Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Gene editing in cancer therapy: overcoming drug resistance and enhancing precision medicine

Abstract

The CRISPR system has revolutionized cancer gene therapy, offering unparalleled precision in genetic manipulation for targeted oncogene disruption, mutation correction, and immune system modulation. This breakthrough tool has demonstrated remarkable potential in overcoming drug resistance, enhancing chemotherapy sensitivity, and improving immunotherapy strategies such as CRISPR-engineered CAR-T cells. Additionally, oncolytic virus-mediated CRISPR delivery has emerged as a novel approach for tumor-specific gene editing, minimizing off-target effects. The rapid transition of CRISPR-based cancer therapeutics from preclinical research to clinical trials underscores its therapeutic potential. This review explores the latest advancements in CRISPR applications for cancer therapy, including gene knockout, base editing for mutation correction, and integration with immune and viral therapies. Despite significant progress, challenges such as off-target effects, immune responses, and delivery limitations remain key hurdles. We discuss current strategies to enhance CRISPR safety and efficacy, emphasizing its potential for personalized cancer treatment.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: The CRISPR/Cas tools.
Fig. 2: Applications of CRISPR technology in cancer therapy.
Fig. 3: Schematic diagram of strategies to overcome the limitations of conventional cancer treatments.
Fig. 4: CRISPR-based genome-wide screening.
Fig. 5: The CRISPR-engineered CAR-T therapy.

Similar content being viewed by others

References

  1. Anand U, Dey A, Chandel AKS, Sanyal R, Mishra A, Pandey DK, et al. Cancer chemotherapy and beyond: current status, drug candidates, associated risks and progress in targeted therapeutics. Genes Dis. 2023;10:1367–401.

    Article  CAS  PubMed  Google Scholar 

  2. Wagle N, Van Allen EM, Treacy DJ, Frederick DT, Cooper ZA, Taylor-Weiner A, et al. MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition. Cancer Discov. 2014;4:61–8.

    Article  CAS  PubMed  Google Scholar 

  3. Mazières J, Peters S, Lepage B, Cortot AB, Barlesi F, Beau-Faller M, et al. Lung cancer that harbors an HER2 mutation: epidemiologic characteristics and therapeutic perspectives. J Clin Oncol. 2013;31:1997–2003.

    Article  PubMed  Google Scholar 

  4. Krepler C, Xiao M, Sproesser K, Brafford PA, Shannan B, Beqiri M, et al. Personalized preclinical trials in BRAF inhibitor-resistant patient-derived xenograft models identify second-line combination therapies. Clin Cancer Res. 2016;22:1592–602.

    Article  CAS  PubMed  Google Scholar 

  5. Cree IA, Knight L, Di Nicolantonio F, Sharma S, Gulliford T. Chemosensitization of solid tumors by modulation of resistance mechanisms. Curr Opin Investig Drugs. 2002;3:634–40.

    CAS  PubMed  Google Scholar 

  6. Pourcel C, Salvignol G, Vergnaud G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology. 2005;151:653–63.

    Article  CAS  PubMed  Google Scholar 

  7. Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. 2005;60:174–82.

    Article  CAS  PubMed  Google Scholar 

  8. Bolotin A, Quinquis B, Sorokin A, Ehrlich SD. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology. 2005;151:2551–61.

    Article  CAS  PubMed  Google Scholar 

  9. Shah SA, Erdmann S, Mojica FJ, Garrett RA. Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol. 2013;10:891–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Mojica FJM, Díez-Villaseñor C, García-Martínez J, Almendros C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology. 2009;155:733–40.

    Article  CAS  PubMed  Google Scholar 

  11. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 2014;507:62–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Lieber MR, Karanjawala ZE. Ageing, repetitive genomes and DNA damage. Nat Rev Mol Cell Biol. 2004;5:69–75.

    Article  CAS  PubMed  Google Scholar 

  14. Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576:149–57.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Matsoukas IG. Commentary: programmable base editing of A.T to G.C in genomic DNA without DNA cleavage. Front Genet. 2018;9:21.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533:420–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Yoon AR, Lee S, Kim JH, Park Y, Koo T, Yun CO. CRISPR-mediated ablation of TP53 and EGFR mutations enhances gefitinib sensitivity and anti-tumor efficacy in lung cancer. Mol Ther. 2024;32:3618–28.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Thuronyi BW, Koblan LW, Levy JM, Yeh WH, Zheng C, Newby GA, et al. Continuous evolution of base editors with expanded target compatibility and improved activity. Nat Biotechnol. 2019;37:1070–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Li X, Qian X, Wang B, Xia Y, Zheng Y, Du L, et al. Programmable base editing of mutated TERT promoter inhibits brain tumour growth. Nat Cell Biol. 2020;22:282–8.

