CRISPR/Cas9-mediated genome editing: from basic research to gene therapy
DOI:
https://doi.org/10.18203/2320-6012.ijrms20241589Keywords:
Gene therapy, CRISPR/Cas9, CAR-T cells, Endonucleases, Homology-directed repair, Non-homologous end joining, Gene knock-out, Gene knock-in, Clinical trials, EthicsAbstract
CRISPR/Cas9 mediated genome editing is one of the most significant molecular tools discovered to edit the desired genes. It has ushered in a new era of novel possibilities of gene therapy. CRISPR/Cas9 system was originally observed as a part of the adaptive immune system in bacteria. It later on was adapted to carry precise and targeted alterations to the DNA in human cells to be used for gene therapy to correct genetic disorders and treat various severe diseases associated with the genetic changes. Besides this, the CRISPR/Cas9 system has been employed in pharmacogenomics to develop new drugs based on the patient’s genes, in modifying the organisms for research and even for diagnostic purposes in developing CRISPR based COVID-9 test. The recent approval of a CRISPR/Cas9 cellular gene therapy by FDA named “Casgevy” to treat sickle cell anemia is a testimonial to the potentials of CRISPR/Cas9 system in developing innovative gene therapies. This review details the mechanisms of CRISPR/Cas9 gene editing and its utilization in the ongoing clinical trials in the treatment of not only the monogenic disorders like sickle cell disease, thalassemia, and genetic blindness but also in treating multi-factorial diseases like cancers, cardiac diseases, diabetes, autoimmune diseases, viral infections such as human immunodeficiency virus (HIV) etc. An attempt has also been made to discuss the various limitations, challenges and ethical frameworks encompassing CRISPR/Cas9 based gene therapy in clinical settings.
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References
Blaese RM, Culver KW, Miller AD, Carter CS, Fleisher T, Clerici M, et al. T lymphocyte-directed gene therapy for ADASCID: Initial trial results after 4 years. Science. 1995;70:475-80.
Bordignon C, Notarangelo LD, Nobili N, Ferrari G, Casorati G, Panina P, et al. Gene therapy in peripheral blood lymphocytes and bone marrow for ADA- immunodeficient patients. Science. 1995;270:470-5.
Verma IM. A tumultuous year for gene therapy. Molecular Therapy. 2000;2(5):415-6.
Sibbald B. Death but one unintended consequence of gene-therapy trial. CMAJ. 2001;164:1612.
Hacein-Bey-Abina S, Von Kalle C, Schmidt M, Mccormack MP, Wulffraat N, Leboulch P, et al. LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science. 2003;302:415-9.
Herzog RW. Gene therapy for SCID-X1: round 2. Mol Ther. 2010;18:1891.
Lukashev AN, Zamyatnin AA. Viral vectors for gene therapy: current state and clinical perspectives. Biochemistry (Moscow). 2016;81:700-8.
Liu C, Zhang L, Zhu W, Guo R, Sun H, Chen X, Deng N. Barriers and strategies of cationic liposomes for cancer gene therapy. Molecular Therapy-Methods & Clinical Development. 2020;18:751-64.
Soleimani M, Al Zaabi AM, Merheb M, Matar R. Nanoparticles in gene therapy. Int J Integr Biol. 2016;17(1).
Schaffert D, Wagner E. Gene therapy progress and prospects: synthetic polymer-based systems. Gene therapy. 2008;15(16):1131-8.
Humbert O, Davis L, Maizels N. Targeted gene therapies: tools, applications, optimization. Crit Rev Biochem Mol Biol. 2012;47(3):264-81.
Niu J, Zhang B, Chen H. Applications of TALENs and CRISPR/Cas9 in human cells and their potentials for gene therapy. Mol Biotechnol. 2014;56:681-8.
Carroll D. Progress and prospects: zinc-finger nucleases as gene therapy agents. Gene Therapy. 2008;15(22):1463-8.
Zhang B. CRISPR/Cas gene therapy. J Cellular Physiol. 2021;236(4):2459-81.
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):10-128.
Strzyz P. CRISPR–Cas9 wins nobel. Nat Rev Mol Cell Biol. 2020;21(12):714.
