Introduction
Discovery Pipeline
Mechanisms of Action
Current Clinical Landscape
Challenges
Future Directions
References
This article explores the science, clinical development, and therapeutic promise of neoantigen vaccines in personalized immunotherapy. It highlights breakthroughs in sequencing, prediction algorithms, and combinatorial strategies that are redefining precision cancer treatment.
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Introduction
Immune checkpoint inhibitors (ICIs) have reshaped modern oncology, yet many solid tumors remain challenging to treat because of limited antigen visibility, extensive genetic heterogeneity, and a profoundly immunosuppressive tumor microenvironment. These challenges have heightened interest in neoantigens, mutation-derived peptides expressed exclusively by cancer cells.
Since neoantigens bypass thymic tolerance, they elicit potent, tumor-directed T-cell responses, making them a strong foundation for emerging immunotherapies.1
High-throughput sequencing and bioinformatics now allow precise mapping of each patient’s neoantigen repertoire. This supports the development of personalized neoantigen vaccines (PNV). Designed to prime durable, tumor-targeted immunity, these vaccines are demonstrating safety, feasibility, and robust T-cell activation in early trials, positioning them as a powerful complement to ICI therapy in solid tumors.1
Importantly, neoantigens can also arise from non-genomic alterations (e.g., aberrant splicing, alternative ORFs, dysregulated post-translational modifications) and from viral ORFs, broadening the actionable antigen space beyond point mutations.5,8
Discovery Pipeline
PNV development commences with genomic profiling of a patient’s tumor. Whole-exome sequencing and ribonucleic acid sequencing (RNA-seq) map somatic mutations and aberrant transcripts. Multi-omics tools, including single-cell sequencing and spatial transcriptomics, aid in confirming expression and refining candidate selection. Immunopeptidomics (mass spectrometry of HLA-bound ligands) directly validates naturally presented peptides and helps uncover noncanonical epitopes.5,8
Predicted neoantigens are then evaluated using major histocompatibility complex (MHC)-binding and antigen-processing algorithms to identify peptides that are most likely to be presented to the patient's human leukocyte antigen (HLA) molecules. Commonly used tools include NetMHC/NetMHCpan, MHCflurry (class I) and NetMHCIIpan/MixMHC2pred (class II), noting that class II predictions remain less accurate due to peptide-length variability and HLA polymorphism.5,8 These prioritized peptides are synthesized or encoded into messenger RNA (mRNA) or deoxyribonucleic acid (DNA) platforms to create PNVs.1,2
Functional validation is essential, with top peptides tested on patient- or donor-derived T cells. Activation is measured by co-stimulatory marker expression (4-1BB, OX-40) or interferon-gamma (IFN-γ) release in enzyme-linked immunosorbent spot (ELISpot) assays. Additional readouts such as intracellular cytokine staining, multimer/tetramer staining, and TCR repertoire tracking are frequently used to confirm antigen specificity and clonotypic expansion.5,8
In murine models, PNVs, particularly when combined with programmed death protein-1 (PD-1) or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) blockade, drive potent T-cell expansion, reshape the tumor microenvironment, and markedly extend survival. Early clinical studies in melanoma and other solid tumors echo these findings, showing that personalized vaccines can activate both pre-existing and naïve T-cell populations. Together, these data underscore their potential as a powerful partner to ICIs.3,4
Despite sophisticated in silico prioritization, experimentally confirmed immunogenicity rates for predicted candidates remain modest, reinforcing the value of orthogonal validation (e.g., immunopeptidomics plus T-cell assays).5,8
Understanding how these vaccines activate T cells is critical to appreciating their therapeutic potential.
Mechanisms of Action
PNVs initiate de novo T-cell priming, driving the expansion of tumor-specific T cells that express cluster of differentiation 4 (CD4+, helper) and CD8+ (cytotoxic) within lymph nodes. Dendritic cells (DCs) present vaccine-encoded peptides to naïve T cells, generating high-affinity effectors that recognize tumor-restricted peptide-MHC (pMHC) complexes not eliminated during thymic development. cDC1-mediated cross-presentation (MHC-I) and cDC2-driven MHC-II presentation coordinate CD8 and CD4 help, enhancing effector function and memory.5,8
With tumor cell destruction, epitope spreading broadens immunity to additional neoantigens and non-vaccine epitopes, an effect documented in NeoVax-treated melanoma patients and in early-phase studies combining NEO-PV-01 with pembrolizumab.2,4 Such spreading has been associated with sustained TCR diversification and durable antitumor surveillance in longitudinal profiling.1
Combining PNVs with ICIs further amplifies responses. PD-1 or CTLA-4 inhibitors release inhibitory brakes on expanding neoantigen-specific T cells, enhancing effector function and enabling responses even in “cold” tumors with limited baseline immunity.
