Gene editing technology, which allows for precise modifications to an organism’s genome, has emerged as a transformative tool in genetic engineering. This review introduces the fundamental concepts and mechanisms of gene editing, with a particular emphasis on CRISPR-Cas systems. The principles and methods used in the development and optimization of gene editing tools, including base editing and prime editing, are discussed. The review also summarizes the applications of gene editing in medicine, agriculture, and biotechnology, highlighting its potential to address complex biological challenges. Finally, the review outlines the current challenges and ethical considerations in the field of gene editing research.
References
[1]
Pacesa, M., Pelea, O. and Jinek, M. (2024) Past, Present, and Future of CRISPR Genome Editing Technologies. Cell, 187, 1076-1100. https://doi.org/10.1016/j.cell.2024.01.042
[2]
Chehelgerdi, M., Chehelgerdi, M., KhorramianGhahfarokhi, M., Shafieizadeh, M., Mahmoudi, E., Eskandari, F., et al. (2024) Correction: Comprehensive Review of Crispr-Based Gene Editing: Mechanisms, Challenges, and Applications in Cancer Therapy. MolecularCancer, 23, Article No. 43. https://doi.org/10.1186/s12943-024-01961-9
[3]
Christian, M., Cermak, T., Doyle, E.L., Schmidt, C., Zhang, F., Hummel, A., et al. (2010) Targeting DNA Double-Strand Breaks with TAL Effector Nucleases. Genetics, 186, 757-761. https://doi.org/10.1534/genetics.110.120717
[4]
Joung, J.K. and Sander, J.D. (2012) Talens: A Widely Applicable Technology for Targeted Genome Editing. NatureReviewsMolecularCellBiology, 14, 49-55. https://doi.org/10.1038/nrm3486
[5]
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A. and Charpentier, E. (2012) A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science, 337, 816-821. https://doi.org/10.1126/science.1225829
[6]
Kim, D., Luk, K., Wolfe, S.A. and Kim, J. (2019) Evaluating and Enhancing Target Specificity of Gene-Editing Nucleases and Deaminases. AnnualReviewofBiochemistry, 88, 191-220. https://doi.org/10.1146/annurev-biochem-013118-111730
[7]
Zetsche, B., Gootenberg, J.S., Abudayyeh, O.O., Slaymaker, I.M., Makarova, K.S., Essletzbichler, P., et al. (2015) Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 Crispr-Cas System. Cell, 163, 759-771. https://doi.org/10.1016/j.cell.2015.09.038
[8]
Kleinstiver, B.P., Sousa, A.A., Walton, R.T., Tak, Y.E., Hsu, J.Y., Clement, K., et al. (2019) Engineered Crispr-cas12a Variants with Increased Activities and Improved Targeting Ranges for Gene, Epigenetic and Base Editing. NatureBiotechnology, 37, 276-282. https://doi.org/10.1038/s41587-018-0011-0
Kaminski, M.M., Abudayyeh, O.O., Gootenberg, J.S., Zhang, F. and Collins, J.J. (2021) CRISPR-Based Diagnostics. NatureBiomedicalEngineering, 5, 643-656. https://doi.org/10.1038/s41551-021-00760-7
[11]
Komor, A.C., Kim, Y.B., Packer, M.S., Zuris, J.A. and Liu, D.R. (2016) Programmable Editing of a Target Base in Genomic DNA without Double-Stranded DNA Cleavage. Nature, 533, 420-424. https://doi.org/10.1038/nature17946
[12]
Gaudelli, N.M., Komor, A.C., Rees, H.A., Packer, M.S., Badran, A.H., Bryson, D.I., et al. (2017) Programmable Base Editing of A∙T to G∙C in Genomic DNA without DNA Cleavage. Nature, 551, 464-471. https://doi.org/10.1038/nature24644
[13]
Anzalone, A.V., Randolph, P.B., Davis, J.R., Sousa, A.A., Koblan, L.W., Levy, J.M., et al. (2019) Search-and-Replace Genome Editing without Double-Strand Breaks or Donor DNA. Nature, 576, 149-157. https://doi.org/10.1038/s41586-019-1711-4
[14]
Yu, X., Huo, G., Yu, J., Li, H. and Li, J. (2023) Prime Editing: Its Systematic Optimization and Current Applications in Disease Treatment and Agricultural Breeding. InternationalJournalofBiologicalMacromolecules, 253, Article ID: 127025. https://doi.org/10.1016/j.ijbiomac.2023.127025
[15]
