Перспективи редагування геному за допомогою CRISPR/Cas, або як опанувати «генетичні ножиці»

Нобелівська премія з хімії 2020 року

Автор(и)

  • Сергій Васильович Комісаренко академік НАН України, директор Інституту біохімії ім. О.В. Палладіна НАН України https://orcid.org/0000-0002-3244-3194
  • Світлана Іванівна Романюк кандидат біологічних наук, старший науковий співробітник Інституту біохімії ім. О.В. Палладіна НАН України https://orcid.org/0000-0002-3900-6755

DOI:

https://doi.org/10.15407/visn2020.12.031

Ключові слова:

Nobel Prize in Chemistry, Emmanuelle Charpentier, Jennifer Doudna, genome editing, CRISPR/Cas9

Анотація

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.

Посилання

Chemistry. Citation Laureates 2020. https://clarivate.com/webofsciencegroup/citation-laureates/chemistry/

Press release: The Nobel Prize in Chemistry 2020. https://www.nobelprize.org/prizes/chemistry/2020/press-release/

Komisarenko S.V., Romanyuk S.I. 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). DOI: https://doi.org/10.15407/visn2020.03.050

Jennifer Doudna. Wikipedia. https://en.wikipedia.org/wiki/Jennifer_Doudna

Emmanuelle Charpentier. Wikipedia. https://en.wikipedia.org/wiki/Emmanuelle_Charpentier

Deltcheva E., Chylinski K., Sharma C.M., Gonzales K., Chao Y., Pirzada Z.A., Eckert M.R., Vogel J., Charpentier E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011. 471(7340): 602–607. DOI: https://doi.org/10.1038/nature09886

Westra E.R., Semenova E., Datsenko K.A., Jackson R.N., Wiedenheft B., Severinov K., Brouns S.J. Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition. PLoS Genet. 2013. 9(9): e1003742. DOI: https://doi.org/10.1371/journal.pgen.1003742

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. DOI: https://doi.org/10.1128/JB.169.12.5429-5433.1987

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. DOI: https://doi.org/10.1128/JB.171.6.3553-3556.1989

Groenen P.M., Bunschoten A.E., van Soolingen D., van Embden J.D. 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. DOI: https://doi.org/10.1111/j.1365-2958.1993.tb00976.x

Mojica F.J., 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. DOI: https://doi.org/10.1046/j.1365-2958.2000.01838.x

Jansen R., Embden J.D., Gaastra W., Schouls L.M. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 2002. 43(6): 1565–1575. DOI: https://doi.org/10.1046/j.1365-2958.2002.02839.x

Mojica F.J., Díez-Villaseñor C., García-Martínez J., Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of Molecular Evolution. 2005. 60(2): 174–182. DOI: https://doi.org/10.1007/s00239-004-0046-3

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. DOI: https://doi.org/10.1099/mic.0.27437-0

Bolotin A., Quinquis B., Sorokin A., Ehrlich S.D. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology. 2005. 151(8): 2551–2561. DOI: https://doi.org/10.1099/mic.0.28048-0

Barrangou R., Fremaux C., Deveau H., Richards M., Boyaval P., Moineau S., Romero D.A., Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007. 315(5819): 1709–1712. DOI: https://doi.org/10.1126/science.1138140

Brouns S.J., Jore M.M., Lundgren M., Westra E.R., Slijkhuis R.J., Snijders A.P., Dickman M.J., Makarova K.S., Koonin E.V., van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008. 321(5891): 960–964. DOI: https://doi.org/10.1126/science.1159689

Marraffini L.A., Sontheimer E.J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science. 2008. 322(5909): 1843–1845. DOI: https://doi.org/10.1126/science.1165771

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).

Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012. 337(6096): 816–821. DOI: https://doi.org/10.1126/science.1225829

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. DOI: https://doi.org/10.1073/pnas.1208507109

Mali P., Yang L., Esvelt K.M., Aach J., Guell M., DiCarlo J.E., Norville J.E., Church G.M. RNA-guided human genome engineering via Cas9. Science. 2013. 339(6121): 823–826. DOI: https://doi.org/10.1126/science.123203372

Cong L., Ran F.A., Cox D., Lin S., Barretto R., Habib N., Hsu P.D., Wu X., Jiang W., Marraffini L.A., Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013. 339(6121): 819–823. DOI: https://doi.org/10.1126/science.1231143

Cho S.W., Kim S., Kim J.M., Kim J.S. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol. 2013. 31(3): 230–232. DOI: https://doi.org/10.1038/nbt.2507

Brown K.V. 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

Lee J., Wang F. Gene-edited baby by Chinese scientist: the opener of the Pandora’s box. Science Insights. 2018. 2018(13): e000178. DOI: https://doi.org/10.15354/si.18.co015

Reardon S. CRISPR gene-editing creates wave of exotic model organisms. Nature. 2019. 568(7753): 441–442. DOI: https://doi.org/10.1038/d41586-019-01300-9

Qi L.S., Larson M.H., Gilbert L.A., Doudna J.A., Weissman J.S., Arkin A.P., Lim W.A. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013. 152(5): 1173–1183. DOI: https://doi.org/10.1016/j.cell.2013.02.022

Kungulovski G., Jeltsch A. Epigenome editing: state of the art, concepts, and perspectives. Trends Genet. 2016. 32(2): 101–113. DOI: https://doi.org/10.1016/j.tig.2015.12.001

Pefanis E., Wang J.G., Rothschild G., Lim J., Kazadi D., Sun J.B., Federation A., Chao J., Elliott O., Liu Z.P., Economides A.N., Bradner J.E., Rabadan R., Basu U. RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell. 2015. 161(4): 774–789. DOI: https://doi.org/10.1016/j.cell.2015.04.034

Elling R., Chan J., Fitzgerald K.A. 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. DOI: https://doi.org/10.1002/eji.201444558

Chen B., Gilbert L.A., Cimini B.A., Schnitzbauer J., Zhang W., Li G.W., Park J., Blackburn E.H., Weissman J.S., Qi L.S., Huang B. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell. 2013. 155(7): 1479–1491. DOI: https://doi.org/10.1016/j.cell.2013.12.001

Hajian R., Balderston S., Tran T., deBoer T., Etienne J., Sandhu M., Wauford N.A., Chung J.Y., Nokes J., Athaiya M., Paredes J., Peytavi R., Goldsmith B., Murthy N., Conboy I.M., 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. DOI: https://doi.org/10.1038/s41551-019-0371-x

CRISPR’s future for point-of-care diagnostics. https://www.diagnosticsworldnews.com/news/2020/02/18/crispr%27s-future-for-point-of-care-diagnostics

Niu Y., Shen B., Cui Y., Chen Y., Wang J., Wang L., Kang Y., Zhao X., Si W., Li W., Xiang A.P., 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. DOI: https://doi.org/10.1016/j.cell.2014.01.027

Baltimore D., Berg P., Botchan M., Carroll D., Charo R.A., Church G., Corn J.E., Daley G.Q., Doudna J.A., Fenner M., Greely H.T., Jinek M., Martin G.S., Penhoet E., Puck J., Sternberg S.H., Weissman J.S., Yamamoto K.R. Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science. 2015. 348(6230): 36–38. DOI: https://doi.org/10.1126/science.aab1028

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

Liang P., Xu Y., Zhang X., Ding C., Huang R., Zhang Z., Lv J., Xie X., 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. DOI: https://doi.org/10.1007/s13238-015-0153-5

Ran F.A., Hsu P.D., Lin C.Y., Gootenberg J.S., Konermann S., Trevino A.E., Scott D.A., 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. DOI: https://doi.org/10.1016/j.cell.2013.08.021

