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Trends and prospects in mitochondrial genome editing

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주제분류생화학

초록

Mitochondria are of fundamental importance in programmed cell death, cellular metabolism, and intracellular calcium concentration modulation, and inheritable mitochondrial disorders via mitochondrial DNA (mtDNA) mutation cause several diseases in various organs and systems. Nevertheless, mtDNA editing, which plays an essential role in the treatment of mitochondrial disorders, still faces several challenges. Recently, programmable editing tools for mtDNA base editing, such as cytosine base editors derived from DddA (DdCBEs), transcription activator-like effector (TALE)-linked deaminase (TALED), and zinc finger deaminase (ZFD), have emerged with considerable potential for correcting pathogenic mtDNA variants. In this review, we depict recent advances in the field, including structural biology and repair mechanisms, and discuss the prospects of using base editing tools on mtDNA to broaden insight into their medical applicability for treating mitochondrial diseases.

Abstract

Mitochondria are of fundamental importance in programmed cell death, cellular metabolism, and intracellular calcium concentration modulation, and inheritable mitochondrial disorders via mitochondrial DNA (mtDNA) mutation cause several diseases in various organs and systems. Nevertheless, mtDNA editing, which plays an essential role in the treatment of mitochondrial disorders, still faces several challenges. Recently, programmable editing tools for mtDNA base editing, such as cytosine base editors derived from DddA (DdCBEs), transcription activator-like effector (TALE)-linked deaminase (TALED), and zinc finger deaminase (ZFD), have emerged with considerable potential for correcting pathogenic mtDNA variants. In this review, we depict recent advances in the field, including structural biology and repair mechanisms, and discuss the prospects of using base editing tools on mtDNA to broaden insight into their medical applicability for treating mitochondrial diseases.

참고문헌 (84)

