HLA micropolymorphisms confine neoantigen conformational adaptability and guide T cell receptor selectivity

T cell receptor (TCR) restriction by highly polymorphic major histocompatibility complex (MHC) proteins is a foundation of cellular immunity. Although the effects of MHC polymorphisms on peptide binding and selection are well established, how micropolymorphisms within MHC supertypes impact immune recognition is poorly understood. Here, we identified a novel mechanism through which the micropolymorphisms in two closely related HLA-A3 superfamily members determine TCR specificity. We previously showed that TCRs specific for a public neoantigen from the PIK3CA oncogene presented by HLA-A*03:01 were unable to recognize the same epitope in the context of HLA-A*03:02. We found here that the micropolymorphisms distinguishing A*03:02 from A*03:01 exert their effect not by altering peptide binding or static structures, but by changing the conformational ensemble of the neoantigen in the groove, preventing it from adopting a conformation compatible with TCR binding. The effect is rooted in how the two polymorphic sites interact with other co-varying, evolutionarily coupled polymorphisms, reflecting a cross-groove network of interactions that controls the conformational adaptability of the peptide/HLA complex. We suggest polymorphism-dependent conformational adaptability reflects an evolved feature of class I MHC proteins that amplifies the impact of peptides in the groove, further diversifying epitopes and contributing to how TCRs and other immunoreceptors differentiate between antigens. Beyond this mechanistic insight, our findings emphasize the need for high-resolution HLA typing in efforts across immunology, including antigen-specific immunotherapy.