    Article  CAS  PubMed  Google Scholar 

  20. Grünewald J, Zhou R, Iyer S, Lareau CA, Garcia SP, Aryee MJ, et al. CRISPR DNA base editors with reduced RNA off-target and self-editing activities. Nat Biotechnol. 2019;37:1041–8.

    Article  PubMed  PubMed Central  Google Scholar 

  21. Hosseini SY, Mallick R, Mäkinen P, Ylä-Herttuala S. Insights into prime editing technology: a deep dive into fundamentals, potentials, and challenges. Hum Gene Ther. 2024;35:649–68.

    Article  CAS  PubMed  Google Scholar 

  22. Abel EL, DiGiovanni J. Multistage carcinogenesis. In: Penning TM, editor. Chemical carcinogenesis. Totowa, NJ: Humana Press; 2011. p 27–51.

  23. Gao Q, Ouyang W, Kang B, Han X, Xiong Y, Ding R, et al. Selective targeting of the oncogenic KRAS G12S mutant allele by CRISPR/Cas9 induces efficient tumor regression. Theranostics. 2020;10:5137–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Yoon AR, Jung BK, Choi E, Chung E, Hong J, Kim JS, et al. CRISPR-Cas12a with an oAd induces precise and cancer-specific genomic reprogramming of EGFR and efficient tumor regression. Mol Ther. 2020;28:2286–96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Jiang M, Hu H, Kai J, Traw MB, Yang S, Zhang X. Different knockout genotypes of OsIAA23 in rice using CRISPR/Cas9 generating different phenotypes. Plant Mol Biol. 2019;100:467–79.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Mizuno Y, Shimada S, Akiyama Y, Watanabe S, Aida T, Ogawa K, et al. DEPDC5 deficiency contributes to resistance to leucine starvation via p62 accumulation in hepatocellular carcinoma. Sci Rep. 2018;8:106.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Richl T, Kuper J, Kisker C. G-quadruplex-mediated genomic instability drives SNVs in cancer. Nucleic Acids Res. 2024;52:2198–211.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Sayed S, Sidorova OA, Hennig A, Augsburg M, Cortes Vesga CP, Abohawya M, et al. Efficient correction of oncogenic KRAS and TP53 mutations through CRISPR base editing. Cancer Res. 2022;82:3002–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Zhao G, Ma Q, Yang H, Jiang H, Xu Q, Luo S, et al. Base editing of the mutated TERT promoter inhibits liver tumor growth. Hepatology. 2024;79:1310–23.

    Article  PubMed  Google Scholar 

  30. Choi E, Hwang HY, Kwon E, Kim D, Koo T. Expanded targeting scope of LbCas12a variants allows editing of multiple oncogenic mutations. Mol Ther Nucleic Acids. 2022;30:131–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Kleinstiver BP, Prew MS, Tsai SQ, Nguyen NT, Topkar VV, Zheng Z, et al. Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nat Biotechnol. 2015;33:1293–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature. 2018;556:57–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Jang G, Kweon J, Kim Y. CRISPR prime editing for unconstrained correction of oncogenic KRAS variants. Commun Biol. 2023;6:681.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Housman G, Byler S, Heerboth S, Lapinska K, Longacre M, Snyder N, et al. Drug resistance in cancer: an overview. Cancers. 2014;6:1769–92.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Holohan C, Van Schaeybroeck S, Longley DB, Johnston PG. Cancer drug resistance: an evolving paradigm. Nat Rev Cancer. 2013;13:714–26.

    Article  CAS  PubMed  Google Scholar 

  36. Wolking S, Schaeffeler E, Lerche H, Schwab M, Nies AT. Impact of genetic polymorphisms of ABCB1 (MDR1, P-Glycoprotein) on drug disposition and potential clinical implications: update of the literature. Clin Pharmacokinet. 2015;54:709–35.

    Article  CAS  PubMed  Google Scholar 

  37. Sui H, Zhou S, Wang Y, Liu X, Zhou L, Yin P, et al. COX-2 contributes to P-glycoprotein-mediated multidrug resistance via phosphorylation of c-Jun at Ser63/73 in colorectal cancer. Carcinogenesis. 2011;32:667–75.

    Article  CAS  PubMed  Google Scholar 

  38. Dong J, Yuan L, Hu C, Cheng X, Qin JJ. Strategies to overcome cancer multidrug resistance (MDR) through targeting P-glycoprotein (ABCB1): an updated review. Pharm Ther. 2023;249:108488.

    Article  CAS  Google Scholar 

  39. Lei ZN, Albadari N, Teng QX, Rahman H, Wang JQ, Wu Z, et al. ABCB1-dependent collateral sensitivity of multidrug-resistant colorectal cancer cells to the survivin inhibitor MX106-4C. Drug Resist Updat. 2024;73. 101065.

