International Journal of Vaccines Review Article
Advancing Cancer Vaccine Development through CRISPR/Cas9 Technologies and Future Opportunities
Abstract
The advent of CRISPR/Cas9 genome editing has revolutionized the cancer immunotherapy market, offering unprecedented precision and versatility in the development of next-generation cancer vaccines. This review examines how CRISPR technologies are being integrated into various stages of cancer vaccine development including neoantigen discovery, dendritic cell engineering, cancer cell reprogramming, and tumor microenvironment modulation. In the area of neoantigen discovery, CRISPR enables rapid identification and validation of tumor-specific mutations, thereby supporting the design of highly personalized vaccines. Engineered dendritic cells, generated through CRISPR-based modifications, demonstrate improved antigen presentation and enhanced activation of T-cell responses. Similarly, reprogramming of cancer cells using targeted gene editing facilitates the development of whole-cell vaccines with increased immunogenicity. Beyond individual cell manipulation, CRISPR also provides opportunities to reshape the tumor microenvironment by knocking out immunosuppressive pathways or introducing immune-stimulatory factors, thereby improving vaccine potency. Newer CRISPR systems, including Cas12 and Cas13, along with advanced strategies such as CRISPRa/i and multiplex gene editing, broaden the scope of cancer vaccine design, offering refined control over gene expression and multi-targeted approaches. The choice of delivery platforms including lipid nanoparticles, viral vectors, electroporation, and exosome-based carriers further influences clinical applicability. Importantly, several ongoing clinical trials are already testing CRISPR- based cancer immunotherapies, underscoring the translational potential of these technologies. Despite promising results, challenges remain, including off-target effects, immunogenicity, ethical issues, and regulatory barriers. Finally, we present future directions, including CRISPR- guided nanotumors and AI-driven neoantigen prioritization, which together highlight the importance of CRISPR.
Keywords
References (136)
- Melief CJ, van Hall T, Arens R, Ossendorp F, van der Burg SH. Therapeutic
- cancer vaccines. The Journal of Clinical Investigation. 2015 Sep 1;125(9):3401-
- Burns KH. Transposable elements in cancer. Nature Reviews Cancer. 2017
- Jul;17(7):415-24.
- 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 Aug 17;337(6096):816-21.
- doi:10.1126/science.1225829
- Doudna JA, Charpentier E. The new frontier of genome engineering with
- CRISPR-Cas9. Science. 2014;346(6213):1258096. doi:10.1126/science.1258096
- Manguso RT, Pope HW, Zimmer MD, Brown FD, Yates KB, Miller BC, et al. In
- vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target.
- Nature. 2017;547(7664):413–8. doi:10.1038/nature23270
- Zhang Y, Zhang Z. The history and advances in cancer immunotherapy:
- understanding the characteristics of tumor-infiltrating immune cells and their
- therapeutic implications. Cell Mol Immunol. 2020;17(8):807–21.
- doi:10.1038/s41423-020-0488-6
- Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, et al.
- CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human
- chimeric antigen receptor T cells. Sci Rep. 2017;7:737. doi:10.1038/s41598-017-
- Liu C, Zhang L, Liu H, Cheng K. Delivery strategies of the CRISPR-Cas9 gene-
- editing system for therapeutic applications. J Control Release. 2022;341:1–15.
- doi:10.1016/j.jconrel.2021.11.034
- 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(7785):149–57. doi:10.1038/s41586-019-1711-4
- Ceccaldi R, Rondinelli B, D’Andrea AD. Repair pathway choices and
- consequences at the double-strand break. Trends Cell Biol. 2016;26(1):52–64.
- doi:10.1016/j.tcb.2015.07.009
- Su S, Zou Z, Chen F, et al. CRISPR-Cas9 mediated efficient PD-1 disruption on
- human primary T cells from cancer patients. Sci Rep. 2016;6:20070.
- doi:10.1038/srep20070
- Peng D, Kryczek I, Nagarsheth N, et al. Epigenetic silencing of TH1-type
- chemokines shapes tumour immunity and immunotherapy. Nature.