Ma H., Marti-Gutierrez N., Park S.W., Wu J., Lee Y., Suzuki K., Koski A., Ji D., Hayama T., Ahmed R., Darby H., Van Dyken C., Li Y., Kang E., Park A.R., Kim D., Kim S.T., Gong J., Gu Y., Xu X., Battaglia D., Krieg S.A., Lee D.M., Wu D.H., Wolf D.P., Heitner S.B., Belmonte J.C.I., Amato P., Kim J.S., Kaul S., Mitalipov S. Correction of a pathogenic gene mutation in human embryos. Nature. 2017. 548(7668): 413–419. DOI: https://doi.org/10.1038/nature23305

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

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

Act now on CRISPR babies. Nature. 2019. 570(137). DOI: https://doi.org/10.1038/d41586-019-01786-3

Citorik R.J., Mimee M., Lu T.K. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat. Biotechnol. 2014. 32(11): 1141–1145. DOI: https://doi.org/10.1038/nbt.3011

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. DOI: https://doi.org/10.1073/pnas.1500107112

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 DOI: https://doi.org/10.1126/science.abb1078

Niu D., Wei H.J., Lin L., George H., Wang T., Lee I.H., Zhao H.Y., Wang Y., Kan Y., Shrock E., Lesha E., Wang G., Luo Y., Qing Y., Jiao D., Zhao H., Zhou X., Wang S., Wei H., G ell M., Church G.M., Yang L. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science. 2017. 357(6357): 1303–1307. DOI: https://doi.org/10.1126/science.aan4187

Gene editing spurs hope for transplanting pig organs into humans. https://www.nytimes.com/2017/08/10/health/gene-editing-pigs-organ-transplants.html

Dash P.K., Kaminski R., Bella R., Su H., Mathews S., Ahooyi T.M., Chen C., Mancuso P., Sariyer R., Ferrante P., Donadoni M., Robinson J.A., Sillman B., Lin Z., Hilaire J.R., Banoub M., Elango M., Gautam N., Mosley R.L., Poluektova L.Y., McMillan J., Bade A.N., Gorantla S., Sariyer I.K., Burdo T.H., Young W.B., Amini S., Gordon J., Jacobson J.M., Edagwa B., Khalili K., Gendelman H.E. Sequential LASER ART and CRISPR treatments eliminate HIV-1 in a subset of infected humanized mice. Nat. Commun. 2019. 10(1): 2753. DOI: https://doi.org/10.1038/s41467-019-10366-y

Yuan M., Webb E., Lemoine N.R., Wang Y. CRISPR-Cas9 as a powerful tool for efficient creation of oncolytic viruses. Viruses. 2016. 8(3): E72. DOI: https://doi.org/10.3390/v8030072

Miller J.F., Sadelain M. The journey from discoveries in fundamental immunology to cancer immunotherapy. Cancer Cell. 2015. 27(4): 439–449. DOI: https://doi.org/10.1016/j.ccell.2015.03.007

White M.K., Khalili K. CRISPR/Cas9 and cancer targets: future possibilities and present challenges. Oncotarget. 2016. 7(11): 12305–12317. DOI: https://doi.org/10.18632/oncotarget.7104

DeWitt M.A., Magis W., Bray N.L., Wang T., Berman J.R., Urbinati F., Heo S.J., Mitros T., Mu oz D.P., Boffelli D., Kohn D.B., Walters M.C., Carroll D., Martin D.I., Corn J.E. Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Sci. Transl. Med. 2016. 8(360): 360ra134. DOI: https://doi.org/10.1126/scitranslmed.aaf9336

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/

Haridy R. First CRISPR therapy administered in landmark human trial. https://newatlas.com/crispr-trial-underway-vertex-gene-therapy/58643/

The Future of CRISPR. http://www.fwreports.com/dossier/the-future-of-crispr/#.XmgL-kFR2Uk

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

Pennisi E. The CRISPR craze. Science. 2013. 341(6148): 833–836. DOI: https://doi.org/10.1126/science.341.6148.833

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

Chatterjee P., Jakimo N., Jacobson J.M. Minimal PAM specificity of a highly similar SpCas9 ortholog. Sci. Adv. 2018. 4(10): eaau0766. DOI: https://doi.org/10.1126/sciadv.aau0766

