoTev-TALE: a monomeric DNA editing enzyme to reduce mu-tant mitochondrial DNA levels. EMBO Mol Med 10, e8084 
  36. Zekonyte U, Bacman SR, Smith J et al (2021) Mitochondrial targeted meganuclease as a platform to eliminate mutant mtDNA in vivo. Nat Commun 12, 3210 
  37. Minczuk M, Papworth MA, Miller JC, Murphy MP and Klug A (2008) Development of a single-chain, quasidimeric zinc-finger nuclease for the selective degradation of mutated human mitochondrial DNA. Nucleic Acids Res 36, 3926-3938  https://doi.org/10.1093/nar/gkn313
  38. Mok BY, de Moraes MH, Zeng J et al (2020) A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature 583, 631-637  https://doi.org/10.1038/s41586-020-2477-4
  39. Cho SI, Lee S, Mok YG et al (2022) Targeted A-to-G base editing in human mitochondrial DNA with programmable deaminases. Cell 185, 1764-1776 e1712 
  40. Richter MF, Zhao KT, Eton E et al (2020) Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat Biotechnol 38, 883-891  https://doi.org/10.1038/s41587-020-0453-z
  41. Yin L, Shi K and Aihara H (2023) Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA. Nat Struct Mol Biol 30, 1153-1159  https://doi.org/10.1038/s41594-023-01034-3
  42. Mok BY, Kotrys AV, Raguram A, Huang TP, Mootha VK and Liu DR (2022) CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA. Nat Biotechnol 40, 1378-1387  https://doi.org/10.1038/s41587-022-01256-8
  43. Mi L, Shi M, Li YX et al (2023) DddA homolog search and engineering expand sequence compatibility of mitochondrial base editing. Nat Commun 14, 874 
  44. Sun H, Wang Z, Shen L et al (2023) Developing mitochondrial base editors with diverse context compatibility and high fidelity via saturated spacer library. Nat Commun 14, 6625 
  45. Cheng K, Li C, Jin J et al (2023) Engineering RsDddA as mitochondrial base editor with wide target compatibility and enhanced activity. Mol Ther Nucleic Acids 34, 102028 
  46. Guo J, Yu W, Li M et al (2023) A DddA ortholog-based and transactivator-assisted nuclear and mitochondrial cytosine base editors with expanded target compatibility. Mol Cell 83, 1710-1724 e1717 
  47. Huang J, Lin Q, Fei H et al (2023) Discovery of deaminase functions by structure-based protein clustering. Cell 186, 3182-3195 e3114 
  48. Lee S, Lee H, Baek G et al (2022) Enhanced mitochondrial DNA editing in mice using nuclear-exported TALE-linked deaminases and nucleases. Genome Biol 23, 211 
  49. Lim K, Cho SI and Kim JS (2022) Nuclear and mitochondrial DNA editing in human cells with zinc finger deaminases. Nat Commun 13, 366 
  50. Willis JCW, Silva-Pinheiro P, Widdup L, Minczuk M and Liu DR (2022) Compact zinc finger base editors that edit mitochondrial or nuclear DNA in vitro and in vivo. Nat Commun 13, 7204 
  51. Mok YG, Lee JM, Chung E et al (2022) Base editing in human cells with monomeric DddA-TALE fusion deaminases. Nat Commun 13, 4038 
  52. Wei Y, Li Z, Xu K et al (2022) Mitochondrial base editor DdCBE causes substantial DNA off-target editing in nuclear genome of embryos. Cell Discov 8, 27 
  53. Lei Z, Meng H, Liu L et al (2022) Mitochondrial base editor induces substantial nuclear off-target mutations. Nature 606, 804-811  https://doi.org/10.1038/s41586-022-04836-5
  54. Lee S, Lee H, Baek G and Kim JS (2023) Precision mitochondrial DNA editing with high-fidelity DddA-derived base editors. Nat Biotechnol 41, 378-386  https://doi.org/10.1038/s41587-022-01486-w
