PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure

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dc.citation.articleNumber1108303
dc.citation.journalTitleFrontiers in Immunology
dc.citation.volumeNumber14
dc.contributor.authorHall-Swan, Sarah
dc.contributor.authorSlone, Jared
dc.contributor.authorRigo, Mauricio M.
dc.contributor.authorAntunes, Dinler A.
dc.contributor.authorLizée, Gregory
dc.contributor.authorKavraki, Lydia E.
dc.date.accessioned2023-07-21T16:13:51Z
dc.date.available2023-07-21T16:13:51Z
dc.date.issued2023
dc.description.abstractIntroductionPeptide-HLA class I (pHLA) complexes on the surface of tumor cells can be targeted by cytotoxic T-cells to eliminate tumors, and this is one of the bases for T-cell-based immunotherapies. However, there exist cases where therapeutic T-cells directed towards tumor pHLA complexes may also recognize pHLAs from healthy normal cells. The process where the same T-cell clone recognizes more than one pHLA is referred to as T-cell cross-reactivity and this process is driven mainly by features that make pHLAs similar to each other. T-cell cross-reactivity prediction is critical for designing T-cell-based cancer immunotherapies that are both effective and safe.MethodsHere we present PepSim, a novel score to predict T-cell cross-reactivity based on the structural and biochemical similarity of pHLAs.Results and discussionWe show our method can accurately separate cross-reactive from non-crossreactive pHLAs in a diverse set of datasets including cancer, viral, and self-peptides. PepSim can be generalized to work on any dataset of class I peptide-HLAs and is freely available as a web server at pepsim.kavrakilab.org.
dc.identifier.citationHall-Swan, Sarah, Slone, Jared, Rigo, Mauricio M., et al.. "PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure." <i>Frontiers in Immunology,</i> 14, (2023) Frontiers Media S.A.: https://doi.org/10.3389/fimmu.2023.1108303.
dc.identifier.digitalfimmu-14-1108303
dc.identifier.doihttps://doi.org/10.3389/fimmu.2023.1108303
dc.identifier.urihttps://hdl.handle.net/1911/114993
dc.language.isoeng
dc.publisherFrontiers Media S.A.
dc.rightsExcept where otherwise noted, this work is licensed under a Creative Commons Attribution (CC BY) license.  Permission to reuse, publish, or reproduce the work beyond the terms of the license or beyond the bounds of Fair Use or other exemptions to copyright law must be obtained from the copyright holder.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titlePepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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