Koronavirüs (COVID 19) ve İnfluenza’nın Proflaktik Tedavisinde CRISPR-Cas13 Sistemlerinin Rolü ve Geliştirilmesi

Year 2021, Volume: 8 Issue: 2, 69 - 78, 30.12.2021

Mikail Yeniçeri

Abstract

İnfluenza, insanlarda influenza A ve influenza B virüslerinin neden olduğu bulaşıcı bir solunum yolu hastalığıdır.
Genellikle yıllık mevsimsel salgınlarla karakterize edilen sporadik salgınları, zoonotik kökenli influenza A virüs suşlarını içerir. Dünya Sağlık Örgütü (DSÖ), yıllık grip salgınının yaklaşık 1 milyar enfeksiyon, 3-5 milyon ağır hastalık vakası ve 300.000-500.000 ölümle sonuçlanmaktadır. İlk olarak Wuhan (Çin) eyaletinde bildirilen, daha önce tanımlanmamış yeni bir Koronavirüs, orta derecede solunum yolu sendromu (MERS) ve Şiddetli Akut Solunum Yolu Sendromu'na (SARS) neden olanların yanı sıra hafif enfektif virüsleri içeren bir virüs ailesidir. Hastalık Kontrol ve Korunma Merkezi göre, virüsün resmi adı artık SARS-CoV-2 ve Koronavirüs hastalığı 2019 (COVID-19)’dur. Kümelenmiş Düzenli Olarak Aralıklı Kısa Palindromik Tekrarlar (CRISPR)-CRISPR ile ilişkili (Cas) sistemleri modern moleküler biyolojide devrim yaratmıştır. Bugüne kadar bu sistemlerin çok sayıda türü keşfedilmiştir. Şimdiye kadarki tüm CRISPR yaklaşımları DNA'yı hedeflemiştir. Ancak araştırma gruplarınca yapılan çalışmalarda, DNA yerine RNA'yı hedefleyen ve yeni karakterize edilmiş CRISPR ile ilişkili bir enzim kullanarak, haberci RNA'yı (mRNA) hedefleyebilen yeni bir düzenleme aracı geliştirmişlerdir. Bu yaklaşım ile genomu değiştirmeden bir hücrenin gen ekspresyonunda değişiklikler yapmak, genom düzenlemesinin hedef dışı etkileriyle ilişkili riskleri azaltmak için kullanılabilecektir. CRISPR-Cas13 sistemi, bakterileri virüslerden koruyan bakteriyel bağışıklık sistemine dayanan bir RNA hedefleme ve düzenleme sistemidir. CRISPR-Cas13 sistemi, CRISPR-Cas9 sistemine benzemektedir. Bununla birlikte, DNA'yı hedefleyen Cas-9'un aksine, Cas-13 tek sarmallı RNA'yı hedefler ve ayırır. Cas13, Cas13a ve Cas13b üyeleri, RNA seviyesinde terapötik gen düzeltmesi ve viral patojenlerin (yeni koronavirüs (SARS-CoV-2) gibi bu retrovirüslerin RNA bazlı genomlarında) kullanılabileceği yönünde geliştirilmektedir. Bu derlemede CRISPR-Cas13 sisteminin proflaktik tedavide kullanılmasının önemi amaçlanmıştır.

