Properties of CD8 T-cell-recognized neoantigens in different tumor types

Our plain-English summary of Properties of CD8 T-cell-recognized neoantigens in different tumor types, by S.L.C. Ketelaars, M.M. van Buuren, A. Gangaev, et al (Immuno-oncology Technology, 2025).

The study

• Authors: S.L.C. Ketelaars, M.M. van Buuren, A. Gangaev, N. van Rooij, S. Patiwael, K. Hoefakker, L.F. Fanchi, P. Baas, M. van der Heijden, M. Kok, T.N. Schumacher, P. Kvistborg, J.B.A.G. Haanen
• Journal: Immuno-oncology Technology
• Published: 2025;27:101062
• Cited by: 2 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Background: Neoantigen-based immunotherapies rely on computational tools predicting peptide immunogenicity based on properties such as its expression level, binding affinity to human leukocyte antigen (HLA), likelihood of proteasomal cleavage and dissimilarity from wild-type peptide. However, current datasets are scarce and limited to highly mutated tumor types such as melanoma and lung cancer, leaving uncertainty about the value of these properties in other tumor types.

Materials And Methods: To investigate this, we retrospectively analyzed the properties of immunogenic neoantigens identified in CD8 T-cell recognition screens of predicted neoantigens in tumor-infiltrating lymphocytes (TILs) from 12 melanoma patients and peripheral blood mononuclear cells (PBMCs) from 14 patients with mesothelioma, triple-negative breast cancer or urothelial cancer. In both experimental settings, CD8 T-cell recognition was assessed using a combinatorial peptide-HLA (pHLA) multimer-based technology.

Results: CD8 T-cell responses were detected against in total 34 of the 8103 predicted neoantigens (0.4%). In both PBMCs and TILs, the eluted ligand (EL) score-the predicted likelihood of a pHLA being presented on the cell surface-was the strongest predictor of immunogenicity, followed by predicted HLA binding affinity. Moreover, in the TILs, the frequency of neoantigen-specific CD8 T cells was strongly correlated with these properties across the 12 patients.

Conclusions: These findings underscore the value of both EL score and HLA binding affinity as key predictors of neoantigen immunogenicity in different tumor types. Furthermore, we demonstrate for the first time an immunodominance hierarchy of neoantigen-specific CD8 T-cell responses across patients in ex vivo expanded TIL cultures.

© 2025 The Authors.

In plain English

This was a retrospective analysis of two previously generated datasets in which predicted tumour neoantigens were tested for recognition by CD8 T cells using a combinatorial peptide-HLA (pHLA) multimer screening method. The authors studied ex vivo expanded tumour-infiltrating lymphocytes (TILs) from 12 melanoma patients and blood cells (PBMCs) taken during immune checkpoint blockade from 14 patients with malignant pleural mesothelioma (7), triple-negative breast cancer (3) or urothelial cancer (4). In the TIL samples, CD8 T-cell responses were found against 21 of 6553 tested pHLA (0.32%) in 10 of 12 patients; in the PBMC samples, against 13 of 1550 (0.84%) in 9 of 14 patients, 34 of 8103 overall. The eluted ligand (EL) score best separated recognised from unrecognised neoantigens (TIL AUC 0.77; PBMC AUC 0.89), followed by predicted HLA binding affinity (TIL AUC 0.76; PBMC AUC 0.88). Measures of "non-selfness" showed no significant association. The authors concluded that EL score and HLA binding affinity are key predictors of neoantigen immunogenicity across tumour types.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Retrospective analysis of neoantigen properties from two previously conducted CD8 T-cell recognition screens (pHLA multimer screening)
• Who was studied: 26 patients: ex vivo expanded TILs from 12 melanoma patients and PBMCs from 14 patients treated with immune checkpoint blockade who had malignant pleural mesothelioma (n = 7), triple-negative breast cancer (n = 3) or urothelial cancer (n = 4)
• Exposure: Not an environmental exposure study; the variables examined were predicted neoantigen properties: HLA binding affinity, eluted ligand (EL) score, RNA expression, proteasomal cleavage likelihood, and 'non-selfness' measures (agretopicity, foreignness, dissimilarity)
• Main results:
  • In the melanoma TIL samples, CD8 T-cell responses were detected against 21 (0.32%) of 6553 tested pHLA, in 10 of 12 patients
  • In the PBMC samples (mesothelioma, TNBC, urothelial cancer), responses were detected against 13 (0.84%) of 1550 tested pHLA, in 9 of 14 patients
  • Across both datasets, CD8 T-cell recognition was detected for 34 of 8103 candidate neoantigens (0.4%)
  • EL score was the strongest predictor of immunogenicity in both settings, followed by predicted HLA binding affinity
  • RNA expression predicted immunogenicity only in the TIL dataset; proteasomal cleavage did not predict it in the TIL dataset
  • In the mesothelioma (MPM) and urothelial cancer subsets of the PBMC dataset, recognised neoantigens had higher predicted HLA binding affinity and higher EL scores than non-recognised ones
  • Tumour mutational burden of the mesothelioma tumours ranged from 1.2 to 2.7 nonsynonymous mutations per megabase (median 1.2)
  • In the TIL dataset the frequency of neoantigen-specific CD8 T cells correlated with predicted HLA binding affinity and EL score across patients, and more weakly with expression level
  • No statistically significant correlations of this kind were found in the PBMC dataset
  • Measures of 'non-selfness' were not significantly associated with immunogenicity in these datasets
• The authors' conclusion: The authors concluded that EL score and HLA binding affinity are key predictors of neoantigen immunogenicity in different tumour types, and that they observed, for the first time in their view, an immunodominance hierarchy across patients in ex vivo expanded TIL cultures
• Limitations the authors state:
  • The authors state that blood samples were taken during checkpoint blockade and were selected on clinical response, so other settings may show absent or undetectable responses
  • The authors state the number of potentially immunogenic neoantigens is likely underestimated
  • The authors note that differences between the two datasets complicate direct comparisons
  • The authors state the TIL immunodominance finding needs validation in other TIL cultures
  • The authors note only CD8 responses were measured and CD4 responses may be more prevalent

Topics

Medical terms in this study, explained in our Lexicon: Lung Cancer, Tumor-Infiltrating Lymphocytes, Mesothelioma.

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