PXD003051

PXD003051 is an original dataset announced via ProteomeXchange.

Title	Identification of In Vivo HLA-DR-Presented Self-Peptides (T Cell Epitopes) in Synovial Tissue, Synovial Fluid and Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis
Description	HLA-DR molecules are highly expressed in synovial tissue (ST), the target of the immune response in chronic inflammatory arthritides, including in rheumatoid arthritis (RA) and Lyme arthritis (LA). In the current study, we identified HLA-DR-presented self-peptides (T cell epitopes) in ST, synovial fluid mononuclear cells (SF), and peripheral blood mononuclear cells (PB) from five patients with RA and eight with LA. Altogether, from 22 samples, 1,532 non-redundant HLA-DR-presented peptides were identified that were derived from 778 source proteins. Moreover, as the study progressed, application of newer, high sensitivity LC-MS instruments resulted in the identification of larger numbers of HLA-DR-presented peptides. Surprisingly, the source proteins for HLA-DR-presented peptides were as likely to have intracellular as extracellular locations. Although the number of peptides identified was greater in ST than in SF or PB, 68% of the peptides identified in SF were found in ST, and 55% of the peptides in PB were found in ST. Two RA patients had the same HLA-DR genotype (DRB1*0401 and 0101), and 44% of the peptides identified in these two patients were the same. In contrast, among the patients with RA or LA who had no shared HLA-DR alleles, only 6% of the peptides were the same. In the RA patients, HLA-DR-presented peptides were identified from source proteins that are thought to serve as potential autoantigens: collagen, enolase, fibrinogen, fibronectin, immunoglobulin and vimentin. Interestingly, peptides from these same source proteins were also commonly found in LA patients. However, citrullinated T cell epitopes were not identified in any patient. Thus, LC-MS/MS techniques are now sensitive enough to identify large numbers of T cell epitopes from tissue or fluids in individual patients. Importantly, analysis of SF or PB allowed us to identify a broader range of HLA-DR-presented self-peptides from individual patients and from patients seen earlier in the disease.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:25:34.965.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Qi Wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	2-pyrrolidone-5-carboxylic acid (Glu); cysteinylation (disulfide with free L-cysteine); monohydroxylated residue; L-citrulline; deamidated residue
Instrument	Q Exactive; LTQ Orbitrap; 6520A Quadrupole Time-of-Flight LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2015-10-14 01:36:10	ID requested
1	2016-10-13 06:30:03	announced
2	2017-06-06 00:30:30	announced	Updated project metadata.
3	2017-10-24 01:54:19	announced	Updated project metadata.
⏵ 4	2024-10-22 04:25:37	announced	2024-10-22: Updated project metadata.

Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE, Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis. J Proteome Res, 16(1):122-136(2017) [pubmed]

ProteomeXchange project tag: Human Immuno-Peptidome Project (HUPO-HIPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

curator keyword: Biomedical

submitter keyword: synovial tissue, synovial fluid,human, peripheral blood, LC-MS/MS

Catherine E. Costello
contact affiliation	Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine
contact email	cecmsms@bu.edu
lab head
Qi Wang
contact affiliation	Boston University
contact email	qwang616@bu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD003051
     1. Label: PRIDE project
     2. Name: Identification of In Vivo HLA-DR-Presented Self-Peptides (T Cell Epitopes) in Synovial Tissue, Synovial Fluid and Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis