A generalizable system for antigenic peptide targeting across HLA-I allotypes

Blackson, W.; Small, E. L.; Sun, S. M.; Shinde, O.; Pantula, R.; Wang, S. J.; Rotsides, P.; Du, H.; Sun, Y.; Hwang, D.; Wang, C. S.; Lu, T.; Laskawy, E.; Kapoor, R.; Want, M. Y.; June, C. H.; Young, R. M.; Maris, J. M.; Huang, P.-S.; Sgourakis, N. G.

doi:10.64898/2026.05.21.726655

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bioRxiv · 10.64898/2026.05.21.726655

A generalizable system for antigenic peptide targeting across HLA-I allotypes

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Abstract

T cell receptors (TCRs) and TCR-mimicking antibodies recognize peptide antigens in the context of specific Human Leucocyte Antigen (HLA-I) allotypes, and the extreme polymorphism of the HLA locus limits the breadth of immunotherapy development. Key barriers include divergent molecular surfaces on HLA proteins and differences in the peptide structure. As a result, existing modalities cannot confer therapeutic coverage across patients of divergent genetic backgrounds. Here, we develop an approach which combines a peptide conformational prediction tool, PepPred, with a cross-HLA binding protein engineering system, TRACeR-I1, to outline a generalized framework for developing binders (xTRACeRs) with compatibility across HLA allotypes while maintaining high levels of specificity towards the peptide antigen. We use our system to develop and validate xTRACeRs against clinically relevant, established peptide antigens presented across common alleles within five HLA-A/B/C supertypes2. Cryo-EM structures of xTRACeR-pHLA complexes for an oncofetal antigen from PRAME and a neuroblastoma-specific peptide from PHOX2B reveal effective mechanisms to navigate polymorphic HLA surface residues, and extensive interactions with the peptide. We implemented these two xTRACeRs as Chimeric Antigen Receptor (CAR) T cells and demonstrated their potent killing efficacy and specificity. Overcoming restriction across HLA supertypes lifts a key barrier in HLA-targeted immunotherapy by expanding patient coverage.

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Blackson, W., Small, E. L., Sun, S. M., Shinde, O., Pantula, R., Wang, S. J., Rotsides, P., Du, H., Sun, Y., Hwang, D., Wang, C. S., Lu, T., Laskawy, E., Kapoor, R., Want, M. Y., June, C. H., Young, R. M., Maris, J. M., Huang, P.-S., Sgourakis, N. G.. 2026-05-22. A generalizable system for antigenic peptide targeting across HLA-I allotypes. https://doi.org/10.64898/2026.05.21.726655

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