  1. Schell, J. C., "A role for the mitochondrial pyruvate carrier as a repressor of the Warburg effect and colon cancer cell growth", Mol. Cell, 56, pp.400~413 (2014)
  2. Herzig, S., "Identification and functional expression of the mitochondrial pyruvate carrier", Science, 337, pp.93~96 (2012)
  3. Filippi, M. -D., "Mitochondria in the maintenance of hematopoietic stem cells : new perspectives and opportunities", Blood, 133, pp.1943~1952 (2019)
  4. Liu, X., "Induction of apoptotic program in cell-free extracts : requirement for dATP and cytochrome c", Cell, 86, pp.147~157 (1996)
  5. Gomes, L. C., "During autophagy mitochondria elongate, are spared from degradation and sustain cell viability", Nat. Cell Biol, 13, pp.589~598 (2011)
  6. Rambold Angelika, S., "Tubular network formation protects mitochondria from autophagosomal degradation during nutrient starvation", Proc. Natl Acad. Sci. USA, 108, pp.10190~10195 (2011)
  7. i signalling in rat cerebellar granule neurones aged in vitro, "Neurobiol. Aging", 2004, 349~359
  8. Tang, S., "Mitochondrial Ca²+ uniporter is critical for store-operated Ca2+entry-dependent breast cancer cell migration", Biochem. Biophys. Res. Commun, 458, pp.186~193 (2015)
  9. Yasukawa, K., "Mitofusin 2 inhibits mitochondrial antiviral signaling", Sci. Signal, 2, pp.ra47~ (2009)
  10. Kaniak-Golik, A., "Mitochondria–nucleus network for genome stability", Free Radic. Biol. Med, 82, pp.73~104 (2015)
  11. Chen, X., "Rearranged mitochondrial genomes are present in human oocytes", Am. J. Hum. Genet, 57, pp.239~247 (1995)
  12. D’Erchia, A. M., "Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity", Mitochondrion, 20, pp.13~21 (2015)
  13. Anderson, S., "Sequence and organization of the human mitochondrial genome", Nature, 290, pp.457~465 (1981)
  14. Schon, K. R., "Mitochondrial diseases : a diagnostic revolution", Trends Genet, 36, pp.702~717 (2020)
  15. Tuppen, H. A. L., "Mitochondrial DNA mutations and human disease", Biochim. Biophys. Acta Bioenerg, 1797, pp.113~128 (2010)
  16. El-Hattab, A. W., "Mitochondrial cytopathies", Cell Calcium, 60, pp.199~206 (2016)
  17. Leber, T., "Ueber hereditäre und congenital-angelegte Sehnervenleiden", Albrecht Graef. Arch. Ophthalmol, 17, pp.249~291 (1871)
  18. Man, P. Y. W., "Leber hereditary optic neuropathy", J. Med. Genet, 39, pp.162~ (2002)
  19. Shoffner, J. M., "Myoclonic epilepsy and ragged-red fiber disease(MERRF)is associated with a mitochondrial DNA tRNALys mutation", Cell, 61, pp.931~937 (1990)
  20. Pfeffer, G., "Mutations in the SPG7 gene cause chronic progressive external ophthalmoplegia through disordered mitochondrial DNA maintenance", Brain, 137, pp.1323~1336 (2014)
  21. Kauppila, J. H. K., "A phenotype-driven approach to generate mouse models with pathogenic mtDNA mutations causing mitochondrial disease", Cell Rep, 16, pp.2980~2990 (2016)
  22. Srivastava, S., "Manipulating mitochondrial DNA heteroplasmy by a mitochondrially targeted restriction endonuclease", Hum. Mol. Genet, 10, pp.3093~3099 (2001)
  23. Tanaka, M., "Gene therapy for mitochondrial disease by delivering restriction endonuclease SmaI into mitochondria", J. Biomed. Sci, 9, pp.534~541 (2002)
  24. Bayona-Bafaluy Maria, P., "Rapid directional shift of mitochondrial DNA heteroplasmy in animal tissues by a mitochondrially targeted restriction endonuclease", Proc. Natl Acad. Sci. USA, 102, pp.14392~14397 (2005)
  25. Wang, H., "CRISPR", Cas9 in genome editing and beyond, 2016, pp.85, 227~264
  26. Jo, A., "Efficient mitochondrial genome editing by CRISPR", Cas9, 2015, pp.2015, 305716~305716
  27. Bian, W. -P., "Knock-in strategy for editing human and zebrafish mitochondrial DNA using mito-CRISPR", Cas9 system, 2019, pp.8, 621~632
  28. Gammage, P. A., "Mitochondrial genome engineering : the revolution may not be CRISPR-Ized", Trends Genet, 34, pp.101~110 (2018)
  29. Hussain, S. A., "Adapting CRISPR", Cas9 system for targeting mitochondrial genome, 2021, pp.12, 627050~
