Ukr.Biochem.J. 2021; Том 93, № 1, січень-лютий, c. 113-128

doi: https://doi.org/10.15407/ubj93.01.113

Перспективи редагування геному за допомогою CRISPR/CAS, або як опанувати «генетичні ножиці». Нобелівська премія з хімії 2020 року

С. В. Комісаренко, С. І. Романюк

Інститут біохімії ім. О. В. Палладіна НАН України, Київ;
e-mail: svk@biochem.kiev.ua

Нобелівську премію з хімії у 2020 р. присуджено двом дослідницям у галузі молекулярної біології – француженці Еммануель Шарпантьє (Emmanuelle Charpentier), яка нині очолює Відділення наук про патогени при Товаристві Макса Планка в Берліні, та американці Дженніфер Дудні (Jennifer Doudna) з Каліфорнійського університету в Берклі – за «розвиток методу редагування геному». У пресрелізі Нобелівського комітету зазначено, що лауреатки відкрили один з найпотужніших інструментів генної технології – CRISPR/Cas9 – або так звані «генетичні ножиці». Цей метод сприяв отриманню у фундаментальних дослідженнях багатьох важливих результатів. Зокрема, дослідники рослин змогли створити культури, стійкі до цвілі, шкідників та посухи. У медицині тривають клінічні випробування нових методів лікування раку, а мрія про те, щоб вилікувати спадкові захворювання, ось-ось стане реальністю. «Генетичні ножиці» вивели нау­ки про життя на новий етап розвитку і дають людству величезну користь.

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Посилання:

