Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing

References

• Porteus M. Genome editing: a new approach to human therapeutics. Annu Rev Pharmacol Toxicol. 2016;56:163–190. doi:10.1146/annurev-pharmtox-010814-124454
   PubMed Web of Science ®Google Scholar
• Hille F, Charpentier E. CRISPR-cas: biology, mechanisms, and relevance. Philos Trans R Soc B Biol Sci. 2016;371(170):54–77. doi:10.1098/rstb.2015.0496
   Web of Science ®Google Scholar
• Ishino Y, Krupovic M, Forterre P. History of CRISPR-Cas from encounter with a mysterious repeated sequence to genome editing technology. J Bacteriol. 2018;200(7):580–617. doi:10.1128/jb.00580-17
   PubMed Web of Science ®Google Scholar
• Ibrahim AU, Özsöz M, Saeed Z, Tirah G, Gideon O. Genome engineering using the CRISPR Cas9 system. Biomed Pharm Sci. 2019;2(2):1–7.
   Google Scholar
• Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms, and applications. Biochimie. 2015;117:119–128. doi:10.1016/j.biochi.2015.03.025
   PubMed Web of Science ®Google Scholar
• Gaj T, Ss J, Liu J. Genome-editing technologies: principles and applications. Cold Spring Harb Perspect Biol. 2016;8:105–122. doi:10.1101/cshperspect.a023754
   Web of Science ®Google Scholar
• Gaj T, Gersbach CA, Barbas CF. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013;31(7):397–405. doi:10.1016/j.tibtech.2013.04.004
   PubMed Web of Science ®Google Scholar
• Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA – guided. Science. 2012;337(6096):816–822. doi:10.1126/science.1225829
   PubMed Web of Science ®Google Scholar
• The AM. CRISPR tool kit for genome editing and beyond. Nat Commun. 2018;9(1):1911. doi:10.1038/s41467-018-04252-2
   Web of Science ®Google Scholar
• Liu Z, Dong H, Cui Y, Cong L, Zhang D. Application of different types of CRISPR/Cas-based systems in bacteria. Microb Cell Fact. 2020;19(1):1–14. doi:10.1186/s12934-020-01431-z
   Web of Science ®Google Scholar
• Mei Y, Wang Y, Chen H, Sun ZS, Da JX. Recent progress in CRISPR/Cas9 technology. J Genet Genomics. 2016;43(2):63–75. doi:10.1016/j.jgg.2016.01.001
   Web of Science ®Google Scholar
• Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata S, Dohmae N. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell. 2017;176(12):139–148.
   Google Scholar
• Shao M, Xu T, Chen C. The big bang of genome editing technology: development and application of the CRISPR/CAS9 system in disease animal models. Sci Press Zool Res. 2016;37(2):1–11.
   Google Scholar
• Ceasar SA, Rajan V, Prykhozhij SV, Berman JN, Ignacimuthu S. Insert, remove or replace: a highly advanced genome editing system using CRISPR/Cas9. Biochim Biophys Acta Mol Cell. 2016;1863(9):2333–2344. doi:10.1016/j.bbamcr.2016.06.009
   PubMed Web of Science ®Google Scholar
• Jiang F, Doudna JA. CRISPR-Cas9 structures and mechanisms. Annu Rev Biophys. 2017;46(1):505–529. doi:10.1146/annurev-biophys-062215-010822
   PubMed Web of Science ®Google Scholar
• Liu M, Rehman S, Tang X, et al. Methodologies for improving HDR efficiency. Front Genet. 2019;9:1–9. doi:10.3389/fgene.2018.00691
   Web of Science ®Google Scholar
• Yang H, Ren S, Yu S, et al. Methods favoring homology-directed repair choice in response to CRISPR/cas9 induced-double strand breaks. Int J Mol Sci. 2020;21(18):1–20. doi:10.3390/ijms21186461
   Web of Science ®Google Scholar
• Hsu P, Lander E, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. PMC. 2014;157(6):1262–1278. doi:10.1016/j.cell.2014.05.010
   Web of Science ®Google Scholar
• Jackson M, Marks L, May GHW, Wilson JB. The genetic basis of disease. Essays Biochem. 2018;62(5):643–723. doi:10.1042/ebc20170053
   PubMed Web of Science ®Google Scholar
• Ma CC, Wang ZL, Xu T, He ZY, Wei YQ. The approved gene therapy drugs worldwide: from 1998 to 2019. Biotechnol Adv. 2020;40:107502. doi:10.1016/j.biotechadv.2019.107502
   PubMed Web of Science ®Google Scholar
• Pandey VK, Tripathi A, Bhushan R. Application of CRISPR/Cas9 genome editing in genetic disorders: a systematic review up to date. J Genet Syndr Gene Ther. 2017;08(02):57–74. doi:10.4172/2157-7412.1000321
