PXD079646

PXD079646 is an original dataset announced via ProteomeXchange.

Title	HLA class I-naturally presented synovial tissue peptides are recognized by CD8+ T lymphocytes from rheumatoid arthritis patients
Description	Introduction: Rheumatoid arthritis (RA) is an autoimmune disease resulting from a response driven by self-reactive CD4+ T cells that recognize autoantigenic peptides presented by antigen-presenting cells (APCs). Recent evidence suggests that CD8+ T cells are also important players in this process. This study aims to define the immunopeptidome of HLA class I molecules from RA synovial tissue (ST)- APCs and synovial fluid (SF)-pulsed monocyte-derived dendritic cells (DCs), and to prove the suitability of this approach to identify peptides recognized by CD8+ T cells from RA patients. Methods: HLA-ABC/peptide complexes were obtained from DCs generated from healthy subjects (HS), which were pulsed with a pool of RA SF (SF-DCs) or left unpulsed (UP-DCs), or obtained directly from RA ST. Isolated peptides were sequenced by mass spectrometry. The autoantigenicity of a set of ten peptides selected from this repertoire was estimated by their ability to activate CD8+ T cells from RA patients, as measured by the induction of intracellular IFN-γ expression and surface exposure of CD107a by flow cytometry. Results: Between 107 to 663 peptides were obtained from DC samples, while over 3,500 class I peptides were identified from each ST sample. The number of peptides was narrowed down based on prioritization steps that included the selection of sequences derived from RA-relevant, immune-related proteins, for further CD8+ T-cell stimulation assays. The frequencies of CD8+ T cells co-stained for IFN-γ and CD107a were significantly higher in RA patients than in HS in response to peptides derived from the proteins MIF, ETS1, USF1, VIM, and AHR. Discussion: In the present work, we validated the use of an immunopeptidomic strategy to identify a series of novel autoantigenic CD8+ T-cell epitopes for RA, derived from synovial, mostly immune-related proteins, which may be useful for future clinical applications.
HostingRepository	PRIDE
AnnounceDate	2026-08-27
AnnouncementXML	Submission_2026-08-27_02:29:39.078.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jaxaira Maggi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2026-06-12 10:20:10	ID requested
⏵ 1	2026-08-27 02:29:40	announced

10.3389/fimmu.2026.1843318;

submitter keyword: CD8+ T cells, HLA class I,Rheumatoid arthritis, Autoantigens, Immunopeptidomics

Jaxaira Maggi
contact affiliation	IIBB-CSIC, Spain
contact email	jaxaira.maggi@iibb.csic.es
lab head
Jaxaira Maggi
contact affiliation	IIBB-CSIC
contact email	jaxaira.maggi@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD079646
     1. Label: PRIDE project
     2. Name: HLA class I-naturally presented synovial tissue peptides are recognized by CD8+ T lymphocytes from rheumatoid arthritis patients