PXD068446-2

PXD068446 is an original dataset announced via ProteomeXchange.

Title	Immunopeptidomics analysis of human atherosclerosis plaques identifies antigenic drivers of atherosclerosis
Description	Atherosclerosis has an auto-immune component driven by self-reactive T and B cells. Identifying their antigenic drivers may lead to new diagnosis and treatment approaches. Here, we aim to identify immunogenic T cell epitopes derived from atherosclerosis-relevant proteins such as ApoB100 by studying the repertoire of peptides presented by HLA in human plaques. We used immunopeptidomics to identify peptides presented by HLA-DR molecules in 51 plaques from patients that underwent endarterectomy surgery. We selected a set of 20 peptides derived from ApoB100 and studied the presence and cytokine profile of ApoB100-specific CD4+ T cells in peripheral blood mononuclear cells (PBMCs) from atherosclerosis patients. Results revealed significant CD4+ T cell activation in response to these ApoB100 peptides in 22.4% of the patients, and this T cell response correlated positively with plaque vulnerability. Furthermore, the cytokine profile of these cells was characterized by production both pro- and anti-inflammatory cytokines.
HostingRepository	PRIDE
AnnounceDate	2025-09-22
AnnouncementXML	Submission_2025-09-22_07:06:26.213.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rayman Tjokrodirijo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-17 03:56:31	ID requested
1	2025-09-18 01:39:18	announced
⏵ 2	2025-09-22 07:06:27	announced	2025-09-22: Updated project metadata.

10.1016/j.atherosclerosis.2025.120509;

Lozano Vigario F, Molenaar J, Sim, ó, Vesperinas I, van der Zon M, Crone NSA, de Jong MJM, Hemme E, Depuydt MAC, Delfos L, de Mol J, Bernab, é, Kleijn MN, Peeters JAHM, Wezel A, Smeets HJ, Tjokrodirijo RTN, de Ru AH, Kros A, Quax PHA, de Vries MR, Kuiper J, Bot I, van Veelen P, Sl, ü, tter B, Immunopeptidomics analysis of human atherosclerosis plaques identifies antigenic drivers of atherosclerosis. Atherosclerosis, 409():120509(2025) [pubmed]

submitter keyword: Immunopeptidomics, PBMCs, ApoB100, antigen-specific T cells

Peter A. van Veelen
contact affiliation	Head Proteomics Group, Leiden University Medical Center, Center for Proteomics and Metabolomics, PO Box 9600, Postal zone P1-Q, 2300 RC Leiden, The Netherlands
contact email	P.A.van_Veelen@lumc.nl
lab head
Rayman Tjokrodirijo
contact affiliation	Leiden University Medical Center, Proteomics group
contact email	r.t.n.tjokrodirijo@lumc.nl
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/2025/09/PXD068446

PRIDE project URI

• PRIDE
  1. PXD068446
     1. Label: PRIDE project
     2. Name: Immunopeptidomics analysis of human atherosclerosis plaques identifies antigenic drivers of atherosclerosis