Scienceline Publication Journal of Life Science and Biomedicine 2251-9939 10 1 2020 1 25 CRISPR/Cas9 gene editing technology and its application to the coronavirus disease (COVID-19), a review 01 09 10.29252/scil.2020.jlsb1 EN Saeid CHEKANI-AZAR PhD, Faculty of Veterinary Medicine, Animal Physiology, Atatürk University, Turkey Ehsan GHARIB MOMBENI Department of Pathobiology, Shahid Chamran University of Ahvaz, Iran Mastewal BIRHAN College of Veterinary Medicine and Animal Science, Department of Veterinary Paraclinical Studies, University of Gondar, Ethiopia Mahshad YOUSEFI MD, Hamadan University of Medical Sciences, Hamadan, Iran Journal Article S225199392000001-10 10.29252/scil.2020.jlsb1 2019 12 22 2020 01 15 2020 01 25 Clustered-Regularly Interspaced Short Palindromic Repeats (CRISPR), and CRISPR associated (Cas) protein (CRISPR/Cas) structures were first identified in E. coli in 1987 and guard prokaryotic cells from any invading pathogens, harmful events and plasmids by recognizing and cutting foreign nucleic acid sequences that contain short palindromic repeats spacer sequences. Several genome editing approaches have been developed based on these mechanisms; the most recent is known as CRISPR/Cas. Before the CRISPR technique was revealed in 2012, editing the genomes of plants and animals took many years and cost hundreds of thousands of dollars. Thus, CRISPR/Cas has attracted significant interest in the scientific community, especially for disease diagnosis and treatment, as it is quicker, less expensive and more precise than other genome editing approaches. The evidence from gene mutations in specific patients generated using CRISPR/Cas can assist in the prediction of the optimal treatment schedule for individual patients and for innovation purposes in other researches like replication in cell culture of coronaviruses like severe acute respiratory syndrome coronavirus-2 (SARS-CoV2 or COVID-19). However, in numerous situations, the effects of the furthermost significant driver mutations are not yet understood and interpretation of the optimal treatment is impossible. CRISPR/Cas classifications feature highly sensitive and selective tools for the detection of various target genes. When we see the next steps of genomic research, it is obvious that genome-wide association studies are relatively new way to identify the genes involved in human disease. Furthermore, CRISPR/Cas provides a tool to manipulate non-coding regions and will thus accelerate examination of these poorly characterized regions of the genome and play a vital role in the progress of whole genome libraries. We aimed to review the history of CRISPR/Cas, the mechanisms of CRISPR techniques, its current status as a tool for studying both natural mutations and genomic manipulations, and explore how CRISPR/Cas may improve the treatment of diseases. Pan A and Kraschel KL. Kraschel. CRISPR diagnostics: Underappreciated uses in perinatology. in Seminars in perinatology. 2018. Elsevier. 30415764 10.1053/j.semperi.2018.09.016 Hidalgo-Cantabrana C, Goh YJ and Barrangou R. Barrangou, Characterization and repurposing of type I and type II CRISPR-Cas systems in bacteria. J Mol Biol. 2018; 431(1): 21-33. 30261168 10.1016/j.jmb.2018.09.013 Qu D, Lu S, Wang P, Jiang M, Yi S, et al. Analysis of CRISPR/Cas system of Proteus and the factors affected the functional mechanism. Life Sci. 2019; 231: 116531. 