Keywords

İnfluenza, Covid 19, CRISPR-Cas13 sistemi

References

• 1. Sellers SA, Hagan RS, Hayden FG, Fischer WA (2017). The hidden burden of influenza: A review of the extra- pulmonary complications of influenza infection. Influenza Other Respir. Viruses 11: 372-393.
• 2. Kwong JC, Schwartz KL, Campitelli MA, Chung H, Crowcroft NS, Karnauchow T, Katz K, Ko DT, McGeer AJ, McNally D, Richardson DC, Rosella LC, Simor A, Smieja M, Zahariadis G, Gubbay JB (2018). Acute myocardial infarction after laboratory-confirmed influenza infection. N. Engl. J. Med. 378: 345-353.
• 3. Forni D, Cagliani R, Clerici M, Sironi M (2017). Molecular Evolution of Human Coronavirus Genomes. Trends Microbiol. 25: 35-48.
• 4. Ashour HM, Elkhatib WF, Rahman MM, Elshabrawy HA (2020). Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks. Pathogens. 9 (3):186.
• 5. Burmistrz M, Krakowski K, Krawczyk-Balska A (2020). RNA-Targeting CRISPR–Cas Systems and Their Applications. Int. J. Mol. Sci. 21:1122.
• 6. Krammer F, Smith G, Fouchier R, Peiris M, Kedzierska K, Doherty PC, Palese P, Shaw ML, Treanor J, Webster RG, García-Sastre A (2018). Influenza. Nat Rev Dis Primers 4: 3.
• 7. Ma W, García- Sastre A, Schwemmle M (2015). Expected and unexpected features of the newly discovered bat influenza A- like viruses. PLOS Pathog. 11: e1004819.
• 8. Fehr AR, Perlman S (2015). Coronaviruses: An overview of their replication and pathogenesis. Methods Mol. Biol. 1282: 1-23.
• 9. Izaguirre G (2019). The Proteolytic Regulation of Virus Cell Entry by Furin and Other Proprotein Convertases. Viruses. 11: 837.
• 10. URL 1: https://www.legacyias.com/wp-content/uploads/2020/04/Covid.png Erişim tarihi: 05.04.2020.
• 11. de Wit E, van Doremalen N, Falzarano D, Munster, VJ (2016). SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol. 14 (8): 523-34.
• 12. URL 2: https://zlab.bio/cas13 Erişim tarihi: 12.04.2020.
• 13. Makarova KS, Wolf YI, Alkhnbashi, OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJM, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, Oost J, Backofen R, Koonin EV (2015). An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol. 13: 722-736.
• 14. Burmistrz M, Rodriguez Martinez JI, Krochmal D, Staniec D, Pyrc K (2017). Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs in the Porphyromonas gingivalis CRISPR-Cas I-C System. J. Bacteriol. 199 (23): e00275-17.
• 15. Marraffini LA (2015). CRISPR-Cas immunity in prokaryotes. Nature. 526: 55-61.
• 16. Burmistrz M, Pyr´c K (2015). CRISPR-Cas Systems in Prokaryotes. Pol. J. Microbiol. 64: 193-202.
• 17. Manghwar H, Lindsey K, Zhang X, Jin S (2019). CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing. Trends Plant. Sci. 24: 1102-1125.
• 18. Makarova KS, Wolf YI, Koonin EV (2018). Classification and Nomenclature of CRISPR-Cas Systems: Where from Here? Cris. J. 1: 325-336.
• 19. Brezgin S, Kostyusheva A, Kostyushev D, Chulanov V (2019). Dead Cas Systems: Types, Principles, and Applications. Int. J. Mol. Sci. 20: 6041.
• 20. Khosravi S, Ishii T, Dreissig S, Houben A (2020). Application and prospects of CRISPR/Cas9-based methods to trace defined genomic sequences in living and fixed plant cells. Chromosome Res.28: 7-17.
• 21. Valenti MT, Serena M, Carbonare LD, Zipeto D (2019). CRISPR/Cas system: An emerging technology in stem cell research. World J. Stem Cells. 11: 937-956.
• 22. Banan M (2019). Recent advances in CRISPR/Cas9-mediated knock-ins in mammalian cells. J. Biotechnol. 308:1-9.
• 23. Khanzadi MN, Khan AA. CRISPR/Cas9: Nature’s gift to prokaryotes and an auspicious tool in genome editing. J. Basic Microbiol. 2019.
• 24. Zhu Y, et al. Shooting the messenger: RNA-targetting CRISPR-Cas systems. Biosci. Rep. 2018;38.
• 25. Nickel L, Ulbricht A, Alkhnbashi OS, Förstner KU, Cassidy L, Weidenbach K, Backofen R, Schmitz RA (2018). Cross-cleavage activity of Cas6b in crRNA processing of two di_erent CRISPR-Cas systems in Methanosarcina mazei Gö1. RNA Biol. 16: 492-503.
• 26. Taylor DW, Zhu Y, Staals RH, Kornfeld JE, Shinkai A, van der Oost J, Nogales E, Doudna JA (2015). Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning. Science 348: 581-585.
• 27. Osawa T, Inanaga H, Sato C, Numata T (2015). Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog. Mol. Cell. 58: 418-430.
• 28. Estrella MA, Kuo FT, Bailey S (2016). RNA-activated DNA cleavage by the Type III-B CRISPR-Cas effector complex. Genes Dev. 30: 460-470.
• 29. Maniv I, Jiang W, Bikard D, Marraffini LA (2016). Impact of Different Target Sequences on Type III CRISPR-Cas Immunity. J. Bacteriol. 198: 941-950.