- 2015;527(7577):249–53. doi:10.1038/nature15520
- Tran E, Robbins PF, Rosenberg SA. ‘Final common pathway’ of human cancer
- immunotherapy: targeting random somatic mutations. Nat Immunol.
- 2017;18(3):255–62. doi:10.1038/ni.3682
- Seki A, Rutz S. Optimized RNP transfection for highly efficient CRISPR/Cas9-
- mediated gene knockout in primary T cells. J Exp Med. 2018;215(3):985–97.
- doi:10.1084/jem.20171626
- Gilbert LA, Larson MH, Morsut L, et al. CRISPR-mediated modular RNA-guided
- regulation of transcription in eukaryotes. Cell. 2013;154(2):442–51.
- doi:10.1016/j.cell.2013.06.044
- Zetsche B, Gootenberg JS, Abudayyeh OO, et al. Cpf1 is a single RNA-guided
- endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163(3):759–71.
- doi:10.1016/j.cell.2015.09.038
- Litchfield K, Reading JL, Puttick C, Thakkar K, Abbosh C, Bentham R, et al.
- Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to
- checkpoint inhibition. Cell. 2021;184(3):596–614.e14.
- doi:10.1016/j.cell.2020.12.032
- Yuan Y, Wang H, Wang Y, Huang L, Wu X, Zhou Y, et al. CRISPR-Cas9 screen
- identifies PTPN2 as a key regulator of antigen presentation and tumor immunity
- in lung cancer. J Exp Med. 2023;220(2):e20221135. doi:10.1084/jem.20221135
- Liu Q, Cheng K, Liao Y, Chen Y, Zhao M, Lu Y, et al. DeepHLApan and
- personalized neoantigen discovery using CRISPR-based tumor models. Brief
- Bioinform. 2024;25(1):bbae039. doi:10.1093/bib/bbae039
- Rodrigues PF, Alberti-Servera L, Eremin A, Grajales-Reyes GE, Ivanek R,
- Tussiwand R. Distinct progenitor lineages contribute to the heterogeneity of
- plasmacytoid dendritic cells. Nat Immunol. 2021;22(5):620–35.
- doi:10.1038/s41590-021-00901-0
- Joosse ME, Topham DJ. The role of dendritic cells in shaping adaptive immunity
- and tolerogenic responses. Front Immunol. 2022;13:833982.
- doi:10.3389/fimmu.2022.833982
- 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(7603):420–24. doi:10.1038/nature17946
- Gao Y, Zhang C, Zhou Y, Shen Y, Du Y, Wu Y, et al. Tumor cell-intrinsic PD-L1
- promotes tumor-initiating cell generation and functions in melanoma and breast
- cancer. Cell Rep. 2022;38(2):110249. doi:10.1016/j.celrep.2022.110249
- Chen Y, Zhang Y, Zhang Y, Wang Y, Ding M, Li L, et al. Engineering tumor
- cell-based vaccines with CRISPR-mediated cytokine release for enhanced
- immunogenicity. Adv Sci (Weinh). 2023;10(12):2207024.
- doi:10.1002/advs.202207024
- Wang H, Mooney DJ. Biomaterial-assisted targeted modulation of immune cells
- in cancer immunotherapy. Nat Mater. 2023;22(4):491–503. doi:10.1038/s41563-
- Zhang Y, Chen J, Zhou F, Zhang C, Wang X, Zhang Y, et al. CRISPR-mediated
- knockdown of VEGFA and IL-6 enhances antitumor immunity by remodeling the
- tumor microenvironment. Cancer Res. 2022;82(10):1854–66. doi:10.1158/0008-
- 5472.CAN-21-3966
- Kumari N, Dwarakanath BS, Das A, Bhatt AN. Role of interleukin-6 in cancer
- progression and therapeutic resistance. Tumour Biol.
- 2021;43(1):10104283211041229. doi:10.1177/10104283211041229
- Deng L, Ren J, Liu L, Liu Q, Wang D, Zhang Y, et al. Dual CRISPR-mediated
- knockout of PD-L1 and activation of STING enhances immunogenicity of cold
- tumors. Nat Commun. 2024;15:4711. doi:10.1038/s41467-024-34711-9
- Benci JL, Xu B, Qiu Y, Wu TJ, Dada H, Twyman-Saint Victor C, et al. Tumor
- interferon signaling regulates a multigenic resistance program to immune
- checkpoint blockade. Cell. 2016;167(6):1540–54.e12.