  1. Chemistry. Citation Laureates 2020. https://clarivate.com/webofsciencegroup/citation-laureates/chemistry/
  2. Press release: The Nobel Prize in Chemistry 2020. https://www.nobelprize.org/prizes/chemistry/2020/press-release/
  3. Komisarenko SV, Romanyuk SI. Genome editing, or CRISPR/Cas9 — a panacea for many incurable diseases or the first step to a gene apocalypse? Visn Nac Akad Nauk Ukr. 2020; (3): 50-77 (In Ukrainian).
  4. Jennifer Doudna. Wikipedia. https://en.wikipedia.org/wiki/Jennifer_Doudna
  5. Emmanuelle Charpentier. Wikipedia. https://en.wikipedia.org/wiki/Emmanuelle_Charpentier
  6. Deltcheva E, Chylinski K, Sharma CM, Gonzales  K, Chao Y, Pirzada ZA, Eckert MR, Vogel J. Charpentier E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011; 471(7340): 602-607.
  7. Westra ER, Semenova E, Datsenko KA, Jackson RN, Wiedenheft B, Severinov K, Brouns SJ. Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition. PLoS Genet. 2013; 9(9): e1003742.
  8. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987; 169(12): 5429-5433.
  9. Nakata A, Amemura M, Makino K. Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome. J Bacteriol. 1989; 171(6): 3553-3556.
  10. Groenen PM, Bunschoten AE, van Soolingen D, van Embden JD. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol Microbiol. 1993; 10(5): 1057-1065.
  11. Mojica FJ, Díez-Villaseñor C, Soria E, Juez G. Biological significance of a family of regularly spaced repeats in the genomes of archaea, bacteria and mitochondria. Mol Microbiol. 2000; 36(1): 244-246.
  12. Jansen R, Embden JD, Gaastra W, Schouls LM. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol. 2002; 43(6): 1565-1575.
  13. Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. 2005; 60(2): 174-182.
  14. Pourcel C, Salvignol G, Vergnaud G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology. 2005; 151(3): 653-663.
  15. Bolotin A, Quinquis B, Sorokin A, Ehrlich SD. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology. 2005; 151(8): 2551-2561.
  16. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007; 315(5819): 1709-1712.
  17. Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008; 321(5891): 960-964.
  18. Marraffini LA, Sontheimer EJ. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science. 2008; 322(5909): 1843-1845.
  19. Sontheimer E, Marraffini L. Target DNA interference with crRNA. U.S. Provisional Patent Application 61/009, 317, filed September 23, 2008; later published as US2010/0076057 (abandoned).
  20. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012; 337(6096): 816-821.
  21. Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci USA. 2012; 109(39): E2579-E2586.
  22. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013; 339(6121): 823-826.
  23. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013; 339(6121): 819-823.
  24. Cho SW, Kim S, Kim JM, Kim JS. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol. 2013; 31(3): 230-232.
  25. Brown KV. Why CRISPR-edited food may be in supermarkets sooner than you think. https://gizmodo.com/whycrispr-edited-food-may-be-in-supermarkets-sooner-th-1822025033
  26. Lee J, Wang F. Gene-edited baby by Chinese scientist: the opener of the Pandora’s box. Sci Insigt. 2018; 2018: e000178.
  27. Reardon S. CRISPR gene-editing creates wave of exotic model organisms. Nature. 2019; 568(7753): 441-442.
  28. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013; 152(5): 1173-1183.
  29. Kungulovski G, Jeltsch A. Epigenome editing: state of the art, concepts, and perspectives. Trends Genet. 2016; 32(2): 101-113.
  30. Pefanis E, Wang JG, Rothschild G, Lim J, Kazadi D, Sun JB, Federation A., Chao J, Elliott O, Liu ZP, Economides AN, Bradner JE, Rabadan R, Basu U. RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell. 2015; 161(4): 774-789.
  31. Elling R, Chan J, Fitzgerald KA. Emerging role of long noncoding RNAs as regulators of innate immune cell development and inflammatory gene expression. Eur J Immunol. 2016; 46(3): 504-512.
  32. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman J, Qi LS, Huang B. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell. 2013; 155(7): 1479-1491.
  33. Hajian R, Balderston S, Tran T, deBoer T, Etienne J, Sandhu M., Wauford NA, Chung JY, Nokes J, Athaiya M, Paredes J, Peytavi R, Goldsmith B, Murthy N, Conboy IM, Aran K. Detection of unamplified target genes via CRISPR-Cas9 immobilized on a graphene field-effect transistor. Nat Biomed Eng. 2019;3(6): 427-437.
  34. CRISPR’s future for point-of-care diagnostics. https://www.diagnosticsworldnews.com/news/2020/02/18/crispr%27s-future-for-point-of-care-diagnostics
  35. Niu Y, Shen B, Cui Y, Chen Y, Wang J, Wang L, Kang Y, Zhao X, Si W, Li W, Xiang AP, Zhou J, Guo X, Bi Y, Si C, Hu B, Dong G, Wang H, Zhou Z, Li T, Tan T, Pu X, Wang F, Ji S, Zhou Q, Huang X, Ji W, Sha J. Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos. Cell. 2014; 156(4): 836-843.
  36. Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna JA, Fenner M, Greely HT, Jinek M, Martin GS, Penhoet E, Puck J, Sternberg SH, Weissman JS, Yamamoto KR. Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science. 2015; 348(6230): 36-38.
  37. Collins F.S. NIH Director on Human Gene Editing: ‘We Must Never Allow our Technology to Eclipse our Humanity’. https://www.discovermagazine.com/health/nih-director-on-human-gene-editing-we-must-never-allow-ourtechnology-to
  38. Liang P, Xu Y, Zhang X, Ding C, Huang R. Zhang Z, Lv J, Xie., Chen Y, Li Y, Sun Y, Bai Y, Songyang Z, Ma W, Zhou C, Huang J. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell. 2015; 6(5): 363-372.
  39. Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 2013; 154(6): 1380-1389.
  40. Ma H, Marti-Gutierrez N, Park SW, Wu J, Lee Y, Suzuki K, Koski A, Ji D, Hayama T, Ahmed R, Darby H, Van Dyken C, Li Y, Kang E, Park AR, Kim D, Kim ST, Gong J, Gu Y, Xu X, Battaglia D, Krieg SA, Lee DM, Wu DH, Wolf DP, Heitner SB, Belmonte JCI, Amato P, Kim JS, Kaul S, Mitalipov S. Correction of a pathogenic gene mutation in human embryos. Nature. 2017; 548(7668): 413-419.