    Article  CAS  PubMed  Google Scholar 

  40. Zhang Y, Li L, Mendoza JJ, Wang D, Yan Q, Shi L, et al. Advances in A-to-I RNA editing in cancer. Mol Cancer. 2024;23:280.

    Article  PubMed  PubMed Central  Google Scholar 

  41. Xu S, Zhou G, He Q, Ding J, Liu X, Cheng Y, et al. A-to-I-edited miR-1251-5p restrains tumor growth and metastasis in lung adenocarcinoma through regulating TCF7-mediated Wnt signaling pathway. Discov Oncol. 2024;15:587.

  42. Romano G, Le P, Nigita G, Saviana M, Micalo L, Lovat F, et al. A-to-I edited miR-411-5p targets MET and promotes TKI response in NSCLC-resistant cells. Oncogene. 2023;42:1597–606.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Cox DBT, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung J, et al. RNA editing with CRISPR-Cas13. Science. 2017;358:1019–27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Tieu V, Sotillo E, Bjelajac JR, Chen C, Malipatlolla M, Guerrero JA, et al. A versatile CRISPR-Cas13d platform for multiplexed transcriptomic regulation and metabolic engineering in primary human T cells. Cell. 2024;187:1278–95.e20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Wang L, Han H. Strategies for improving the genome-editing efficiency of class 2 CRISPR/Cas system. Heliyon. 2024;10:e38588.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Cai J, Chen J, Wu T, Cheng Z, Tian Y, Pu C, et al. Genome-scale CRISPR activation screening identifies a role of LRP8 in Sorafenib resistance in hepatocellular carcinoma. Biochem Biophys Res Commun. 2020;526:1170–6.

    Article  CAS  PubMed  Google Scholar 

  47. Belli O, Karava K, Farouni R, Platt RJ. Multimodal scanning of genetic variants with base and prime editing. Nat Biotechnol. 2025;43:1458–70.

  48. Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell. 2015;160:1246–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. June CH, O’Connor RS, Kawalekar OU, Ghassemi S, Milone MC. CAR T cell immunotherapy for human cancer. Science. 2018;359:1361–5.

    Article  CAS  PubMed  Google Scholar 

  50. Dimitri A, Herbst F, Fraietta JA. Engineering the next-generation of CAR T-cells with CRISPR-Cas9 gene editing. Mol Cancer. 2022;21:78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Schuster SJ, Svoboda J, Chong EA, Nasta SD, Mato AR, Anak O, et al. Chimeric antigen receptor T cells in refractory B-cell lymphomas. N Engl J Med. 2017;377:2545–54.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Neelapu SS, Locke FL, Bartlett NL, Lekakis LJ, Miklos DB, Jacobson CA, et al. Axicabtagene ciloleucel CAR T-Cell therapy in refractory large B-cell lymphoma. N Engl J Med. 2017;377:2531–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Maude SL, Laetsch TW, Buechner J, Rives S, Boyer M, Bittencourt H, et al. Tisagenlecleucel in children and young adults with B-cell lymphoblastic leukemia. N Engl J Med. 2018;378:439–48.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Lu Y, Xue J, Deng T, Zhou X, Yu K, Deng L, et al. Safety and feasibility of CRISPR-edited T cells in patients with refractory non-small-cell lung cancer. Nat Med. 2020;26:732–40.

    Article  CAS  PubMed  Google Scholar 

  55. Depil S, Duchateau P, Grupp SA, Mufti G, Poirot L. ‘Off-the-shelf’ allogeneic CAR T cells: development and challenges. Nat Rev Drug Discov. 2020;19:185–99.

    Article  CAS  PubMed  Google Scholar 

  56. Iyer SP, Sica RA, Ho PJ, Hu B, Zain J, Prica A, et al. S262: The cobalt-lym Study Of Ctx130: a phase 1 dose escalation study Of Cd70-targeted allogeneic crispr-Cas9–engineered Car T cells in patients with relapsed/refractory (R/R) T-cell malignancies. HemaSphere. 2022;6:163–4.

    Article  Google Scholar 

  57. Hu Y, Zhou Y, Zhang M, Ge W, Li Y, Yang L, et al. CRISPR/Cas9-engineered universal CD19/CD22 dual-targeted CAR-T cell therapy for relapsed/refractory B-cell acute lymphoblastic leukemia. Clin Cancer Res. 2021;27:2764–72.

    Article  CAS  PubMed  Google Scholar 

  58. Diorio C, Murray R, Naniong M, Barrera L, Camblin A, Chukinas J, et al. Cytosine base editing enables quadruple-edited allogeneic CART cells for T-ALL. Blood. 2022;140:619–29.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Chiesa R, Georgiadis C, Syed F, Zhan H, Etuk A, Gkazi SA, et al. Base-edited CAR7 T cells for relapsed T-cell acute lymphoblastic leukemia. N Engl J Med. 2023;389:899–910.

