PXD058478

PXD058478 is an original dataset announced via ProteomeXchange.

Title	Phage display enables machine learning discovery of cancer antigen specific TCRs
Description	T cells targeting epitopes in infectious diseases or cancer play a central role in spontaneous and therapy-induced immune responses. T-cell epitope recognition is mediated by the binding of the T-Cell Receptor (TCR) and TCRs recognizing clinically relevant epitopes are promising for T-cell based therapies. Starting from one of the few known TCRs targeting the cancer-testis antigen NY-ESO-1 (157–165) epitope, we built large phage display libraries of TCRs with randomized Complementary Determining Region 3 of the β chain. The TCR libraries were panned against the NY-ESO-1 epitope, which enabled us to collect thousands of epitope-specific TCR sequences. We then trained a machine learning TCR-epitope interaction predictor with this data and could identify several epitope-specific TCRs directly from TCR repertoires. Cellular binding and functional assays revealed that the predicted TCRs displayed activity towards the NY-ESO-1 epitope and no detectable cross-reactivity with self-peptides. Overall, our work demonstrates how display technologies combined with machine learning models of TCR-epitope recognition can effectively leverage large TCR repertoires for TCR discovery.
HostingRepository	PRIDE
AnnounceDate	2025-06-20
AnnouncementXML	Submission_2025-06-20_08:33:57.218.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michal Bassani-Sternberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-02 06:39:35	ID requested
⏵ 1	2025-06-20 08:33:58	announced

Croce G, Lani R, Tardivon D, Bobisse S, de Tiani M, Bragina M, Perez MAS, Michaux J, Pak HS, Michel A, Gehret T, Schmidt J, Guillame P, Bassani-Sternberg M, Zoete V, Harari A, Rufer N, Hebeisen M, Dunn SM, Gfeller D, Phage display enables machine learning discovery of cancer antigen-specific TCRs. Sci Adv, 11(24):eads5589(2025) [pubmed]

10.1126/sciadv.ads5589;

submitter keyword: HLA-A*02:01, immunopeptidomics,HLA peptides

Michal Bassani-Sternberg
contact affiliation	Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Rue du Bugnon 25a, CH-1005 Lausanne
contact email	michal.bassani@chuv.ch
lab head
Michal Bassani-Sternberg
contact affiliation	UNIL/CHUV
contact email	michal.bassani@chuv.ch
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/06/PXD058478

PRIDE project URI

• PRIDE
  1. PXD058478
     1. Label: PRIDE project
     2. Name: Phage display enables machine learning discovery of cancer antigen specific TCRs