31175856 10.1016/j.lfs.2019.06.006 Mehravar M, Shirazi A, Nazari M and Banan M. Mosaicism in CRISPR/Cas9-mediated genome editing. Dev Biol. 2018; 445(2): 156-162. 30359560 10.1016/j.ydbio.2018.10.008 Zhan T, Rindtorff N, Betge J, Ebert MP and Boutros M. CRISPR/Cas9 for cancer research and therapy. Semin Cancer Biol. 2019; 55(2019): 106-119. 29673923 10.1016/j.semcancer.2018.04.001 Herai RH. Avoiding the off-target effects of CRISPR/cas9 system is still a challenging accomplishment for genetic transformation. Gene. 2019; 700: 176-178. 30898720 10.1016/j.gene.2019.03.019 King MW and Munger J. Editing the human cytomegalovirus genome with the CRISPR/Cas9 system. Virology. 2019; 529: 186-194. 30716580 10.1016/j.virol.2019.01.021 de Wilde AH, Zevenhoven-Dobbe JC, Beugeling C, Chatterji U, de Jong D, et al. Coronaviruses and arteriviruses display striking differences in their cyclophilin a-dependence during replication in cell culture. Virology. 2018; 517: 148-156. PMC7112125 29249267 10.1016/j.virol.2017.11.022 Ford K, McDonald D and Mali P. Functional genomics via CRISPR–Cas. J Mol Biol. 2019; 431(1): 48-65 PMC6309720 29959923 10.1016/j.jmb.2018.06.034 Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, et al. Evolution and classification of the CRISPR–Cas systems. Nat Rev Microbiol. 2011; 9(6): 467. PMC3380444 21552286 10.1038/nrmicro2577 Khatodia S, Bhatotia K, Passricha N, Khurana S and Tuteja N. The CRISPR/Cas genome-editing tool: application in improvement of crops. Front Plant Sci. 2016; 7: 506. PMC4835450 27148329 10.3389/fpls.2016.00506 Yamaguchi Handde Lecea L. In vivo cell type-specific CRISPR gene editing for sleep research. J Neurosci Methods. 2018; 316: 99-102. PMC6380930 30439390 10.1016/j.jneumeth.2018.10.016 PMC4153410 24768240 10.51145/jlsb.2021.10 Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol, 2008; 190(4): 1390-1400. PMC2238228 18065545 10.1128/JB.01412-07 Ogaugwu CE, Agbo SO and Adekoya MA. CRISPR in sub-Saharan Africa: applications and education. Trends Biotechnol. 2019. 37(3): p. 234-237. PMC6378648 30100229 10.1016/j.tibtech.2018.07.012 Nishiyama J. Genome editing in the mammalian brain using the CRISPR–Cas system. Neurosci Res. 2019; 141: p. 4-12. 30076877 10.1016/j.neures.2018.07.003 Rahman S, Datta M, Kim J and Jan AT. CRISPR/Cas: An intriguing genomic editing tool with prospects in treating neurodegenerative diseases. Semin Cell Dev Biol. 2019. 96: 22-31. 31102655 10.1016/j.semcdb.2019.05.014 Kaushik I, Ramachandran S and Srivastava SK. CRISPR-Cas9: A multifaceted therapeutic strategy for cancer treatment. Semin Cell Dev Biol. Elsevier. 2019; 96:4-12. PMC6829064 31054324 10.1016/j.semcdb.2019.04.018 Pineda M, Lear A, Collins JP and Kiani S. Safe CRISPR: Challenges and Possible Solutions. Trends Biotechnol. 2018; 37(4): 389-401. 30352704 10.1016/j.tibtech.2018.09.010 Chen M, Mao A, Xu M, Weng Q, Mao J, et al. CRISPR-Cas9 for cancer therapy: Opportunities and challenges. Cancer lett. 2019; 447: 48-55. 30684591 10.3390/biomedicines6040105 Thomas M, Parry-Smith DandIyer V. Best practice for CRISPR design using current tools and resources. Methods, 2019; 164–165(15 July): 3-17. 