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bioRxiv · 10.1101/2025.06.05.658000

A high-throughput immunopeptidome platform for MHC II alleles to characterize antigen-specific CD4 + T cells

Chen, J.·Zhu, X.·Huo, J.·Wu, S.·Zhou, T.·Cheng, C.·Dong, H.·Li, Y.·Chen, Y.·Dong, X.
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Abstract

CD4+ T cells play a pivotal role in adaptive immunity, recognizing peptide antigens presented by MHC II molecules during infections and tumor development. Identifying immunodominant MHC II epitopess is essential for understanding CD4+ T cell responses; however, current methods such as mass spectrometry, suffer from low sensitivity and throughput, while computational algorithms show variable accuracy. To overcome these challenges, we developed EliteMHCII, a high-throughput immunopeptidome profiling platform that identifies antigen-derived MHC II epitopes and measures peptide binding affinity across 24 globally common MHC II alleles. Using EliteMHCII, we assessed the immunodominant epitopes of the SARS-CoV-2 RBD protein. Validation in vaccinated individuals and humanized mouse models revealed a strong correlation between high-affinity peptides and robust CD4+ T cell responses, while low-affinity peptides failed to elicit responses. Therefore, our immunopeptidome profiling platform, EliteMHCII, serves as a rapid, high throughput, feasible platform for CD4+ T cell epitope discovery at a global populational level in the context of infectious diseases and cancer immunotherapy.

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Chen, J., Zhu, X., Huo, J., Wu, S., Zhou, T., Cheng, C., Dong, H., Li, Y., Chen, Y., Dong, X.. 2025-06-09. A high-throughput immunopeptidome platform for MHC II alleles to characterize antigen-specific CD4 + T cells. https://doi.org/10.1101/2025.06.05.658000

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