  41. Second woman carrying gene-edited baby, Chinese authorities confirm. https://www.theguardian.com/science/2019/jan/22/second-woman-carrying-gene-edited-baby-chinese-authorities-confirm
  42. CRISPR scientist gets three years of jail time for creating gene-edited babies. https://gizmodo.com/crispr-scientistgets-three-years-of-jail-time-for-crea-1840724277
  43. Act now on CRISPR babies. Nature. 2019; 570(7760): 137.
  44. Citorik RJ, Mimee M, Lu T. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat Biotechnol. 2014; 32(11): 1141-1145.
  45. Yosef I, Manor M, Kiro R, Qimron U. Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria. Proc Natl Acad Sci USA. 2015; 112(23): 7267-7272.
  46. Stokstad E. Genetically engineered moths can knock down crop pests, but will they take off? https://www.sciencemag.org/news/2020/01/genetically-engineered-moths-can-knock-down-crop-pests-will-they-take
  47. Niu D, Wei HJ, Lin L, George H, Wang T, Lee IH, Zhao HY, Wang Y, Kan Y, Shrock E, Lesha E, Wang G, Luo Y, Qing Y, Jiao D, Zhao H, Zhou X, Wang S, Wei H, Güell M, Church GM, Yang L. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science. 2017; 357(6357): 1303-1307.
  48. Gene editing spurs hope for transplanting pig organs into humans. https://www.nytimes.com/2017/08/10/health/gene-editing-pigs-organ-transplants.html
  49. Dash PK, Kaminski R, Bella R, Su H, Mathews S, Ahooyi TM, Chen C, Mancuso P, Sariyer R, Ferrante P, Donadoni M, Robinson JA, Sillman B, Lin Z, Hilaire JR, Banoub M, Elango M, Gautam N, Mosley RL, Poluektova LY, McMillan J, Bade AN, Gorantla S, Sariyer IK, Burdo TH, Young WB, Amini S, Gordon J, Jacobson JM, Edagwa B, Khalili K, Gendelman HE. Sequential LASER ART and CRISPR treatments eliminate HIV-1 in a subset of infected humanized mice. Nat Commun. 2019; 10(1): 2753.
  50. Yuan M, Webb E, Lemoine NR, Wang Y. CRISPR-Cas9 as a powerful tool for efficient creation of oncolytic viruses. Viruses. 2016; 8(3): E72.
  51. Miller JF, Sadelain M. The journey from discoveries in fundamental immunology to cancer immunotherapy. Cancer Cell. 2015; 27(4): 439-449.
  52. White MK, Khalili K. CRISPR/Cas9 and cancer targets: future possibilities and present challenges. Oncotarget. 2016; 7(11): 12305-12317.
  53. DeWitt MA, Magis W, Bray NL, Wang T, Berman JR, Urbinati F, Heo SJ, Mitros T, Muñoz DP, Boffelli D, Kohn DB, Walters MC, Carroll D, Martin DIK, Corn JE. Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Sci Transl Med. 2016; 8(360): 360ra134.
  54. Sanders R. UC rings out 2019 with its 20th CRISPR patent. https://news.berkeley.edu/2019/12/31/uc-rings-out-2019-with-its-20th-crispr-patent/
  55. Haridy R. First CRISPR therapy administered in landmark human trial. https://newatlas.com/crispr-trial-underway-vertex-gene-therapy/58643/
  56. The Future of CRISPR. http://www.fwreports.com/dossier/the-future-of-crispr/#.XmgL-kFR2Uk
  57. Mullin E. Fresh off her Nobel Prize win, Jennifer Doudna predicts what’s next for CRISPR. https://futurehuman.medium.com/fresh-off-her-nobel-prize-win-jennifer-doudna-predicts-whats-next-for-crispr-1fea0225c41d
  58. Pennisi E. The CRISPR craze. Science. 2013; 341(6148): 833-836.
  59. Gene editing like CRISPR is too important to be left to scientists alone. https://www.theguardian.com/commentisfree/2019/oct/22/gene-editing-crispr-scientists
  60. Chatterjee P, Jakimo N, Jacobson JM. Minimal PAM specificity of a highly similar SpCas9 ortholog. Sci Adv. 2018; 4(10): eaau0766.
  61. Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF. New CRISPR-Cas systems from unculti­vated microbes. Nature. 2017; 542(7640): 237-241.
  62. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015; 163(3): 759-771.
  63. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016; 353(6299): aaf5573.
  64. Smargon AA, Cox DB, Pyzocha NK, Zheng K, Slaymaker IM, Gootenberg JS, Abudayyeh OA, Essletzbichler P, Shmakov S, Makarova KS, Koonin EV, Zhang F. Cas13b is a type VI-B CRISPR-associated RNAguided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol Cell. 2017; 65(4): 618-630.e7.
  65. Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, Scott DA. Cas13d is a compact RNAtargeting type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Mol Cell. 2018; 70(2): 327-339.
  66. Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA. Programmed DNA Destruction by Miniature CRISPR-Cas14 Enzymes. Science. 2018; 362(6416): 839-842.
  67. Anzalone AV, Koblan LW, Liu DR. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol. 2020; 38(7): 824-844.
  68. Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F. RNA-guided DNA insertion with CRISPR-associated transposases. Science. 2019; 365(6448): 48-53.
  69. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016; 533(7603): 420-424.
  70. Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature. 2017; 551(7681): 464-471.
  71. Stafforst T, Schneider MF. An RNA-deaminase conjugate selectively repairs point mutations. Angew Chem Int Ed Engl. 2012; 51(44): 11166-11169.
  72. Reardon S. Step aside CRISPR, RNA editing is taking off. Nature. 2020; 578(7793): 24–27.
  73. Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A, Liu DR. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019; 576(7785): 149-157.
  74. Pennis E. Microbes’ mystery DNA helps defeat viruses – and has genome-editing potential. https://www.sciencemag.org/news/2020/11/microbes-mystery-dna-helps-defeat-viruses-and-has-genome-editing-potential
  75. Sharon E, Chen SA, Khosla NM, Smith JD, Pritchard JK, Fraser HB. Functional genetic variants revealed by massively parallel precise genome editing. Cell. 2018; 175(2): 544-557.e16.
  76. Fan S. Everything You Need to Know About Superstar CRISPR Prime Editing https://singularityhub.com/2019/11/05/everything-you-need-to-know-about-superstar-crispr-prime-editing/

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