Across tumor types, combination therapy has repeatedly shown enhanced intratumoral T-cell infiltration, broadened TCR clonality, and higher rates of de novo responses relative to vaccine or ICI alone.3,5 Clinical trials demonstrate that combining personalized vaccines with ICIs, such as nivolumab, pembrolizumab, or dual blockade, can enhance T-cell infiltration and immune responses, improving progression-free survival.3
Current Clinical Landscape
Clinical translation of PNVs has accelerated rapidly, led by major programs from BioNTech, Moderna, and Genentech. Early evidence came from a 2017 pilot study of NeoVax in patients with stage IIIB/C or IV melanoma (NCT01970358). Six patients received a personalized long-peptide vaccine after surgery; four remained recurrence-free at 25 months, while two achieved complete responses after subsequent anti–PD-1 therapy.1
Genentech’s NEO-PV-01 program expanded clinical testing in a Phase Ib trial involving 82 patients with advanced melanoma, non-small cell lung cancer (NSCLC), and bladder cancer. Vaccination combined with pembrolizumab induced de novo and neoantigen-specific CD4+ and CD8+ T cell responses, along with robust epitope spreading.
In the present scenario, mRNA platforms, led by Moderna and BioNTech, are at the forefront. Moderna’s mRNA-4157/V940, delivered with pembrolizumab, achieved a 44 % reduction in recurrence risk in the phase IIb KEYNOTE-942 melanoma trial, prompting breakthrough therapy designation and progression to phase III evaluation.1,5
Challenges
Despite accelerating clinical progress, PNVs face several obstacles. Inter- and intratumoral heterogeneity creates shifting mutational landscapes that fuel immune evasion and complicate antigen selection. Moreover, manufacturing personalized vaccines remains resource-intensive, requiring rapid sequencing, neoantigen prediction, and individualized good manufacturing practice (GMP) production.5,6
Reliable biomarkers are also limited. While tumor mutational burden (TMB) estimates neoantigen load, only a fraction of nonsynonymous mutations may generate peptides that are effectively processed and presented on MHC molecules.5,6,8
Future Directions
Advances in next-generation sequencing and cancer bioinformatics have accelerated neoantigen discovery, and artificial intelligence (AI)-driven epitope prediction is now refining the selection of high-value targets for personalized vaccines.6,7
Alongside algorithmic improvements, future progress will rely on rational combination strategies. Pairing personalized vaccines with ICIs, radiotherapy, chemotherapy, or adoptive cell transfer may address tumor heterogeneity and strengthen T-cell priming, infiltration, and persistence.
References
- Li, X., You, J., Hong, L., Liu, W., Guo, P., & Hao, X. (2023). Neoantigen cancer vaccines: A new star on the horizon. Cancer Biology & Medicine, 21(4), 274. DOI:10.20892/j.issn.2095-3941.2023.0395, https://www.cancerbiomed.org/content/early/2023/12/29/j.issn.2095-3941.2023.0395
- Perrinjaquet, M., & Richard Schlegel, C. (2023). Personalized neoantigen cancer vaccines: An analysis of the clinical and commercial potential of ongoing development programs. Drug Discovery Today, 28(11), 103773. DOI:10.1016/j.drudis.2023.103773, https://www.sciencedirect.com/science/article/pii/S1359644623002891
- Liao, Y., & Zhang, S. (2021). Safety and Efficacy of Personalized Cancer Vaccines in Combination with Immune Checkpoint Inhibitors in Cancer Treatment. Frontiers in Oncology, 11, 663264. DOI:10.3389/fonc.2021.663264, https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2021.663264/full
- Richard, G., Ruggiero, N., Steinberg, G. D., Martin, W. D., & De Groot, A. S. (2024). Neoadjuvant personalized cancer vaccines: the final frontier? Expert Review of Vaccines, 23(1), 205–212. DOI:10.1080/14760584.2024.2303015, https://www.tandfonline.com/doi/full/10.1080/14760584.2024.2303015
- Zhou, Y., Wei, Y., Tian, X. et al. (2025). Cancer vaccines: current status and future directions. J Hematol Oncol, 18, 18. DOI:10.1186/s13045-025-01670-w, https://jhoonline.biomedcentral.com/articles/10.1186/s13045-025-01670-w
- Shen, Y., Yu, L., Xu, X., Yu, S., & Yu, Z. (2022). Neoantigen vaccine and neoantigen-specific cell adoptive transfer therapy in solid tumors: Challenges and future directions. Cancer Innovation, 1(2), 168-182. DOI:10.1002/cai2.26, https://onlinelibrary.wiley.com/doi/full/10.1002/cai2.26
- Garg, P., Pareek, S., Kulkarni, P., Horne, D., Salgia, R., & Singhal, S. S. (2023). Next-Generation Immunotherapy: Advancing Clinical Applications in Cancer Treatment. Journal of Clinical Medicine, 13(21), 6537. DOI:10.3390/jcm13216537, https://www.mdpi.com/2077-0383/13/21/6537
- Xie, N., Shen, G., Gao, W., Huang, Z., Huang, C., & Fu, L. (2023). Neoantigens: Promising targets for cancer therapy. Signal Transduction and Targeted Therapy, 8(1), 9. DOI:10.1038/s41392-022-01270-x, https://www.nature.com/articles/s41392-022-01270-x
Further Reading
Last Updated: Dec 16, 2025