Mota DS, Marques JM, Guimarães JM, Mariúba LA. CRISPR/Cas Class 2 systems and their applications in biotechnological processes. Genet Mol Res. 2020;20:1-10.
Xu Y, Li Z. CRISPR-Cas systems: Overview, innovations and applications in human disease research and gene therapy. Computational Structural Biotechnol J. 2020;18:2401-15.
Leonard A, Tisdale JF. A new frontier: FDA approvals for gene therapy in sickle cell disease. Mol Therapy. 2024;32(2):264-7.
Uddin F, Rudin CM, Sen T. CRISPR gene therapy: applications, limitations, and implications for the future. Front Oncol. 2020;10:1387.
Charpentier E. CRISPR‐Cas9: how research on a bacterial RNA‐guided mechanism opened new perspectives in biotechnology and biomedicine. EMBO Mol Med. 2015;7(4):363-5.
Garcia-Doval C, Jinek M. Molecular architectures and mechanisms of Class 2 CRISPR-associated nucleases. Curr Opinion Structural Biol. 2017;47:157-66.
Jiang F, Doudna JA. CRISPR–Cas9 structures and mechanisms. Annual Rev Biophysics. 2017;46:505-29.
Barman A, Deb B, Chakraborty S. A glance at genome editing with CRISPR–Cas9 technology. Curr Genetics. 2020;66:447-62.
Janik E, Niemcewicz M, Ceremuga M, Krzowski L, Saluk-Bijak J, Bijak M. Various aspects of a gene editing system—crispr–cas9. Int J Mol Sci. 2020;21(24):9604.
Yao X, Wang X, Hu X, Liu Z, Liu J, Zhou H, et al. Homology-mediated end joining-based targeted integration using CRISPR/Cas9. Cell Res. 2017;27(6):801-14.
Guo T, Feng YL, Xiao JJ, Liu Q, Sun XN, Xiang JF, et al. Harnessing accurate non-homologous end joining for efficient precise deletion in CRISPR/Cas9-mediated genome editing. Genome Biol. 2018;19:1-20.
Ceasar SA, Rajan V, Prykhozhij SV, Berman JN, Ignacimuthu S. Insert, remove or replace: A highly advanced genome editing system using CRISPR/Cas9. Biochimica et Biophysica Acta (BBA)-Mol Cell Res. 2016;1863(9):2333-44.
Liu C, Zhang L, Liu H, Cheng K. Delivery strategies of the CRISPR-Cas9 gene-editing system for therapeutic applications. J Controlled Release. 2017;266:17-26.
Taha EA, Lee J, Hotta A. Delivery of CRISPR-Cas tools for in vivo genome editing therapy: Trends and challenges. J Controlled Release. 2022;342:345-61.
Yip BH. Recent advances in CRISPR/Cas9 delivery strategies. Biomolecules. 2020;10(6):839.
Minkenberg B, Wheatley M, Yang Y. CRISPR/Cas9-enabled multiplex genome editing and its application. Prog Mol Biol Transl Sci. 2017;149:111-32.
Gonçalves E, Segura‐Cabrera A, Pacini C, Picco G, Behan FM, Jaaks P, et al. Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens. Mol Systems Biol. 2020;16(7):e9405.
Auwerx C, Sadler MC, Reymond A, Kutalik Z. From pharmacogenetics to pharmaco-omics: Milestones and future directions. Human Genet Genom Adv. 2022;3(2).
Ma Y, Zhang L, Huang X. Genome modification by CRISPR/Cas9. FEBS J. 2014;281(23):5186-93.
Rahimi H, Salehiabar M, Barsbay M, Ghaffarlou M, Kavetskyy T, Sharafi A, et al. CRISPR systems for COVID-19 diagnosis. ACS Sensors. 2021;6(4):1430-45.
Luthra R, Kaur S, Bhandari K. Applications of CRISPR as a potential therapeutic. Life Sci. 2021;284:119908.
Martinez-Lage M, Torres-Ruiz R, Puig-Serra P, Moreno-Gaona P, Martin MC, Moya FJ, et al. In vivo CRISPR/Cas9 targeting of fusion oncogenes for selective elimination of cancer cells. Nat Comm. 2020;11(1):5060.
