Non-Enzymatic Structural Modifications Reshape Peptide Presentation and Antigen Recognition

Cytotoxic T lymphocytes recognize infected or transformed cells through peptide antigens presented by major histocompatibility complex class I (MHC-I) molecules. Although antigen recognition is typically defined by peptide sequence, chemical modifications to amino acid sidechains can generate structurally distinct epitopes that alter immune recognition. Here, we investigated how endogenous and exogenous electrophiles can install non-enzymatic post-translational modifications (PTMs), thereby influencing antigen presentation and T cell activation. Notably, these structural modifications are typically irreversible and can persist through protein processing and subsequent peptide presentation. We comprehensively mapped out these potential modifications found that peptide variants bearing non-enzymatic PTMs altered MHC-I stability and disrupted T cell recognition, particularly when modifications occurred at TCR-contact residues. To identify such species on MHC-I of cells, we developed a chemical enrichment strategy using an alkyne-tagged probe to capture non-enzymatically acylated peptides associated with MHC-I. Finally, we show that electrophilic environmental chemicals and dietary isothiocyanates (ITCs) can covalently modify antigenic peptides and abolish T cell activation despite preserved MHC-I binding. Together, these findings demonstrate that endogenous and exogenous chemical modifications can reshape the immunopeptidome and generate chemically distinct peptide antigens that alter adaptive immune recognition.