Burstein D., Harrington L.B., Strutt S.C., Probst A.J., Anantharaman K., Thomas B.C., Doudna J.A., Banfield J.F. New CRISPR-Cas systems from uncultivated microbes. Nature. 2017. 542(7640): 237–241. DOI: https://doi.org/10.1038/nature21059

Zetsche B., Gootenberg J.S., Abudayyeh O.O., Slaymaker I.M., Makarova K.S., Essletzbichler P., Volz S.E., Joung J., van der Oost J., Regev A., Koonin E.V., Zhang F. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015. 163(3): 759–771. DOI: https://doi.org/10.1016/j.cell.2015.09.038

Abudayyeh O.O., Gootenberg J.S., Konermann S., Joung J., Slaymaker I.M., Cox D.B., Shmakov S., Makarova K.S., Semenova E., Minakhin L., Severinov K., Regev A., Lander E.S., Koonin E.V., Zhang F. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016. 353(6299): aaf5573. DOI: https://doi.org/10.1126/science.aaf5573

Smargon A.A., Cox D.B., Pyzocha N.K., Zheng K., Slaymaker I.M., Gootenberg J.S., Abudayyeh O.A., Essletzbichler P., Shmakov S., Makarova K.S., Koonin E.V., 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. DOI: https://doi.org/10.1016/j.molcel.2016.12.023

Yan W.X., Chong S., Zhang H., Makarova K.S., Koonin E.V., Cheng D.R., Scott D.A. 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. DOI: https://doi.org/10.1016 / j.molcel.2018.02.028

Harrington L.B., Burstein D., Chen J.S., Paez-Espino D., Ma E., Witte I.P., Cofsky J.C., Kyrpides N.C., Banfield J.F., Doudna J.A. Programmed DNA Destruction by Miniature CRISPR-Cas14 Enzymes. Science. 2018. 362(6416): 839–842. DOI: https://doi.org/10.1126/science.aav4294

Anzalone A.V., Koblan L.W., Liu D.R. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol. 2020. 38(7): 824–844. DOI: https://doi.org/10.1038/s41587-020-0561-9

Strecker J., Ladha A., Gardner Z., Schmid-Burgk J.L., Makarova K.S., Koonin E.V., Zhang F. RNA-guided DNA insertion with CRISPR-associated transposases. Science. 2019. 365(6448): 48–53. DOI: https://doi.org/10.1126/science.aax9181

Komor A.C., Kim Y.B., Packer M.S., Zuris J.A., Liu D.R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016. 533(7603): 420–424. DOI: https://doi.org/10.1038/nature17946

Gaudelli N.M., Komor A.C., Rees H.A., Packer M.S., Badran A.H., Bryson D.I., Liu D.R. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature. 2017. 551(7681): 464–471. DOI: https://doi.org/10.1038/nature24644

Stafforst T., Schneider M.F. An RNA-deaminase conjugate selectively repairs point mutations. Angew. Chem. Int. Ed. Engl. 2012. 51(44): 11166–11169. DOI: https://doi.org/10.1002/anie.201206489

Reardon S. Step aside CRISPR, RNA editing is taking off. Nature. 2020. 578(7793): 24–27. DOI: https://doi.org/10.1038/d41586-020-00272-5

Anzalone A.V., Randolph P.B., Davis J.R., Sousa A.A., Koblan L.W., Levy J.M., Chen P.J., Wilson C., Newby G.A., Raguram A., Liu D.R. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019. 576(7785): 149-157. DOI: https://doi.org/10.1038/s41586-019-1711-4

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

Sharon E., Chen S.A., Khosla N.M., Smith J.D., Pritchard J.K., Fraser H.B. Functional genetic variants revealed by massively parallel precise genome editing. Cell. 2018. 175(2): 544–557.e16. DOI: https://doi.org/10.1016/j.cell.2018.08.057.

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/

##submission.downloads##

Опубліковано

2023-03-07