CRISPR-Cas9 Mediated Genome Editing a Promise to Cure HIV: A Systematic Review

Authors

DOI:

https://doi.org/10.23918/eajse.v11i3p14

Keywords:

CRISPR-Cas9, HIV, CCR5, CXCR4, Genome Editing

Abstract

Human Immunodeficiency Virus (HIV-1) infection might be controlled using long-term antiretroviral therapy. However, it causes various side effects rather than its cost-effectiveness. Thus, the development of a permanent cure for HIV-1 that most probably relies on gene therapy is highly required. Relying on that, genome editing approaches like Clustered Regularly Interspaced Short Palindromic Repeats associated with Cas9 (CRISPR-Cas9) have been utilized to target coreceptors, including CCR5 and CXCR4, hoping to find a curative method against HIV infection. Accordingly, the current study aims to systematically review CRISPR-Cas9 mediating genome editing studies, mainly CCR5 or CXCR4 or simultaneous genome editing to make HIV resistant primary human CD4+ T cells. A systematic review was conducted on original articles focusing on CRISPR-Cas9 mediated genome editing in HIV, published between 2015 and 2023. As a result, the CRISPR-Cas9 technology has demonstrated effective gene editing to confer HIV-1 resistance by targeting CCR5 and CXCR4 receptors in CD4+ T cells. Studies show that knockout of CCR5 or CXCR4, through CRISPR-Cas9 mediated frameshift insertions, base editing, and other genetic interventions, provides substantial resistance to HIV-1, with no major cytotoxic effects observed in primary T cells. Dual knockout of CXCR4 and CCR5 offers resistance to both X4- and R5-tropic HIV strains, suggesting enhanced protective potential. However, challenges remain, particularly due to CXCR4's crucial cellular roles, necessitating careful assessment of functional impacts and off-target effects. Additionally, leveraging natural mutations like CCR5∆32 has inspired promising avenues for durable HIV-1 resistance. While targeting viral genomes, especially latent reservoirs, appears safer by avoiding host genome alterations, reinfection risks persist. These findings highlight the promise of CRISPR-based HIV therapies, though clinical translation will require rigorous optimization and evaluation.

References

[1] Carbone A, Vaccher E, Gloghini A, Pantanowitz L, Abayomi A, De Paoli P, et al. Diagnosis and management of lymphomas and other cancers in HIV-infected patients. Nature reviews Clinical oncology. 2014;11(4):223-38. doi:https://doi.org/10.1038/nrclinonc.2014.31

[2] Chen LF, Hoy J, Lewin SR. Ten years of highly active antiretroviral therapy for HIV infection. Medical Journal of Australia. 2007;186(3):146-51.

[3] Andrade HB, Shinotsuka CR, da Silva IRF, Donini CS, Yeh Li H, de Carvalho FB, et al. Highly active antiretroviral therapy for critically ill HIV patients: a systematic review and meta-analysis. PLoS One. 2017;12(10):e0186968. doi:https://doi.org/10.1371/journal.pone.0186968

[4] Costiniuk CT, Jenabian M-A. HIV reservoir dynamics in the face of highly active antiretroviral therapy. AIDS patient care and STDs. 2015;29(2):55-68. doi:https://doi.org/10.1089/apc.2014.0173

[5] Vidya Vijayan K, Karthigeyan KP, Tripathi SP, Hanna LE. Pathophysiology of CD4+ T-cell depletion in HIV-1 and HIV-2 infections. Frontiers in immunology. 2017;8:580. doi:https://doi.org/10.3389/fimmu.2017.00580

[6] Chen B. Molecular mechanism of HIV-1 entry. Trends in microbiology. 2019;27(10):878-91. doi:https://doi.org/10.1016/j.tim.2019.06.002

[7] Connor RI, Sheridan KE, Ceradini D, Choe S, Landau NR. Change in coreceptor use correlates with disease progression in HIV-1–infected individuals. The Journal of Experimental Medicine. 1997;185(4):621-8. doi:https://doi.org/10.1084%2Fjem.185.4.621

[8] Lim JK, McDermott DH, Lisco A, Foster GA, Krysztof D, Follmann D, et al. CCR5 deficiency is a risk factor for early clinical manifestations of West Nile virus infection but not for viral transmission. The Journal of Infectious Diseases. 2010;201(2):178-85. doi:https://doi.org/10.1086/649426