  55. Guo J, Chen X, Liu Z et al (2022) DdCBE mediates efficient and inheritable modifications in mouse mitochondrial genome. Mol Ther Nucleic Acids 27, 73-80  https://doi.org/10.1016/j.omtn.2021.11.016
  56. Chen X, Liang D, Guo J et al (2022) DdCBE-mediated mitochondrial base editing in human 3PN embryos. Cell Discov 8, 8 
  57. Yi Z, Zhang X, Tang W et al (2023) Strand-selective base editing of human mitochondrial DNA using mitoBEs. Nat Biotechnol, 1-12. https://doi.org/10.1038/s41587-023-01791-y 
  58. Hu J, Sun Y, Li B et al (2023) Strand-preferred base editing of organellar and nuclear genomes using CyDENT. Nat Biotechnol, 1-10. https://doi.org/10.1038/s41587-023-01910-9 
  59. Paunovska K, Loughrey D and Dahlman JE (2022) Drug delivery systems for RNA therapeutics. Nat Rev Genet 23, 265-280  https://doi.org/10.1038/s41576-021-00439-4
  60. Degors IMS, Wang C, Rehman ZU and Zuhorn IS (2019) Carriers break barriers in drug delivery: endocytosis and endosomal escape of gene delivery vectors. Acc Chem Res 52, 1750-1760  https://doi.org/10.1021/acs.accounts.9b00177
  61. Lee H, Lee S, Baek G et al (2021) Mitochondrial DNA editing in mice with DddA-TALE fusion deaminases. Nat Commun 12, 1190 
  62. Silva-Pinheiro P, Mutti CD, Van Haute L et al (2023) A library of base editors for the precise ablation of all protein-coding genes in the mouse mitochondrial genome. Nat Biomed Eng 7, 692-703  https://doi.org/10.1038/s41551-022-00968-1
  63. Guo J, Zhang X, Chen X et al (2021) Precision modeling of mitochondrial diseases in zebrafish via DdCBE-mediated mtDNA base editing. Cell Discov 7, 78 
  64. Sabharwal A, Kar B, Restrepo-Castillo S et al (2021) The FusX TALE Base Editor (FusXTBE) for rapid mitochondrial DNA programming of human cells in vitro and zebrafish disease models in vivo. CRISPR J 4, 799-821 
  65. Qi X, Chen X, Guo J et al (2021) Precision modeling of mitochondrial disease in rats via DdCBE-mediated mtDNA editing. Cell Discov 7, 95 
  66. Qi X, Tan L, Zhang X et al (2023) Expanding DdCBE-mediated targeting scope to aC motif preference in rat. Mol Ther Nucleic Acids 32, 1-12  https://doi.org/10.1016/j.omtn.2023.02.028
  67. Tan L, Qi X, Kong W et al (2023) A conditional knockout rat resource of mitochondrial protein-coding genes via a DdCBE-induced premature stop codon. Sci Adv 9, eadf2695 
  68. Wei Y, Xu C, Feng H et al (2022) Human cleaving embryos enable efficient mitochondrial base-editing with DdCBE. Cell Discov 8, 7 
  69. Wang D, Tai PWL and Gao G (2019) Adeno-associated virus vector as a platform for gene therapy delivery. Nat Rev Drug Discov 18, 358-378  https://doi.org/10.1038/s41573-019-0012-9
  70. Silva-Pinheiro P, Nash PA, Van Haute L, Mutti CD, Turner K and Minczuk M (2022) In vivo mitochondrial base editing via adeno-associated viral delivery to mouse postmitotic tissue. Nat Commun 13, 750 
  71. Lek A, Wong B, Keeler A et al (2023) Death after High-Dose rAAV9 gene therapy in a patient with Duchenne's Muscular Dystrophy. N Engl J Med 389, 1203-1210  https://doi.org/10.1056/NEJMoa2307798
  72. Kang BC, Bae SJ, Lee S et al (2021) Chloroplast and mitochondrial DNA editing in plants. Nat Plants 7, 899-905 https://doi.org/10.1038/s41477-021-00943-9