Deep learning predictions of TCR-epitope interactions reveal epitope-specific chains in dual alpha T cells.

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Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_5F1F27C4B8D4
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Deep learning predictions of TCR-epitope interactions reveal epitope-specific chains in dual alpha T cells.
Journal
Nature communications
Author(s)
Croce G., Bobisse S., Moreno D.L., Schmidt J., Guillame P., Harari A., Gfeller D.
ISSN
2041-1723 (Electronic)
ISSN-L
2041-1723
Publication state
Published
Issued date
13/04/2024
Peer-reviewed
Oui
Volume
15
Number
1
Pages
3211
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
T cells have the ability to eliminate infected and cancer cells and play an essential role in cancer immunotherapy. T cell activation is elicited by the binding of the T cell receptor (TCR) to epitopes displayed on MHC molecules, and the TCR specificity is determined by the sequence of its α and β chains. Here, we collect and curate a dataset of 17,715 αβTCRs interacting with dozens of class I and class II epitopes. We use this curated data to develop MixTCRpred, an epitope-specific TCR-epitope interaction predictor. MixTCRpred accurately predicts TCRs recognizing several viral and cancer epitopes. MixTCRpred further provides a useful quality control tool for multiplexed single-cell TCR sequencing assays of epitope-specific T cells and pinpoints a substantial fraction of putative contaminants in public databases. Analysis of epitope-specific dual α T cells demonstrates that MixTCRpred can identify α chains mediating epitope recognition. Applying MixTCRpred to TCR repertoires from COVID-19 patients reveals enrichment of clonotypes predicted to bind an immunodominant SARS-CoV-2 epitope. Overall, MixTCRpred provides a robust tool to predict TCRs interacting with specific epitopes and interpret TCR-sequencing data from both bulk and epitope-specific T cells.
Keywords
Humans, T-Lymphocytes, Epitopes, Deep Learning, Immunodominant Epitopes, COVID-19
Pubmed
Web of science
Open Access
Yes
Create date
19/04/2024 7:39
Last modification date
07/05/2024 6:17
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