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., et al. (2007) CRISPR Provides Acquired Resistance against Viruses in Prokaryotes. Science, 315, 1709-1712. https://doi.org/10.1126/science.1138140
[16]
Nishimasu, H., Ran, F.A., Hsu, P.D., Konermann, S., Shehata, S.I., Dohmae, N., et al. (2014) Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Cell, 156, 935-949. https://doi.org/10.1016/j.cell.2014.02.001
[17]
Lieber, M.R. (2010) The Mechanism of Double-Strand DNA Break Repair by the Nonhomologous DNA End-Joining Pathway. AnnualReviewofBiochemistry, 79, 181-211. https://doi.org/10.1146/annurev.biochem.052308.093131
[18]
Attar, N. (2015) An Intriguing New Bacterial Phylum. NatureReviewsMicrobiology, 13, 459-459. https://doi.org/10.1038/nrmicro3534
[19]
Pickar-Oliver, A. and Gersbach, C.A. (2019) The Next Generation of Crispr-cas Technologies and Applications. NatureReviewsMolecularCellBiology, 20, 490-507. https://doi.org/10.1038/s41580-019-0131-5
[20]
Janik, E., Niemcewicz, M., Ceremuga, M., Krzowski, L., Saluk-Bijak, J. and Bijak, M. (2020) Various Aspects of a Gene Editing System—CRISPR-Cas9. InternationalJournalofMolecularSciences, 21, Article No. 9604. https://doi.org/10.3390/ijms21249604
[21]
Sternberg, S.H., LaFrance, B., Kaplan, M. and Doudna, J.A. (2015) Conformational Control of DNA Target Cleavage by CRISPR-Cas9. Nature, 527, 110-113. https://doi.org/10.1038/nature15544
[22]
Fiflis, D.N., Rey, N.A., Venugopal-Lavanya, H., Sewell, B., Mitchell-Dick, A., Clements, K.N., et al. (2024) Repurposing Crispr-Cas13 Systems for Robust mRNA Trans-splicing. NatureCommunications, 15, Article No. 2325. https://doi.org/10.1038/s41467-024-46172-4
[23]
Kick, L.M., von Wrisberg, M., Runtsch, L.S. and Schneider, S. (2022) Structure and Mechanism of the RNA Dependent Rnase Cas13a from Rhodobacter Capsulatus. CommunicationsBiology, 5, Article No. 71. https://doi.org/10.1038/s42003-022-03025-4
[24]
Kim, S., Yuan, J.B., Woods, W.S., Newton, D.A., Perez-Pinera, P. and Song, J.S. (2023) Chromatin Structure and Context-Dependent Sequence Features Control Prime Editing Efficiency. FrontiersinGenetics, 14, Article ID: 1222112. https://doi.org/10.3389/fgene.2023.1222112
[25]
Vakulskas, C.A., et al. (2018) A High-Fidelity Cas9 Mutant Delivered as a Ribonucleoprotein Complex Enables Efficient Gene Editing in Human Hematopoietic Stem and Progenitor Cells. Nature Medicine, 24, 1216-1224. https://doi.org/10.1038/s41591-018-0137-0
[26]
Musunuru, K., Chadwick, A.C., Mizoguchi, T., Garcia, S.P., DeNizio, J.E., Reiss, C.W., et al. (2021) InVivo CRISPR Base Editing of PCSK9 Durably Lowers Cholesterol in Primates. Nature, 593, 429-434. https://doi.org/10.1038/s41586-021-03534-y
[27]
Koeppel, J., Weller, J., Peets, E.M., Pallaseni, A., Kuzmin, I., Raudvere, U., et al. (2023) Prediction of Prime Editing Insertion Efficiencies Using Sequence Features and DNA Repair Determinants. NatureBiotechnology, 41, 1446-1456. https://doi.org/10.1038/s41587-023-01678-y
[28]
Petrova, I.O. and Smirnikhina, S.A. (2023) The Development, Optimization and Future of Prime Editing. InternationalJournalofMolecularSciences, 24, Article No. 17045. https://doi.org/10.3390/ijms242317045
[29]
Zeng, H., Daniel, T.C., Lingineni, A., Chee, K., Talloo, K. and Gao, X. (2024) Recent Advances in Prime Editing Technologies and Their Promises for Therapeutic Applications. CurrentOpinioninBiotechnology, 86, Article ID: 103071. https://doi.org/10.1016/j.copbio.2024.103071
[30]
Doudna, J.A. and Charpentier, E. (2014) The New Frontier of Genome Engineering with CRISPR-Cas9. Science, 346, Article ID: 1258096. https://doi.org/10.1126/science.1258096
[31]
Frangoul, H., Altshuler, D., Cappellini, M.D., Chen, Y., Domm, J., Eustace, B.K., et al. (2021) CRISPR-Cas9 Gene Editing for Sickle Cell Disease and Β-Thalassemia. NewEnglandJournalofMedicine, 384, 252-260. https://doi.org/10.1056/nejmoa2031054
