PXD062551

PXD062551 is an original dataset announced via ProteomeXchange.

Title	An mRNA-based workflow for validation of Neo-Epitope Presentation by HLA-I/Peptide Affinity Purification
Description	Human leukocyte antigen (HLA) class I restricted neo-epitopes play a key role in inducing an adaptive cytotoxic T lymphocyte response against cancer. To enhance therapeutic and personalized cancer vaccination strategies, the identification of these cancer-specific neo-epitopes is essential. Current workflows for the neo-epitope identification are often laborious and still require computational deconvolution to determine the correct peptide sequence and its corresponding restriction element. In this study, we evaluated the use of an mRNA-based workflow, which allows for more precise purification of HLA-I/peptide (pHLA) complexes and potentially facilitates peptide identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The approach uses mRNA encoding a specific HLA-I molecule linked with a Twin-Strep-Tag (HLA-TST), allowing affinity-based purification and downstream analysis of pHLA. We delivered a proof-of-concept for this approach by co-delivering mRNA encoding a TST-coupled HLA-A*0201 with mRNA encoding the HLA-A*0201-restricted p53 epitope via electroporation in HLA-A*0201- K562 cells. The findings of this study show the promise of the mRNA-based strategy in neo-epitope research. However, further studies are necessary to fully understand the technical factors that can affect the peptides identified by LC-MS/MS.
HostingRepository	PRIDE
AnnounceDate	2025-06-23
AnnouncementXML	Submission_2025-06-22_16:08:27.326.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kurt Boonen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-03 01:02:50	ID requested
⏵ 1	2025-06-22 16:08:28	announced

Esprit A, Autaers D, Thielemans K, Pepermans E, Boonen K, Baggerman G, Franceschini L, Breckpot K, An mRNA-based workflow validating neo-epitope presentation through HLA-I/peptide affinity purification. Front Immunol, 16():1566461(2025) [pubmed]

10.3389/fimmu.2025.1566461;

submitter keyword: p53 epitope, HLA-A*0201, immunopeptidomics, mRNA

Karine Breckpot
contact affiliation	Translational Oncology Research Center, Vrije Universiteit Brussel (VUB), Brussels, Belgium
contact email	Karine.Breckpot@vub.be
lab head
Kurt Boonen
contact affiliation	University of Antwerp, VITO
contact email	kurt.boonen@uantwerpen.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD062551
     1. Label: PRIDE project
     2. Name: An mRNA-based workflow for validation of Neo-Epitope Presentation by HLA-I/Peptide Affinity Purification