• 30. Kazlauskiene M, Tamulaitis G, Kostiuk G, Venclovas Č, Siksnys V (2016). Spatiotemporal Control of Type III-A CRISPR-Cas Immunity: Coupling DNA Degradation with the Target RNA Recognition. Mol. Cell 62: 295-306.
• 31. Niewoehner O, Garcia-Doval C, Rostøl JT, Berk C, Schwede F, Bigler L, Hall J, Marraffini LA, Jinek M (2017). Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers. Nature 548: 543-548.
• 32. Kazlauskıene M, Kostıuk G, Venclovas Č, Tamulaıtıs G, Sıksnys V (2017). A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems. Science. 357:605-609.
• 33. Sheppard NF, Glover CV, Terns RM, Terns MP (2016). The CRISPR-associated Csx1 protein of Pyrococcus furiosus is an adenosine-specific endoribonuclease. RNA. 22: 216-224.
• 34. Goldberg GW, McMillan EA, Varble A, Modell JW, Samai P, Jiang W, Marraffini LA (2018).Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts. Nat. Commun. 9: 61.
• 35. Jiang W, Samai P, Marraffini LA (2016). Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity. Cell. 164:710-721.
• 36. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DBT, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F (2016). C2c2 is a single-component programmable RNA-guidedRNA-targeting CRISPR effector. Science. 353:aaf5573.
• 37. Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV (2015). Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. Mol. Cell. 60: 385-397.
• 38. Smargon AA, Cox D, Pyzocha NK, Zheng K, Slaymaker IM, Gootenberg JS, Abudayyeh OA, Essletzbichler P, Shmakov S, Makarova KS, Koonin EV ,Zhang F (2017). Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Di_erentially Regulated by Accessory Proteins Csx27 and Csx28. Mol. Cell. 65: 618-630.
• 39. Shmakov S, Smargon AA, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova, KS, Wolf YI, Severinov K, Zhang F, Koonin EV (2017). Diversity and evolution of class 2 CRISPR-Cas systems. Nat. Rev. Microbiol. 15: 169-182.
• 40. East-Seletsky A, O'Connell MR, Burstein D, Knott GJ, Doudna JA (2017). RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes. Mol. Cell. 66: 373-383.
• 41. Liu L, Li X, Ma J, Li Z, You L, Wang J, Wang M, Zhang X, Wang Y (2017). The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a. Cell. 170: 714-726.
• 42. Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, Scott DA (2018). Cas13d Is a Compact RNA-Targeting Type VI CRISPR E_ector Positively Modulated by a WYL-Domain-Containing Accessory Protein. Mol. Cell. 70: 327-339.
• 43. Omar O. Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A, Lander ES, Voytas DF, Ting AY, Zhang F (2017). RNA targeting with CRISPR-Cas13. Nature. 550: 280–284.
• 44. Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU, Beisel CL, Sharma CM (2018). CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9. Mol. Cell. 69: 893-905.
• 45. Rousseau BA, Hou Z, Gramelspacher MJ, Zhang Y (2018). Programmable RNA Cleavage and Recognition by a Natural CRISPR-Cas9 System from Neisseria meningitidis. Mol. Cell. 69: 906-914.
• 46. Strutt SC, Torrez RM, Kaya E, Negrete OA, Doudna JA (2018). RNA-dependent RNA targeting by CRISPR-Cas9. Elife. 7: e32724.
• 47. Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD (2018). Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors. Cell. 173: 665-676.
• 48. Cox DBT, Gootenberg JS, Abudayyeh OO, Franklın B, Kellner MJ, Joung J, Zhang F (2017). RNA editing with CRISPR-Cas13. Science. 358: 1019-1027.
• 49. Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbıchler P, Dy AJ, Joung J, Verdıne V, Donghıa N, Darınger NM, Freıje CA, Myhrvold C, Bhattacharyya RP, Lıvny J, Regev A, Koonın EV, Hung DT, Sabetı PC, Collıns JJ, Zhang F (2017). Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 356: 438-442.
• 50. Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collıns JJ, Zhang F (2018). Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science. 360: 439-444.
• 51. Rashid Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M (2018). RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol. 19:1.
• 52. Zhang C, Konermann S, Brideau NJ, Lotfy P, Wu X, Novick SJ, Strutzenberg T, Griffin PR, Hsu PD, Lyumkis D (2018). Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d. Cell. 175: 212-223.
• 53. Abbott TR, Dhamdhere G, Liu Y, Lin X, Goudy L, Zeng L, Chemparathy A, Chmura S, Heaton NS, Debs R, Pande T, Endy D, Russa ML, Lewis DB, Qi LS (2020). Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza. BioRxiv. 03.13.991307.