Ranking neoantigens for escape-resilience rather than predicted immunogenicity: Associated changes in vaccine design.

Bryan ME., Weatherseed M., Gandhi OH., Ince W., Vavoulis D., Schuh A., Lee SM., Adamopoulou E., Watson RA., Mair R., Leung CSK., Lee LY., Elliott T.

Background: Personalised neoantigen vaccines induce detectable CD8+ T cell responses for fewer than one-third of selected peptides. Current pipelines prioritise candidates by predicted immunogenicity and select peptides independently, overlooking two constraints: efficacy depends on the peptide set as a whole, and tumours adapt antigen processing under immune pressure. We developed a framework that optimises peptide combinations for resilience to tumour escape and tested whether escape-resilience predicts clinical immunogenicity. Methods: We modelled peptide susceptibility to five antigen-processing escape mechanisms: TAP downregulation, immunoproteasome-to-constitutive proteasome switching, aminopeptidase upregulation, tapasin loss, and HLA loss of heterozygosity. Selection was formulated as a minimax optimisation, maximising predicted efficacy under worst-case tumour adaptation. We analysed five neoantigen vaccine trials with per-epitope CD8+ T cell response data, consisting of 571 neoantigens, 3, 806 peptides, and 174 patients. Mixed-effects models tested associations between escape-resilience and immunogenicity, adjusting for binding affinity (NetMHCpan-4.1 %rank), pMHC stability (NetMHCstabpan), mutation type, and clonality. Six hypotheses were pre-registered with Bonferroni correction. Results: Escape-resilience predicted immunogenicity independently of established features. After adjustment, vulnerability to TAP loss (OR 0.42 per SD, 95% CI 0.24–0.71, p=0.0018) and proteasome switching (OR 0.54 per SD, 95% CI 0.34–0.86, p=0.0089) were associated with failure to elicit CD8+ responses. Among peptides with comparable predicted binding affinity, escape-resilient peptides were significantly more likely to be immunogenic. Composite escape-resilience scores discriminated immunogenic from non-immunogenic peptides (AUC 0.71, 95% CI 0.66–0.76), outperforming binding affinity alone (AUC 0.58) and an affinity-stability model (AUC 0.64). Adding escape-resilience improved discrimination (ΔAUC 0.07, p=0.003). Retrospective re-ranking altered 38% (95% CI 31–45%) of vaccine compositions, replacing high-affinity but escape-vulnerable peptides with lower-affinity, processing-robust alternatives. Associations were stronger for truncal mutations (OR 2.8, 95% CI 1.6–4.9) than subclonal mutations (OR 1.4, 95% CI 0.8–2.4; interaction p=0.041), indicating that processing robustness is most consequential for clonally dominant neoantigens. Conclusions: Optimising neoantigen selection against tumour escape identifies peptides more likely to elicit CD8+ T cell responses, independent of binding affinity and stability. The stronger effects in truncal mutations suggest escape-aware ranking may be particularly valuable for durable, clone-targeted vaccination strategies. Prospective trials are needed to assess clinical impact.

DOI

10.1200/JCO.2026.44.16_suppl.2654

Type

Journal article

Publication Date

2026-06-01T00:00:00+00:00

Volume

44

Pages

2654 - 2654

Total pages

0

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