[32]
Tabebordbar, M., Zhu, K., Cheng, J.K.W., Chew, W.L., Widrick, J.J., Yan, W.X., et al. (2016) InVivo Gene Editing in Dystrophic Mouse Muscle and Muscle Stem Cells. Science, 351, 407-411. https://doi.org/10.1126/science.aad5177
[33]
Huang, Y., Xuan, H., Yang, C., Guo, N., Wang, H., Zhao, J., et al. (2019) GmHsp90A2 Is Involved in Soybean Heat Stress as a Positive Regulator. PlantScience, 285, 26-33. https://doi.org/10.1016/j.plantsci.2019.04.016
[34]
Chohan, K.L., Siegler, E.L. and Kenderian, S.S. (2023) CAR-T Cell Therapy: The Efficacy and Toxicity Balance. CurrentHematologicMalignancyReports, 18, 9-18. https://doi.org/10.1007/s11899-023-00687-7
[35]
Dimitri, A., Herbst, F. and Fraietta, J.A. (2022) Engineering the Next-Generation of CAR T-Cells with CRISPR-Cas9 Gene Editing. MolecularCancer, 21, Article No. 78. https://doi.org/10.1186/s12943-022-01559-z
[36]
Hockemeyer, D. and Jaenisch, R. (2016) Induced Pluripotent Stem Cells Meet Genome Editing. CellStemCell, 18, 573-586. https://doi.org/10.1016/j.stem.2016.04.013
[37]
Wang, F., Wang, C., Liu, P., Lei, C., Hao, W., Gao, Y., et al. (2016) Enhanced Rice Blast Resistance by Crispr/cas9-Targeted Mutagenesis of the ERF Transcription Factor Gene Oserf922. PLOSONE, 11, e0154027. https://doi.org/10.1371/journal.pone.0154027
[38]
Zsögön, A., Čermák, T., Naves, E.R., Notini, M.M., Edel, K.H., Weinl, S., et al. (2018) De Novo Domestication of Wild Tomato Using Genome Editing. NatureBiotechnology, 36, 1211-1216. https://doi.org/10.1038/nbt.4272
[39]
Le, Y., Zhang, M., Wu, P., Wang, H. and Ni, J. (2024) Biofuel Production from Lignocellulose via Thermophile-Based Consolidated Bioprocessing. EngineeringMicrobiology, 4, Article ID: 100174. https://doi.org/10.1016/j.engmic.2024.100174
[40]
Mescouto, V.A.D., Ferreira, L.D.C., Paiva, R.D.J., Oliveira, D.T.D., de Oliveira, M.S., Rocha Filho, G.N.D., et al. (2024) Review of Recent Advances in Improvement Strategies for Biofuels Production from Cyanobacteria. Heliyon, 10, e40293. https://doi.org/10.1016/j.heliyon.2024.e40293
[41]
Baeshen, N.A., Baeshen, M.N., Sheikh, A., Bora, R.S., Ahmed, M.M.M., Ramadan, H.A.I., et al. (2014) Cell Factories for Insulin Production. MicrobialCellFactories, 13, Article No. 141. https://doi.org/10.1186/s12934-014-0141-0
[42]
Diep, P., Mahadevan, R. and Yakunin, A.F. (2018) Heavy Metal Removal by Bioaccumulation Using Genetically Engineered Microorganisms. FrontiersinBioengineeringandBiotechnology, 6, Article No. 157. https://doi.org/10.3389/fbioe.2018.00157
[43]
Modell, A.E., Lim, D., Nguyen, T.M., Sreekanth, V. and Choudhary, A. (2022) Crispr-based Therapeutics: Current Challenges and Future Applications. TrendsinPharmacologicalSciences, 43, 151-161. https://doi.org/10.1016/j.tips.2021.10.012
[44]
Wang, D., Tai, P.W.L. and Gao, G. (2019) Adeno-Associated Virus Vector as a Platform for Gene Therapy Delivery. NatureReviewsDrugDiscovery, 18, 358-378. https://doi.org/10.1038/s41573-019-0012-9
[45]
Huang, X., et al. (2024) A Brain-Wide CRISPR Screen Identifies Neuronal Circuits Regulating Sleep. Cell, 187, 398-412.
[46]
Yin, et al. (2023) Efficient Genome Editing in Plants Using a CRISPR/Cas9 System with tRNA-sgRNA Fusions. ScienceAdvances, 9, eadf4561.
[47]
Stadtmauer, E.A., Fraietta, J.A., Davis, M.M., Cohen, A.D., Weber, K.L., Lancaster, E., et al. (2020) CRISPR-Engineered T Cells in Patients with Refractory Cancer. Science, 367, eaba7365. https://doi.org/10.1126/science.aba7365
[48]
Yin, H., Song, C., Dorkin, J.R., Zhu, L.J., Li, Y., Wu, Q., et al. (2016) Therapeutic Genome Editing by Combined Viral and Non-Viral Delivery of CRISPR System Components inVivo. NatureBiotechnology, 34, 328-333. https://doi.org/10.1038/nbt.3471
[49]
Rim, J.H., et al. (2021) CRISPR-Cas9 inVivo Gene Editing for Transthyretin Amyloidosis. The New England Journal of Medicine, 385, 1722.