Mollanoori H, Shahraki H, Rahmati Y, Teimourian S. CRISPR/Cas9 and CAR-T cell, collaboration of two revolutionary technologies in cancer immunotherapy, an instruction for successful cancer treatment. Hum Immunol. 2018;79(12):876-82.
Wang J, Xu ZW, Liu S, Zhang RY, Ding SL, Xie XM, et al. Dual gRNAs guided CRISPR/Cas9 system inhibits hepatitis B virus replication. World J Gastroenterol. 2015;21(32):9554.
Alkanli SS, Alkanli N, Ay A, Albeniz I. CRISPR/Cas9 mediated therapeutic approach in Huntington’s disease. Mol Neurobiol. 2023;60(3):1486-98.
Varela MD, de Guimaraes TA, Georgiou M, Michaelides M. Leber congenital amaurosis/early-onset severe retinal dystrophy: current management and clinical trials. Br J Ophthalmol. 2022;106(4):445-51.
Frangoul H, Bobruff Y, Cappellini MD, Corbacioglu S, Fernandez CM, De la Fuente J, et al. Safety and efficacy of CTX001 in patients with transfusion-dependent β-thalassemia and sickle cell disease: early results from the climb THAL-111 and climb SCD-121 studies of autologous CRISPR-CAS9-modified CD34+ hematopoietic stem and progenitor cells. Blood. 2020;136:3-4.
Foy SP, Jacoby K, Bota DA, Hunter T, Pan Z, Stawiski E, et al. Non-viral precision T cell receptor replacement for personalized cell therapy. Nature. 2023;615(7953):687-96.
Frangoul H, Altshuler D, Cappellini MD, Chen YS, Domm J, Eustace BK, et al. CRISPR-Cas9 Gene Editing for Sickle Cell Disease and β-Thalassemia. N Engl J Med. 2021;384(3):252-60.
Partridge M, Pai M. Vertex and CRISPR Therapeutics Present New Data on More Patients With Longer Follow-Up Treated With exagamglogene autotemcel (exa-cel). European Hematology Association (EHA) Congress. 2022. Available at: https://news.vrtx.com/node/29996/pdf. Accessed on 08 March 2024.
Sheridan C. The world's first CRISPR therapy is approved: who will receive it? Nat Biotechnol. 2024;42(1):3-4.
Foy SP, Jacoby K, Bota DA, Hunter T, Pan Z, Stawiski E, et al. Non-viral precision T cell receptor replacement for personalized cell therapy. Nature. 2023;615(7953):687-96.
Cristea M, Chmielowski B, Funke R, Stallings-Schmitt T, Denker M, Frohlich M, et al. CT250: A Phase 1a/1b, open-label first-in-human study of the safety, tolerability, and feasibility of gene-edited autologous NeoTCR-T cells (NeoTCR-P1) administered to patients with locally advanced or metastatic solid tumors. Cancer Res. 2020;80(16):CT250.
O'Brien S, Nastoupil LJ, Essell J, Dsouza L, Hart D, Matsuda E, et al. A First-in-Human Phase 1, Multicenter, Open-Label Study of CB-010, a Next-Generation CRISPR-Edited Allogeneic Anti-CD19 CAR-T Cell Therapy with a PD-1 Knockout, in Patients with Relapsed/Refractory B Cell Non-Hodgkin Lymphoma (ANTLER Study). Blood. 2022;140(1):9457-8.
Zhan T, Rindtorff N, Betge J, Ebert MP, Boutros M. CRISPR/Cas9 for cancer research and therapy. Semin Cancer Biol. 2019;55:106-19.
Roper J, Tammela T, Akkad A, Almeqdadi M, Santos SB, Jacks T, et al. Colonoscopy-based colorectal cancer modeling in mice with CRISPR-Cas9 genome editing and organoid transplantation. Nat Protoc. 2018;13:217-34.
Wallace E, Howard L, Liu M, O'Brien T, Ward D, Shen S, et al. Long QT Syndrome: Genetics and Future Perspective. Pediatr Cardiol. 2019;40(7):1419-30.
Ding Q, Strong A, Patel KM, Ng SL, Gosis BS, Regan SN, et al. Permanent alteration of PCSK9 with in vivo CRISPR-Cas9 genome editing. Circ Res. 2014;115:488-92.