   Google Scholar
• Cai L, Fisher AL, Huang H, Xie Z. CRISPR-mediated genome editing and human diseases. Genes Dis. 2016;3(4):244–251. doi:10.1016/j.gendis.2016.07.003
   Google Scholar
• Frangoul H, Altshuler D, Cappellini MD, et al. CRISPR-Cas9 gene editing for sickle cell disease and β-thalassemia. N Engl J Med. 2021;384(3):252–260. doi:10.1056/nejmoa2031054
   PubMed Web of Science ®Google Scholar
• Shah F, Dwivedi M. Pathophysiology and recent therapeutic insights of sickle cell disease. Ann Hematol. 2020;99(5):925–935. doi:10.1007/s00277-020-03977-9
   PubMed Web of Science ®Google Scholar
• Demirci S, Leonard A. CRISPR/Cas9 for sickle cell disease: applications, future possibilities, and challenges. Adv Exp Med Biol. 2019;1144:37–52. doi:10.1007/5584_2018_331
   Web of Science ®Google Scholar
• Ali M, Abbasalipour M, Concordet J, et al. Expression analysis data of BCL11A and g -globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion. Sci Direct. 2020;28:1049–1074. doi:10.1016/j.dib.2019.104974
   Web of Science ®Google Scholar
• Dame C, Juul SE. The switch from fetal to adult hemoglobin. Clin Perinatol. 2013;27(3):507–526. doi:10.1016/S0095-5108(05)70036-1
   Web of Science ®Google Scholar
• Esrick EB, Lehmann LE, Biffi A, et al. Post-transcriptional genetic silencing of BCL11A to treat sickle cell disease. N Engl J Med. 2021;384(3):205–215. doi:10.1056/nejmoa2029392
   PubMed Web of Science ®Google Scholar
• Conese M, Beccia E, Castellani S. The long and winding road: stem cells for cystic fibrosis. Expert Opin Biol Ther. 2018;18(3):1–12. doi:10.1080/14712598.2018.1413087
   Web of Science ®Google Scholar
• Csanády L, Vergani P, Gadsby DC. Structure, gating, and regulation of the CFTR anion channel. Physiol Rev. 2019;99(1):707–738. doi:10.1152/physrev.00007.2018
   PubMed Web of Science ®Google Scholar
• Somayaji R, Nichols DP, Bell SC. Cystic fibrosis–Ten promising therapeutic approaches in the current era of care. Expert Opin Investig Drugs. 2020;29(10):1107–1124. doi:10.1080/13543784.2020.1805733
   PubMed Web of Science ®Google Scholar
• Bergeron C, Cantin AM. New therapies to correct the cystic fibrosis basic defect. Int J Mol Sci. 2021;22(12):1–21. doi:10.3390/ijms22126193
   Web of Science ®Google Scholar
• Schwank G, Koo BK, Sasselli V, et al. Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell. 2013;13(6):653–658. doi:10.1016/j.stem.2013.11.002
   PubMed Web of Science ®Google Scholar
• Li HL, Fujimoto N, Sasakawa N, et al. Precise correction of the dystrophin gene in Duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9. Stem Cell Reports. 2015;4(1):143–154. doi:10.1016/j.stemcr.2014.10.013
   PubMed Web of Science ®Google Scholar
• Fortunato F, Rossi R, Falzarano MS, Ferlini A. Innovative therapeutic approaches for DMD. J Clin Med. 2021;10(4):820. doi:10.3390/jcm10040820
   Web of Science ®Google Scholar
• Shimizu-Motohashi Y, Komaki H, Motohashi N, Takeda S, Yokota T, Aoki Y. Restoring dystrophin expression in Duchenne muscular dystrophy: current status of therapeutic approaches. J Pers Med. 2019;9(1):1–14. doi:10.3390/jpm9010001
   PubMed Web of Science ®Google Scholar
• Mollanoori H, Rahmati Y, Hassani B, Havasi Mehr M, Teimourian S. Promising therapeutic approaches using CRISPR/Cas9 genome editing technology in the treatment of Duchenne muscular dystrophy. Genes Dis. 2021;8(2):146–156. doi:10.1016/j.gendis.2019.12.007
   Web of Science ®Google Scholar
• Kantor A, Mcclements ME. CRISPR-Cas9 DNA base-editing and prime-editing. Int J Mol Sci. 2020;21(17):6240. doi:10.3390/ijms21176240
   PubMed Web of Science ®Google Scholar
• Yang L, Tang J, Ma X, et al. Progression and application of CRISPR-Cas genomic editors. Methods. 2021. doi:10.1016/j.ymeth.2021.03.013
   Web of Science ®Google Scholar
• Adlat S, Hayel F, Yang P, et al. CRISPR-mediated base editing in mice using cytosine deaminase base editor 4. Electron J Biotechnol. 2021;52:59–66. doi:10.1016/j.ejbt.2021.04.010
   Web of Science ®Google Scholar