- doi:10.1016/j.cell.2016.11.022
- Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, Barcena C, et
- al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9
- complex. Nature. 2015;517(7536):583–88. doi:10.1038/nature14136
- Bowling S, Sritharan D, Osorio FG, Nguyen M, Cheung P, Rodriguez-Fraticelli
- AE, et al. An engineered CRISPR-Cas9 mouse line for simultaneous readout of
- lineage histories and gene expression profiles in single cells. Cell.
- 2020;181(2):325–40.e24. doi:10.1016/j.cell.2020.02.043
- Han X, Liu Z, Jo MC, Zhang K, Li Y, Zeng Z, et al. CRISPR-Cas9 delivery
- mediated with synthetic hybrid lipid nanoparticles for cancer immunotherapy.
- Adv Mater. 2019;31(52):e1902952. doi:10.1002/adma.201902952
- Klompe SE, Vo PLH, Halpin-Healy TS, Sternberg SH. Transposon-encoded
- CRISPR–Cas systems direct RNA-guided DNA integration. Nature.
- 2019;571(7764):219–25. doi:10.1038/s41586-019-1323-z
- Pardi N, Hogan MJ, Porter FW, Weissman D. mRNA vaccines—a new era in
- vaccinology. Nat Rev Drug Discov. 2018;17(4):261–79.
- doi:10.1038/nrd.2017.243
- Zhao X, Yang K, Zhao R, Ji T, Wang X, Yang X, et al. Inducing enhanced
- immunogenic tumor cell death with nanocarrier-mediated codelivery of epigenetic
- drugs and TLR agonists. Biomaterials. 2020;232:119681.
- doi:10.1016/j.biomaterials.2019.119681
- Wang H, Zhang X, Zuo Y, Wang J, Li L, Yu T, et al. Co-delivery of mRNA
- vaccine and CRISPR/Cas9 system using lipid nanoparticles for cancer
- immunotherapy. Biomaterials. 2023;295:121999.
- doi:10.1016/j.biomaterials.2022.121999
- Li C, Liu H, Sun Y, Wang J, Yang J, Zheng S, et al. A CRISPR-based STING
- pathway booster enhances mRNA vaccine-induced immunity against cold tumors.
- Nat Biomed Eng. 2024;8(1):112–25. doi:10.1038/s41551-023-01131-2
- Abbasi J. Programmable mRNA translation for future vaccines. JAMA.
- 2023;329(22):1892. doi:10.1001/jama.2023.6963
- Liu X, Tang X, Li H, Li R, Fan H, Lu J, et al. Artificial intelligence-augmented
- CRISPR design streamlines personalized neoantigen vaccine development. Nat
- Commun. 2023;14(1):2921. doi:10.1038/s41467-023-38685-3
- Hou X, Zaks T, Langer R, Dong Y. Lipid nanoparticles for mRNA delivery. Nat
- Rev Mater. 2021;6(12):1078–94. doi:10.1038/s41578-021-00358-0
- Kulkarni JA, et al. The current landscape of nucleic acid delivery via lipid
- nanoparticles. Nat Nanotechnol. 2021;16(6):630–43.
- Wang D, Tai PWL, Gao G. Adeno-associated virus vector as a platform for gene
- therapy delivery. Nat Rev Drug Discov. 2019;18(5):358–75.
- Milone MC, O’Doherty U. Clinical use of lentiviral vectors. Leukemia.
- 2018;32(7):1529–46.
- Stadtmauer EA, et al. CRISPR-engineered T cells in patients with refractory
- cancer. Science. 2020;367(6481):eaba7365.
- Wang P, et al. Gold nanoparticle-based gene therapy: recent advances and future
- prospects. ACS Appl Bio Mater. 2018;1(4):561–75.
- Kamerkar S, et al. Exosomes facilitate therapeutic targeting of oncogenic KRAS
- in pancreatic cancer. Nature. 2017;546(7659):498–503.