  30. Yin, T., "Current Progress of Mitochondrial Genome Editing by CRISPR", Front. Physiol (2022)[DOI]
  31. Antón, Z., "Mitochondrial import, health and mtDNA copy number variability seen when using type II and type V CRISPR effectors", J. Cell Sci (2020)[DOI]
  32. Kim, Y. G., "Hybrid restriction enzymes : zinc finger fusions to Fok I cleavage domain", Proc. Natl Acad. Sci. USA, 93, pp.1156~1160 (1996)
  33. Smith, J., "Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains", Nucleic Acids Res, 28, pp.3361~3369 (2000)
  34. Christian, M., "Targeting DNA double-strand breaks with TAL effector nucleases", Genetics, 186, pp.757~761 (2010)
  35. Gammage, P. A., "Mitochondrially targeted ZFNs for selective degradation of pathogenic mitochondrial genomes bearing large-scale deletions or point mutations", EMBO Mol. Med, 6, pp.458~466 (2014)
  36. Bacman, S. R., "Specific elimination of mutant mitochondrial genomes in patient-derived cells by mitoTALENs", Nat. Med, 19, pp.1111~1113 (2013)
  37. Beerli, R. R, "Toward controlling gene expression at will: specific regulation of the erbB-2", HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks, 1998, pp.95, 14628~14633
  38. Beerli, R. R., "Positive and negative regulation of endogenous genes by designed transcription factors", Proc. Natl Acad. Sci. USA, 97, pp.1495~1500 (2000)
  39. Gersbach, C. A., "Synthetic zinc finger proteins : the advent of targeted gene regulation and genome modification technologies", Acc. Chem. Res, 47, pp.2309~2318 (2014)
  40. Minczuk, M., "Sequence-specific modification of mitochondrial DNA using a chimeric zinc finger methylase", Proc. Natl Acad. Sci. USA, 103, pp.19689~19694 (2006)
  41. Minczuk, M., "Development of a single-chain, quasi-dimeric zinc-finger nuclease for the selective degradation of mutated human mitochondrial DNA", Nucleic Acids Res, 36, pp.3926~3938 (2008)
  42. Minczuk, M., "Construction and testing of engineered zinc-finger proteins for sequence-specific modification of mtDNA", Nat. Protoc, 5, pp.342~356 (2010)
  43. Gammage, P. A., "Near-complete elimination of mutant mtDNA by iterative or dynamic dose-controlled treatment with mtZFNs", Nucleic Acids Res, 44, pp.7804~7816 (2016)
  44. Gaude, E., "NADH shuttling couples cytosolic reductive carboxylation of glutamine with glycolysis in cells with mitochondrial dysfunction", Mol. Cell, 69, pp.581~593 (2018)
  45. Gammage, P. A., "Genome editing in mitochondria corrects a pathogenic mtDNA mutation in vivo", Nat. Med, 24, pp.1691~1695 (2018)
  46. Lim, K., "Nuclear and mitochondrial DNA editing in human cells with zinc finger deaminases", Nat. Commun, 13, pp.366~ (2022)
  47. Perez-Quintero, A. L., "A decade decoded : spies and hackers in the history of TAL effectors research", Annu. Rev. Phytopathol, 57, pp.459~481 (2019)
  48. Boch, J., "Breaking the code of DNA binding specificity of TAL-type III effectors", Science, 326, pp.1509~1512 (2009)
  49. Bogdanove, A. J., "TAL effectors: customizable proteins for DNA targeting", Science, 333, pp.1843~1846 (2011)
  50. Richter, A., "TALENs: Methods and Protocols", pp.9~25 (2016), Springer
  51. Gaj, T., "ZFN, TALEN, and CRISPR", Cas-based methods for genome engineering, 2013, pp.31, 397~405
  52. Hashimoto, M., "MitoTALEN : a general approach to reduce mutant mtDNA loads and restore oxidative phosphorylation function in mitochondrial diseases", Mol. Ther, 23, pp.1592~1599 (2015)
  53. Yahata, N., "TALEN-mediated shift of mitochondrial DNA heteroplasmy in MELAS-iPSCs with m.13513G>A mutation", Sci. Rep, 7, pp.15557~ (2017)
  54. Yang, Y., "Targeted elimination of mutant mitochondrial DNA in MELAS-iPSCs by mitoTALENs", Protein Cell, 9, pp.283~297 (2018)
  55. Phillips, A. F., "Single-molecule analysis of mtDNA replication uncovers the basis of the common deletion", Mol. Cell, 65, pp.527~538 (2017)
  56. Tonin, Y., "Modeling of antigenomic therapy of mitochondrial diseases by mitochondrially addressed RNA targeting a pathogenic point mutation in mitochondrial DNA*", J. Biol. Chem, 289, pp.13323~13334 (2014)