    Article  CAS  PubMed  Google Scholar 

  60. Chen R, Chen L, Wang C, Zhu H, Gu L, Li Y, et al. CAR-T treatment for cancer: prospects and challenges. Front Oncol. 2023;13:1288383.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Bonneaud TL, Lefebvre CC, Nocquet L, Basseville A, Roul J, Weber H, et al. Targeting of MCL-1 in breast cancer-associated fibroblasts reverses their myofibroblastic phenotype and pro-invasive properties. Cell Death Dis. 2022;13:787.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Tang N, Cheng C, Zhang X, Qiao M, Li N, Mu W, et al. TGF-beta inhibition via CRISPR promotes the long-term efficacy of CAR T cells against solid tumors. JCI Insight. 2020;5:e133977.

  63. Pol J, Kroemer G, Galluzzi L. First oncolytic virus approved for melanoma immunotherapy. Oncoimmunology. 2016;5:e1115641.

    Article  PubMed  Google Scholar 

  64. Chen Y, Chen X, Bao W, Liu G, Wei W, Ping Y. An oncolytic virus-T cell chimera for cancer immunotherapy. Nat Biotechnol. 2024;42:1876–87.

    Article  CAS  PubMed  Google Scholar 

  65. Gryciuk A, Rogalska M, Baran J, Kuryk L, Staniszewska M. Oncolytic adenoviruses armed with co-stimulatory molecules for cancer treatment. Cancers. 2023;15:1947.

  66. Hong J, Yun CO. Overcoming the limitations of locally administered oncolytic virotherapy. BMC Biomed Eng. 2019;1:17.

    Article  PubMed  PubMed Central  Google Scholar 

  67. Masarwy R, Breier D, Stotsky-Oterin L, Ad-El N, Qassem S, Naidu GS, et al. Targeted CRISPR/Cas9 lipid nanoparticles elicit therapeutic genome editing in head and neck cancer. Adv Sci. 2025;12:e2411032.

    Article  Google Scholar 

  68. Bairqdar A, Karitskaya PE, Stepanov GA. Expanding horizons of CRISPR/Cas technology: clinical advancements, therapeutic applications, and challenges in gene therapy. Int J Mol Sci. 2024;25:13321.

  69. McAndrews KM, Xiao F, Chronopoulos A, LeBleu VS, Kugeratski FG, Kalluri R. Exosome-mediated delivery of CRISPR/Cas9 for targeting of oncogenic Kras(G12D) in pancreatic cancer. Life Sci Alliance. 2021;4:e202000875.

  70. Balaraman AK, Babu MA, Moglad E, Mandaliya V, Rekha MM, Gupta S, et al. Exosome-mediated delivery of CRISPR-Cas9: A revolutionary approach to cancer gene editing. Pathol Res Pract. 2025;266:155785.

    Article  CAS  PubMed  Google Scholar 

  71. Di Carlo E, Sorrentino C. State of the art CRISPR-based strategies for cancer diagnostics and treatment. Biomark Res. 2024;12:156.

    Article  PubMed  PubMed Central  Google Scholar 

  72. Han J, Zhu L, Zhang J, Guo L, Sun X, Huang C, et al. Rational engineering of adeno-associated virus capsid enhances human hepatocyte tropism and reduces immunogenicity. Cell Prolif. 2022;55:e13339.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Lee BR, Jo E, Yoon HY, Yoon CJ, Lee HJ, Kwon KC, et al. Nonimmunogenetic viral capsid carrier with cancer targeting activity. Adv Sci. 2018;5:1800494.

    Article  Google Scholar 

  74. Barnes C, Scheideler O, Schaffer D. Engineering the AAV capsid to evade immune responses. Curr Opin Biotechnol. 2019;60:99–103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Chehelgerdi M, Chehelgerdi M, Khorramian-Ghahfarokhi M, Shafieizadeh M, Mahmoudi E, Eskandari F, et al. Comprehensive review of CRISPR-based gene editing: mechanisms, challenges, and applications in cancer therapy. Mol Cancer. 2024;23:9.

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Funding

This work was supported by a grant from Kyung Hee University in 2023 [KHU-20230920].

Author information

Authors and Affiliations

Authors

Contributions

TK designed, supervised, and wrote the manuscript. HP and SY provided conceptualization and wrote the manuscript. HP edited the manuscript and generated the figures and table.

Corresponding author

Correspondence to Taeyoung Koo.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Park, H., Yu, S. & Koo, T. Gene editing in cancer therapy: overcoming drug resistance and enhancing precision medicine. Cancer Gene Ther (2025). https://doi.org/10.1038/s41417-025-00959-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/s41417-025-00959-9

Search

Quick links