31152780 10.1016/j.ymeth.2019.05.019 Fu BXH, Smith JD, Fuchs RT, Mabuchi M, Curcuru J, et al. Target-dependent nickase activities of the CRISPR-Cas nucleases Cpf1 and Cas9. Nat Microbiol. 2019; 4(5): 888-897. PMC6512873 30833733 10.1038/s41564-019-0382-0 Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014; 343(6166): 84-87. PMC4089965 24336571 10.1126/science.1247005 Rezaei H, Farahani N, Hosseingholi EZ, Sathyapalan T and Hossein Sahebkar A. Harnessing CRISPR/Cas9 technology in cardiovascular disease. Trends Cardiovasc Med. 2019; 30(2): 93-101. 30935726 10.1016/j.tcm.2019.03.005 Wang W, Zhang L, Wang X and Zeng Y. The advances in CRISPR technology and 3D genome. Semin Cell Dev Biol. 2019 Jun; 90:54-61. 30004018 10.1016/j.semcdb.2018.07.009 Ai J-W, Zhou X, Xu T, Yang M, Chen Y, et al. CRISPR-based rapid and ultra-sensitive diagnostic test for Mycobacterium tuberculosis. Emerg Microbes Infect. 2019; 8(1): 1361-1369. PMC6758691 31522608 10.1080/22221751.2019.1664939 Strich JR and Chertow DS. CRISPR-Cas biology and its application to infectious diseases. Diseases. J Clin Microbiol. 2019; 57(4): e01307-18. PMC6440769 30429256 10.1128/JCM.01307-18 Hui DS and Zumla A. Severe Acute Respiratory Syndrome: Historical, Epidemiologic, and Clinical Features. Infect Dis Clin North Am. 2019; 33(4): 869-889. 10.1016/j.idc.2019.07.001 Azhar EI, Hui DS, Memish ZA, Drosten C and Zumla A. The Middle East Respiratory Syndrome (MERS). Infect Dis Clin North Am. 2019; 33(4): 891-905. PMC7127753 31668197 10.18683/germs.2019.1155 Organization WH. Novel Coronavirus (‎2019-nCoV)‎: situation report, 3. 2020. Huang C, Wang Y, Li X, Ren L, Zhao J, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020; 395(10223): 497-506. PMC7159299 31986264 10.1016/S0140-6736(20)30183-5 Zumla A, Hui DS, Azhar EI, Memish ZA and Maeurer M. Reducing mortality from 2019-nCoV: host-directed therapies should be an option. Lancet. 2020; 395(10224): e35-e36. PMC7133595 32035018 10.1016/S0140-6736(20)30305-6 Li G, Fan Y, Lai Y, Han T, Li Z, et al. Coronavirus infections and immune responses. J Med Virol. 2020; 92(4):424-432. PMC7166547 31981224 10.1002/jmv.25685 Channappanavar R and Perlman S. Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology. Semin Immunopathol. 2017. 39(5): 529-539. PMC7079893 28466096 10.1007/s00281-017-0629-x Batawi S, Tarazan N, Al-Raddadi R, Al Qasim E, Sindi A, et al. Quality of life reported by survivors after hospitalization for Middle East respiratory syndrome (MERS). Health Qual Life Outcomes. 2019; 17(1):101. PMC6560892 31186042 10.1186/s12955-019-1165-2 Ngai JC, Ko FW, Ng SS, TO KW, Tong M, et al. The long‐term impact of severe acute respiratory syndrome on pulmonary function, exercise capacity and health status. Respirology. 2010; 15(3): 543-550. PMC7192220 20337995 10.1111/j.1440-1843.2010.01720.x Zumla A, Chan JF, Azhar EI, Hui DS and Yuen K-Y. Coronaviruses—drug discovery and therapeutic options. Nat Rev Drug Discov. 