Identification and profiling of HLA-A*02:01-restricted Toxoplasma gondii peptides through immunopeptidomics in HLA-A2.1 transgenic mice

HLA class I presentation of pathogen-derived peptides is essential for CD8+ T-cell recognition of Toxoplasma gondii. While in vitro MHC ligands have been documented, the in vivo epitope landscape during infection progression remains poorly characterized. Here, we employed an MS-based immunopeptidomics approach to directly profile the T. gondii immunopeptidome presented by HLA-A*02:01 in transgenic mice. By employing a hierarchical discovery funnel, our analysis identified a comprehensive repertoire of 3,744 unique T. gondii-derived peptides. Subsequent filtering for canonical 8–12mers, matching the typical binding length for HLA-A*02:01 ligands, established a high-confidence foundational ligandome of 3,433 peptides. Source protein analysis revealed that these peptides originate from diverse parasite proteins, including a substantial proportion of previously uncharacterized hypothetical proteins. Notably, specific ligands were consistently detected across both acute and chronic stages, suggesting stable MHC-I presentation throughout the infection cycle. By integrating in silico predictions with experimental validation, we prioritized 73 high-affinity candidates, five of which exhibited robust HLA-A*02:01 binding capacity in vitro and in vivo. Specifically, we identified a novel ligand derived from glycogen synthase (PGS) and determined its co-crystal structure with HLA-A*02:01, revealing favorable binding architecture. Overall, these findings expand the known HLA-A*02:01-restricted ligand landscape of T. gondii and provide a high-priority list of candidates for future functional validation of CD8+ T-cell immunogenicity.