Crosby J, Peloso GM, Auer PL, Crosslin DR, Stitziel NO, Lange LA, et al. Loss-of-function mutations in APOC3, triglycerides, and coronary disease. N Engl J Med. 2014;371:22-31.
Vethe H, Bjørlykke Y, Ghila LM, Paulo JA, Scholz H, Gygi SP, et al. Probing the missing mature β-cell proteomic landscape in differentiating patient iPSC-derived cells. Sci Rep. 2017;7:4780.
Gillmore JD, Gane Ed, Taubel J, Kao J, Fontana M, Maitland ML, et.al. CRISPR-Cas9 In Vivo Gene Editing for Transthyretin Amyloidosis. N Engl J Med. 2021;385(6):493-502.
Karpov DS, Sosnovtseva AO, Pylina SV, Bastrich AN, Petrova DA, Kovalev MA, et al. Challenges of CRISPR/Cas-Based Cell Therapy for Type 1 Diabetes: How Not to Engineer a "Trojan Horse". Int J Mol Sci. 2023;24(24):17320.
Maeder ML, Stefanidakis M, Wilson CJ, Baral R, Barrera LA, Bounoutas GS, et al. Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10. Nat Med. 2019;25:229-33.
Harris VM, Koelsch KA, Kurien BT, Harley ITW, Wren JD, Harley JB, et al. Characterization of cxorf21 provides molecular insight into female-bias immune response in sle pathogenesis. Front Immunol. 2019;10:2160.
Odqvist L, Jevnikar Z, Riise R, Oberg L, Rhedin M, Leonard D, et al. Genetic variations in a20 dub domain provide a genetic link to citrullination and neutrophil extracellular traps in systemic lupus erythematosus. Ann Rheum Dis. 2019;78:1363-70.
CRISPR Therapeutics. CRISPR Therapeutics Announces Updates to Immuno-Oncology Pipeline and Expansion into Autoimmune Disease. Available at: https://ir.crisprtx.com/news-releases/news-release-details/crispr-therapeutics-announces-updates-immuno-oncology-pipeline. Accessed on 02 May 2024.
Abbott TR, Dhamdhere G, Liu Y, Lin X, Goudy L, Zeng L, et al. Development of CRISPR as an antiviral strategy to combat SARS-CoV-2 and influenza. Cell. 2020;181:865-76.
Ebina H, Misawa N, Kanemura Y, Koyanagi Y. Harnessing the CRISPR/ Cas9 system to disrupt latent HIV-1 provirus. Sci Rep. 2013;3:2510.
Hu W, Kaminski R, Yang F, Zhang Y, Cosentino L, Li F, et al. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc Natl Acad Sci USA. 2014;111:11461-6.
Presti R, Baxter J, Sivapalasingam S, Gordon J, Gordon TJ, Kennedy WP. First-in-human trial of systemic CRISPR-Cas9 multiplex gene therapy for functional cure of HIV. Presented at: 30th Annual ESGCT Congress; Brussels, Belgium. 2023.
Kim P, Sanchez A, Kime J, Ousterout D. Phase 1b Results of Pharmacokinetics, Pharmacodynamics, and Safety for LBP-EC01, a CRISPR-Cas3 Enhanced Bacteriophage Cocktail Targeting Escherichia coli that Cause Urinary Tract Infections. Open Forum Infect Dis. 2021;8(1):S633.
Pacia DM, Brown BL, Minssen T, Darrow JJ. CRISPR-phage antibacterials to address the antibiotic resistance crisis: scientific, economic, and regulatory considerations. J Law Biosci. 2024;11(1):lsad030.
Longhurst HJ, Lindsay K, Petersen RS, Fijen LM, Gurugama P, Maag D. CRISPR-Cas9 In Vivo Gene Editing of KLKB1 for Hereditary Angioedema. N Engl J Med. 2024;390(5):432-44.
Yin J, Lu R, Xin C, Wang Y, Ling X, Li D, et al. Cas9 exo-endonuclease eliminates chromosomal translocations during genome editing. Nat Comm. 2022;13:1204.
Gkazi SA. Quantifying CRISPR off-target effects. Emerg. Top. Life Sci. 2019;3:327-34.