2016; 15(5):327-47. PMC7097181 26868298 10.1038/nrd.2015.37 Beigel JH, Nam HH, Adams PL, Krafft A, Ince WL, et al. Advances in respiratory virus therapeutics–A meeting report from the 6th isirv Antiviral Group conference. Antiviral Res. 2019 Jul; 167:45-67. PMC7132446 30974127 10.1016/j.antiviral.2019.04.006 Zumla A, Azhar EI, Arabi Y, Alotaibi B, Rao M, et al. Host-directed therapies for improving poor treatment outcomes associated with the middle east respiratory syndrome coronavirus infections. Int J Infect Dis. 2015 Nov;40:71-4. PMC7128983 26365771 10.1016/j.ijid.2015.09.005 Gorbalenya AE, Enjuanes L, Ziebuhr J and Snijder EJ. Nidovirales: Evolving the largest RNA virus genome. Virus Res. 2006; 117(1):17-37. PMC7114179 16503362 10.1016/j.virusres.2006.01.017 Nga PT, del Carmen Parquet M, Lauber C, Parida M, Nabeshima T, et al. Discovery of the first insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus genomes. PLoS Pathog. 2011; 7(9):e1002215. PMC3169540 21931546 10.1371/journal.ppat.1002215 de Wit E, van Doremalen N, Falzarano D and Munster VJ. SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol. 2016; 14(8):523-34. PMC7097822 27344959 10.1038/nrmicro.2016.81 Snijder EJ, Kikkert MandFang Y. Arterivirus molecular biology and pathogenesis. J Gen Virol. 2013; 94(Pt 10):2141-2163. 23939974 10.1099/vir.0.056341-0 Gosert R, Kanjanahaluethai A, Egger D, Bienz K and Baker SC. RNA replication of mouse hepatitis virus takes place at double-membrane vesicles. J Virol. 2002; 76(8):3697-708. PMC136101 11907209 10.1128/JVI.76.8.3697-3708.2002 Hagemeijer MC, Vonk AM, Monastyrska I, Rottier PJ and de Haan CA. Visualizing coronavirus RNA synthesis in time by using click chemistry. J Virol. 2012; 86(10):5808-16. PMC3347275 22438542 10.1128/JVI.07207-11 Pedersen KW, van der Meer Y, Roos N, Snijder EJ. Open reading frame 1a-encoded subunits of the arterivirus replicase induce endoplasmic reticulum-derived double-membrane vesicles which carry the viral replication complex. J Virol. 1999; 73(3):2016-26. PMC104444 9971782 10.1128/JVI.73.3.2016-2026.1999 van Hemert MJ, van den Worm SHE, Knoops K, Mommaas AM, Gorbalenya AE, et al. SARS-Coronavirus Replication/Transcription Complexes Are Membrane-Protected and Need a Host Factor for Activity In Vitro. PLOS Pathog, 2008; 4(5): e1000054. PMC2322833 18451981 10.1371/journal.ppat.1000054 Knoops K, Bárcena M, Limpens RW, Koster AJ, Mommaas AM, et al. Ultrastructural characterization of arterivirus replication structures: reshaping the endoplasmic reticulum to accommodate viral RNA synthesis. J Virol. 2012; 86(5):2474-87. 22190716 10.1128/JVI.06677-11 Maier HJ, Hawes PC, Cottam EM, Mantell J, Verkade P, et al. Infectious bronchitis virus generates spherules from zippered endoplasmic reticulum membranes. mBio. 2013 Oct 22;4(5):e00801-13. PMC3812713 24149513 10.1128/mBio.00801-13 Ulasli M, Verheije MH, de Haan CAM and Reggiori F. Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus. Cell Microbiol. 2010; 12(6):844-61. PMC7159092 20088951 10.1111/j.1462-5822.2010.01437.x de Wilde AH, Snijder EJ, Kikkert Mandvan Hemert MJ. Host factors in coronavirus replication. Curr Top Microbiol Immunol. 2018;419:1-42. PMC7119980 28643204 10.1007/82_2017_25 van der Hoeven B, Oudshoorn D, Koster AJ, Snijder EJ, Kikkert M, et al. Biogenesis and architecture of arterivirus replication organelles. Virus Res. 2016; 220:70-90. PMC7111217 27071852 10.1016/j.virusres.2016.04.001 Zhong Y, Tan YW and Liu DX. Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions. Viruses. 2012 Jun;4(6):980-1010. PMC3397358 22816036 10.3390/v4060980 Naoumov NV. Cyclophilin inhibition as potential therapy for liver diseases. J Hepatol. 2014 Nov;61(5):1166-74. 