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

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dc.citation.articleNumber1108303en_US
dc.citation.journalTitleFrontiers in Immunologyen_US
dc.citation.volumeNumber14en_US
dc.contributor.authorHall-Swan, Sarahen_US
dc.contributor.authorSlone, Jareden_US
dc.contributor.authorRigo, Mauricio M.en_US
dc.contributor.authorAntunes, Dinler A.en_US
dc.contributor.authorLizée, Gregoryen_US
dc.contributor.authorKavraki, Lydia E.en_US
dc.date.accessioned2023-07-21T16:13:51Zen_US
dc.date.available2023-07-21T16:13:51Zen_US
dc.date.issued2023en_US
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.en_US
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.en_US
dc.identifier.digitalfimmu-14-1108303en_US
dc.identifier.doihttps://doi.org/10.3389/fimmu.2023.1108303en_US
dc.identifier.urihttps://hdl.handle.net/1911/114993en_US
dc.language.isoengen_US
dc.publisherFrontiers Media S.A.en_US
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.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titlePepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structureen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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