• Liu Z, Chen S, Jia Y, et al. Efficient and high-fidelity base editor with expanded PAM compatibility for cytidine dinucleotide. Sci China Life Sci. 2021;64(8):1355–1367. doi:10.1007/s11427-020-1775-2
   Web of Science ®Google Scholar
• Lv X, Qiu K, Tu T, et al. Development of a simple and quick method to assess base editing in human cells. Mol Ther - Nucleic Acids. 2020;20:580–588. doi:10.1016/j.omtn.2020.03.004
   Google Scholar
• Matsoukas IG. Prime editing: genome editing for rare genetic diseases without double-strand breaks or donor DNA. Front Genet. 2020;11(528):1–6. doi:10.3389/fgene.2020.00528
   PubMed Web of Science ®Google Scholar
• Schole J, Harrison PT, Harrison PT. Prime editing – an update on the field. Gene Ther. 2021. doi:10.1038/s41434-021-00263-9
   Web of Science ®Google Scholar
• Stadtmauer EA, Fraietta JA, Davis MM, et al. CRISPR-engineered T cells in patients with refractory cancer. Science. 2020;367(6481):777–780. doi:10.1126/science.aba7365
   Web of Science ®Google Scholar
• Strich JR, Chertow DS. CRISPR-cas biology and its application to infectious diseases. J Clin Microbiol. 2018;57(4):1307–1318. doi:10.1128/jcm.01307-18
   Web of Science ®Google Scholar
• Yin C, Zhang T, Qu X, et al. In vivo excision of HIV-1 provirus by saCas9 and multiplex single-guide RNAs in animal models. Mol Ther. 2017;25(5):1168–1186. doi:10.1016/j.ymthe.2017.03.012
   PubMed Web of Science ®Google Scholar
• Liu Z, Chen S, Jin X, et al. Genome editing of the HIV co-receptors CCR5 and CXCR4 by CRISPR-Cas9 protects CD4+ T cells from HIV-1 infection. Cell Biosci. 2017;7(1):1–15. doi:10.1186/s13578-017-0174-2
   Web of Science ®Google Scholar
• Adhikari P, Poudel M. CRISPR-Cas9 in agriculture: approaches, applications, future perspectives, and associated challenges. Malaysian J Halal Res. 2020;3(1):6–16. doi:10.2478/mjhr-2020-0002
   Google Scholar
• Dominguez A, Lim W, Lei Q. Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation. Physiol Behav. 2016;176(1):100–106. doi:10.1038/nrm.2015.2
   Web of Science ®Google Scholar
• Anton T, Karg E, Bultmann S. Applications of the CRISPR/Cas system beyond gene editing. Biol Methods Protoc. 2018;3(1):1–10. doi:10.1093/biomethods/bpy002
   Google Scholar
• Kotagama OW, Jayasinghe CD, Abeysinghe T. Era of genomic medicine: a narrative review on CRISPR technology as a potential therapeutic tool for human diseases. Biomed Res Int. 2019;201:1–15. doi:10.1155/2019/1369682
   Web of Science ®Google Scholar
• Charlesworth C, Deshpande P, Dever D, et al. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat Med. 2020;25(2):249–254. doi:10.1101/243345
   Web of Science ®Google Scholar
• Yip BH. Recent Advances in CRISPR/Cas9 delivery strategies. Biomolecules. 2020;10(6):839. doi:10.3390/biom10060839
   PubMed Web of Science ®Google Scholar
• Zhang S, Shen J, Li D, Cheng Y. Strategies in the delivery of Cas9 ribonucleoprotein for CRISPR/Cas9 genome editing. Theranostics. 2020;11(2):614–648. doi:10.7150/thno.47007
   Web of Science ®Google Scholar
• Fajrial AK, He QQ, Wirusanti NI, Slansky JE, Ding X. A review of emerging physical transfection methods for CRISPR/Cas9-mediated gene editing. Theranostics. 2020;10(12):5532–5549. doi:10.7150/thno.43465
   Web of Science ®Google Scholar
• Lino CA, Harper JC, Carney JP, Timlin JA. Delivering CRISPR: a review of the challenges and approaches. Drug Deliv. 2018;25(1):1234–1257. doi:10.1080/10717544.2018.1474964
   PubMed Web of Science ®Google Scholar
• Shah A, Aftab S, Nisar J, Naeem M, Jan F. Lipid- and polymer-based nanoparticle systems for the delivery of CRISPR/ Cas9. J Drug Deliv Sci Technol. 2021;65:102728. doi:10.1016/j.jddst.2021.102426
   Web of Science ®Google Scholar
• Xu X, Wan T, Xin H, et al. Delivery of CRISPR/Cas9 for therapeutic genome editing. J Gene Med. 2019;21(7):1–18. doi:10.1002/jgm.3107
   Web of Science ®Google Scholar
• Duan L, Ouyang K, Xu X, et al. Nanoparticle delivery of CRISPR/Cas9 for genome editing. Front Genet. 2021:12. doi:10.3389/fgene.2021.673286.