[9] Didigu CA, Wilen CB, Wang J, Duong J, Secreto AJ, Danet-Desnoyers GA, et al. Simultaneous zinc-finger nuclease editing of the HIV coreceptors ccr5 and cxcr4 protects CD4+ T cells from HIV-1 infection. Blood, The Journal of the American Society of Hematology. 2014;123(1):61-9. doi:https://doi.org/10.1182/blood-2013-08-521229

[10] Jiang F, Doudna JA. CRISPR–Cas9 structures and mechanisms. Annual review of biophysics. 2017;46:505-29. doi:https://doi.org/10.1146/annurev-biophys-062215-010822

[11] Niu Y, Shen B, Cui Y, Chen Y, Wang J, Wang L, et al. Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos. Cell. 2014;156(4):836-43. doi:https://doi.org/10.1016/j.cell.2014.01.027

[12] Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014;343(6166):84-7. doi:https://doi.org/10.1126/science.1247005

[13] Martinez-Lage M, Puig-Serra P, Menendez P, Torres-Ruiz R, Rodriguez-Perales S. CRISPR/Cas9 for cancer therapy: hopes and challenges. Biomedicines. 2018;6(4):105. doi:https://doi.org/10.3390/biomedicines6040105

[14] Mohammadzadeh I, Qujeq D, Yousefi T, Ferns GA, Maniati M, Vaghari‐Tabari M. CRISPR/Cas9 gene editing: A new therapeutic approach in the treatment of infection and autoimmunity. IUBMB life. 2020;72(8):1603-21. doi:https://doi.org/10.1002/iub.2296

[15] Dhanda S. Applications of CRISPR/Cas9 as a Tool to study Human Diseases caused by Viruses: A review. 2023.

[16] Liu S, Wang Q, Yu X, Li Y, Guo Y, Liu Z, et al. HIV-1 inhibition in cells with a CXCR4 mutant genome created by CRISPR-Cas9 and piggyBac recombinant technologies. Scientific Reports. 2018;8(1):1-11. doi:https://doi.org/10.1038/s41598-018-26894-4

[17] Scheller SH, Rashad Y, Saleh FM, Willingham KA, Reilich A, Lin D, et al. Biallelic, selectable, knock-in targeting of CCR5 via CRISPR-Cas9 mediated homology directed repair inhibits HIV-1 replication. Frontiers in immunology. 2022;13:821190. doi:https://doi.org/10.3389/fimmu.2022.821190

[18] Knipping F, Newby GA, Eide CR, McElroy AN, Nielsen SC, Smith K, et al. Disruption of HIV-1 co-receptors CCR5 and CXCR4 in primary human T cells and hematopoietic stem and progenitor cells using base editing. Molecular Therapy. 2022;30(1):130-44. doi:https://doi.org/10.1016/j.ymthe.2021.10.026

[19] Huang Z, Tomitaka A, Raymond A, Nair M. Current application of CRISPR/Cas9 gene-editing technique to eradication of HIV/AIDS. Gene therapy. 2017;24(7):377-84. doi:https://doi.org/10.1038/gt.2017.35

[20] Boasso A, Shearer G, Chougnet C. Immune dysregulation in human immunodeficiency virus infection: know it, fix it, prevent it? Journal of Internal Medicine. 2009;265(1):78-96. doi:https://doi.org/10.1111/j.1365-2796.2008.02043.x

[21] Aiken C, Rousso I. The HIV-1 capsid and reverse transcription. Retrovirology. 2021;18(1):1-9. doi:https://doi.org/10.1186/s12977-021-00566-0

[22] Freen-van Heeren JJ. Closing the Door with CRISPR: Genome Editing of CCR5 and CXCR4 as a Potential Curative Solution for HIV. BioTech. 2022;11(3):25. doi:https://doi.org/10.3390/biotech11030025

[23] Himmel DM, Arnold E. Non-nucleoside reverse transcriptase inhibitors join forces with integrase inhibitors to combat HIV. Pharmaceuticals. 2020;13(6):122. doi:https://doi.org/10.3390/ph13060122

[24] Voshavar C. Protease inhibitors for the treatment of HIV/AIDS: recent advances and future challenges. Current Topics in Medicinal Chemistry. 2019;19(18):1571-98. doi:https://doi.org/10.2174/1568026619666190619115243

