Predicting Antigen-Specificities of Orphan T Cell Receptors from Cancer Patients with TCRpcDist.
deorphanization
epitope specificity
specificity prediction
t cell receptors (TCRs)
tcr clustering
tumor antigens
Journal
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
ISSN: 2198-3844
Titre abrégé: Adv Sci (Weinh)
Pays: Germany
ID NLM: 101664569
Informations de publication
Date de publication:
19 Aug 2024
19 Aug 2024
Historique:
revised:
19
07
2024
received:
30
05
2024
medline:
19
8
2024
pubmed:
19
8
2024
entrez:
19
8
2024
Statut:
aheadofprint
Résumé
Approaches to analyze and cluster T-cell receptor (TCR) repertoires to reflect antigen specificity are critical for the diagnosis and prognosis of immune-related diseases and the development of personalized therapies. Sequence-based approaches showed success but remain restrictive, especially when the amount of experimental data used for the training is scarce. Structure-based approaches which represent powerful alternatives, notably to optimize TCRs affinity toward specific epitopes, show limitations for large-scale predictions. To handle these challenges, TCRpcDist is presented, a 3D-based approach that calculates similarities between TCRs using a metric related to the physico-chemical properties of the loop residues predicted to interact with the epitope. By exploiting private and public datasets and comparing TCRpcDist with competing approaches, it is demonstrated that TCRpcDist can accurately identify groups of TCRs that are likely to bind the same epitopes. Importantly, the ability of TCRpcDist is experimentally validated to determine antigen specificities (neoantigens and tumor-associated antigens) of orphan tumor-infiltrating lymphocytes (TILs) in cancer patients. TCRpcDist is thus a promising approach to support TCR repertoire analysis and TCR deorphanization for individualized treatments including cancer immunotherapies.
Identifiants
pubmed: 39159239
doi: 10.1002/advs.202405949
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e2405949Subventions
Organisme : Swiss National Science Foundation
ID : 205321_192019
Pays : Switzerland
Organisme : Swiss National Science Foundation
ID : 310030_182384
Pays : Switzerland
Organisme : Swiss National Science Foundation
ID : CRSII5_193749
Pays : Switzerland
Organisme : Cancera Foundation
Organisme : Mats Paulssons Foundation
Organisme : Biltema Foundation
Organisme : Ludwig Institute for Cancer Research
Organisme : University of Lausanne
Informations de copyright
© 2024 The Author(s). Advanced Science published by Wiley‐VCH GmbH.
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