Ketelaars S L C, van Buuren M M, Gangaev A, van Rooij N, Patiwael S, Hoefakker K, Fanchi L F, Baas P, van der Heijden M, Kok M, Schumacher T N, Kvistborg P, Haanen J B A G
Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
Oncode Institute, Utrecht, The Netherlands.
Immunooncol Technol. 2025 Jun 13;27:101062. doi: 10.1016/j.iotech.2025.101062. eCollection 2025 Sep.
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.
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.
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.
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 expanded TIL cultures.
基于新抗原的免疫疗法依赖于计算工具，这些工具根据肽的表达水平、与人白细胞抗原（HLA）的结合亲和力、蛋白酶体切割的可能性以及与野生型肽的差异等特性来预测肽的免疫原性。然而，目前的数据集稀缺，且仅限于黑色素瘤和肺癌等高突变肿瘤类型，这使得这些特性在其他肿瘤类型中的价值存在不确定性。
为了研究这一问题，我们回顾性分析了在12例黑色素瘤患者的肿瘤浸润淋巴细胞（TIL）和14例间皮瘤、三阴性乳腺癌或尿路上皮癌患者的外周血单个核细胞（PBMC）中对预测新抗原进行的CD8 T细胞识别筛选中鉴定出的免疫原性新抗原的特性。在这两种实验设置中，使用基于组合肽-HLA（pHLA）多聚体的技术评估CD8 T细胞识别。
在8103个预测新抗原中，总共检测到针对34个新抗原的CD8 T细胞反应（0.4%）。在PBMC和TIL中，洗脱配体（EL）评分（预测pHLA在细胞表面呈现可能性）是免疫原性的最强预测指标，其次是预测的HLA结合亲和力。此外，在TIL中，新抗原特异性CD8 T细胞的频率与12例患者的这些特性密切相关。
这些发现强调了EL评分和HLA结合亲和力作为不同肿瘤类型中新抗原免疫原性关键预测指标的价值。此外，我们首次在扩大的TIL培养物中证明了不同患者间新抗原特异性CD8 T细胞反应的免疫显性层次结构。