[25] Qi C, Li D, Jiang X, Jia X, Lu L, Wang Y, et al. Inducing CCR5Δ32/Δ32 homozygotes in the human Jurkat CD4+ cell line and primary CD4+ cells by CRISPR-Cas9 genome-editing technology. Molecular Therapy-Nucleic Acids. 2018;12:267-74. doi:https://doi.org/10.1016/j.omtn.2018.05.012

[26] Doudna JA, Charpentier E. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346(6213):1258096. doi:https://doi.org/10.1126/science.1258096

[27] Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences. 2012;109(39):E2579-E86. doi:https://doi.org/10.1073/pnas.1208507109

[28] Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J. RNA-programmed genome editing in human cells. elife. 2013;2:e00471. doi:https://doi.org/10.7554/eLife.00471

[29] Redman M, King A, Watson C, King D. What is CRISPR/Cas9? Archives of Disease in Childhood-Education and Practice. 2016;101(4):213-5. doi:https://doi.org/10.1136/archdischild-2016-310459

[30] Liu Z, Dong H, Cui Y, Cong L, Zhang D. Application of different types of CRISPR/Cas-based systems in bacteria. Microbial cell factories. 2020;19(1):1-14. doi:https://doi.org/10.1186/s12934-020-01431-z

[31] Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013;339(6121):823-6. doi:https://doi.org/10.1126/science.1232033

[32] Guilinger JP, Thompson DB, Liu DR. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nature Biotechnology. 2014;32(6):577-82. doi:https://doi.org/10.1038/nbt.2909

[33] Gupta RM, Musunuru K. Expanding the genetic editing tool kit: ZFNs, TALENs, and CRISPR-Cas9. The Journal of Clinical Investigation. 2014;124(10):4154-61. doi:https://doi.org/10.1172/JCI72992

[34] Moore JP, Kitchen SG, Pugach P, Zack JA. The CCR5 and CXCR4 coreceptors—central to understanding the transmission and pathogenesis of human immunodeficiency virus type 1 infection. AIDS research and human retroviruses. 2004;20(1):111-26. doi:https://doi.org/10.1089/088922204322749567

[35] Yu S, Yao Y, Xiao H, Li J, Liu Q, Yang Y, et al. Simultaneous knockout of CXCR4 and CCR5 genes in CD4+ T cells via CRISPR/Cas9 confers resistance to both X4-and R5-tropic human immunodeficiency virus type 1 infection. Human gene therapy. 2018;29(1):51-67. doi:https://doi.org/10.1089/hum.2017.032

[36] Hütter G, Nowak D, Mossner M, Ganepola S, Müßig A, Allers K, et al. Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. New England Journal of Medicine. 2009;360(7):692-8. doi:https://doi.org/10.1056/NEJMoa0802905

[37] Li C, Guan X, Du T, Jin W, Wu B, Liu Y, et al. Inhibition of HIV-1 infection of primary CD4+ T-cells by gene editing of CCR5 using adenovirus-delivered CRISPR/Cas9. Journal of General Virology. 2015;96(8):2381-93. doi:https://doi.org/10.1099/vir.0.000139

[38] Ellwanger JH, Kulmann-Leal B, de Lima Kaminski V, Rodrigues AG, de Souza Bragatte MA, Chies JAB. Beyond HIV infection: neglected and varied impacts of CCR5 and CCR5Δ32 on viral diseases. Virus research. 2020;286:198040.

[39] Brumme ZL, Goodrich J, Mayer HB, Brumme CJ, Henrick BM, Wynhoven B, et al. Molecular and clinical epidemiology of CXCR4-using HIV-1 in a large population of antiretroviral-naive individuals. The Journal of Infectious Diseases. 2005;192(3):466-74. doi:https://doi.org/10.1086/431519

[40] Hou P, Chen S, Wang S, Yu X, Chen Y, Jiang M, et al. Genome editing of CXCR4 by CRISPR/Cas9 confers cells resistant to HIV-1 infection. Scientific reports. 2015;5(1):15577. doi:https://doi.org/10.1038/srep15577

[41] Wang Q, Chen S, Xiao Q, Liu Z, Liu S, Hou P, et al. Genome modification of CXCR4 by Staphylococcus aureus Cas9 renders cells resistance to HIV-1 infection. Retrovirology. 2017;14:1-12.