Giannoukos G, Ciulla DM, Marco E, Abdulkerim HS, Barrera LA, Bothmer A, et al. UDiTaS™, a genome editing detection method for indels and genome rearrangements. BMC Genom. 2018;19:1-10.
Kantor A, McClements ME, MacLaren RE. CRISPR-Cas9 DNA Base-Editing and Prime-Editing. Int J Mol Sci. 2020;21:6240.
Kuscu C, Parlak M, Tufan T, Yang J, Szlachta K, Wei X, et al. CRISPR-STOP: Gene silencing through base-editing-induced nonsense mutations. Nat Methods. 2017;14:710-2.
Senís E, Fatouros C, Große S, Wiedtke E, Niopek D, Mueller AK, et al. CRISPR/Cas9-mediated genome engineering: An adeno-associated viral (AAV) vector toolbox. Biotechnol. J. 2014;9:1402-12.
Rosenblum D, Gutkin A, Kedmi R, Ramishetti S, Veiga N, Jacobi AM, et al. CRISPR-Cas9 genome editing using targeted lipid nanoparticles for cancer therapy. Sci Adv. 2020;6:eabc9450.
Hayashi H, Kubo Y, Izumida M, Matsuyama T. Efficient viral delivery of Cas9 into human safe harbor. Sci Rep. 2020;10:1-14.
Guenther CM, Kuypers BE, Lam MT, Robinson TM, Zhao J, Suh J, et al. Synthetic virology: engineering viruses for gene delivery. Interdiscip Rev Nanomed Nanobiotechnol. 2014;6:548-58.
Kay MA, He CY, Chen ZY. A robust system for production of minicircle DNA vectors. Nat Biotechnol. 2010;28:1287-9.
Lee K, Conboy M, Park HM, Jiang F, Kim HJ, Dewitt MA, et al. Nanoparticle delivery of Cas9 ribonucleoprotein and donor DNA in vivo induces homology-directed DNA repair. Nat Biomed Eng. 2017;1:889-901.
Janik E, Niemcewicz M, Ceremuga M, Krzowski L, Saluk-Bijak J, Bijak M. Various aspects of a gene editing system crispr cas9. Int J Mol Sci. 2020;21(24):9604.
Yao X, Wang X, Hu X, Liu Z, Liu J, Zhou H, et al. Homology-mediated end joining-based targeted integration using CRISPR/Cas9. Cell Res. 2017;27(6):801-14.
Guo T, Feng YL, Xiao JJ, Liu Q, Sun XN, Xiang JF, et al. Harnessing accurate non-homologous end joining for efficient precise deletion in CRISPR/Cas9-mediated genome editing. Genome Biol. 2018;19:1-20.
Ceasar SA, Rajan V, Prykhozhij SV, Berman JN, Ignacimuthu S. Insert, remove or replace: A highly advanced genome editing system using CRISPR/Cas9. Biochimica et Biophysica Acta (BBA)-Mol Cell Res. 2016;1863(9):2333-44.
Krishan K, Kanchan T, Singh B. Human genome editing and ethical considerations. Sci Eng Ethics. 2016;22(2):597-9.
Knoppers BM, Kleiderman E. "CRISPR babies": What does this mean for science and Canada? CMAJ. 2019;191(4):E91-2.
Khan SH. Genome-editing technologies: concept, pros, and cons of various genome-editing techniques and bioethical concerns for clinical application. Mol Therapy-Nucleic Acids. 2019;16:326-34.
Mahmoudian-sani MR, Farnoosh G, Mahdavinezhad A, Saidijam M. CRISPR genome editing and its medical applications. Biotechnol Biotechnological Equipment. 2018;32(2):286-92.
Rafii S, Tashkandi E, Bukhari N, Al-Shamsi HO. Current Status of CRISPR/Cas9 Application in Clinical Cancer Research: Opportunities and Challenges. Cancers. 2022;14(4):947.
Uddin F, Rudin CM, Sen T. CRISPR gene therapy: applications, limitations, and implications for the future. Front Oncol. 2020;10:1387.
Li H, Yang Y, Hong W, Huang M, Wu M, Zhao X. Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Signal transduction and targeted therapy. 2020;5(1):1.