[50]
Donev, E.N., Derba‐Maceluch, M., Yassin, Z., Gandla, M.L., Pramod, S., Heinonen, E., et al. (2023) Field Testing of Transgenic Aspen from Large Greenhouse Screening Identifies Unexpected Winners. PlantBiotechnologyJournal, 21, 1005-1021. https://doi.org/10.1111/pbi.14012
[51]
Al-Osaimi, H.M., Kanan, M., Marghlani, L., Al-Rowaili, B., Albalawi, R., Saad, A., et al. (2024) A Systematic Review on Malaria and Dengue Vaccines for the Effective Management of These Mosquito Borne Diseases: Improving Public Health. HumanVaccines&Immunotherapeutics, 20, Article ID: 2337985. https://doi.org/10.1080/21645515.2024.2337985
[52]
Wedell, N., Price, T.A.R. and Lindholm, A.K. (2019) Gene Drive: Progress and Prospects. ProceedingsoftheRoyalSocietyB: BiologicalSciences, 286, Article ID: 20192709. https://doi.org/10.1098/rspb.2019.2709
[53]
Adolfi, A., Gantz, V.M., Jasinskiene, N., Lee, H., Hwang, K., Terradas, G., et al. (2020) Efficient Population Modification Gene-Drive Rescue System in the Malaria Mosquito Anopheles stephensi. NatureCommunications, 11, Article No. 5553. https://doi.org/10.1038/s41467-020-19426-0
[54]
Kyrou, K., Hammond, A.M., Galizi, R., Kranjc, N., Burt, A., Beaghton, A.K., et al. (2018) A CRISPR-Cas9 Gene Drive Targeting Doublesex Causes Complete Population Suppression in Caged Anopheles Gambiae Mosquitoes. NatureBiotechnology, 36, 1062-1066. https://doi.org/10.1038/nbt.4245
[55]
Carballar-Lejarazú, R. and James, A.A. (2017) Population Modification of Anopheline Species to Control Malaria Transmission. PathogensandGlobalHealth, 111, 424-435. https://doi.org/10.1080/20477724.2018.1427192
[56]
Li, M., Yang, T., Kandul, N.P., Bui, M., Gamez, S., Raban, R., et al. (2020) Development of a Confinable Gene Drive System in the Human Disease Vector Aedes Aegypti. eLife, 9, e51701. https://doi.org/10.7554/elife.51701
[57]
Li, T., Yang, Y., Qi, H., Cui, W., Zhang, L., Fu, X., et al. (2023) Crispr/cas9 Therapeutics: Progress and Prospects. SignalTransductionandTargetedTherapy, 8, Article No. 36. https://doi.org/10.1038/s41392-023-01309-7
[58]
Yin, H., Kauffman, K.J. and Anderson, D.G. (2017) Delivery Technologies for Genome Editing. NatureReviewsDrugDiscovery, 16, 387-399. https://doi.org/10.1038/nrd.2016.280
[59]
Baylis, F. (2019) Altered Inheritance: CRISPR and the Ethics of Human Genome Editing. Science, 366, 165-166.
[60]
International Society for Stem Cell Research (2021) ISSCR Guidelines for Stem Cell Research and Clinical Translation.
[61]
Cyranoski, D. (2019) The CRISPR-Baby Scandal: What’s Next for Human Gene-Editing. Nature, 566, 440-442. https://doi.org/10.1038/d41586-019-00673-1
[62]
Pew Research Center (2023) Public Views on Gene Editing for Babies and Disease Treatment.
[63]
Saha, K., Hurlbut, J.B., Jasanoff, S., Ahmed, A., Appiah, A., Bartholet, E., et al. (2018) Building Capacity for a Global Genome Editing Observatory: Institutional Design. Trends in Biotechnology, 36, 741-743. https://doi.org/10.1016/j.tibtech.2018.04.008
[64]
U.S. Food and Drug Administration (2023) BLA 125746: Casgevy (exagamglogene autotemcel).
[65]
Knoppers, B.M. and Chadwick, R. (2005) Human Genetic Research: Emerging Trends in Ethics. NatureReviewsGenetics, 6, 75-79. https://doi.org/10.1038/nrg1505
[66]
Rozas, P., Kessi-Pérez, E.I. and Martínez, C. (2022) Genetically Modified Organisms: Adapting Regulatory Frameworks for Evolving Genome Editing Technologies. BiologicalResearch, 55, Article No. 31. https://doi.org/10.1186/s40659-022-00399-x