   Web of Science ®Google Scholar
• Behr M, Zhou J, Xu B, Zhang H. In vivo delivery of CRISPR-Cas9 therapeutics: progress and challenges. Acta Pharm Sin B. 2021. doi:10.1016/j.apsb.2021.05.020
   Web of Science ®Google Scholar
• Ali A, Aslam S, Tabasum S, Aslam R. Overview of delivery of CRISPR/Cas systems, its types, and role in genome editing and immunotherapy. J RNA Genomics. 2021;17:665–672.
   Google Scholar
• Horodecka K, Düchler M. Crispr/cas9: principle, applications, and delivery through extracellular vesicles. Int J Mol Sci. 2021;22(11):6072. doi:10.3390/ijms22116072
   PubMed Web of Science ®Google Scholar
• Zhang XH, Tee LY, Wang XG, Huang QS, Yang SH. Off-target effects in CRISPR/Cas9-mediated genome engineering. Mol Ther-Nucleic Acids. 2015;4(11):2162–2531. doi:10.1038/mtna.2015.37
   Google Scholar
• Chen S, Yao Y, Zhang Y, Fan G. CRISPR system: discovery, development and off-target detection. Cell Signal. 2020;70:109577. doi:10.1016/j.cellsig.2020.109577
   PubMed Web of Science ®Google Scholar
• Han HA, Kah J, Pang S, Soh B. Mitigating off-target effects in CRISPR/Cas9-mediated in vivo gene editing. J Mol Med. 2020;98(5):615–632. doi:10.1007/s00109-020-01893-z
   PubMed Web of Science ®Google Scholar
• Manghwar H, Li B, Ding X, et al. CRISPR/Cas systems in genome editing: methodologies and tools for sgRNA design, off-target evaluation, and strategies to mitigate off-target effects. Adv Sci. 2020;7(6):1902312. doi:10.1002/advs.201902312
   Web of Science ®Google Scholar
• Naeem M, Majeed S, Hoque MZ, Ahmad I. Latest developed strategies to minimize the off-target effects in CRISPR-Cas-mediated genome editing. Cells. 2020;9(7):1–23. doi:10.3390/cells9071608
   Web of Science ®Google Scholar
• Collias D, Beisel CL. CRISPR technologies and the search for the PAM-free nuclease. Nat Commun. 2021;12(1):1–12. doi:10.1038/s41467-020-20633-y
   Web of Science ®Google Scholar
• Wang Q, Liu J, Janssen JM, Le Bouteiller M, Frock RL, Gonçalves MAFV. Precise and broad scope genome editing based on high-specificity Cas9 nickases. Nucleic Acids Res. 2021;49(2):1173–1198. doi:10.1093/nar/gkaa1236
   Web of Science ®Google Scholar
• Paul B, Montoya G. CRISPR-Cas12a: functional overview and applications. Biomed J. 2020;43(1):8–17. doi:10.1016/j.bj.2019.10.005
   PubMed Web of Science ®Google Scholar
• Yılmaz ŞG. Genome editing technologies: CRISPR, LEAPER, RESTORE, ARCUT, SATI, AND RESCUE. EXCL J. 2021;20:19–45. doi:10.17179/excli2020-3070
   Web of Science ®Google Scholar
• Morisaka H, Yoshimi K, Okuzaki Y, et al. CRISPR-Cas3 induces broad and unidirectional genome editing in human cells. Nat Commun. 2019;10(1). doi:10.1038/s41467-019-13226-x
   Web of Science ®Google Scholar
• Liu Q, Zhang H, Huang X. Anti-CRISPR proteins targeting the CRISPR-Cas system enrich the toolkit for genetic engineering. FEBS J. 2020;287(4):626–644. doi:10.1111/febs.15139
   Web of Science ®Google Scholar
• A S, Tanuj G. Anti-CRISPR: a defense strategy of bacteriophages against bacteria. J Entomol Zool Stud. 2020;8(6):1003–1010. doi:10.22271/j.ento.2020.v8.i6n.7968
   Google Scholar