  57. Reddy, P., "Selective elimination of mitochondrial mutations in the germline by genome editing", Cell, 161, pp.459~469 (2015)
  58. Pereira, C. V., "mitoTev-TALE : a monomeric DNA editing enzyme to reduce mutant mitochondrial DNA levels", EMBO Mol. Med, 10, pp.e8084~ (2018)
  59. Mok, B. Y., "A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing", Nature, 583, pp.631~637 (2020)
  60. Wei, Y., "Human cleaving embryos enable efficient mitochondrial baseediting with DdCBE", Cell Discov, 8, pp.7~ (2022)
  61. Sabharwal, A., "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, pp.799~821 (2021)
  62. Guo, J., "Precision modeling of mitochondrial diseases in zebrafish via DdCBEmediated mtDNA base editing", Cell Discov, 7, pp.78~ (2021)
  63. Guo, J., "DdCBE mediates efficient and inheritable modifications in mouse mitochondrial genome", Mol. Ther, 27, pp.73~80 (2022)
  64. Lee, H., "Mitochondrial DNA editing in mice with DddA-TALE fusion deaminases", Nat. Commun, 12, pp.1190~ (2021)
  65. Qi, X., "Precision modeling of mitochondrial disease in rats via DdCBEmediated mtDNA editing", Cell Discov, 7, pp.95~ (2021)
  66. Kang, B. -C., "Chloroplast and mitochondrial DNA editing in plants", Nat. Plants, 7, pp.899~905 (2021)
  67. Silva-Pinheiro, P., "In vivo mitochondrial base editing via adeno-associated viral delivery to mouse post-mitotic tissue", Nat. Commun, 13, pp.750~ (2022)
  68. Nakazato, I., "Targeted base editing in the plastid genome of Arabidopsis thaliana", Nat. Plants, 7, pp.906~913 (2021)
  69. Cho, S. -I., "Targeted A-to-G base editing in human mitochondrial DNA with programmable deaminases", Cell, 185, pp.1764~1776 (2022)
  70. Mok, B. Y., "CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA", Nat. Biotechnol (2022)[DOI]
  71. Wei, Y., "Mitochondrial base editor DdCBE causes substantial DNA off-target editing in nuclear genome of embryos", Cell Discov, 8, pp.27~ (2022)
  72. Lei, Z., "Mitochondrial base editor induces substantial nuclear off-target mutations", Nature (2022)[DOI]
  73. Moraes, C. T., "A magic bullet to specifically eliminate mutated mitochondrial genomes from patients’ cells", EMBO Mol. Med, 6, pp.434~435 (2014)
  74. Smirnov, A., "Biological significance of 5S rRNA import into human mitochondria : role of ribosomal protein MRP-L18", Genes Dev, 25, pp.1289~1305 (2011)
  75. Puranam Ram, S., "The RNase P associated with HeLa cell mitochondria contains an essential RNA component identical in sequence to that of the nuclear RNase P", Mol. Cell. Biol, 21, pp.548~561 (2001)
  76. Mercer, TimR., "The human mitochondrial transcriptome", Cell, 146, pp.645~658 (2011)
  77. Zelenka, J., "Mitochondrial DNA: Methods and Protocols", pp.175~181 (2016), Springer
  78. Towheed, A., "Small mitochondrial-targeted RNAs modulate endogenous mitochondrial protein expression in vivo", Neurobiol. Dis, 69, pp.15~22 (2014)
  79. Smirnov, A., "Two distinct structural elements of 5S rRNA are needed for its import into human mitochondria", RNA, 14, pp.749~759 (2008)
  80. Yu, H., "Gene delivery to mitochondria by targeting modified adenoassociated virus suppresses Leber’s hereditary optic neuropathy in a mouse model", Proc. Natl Acad. Sci. USA, 109, pp.E1238~E1247 (2012)
  81. Banskota, S., "Engineered virus-like particles for efficient in vivo delivery of therapeutic proteins", Cell, 185, pp.250~265 (2022)
  82. Mangeot, P. E., "Genome editing in primary cells and in vivo using viralderived Nanoblades loaded with Cas9-sgRNA ribonucleoproteins", Nat. Commun, 10, pp.45~ (2019)
  83. Wu, Z., "Programmed genome editing by a miniature CRISPR-Cas12f nuclease", Nat. Chem. Biol, 17, pp.1132~1138 (2021)
  84. Wang, Y., "Guide RNA engineering enables efficient CRISPR editing with a miniature Syntrophomonas palmitatica Cas12f1 nuclease", Cell Rep, 40, pp.111418~ (2022)

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