[42] Tian S, Choi W-T, Liu D, Pesavento J, Wang Y, An J, et al. Distinct functional sites for human immunodeficiency virus type 1 and stromal cell-derived factor 1α on CXCR4 transmembrane helical domains. Journal of Virology. 2005;79(20):12667-73. doi:https://doi.org/10.1128/jvi.79.20.12667-12673.2005

[43] Liu Y, Zhou J, Pan J-A, Mabiala P, Guo D. A novel approach to block HIV-1 coreceptor CXCR4 in a non-toxic manner. Molecular biotechnology. 2014;56:890-902. doi:https://doi.org/10.1007/s12033-014-9768-7

[44] Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, et al. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proceedings of the National Academy of Sciences. 2015;112(33):10437-42. doi:https://doi.org/10.1073/pnas.1512503112

[45] Xie F, Ye L, Chang JC, Beyer AI, Wang J, Muench MO, et al. Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac. Genome research. 2014;24(9):1526-33. doi:http://www.genome.org/cgi/doi/10.1101/gr.173427.114

[46] Zhu S, Rong Z, Lu X, Xu Y, Fu X. Gene targeting through homologous recombination in monkey embryonic stem cells using CRISPR/Cas9 system. Stem cells and development. 2015;24(10):1147-9. doi:https://doi.org/10.1089/scd.2014.0507

[47] Karuppusamy KV, Demosthenes JP, Venkatesan V, Christopher AC, Babu P, Azhagiri MK, et al. The CCR5 gene-edited CD34+ CD90+ hematopoietic stem cell population serves as an optimal graft source for HIV gene therapy. Frontiers in Immunology. 2022;13:792684. doi:https://doi.org/10.3389/fimmu.2022.792684

[48] Liu Z, Chen S, Jin X, Wang Q, Yang K, Li C, et al. Genome editing of the HIV co-receptors CCR5 and CXCR4 by CRISPR-Cas9 protects CD4+ T cells from HIV-1 infection. Cell & bioscience. 2017;7:1-15. doi:https://doi.org/10.1186/s13578-017-0174-2

[49] Li S, Holguin L, Burnett JC. CRISPR-Cas9-mediated gene disruption of HIV-1 co-receptors confers broad resistance to infection in human T cells and humanized mice. Molecular Therapy-Methods & Clinical Development. 2022;24:321-31. doi:https://doi.org/10.1016/j.omtm.2022.01.012

[50] Llewellyn GN, Seclén E, Wietgrefe S, Liu S, Château M, Pei H, et al. Humanized mouse model of HIV-1 latency with enrichment of latent virus in PD-1+ and TIGIT+ CD4 T cells. Journal of Virology. 2019;93(10):10.1128/jvi. 02086-18. doi:https://doi.org/10.1128/jvi.02086-18

[51] Barton K, Winckelmann A, Palmer S. HIV-1 reservoirs during suppressive therapy. Trends in microbiology. 2016;24(5):345-55. doi:https://doi.org/10.1016/j.tim.2016.01.006

[52] Freen‐van Heeren JJ. Addressing HIV‐1 latency with flow‐FISH: finding, characterizing, and targeting HIV‐1 infected cells. Wiley Online Library; 2021. p. 861-5.

[53] Zhu W, Lei R, Le Duff Y, Li J, Guo F, Wainberg MA, et al. The CRISPR/Cas9 system inactivates latent HIV-1 proviral DNA. Retrovirology. 2015;12:1-7. doi:https://doi.org/10.1186/s12977-015-0150-z

[54] Kaminski R, Chen Y, Fischer T, Tedaldi E, Napoli A, Zhang Y, et al. Elimination of HIV-1 genomes from human T-lymphoid cells by CRISPR/Cas9 gene editing. Scientific reports. 2016;6(1):22555. doi:https://doi.org/10.1038/srep22555

[55] Herskovitz J, Hasan M, Patel M, Blomberg WR, Cohen JD, Machhi J, et al. CRISPR-Cas9-mediated exonic disruption for HIV-1 elimination. EBioMedicine. 2021;73. doi:https://doi.org/10.1016/j.ebiom.2021.103678

Downloads

Published

2026-02-26

Data Availability Statement

This is a systematic review which reviewed the published article related with the topic.

How to Cite

Ali, H. (2026). CRISPR-Cas9 Mediated Genome Editing a Promise to Cure HIV: A Systematic Review. EURASIAN JOURNAL OF SCIENCE AND ENGINEERING, 11(3), 225-240. https://doi.org/10.23918/eajse.v11i3p14