25048953 10.1016/j.jhep.2014.07.008 Nigro P, Pompilio G and Capogrossi MC. Cyclophilin A: a key player for human disease. Cell Death Dis. 2013 Oct 31;4(10):e888. PMC3920964 24176846 10.1038/cddis.2013.410 Hopkins S and Gallay PA. The role of immunophilins in viral infection. Biochim Biophys Acta. 2015 Oct;1850(10):2103-10. PMC4491039 25445708 10.1016/j.bbagen.2014.11.011 Carbajo-Lozoya J, Ma-Lauer Y, Malešević M, Theuerkorn M, Kahlert V, et al. Human coronavirus NL63 replication is cyclophilin A-dependent and inhibited by non-immunosuppressive cyclosporine A-derivatives including Alisporivir. Virus Res. 2014; 184:44-53. PMC7114444 24566223 10.1016/j.virusres.2014.02.010 de Wilde AH, Falzarano D, Zevenhoven-Dobbe JC, Beugeling C, Fett C, et al. Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model. Virus Res. 2017; 228:7-13. PMC7114565 27840112 10.1016/j.virusres.2016.11.011 de Wilde AH, Raj VS, Oudshoorn D, Bestebroer TM, van Nieuwkoop S, et al. MERS-coronavirus replication induces severe in vitro cytopathology and is strongly inhibited by cyclosporin A or interferon-α treatment. J Gen Virol. 2013; 94(Pt 8):1749-1760. PMC3749523 23620378 10.1099/vir.0.052910-0 de Wilde AH, Zevenhoven-Dobbe JC, van der Meer Y, Thiel V, Narayanan K, et al. Cyclosporin A inhibits the replication of diverse coronaviruses. J Gen Virol. 2011; 92(Pt 11):2542-2548. PMC3352363 21752960 10.1099/vir.0.034983-0 Kim Y, Lee C. Porcine epidemic diarrhea virus induces caspase-independent apoptosis through activation of mitochondrial apoptosis-inducing factor. Virology. 2014; 460-461:180-93. PMC7127720 25010284 10.1016/j.virol.2014.04.040 Tanaka Y, Sato Y, Osawa S, Inoue M, Tanaka S, et al. Suppression of feline coronavirus replication in vitro by cyclosporin A. Vet Res. 2012 Apr 30; 43(1):41. PMC3403912 22546085 10.1186/1297-9716-43-41 von Brunn A. Editorial overview: Engineering for viral resistance. Current Opinion in Virology, 2015. 14. von Brunn A. Editorial overview: Engineering for viral resistance. Curr Opin Virol. 2015; 14:v-vii. PMC7128793 26320757 10.1016/j.coviro.2015.08.009 von Brunn A, Ciesek S, von Brunn B and Carbajo-Lozoya J. Genetic deficiency and polymorphisms of cyclophilin A reveal its essential role for Human Coronavirus 229E replication. Curr Opin Virol. 2015 Oct;14:56-61. PMC7102849 26318518 10.1016/j.coviro.2015.08.004 Tanaka Y, Sato Y and Sasaki T. Feline coronavirus replication is affected by both cyclophilin A and cyclophilin B. J Gen Virol. 2017 Feb; 98(2):190-200. PMC7079567 27902373 10.1099/jgv.0.000663 de Wilde AH, Li Y, van der Meer Y, Vuagniaux G, Lysek R, et al. Cyclophilin inhibitors block arterivirus replication by interfering with viral RNA synthesis. J Virol. 2013 Feb; 87(3):1454-64. PMC3554155 23152531 10.1128/JVI.02078-12 Foss DV, Hochstrasser ML and Wilson RC. Clinical applications of CRISPR‐based genome editing and diagnostics. Transfusion. 2019; 59(4):1389-1399. 30600536 10.1111/trf.15126 Brokowski C and Adli M. CRISPR ethics: moral considerations for applications of a powerful tool. J Mol Biol. 2019 Jan 4; 431(1):88-101. PMC6286228 29885329 10.1016/j.jmb.2018.05.044 Sugarman J. Ethics and germline gene editing. EMBO Rep. 2015 Aug;16(8):879-80. PMC4552475 26138102 10.15252/embr.201540879 Brokowski C. Do CRISPR germline ethics statements cut it? CRISPR J. 2018; 1(2):115-125. PMC6694771 31021208 10.1089/crispr.2017.0024