PXD039166

PXD039166 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiling of Extracellular Vesicles in synovial fluid and plasma from Oligoarticular Juvenile Idiopathic Arthritis patients reveals novel immunopathogenic biomarkers
Description	New early low-invasive biomarkers are highly demanded for the management of Oligoarticular Juvenile Idiopathic Arthritis (OJIA), the most common chronic pediatric rheumatic disease in Western countries and a leading cause of disability. Despite recent significant advances in OJIA treatment, a high percentage of patients undergo arthritis recurrence and/or extension to other joints by one-two years after onset. A deeper understanding of the molecular basis of OJIA pathophysiology is essential for the identification of biomarkers for early disease detection and patient stratification and to guide targeted therapeutic intervention to allow the development of diagnostic and therapeutic interventions earlier in disease course. Proteomic profiling of extracellular vesicles (EVs) released in biological fluids has recently emerged as a minimally invasive approach to elucidate adult arthritis pathogenic mechanisms and for new biomarker discovery. However, EV-prot expression and potential as biomarkers in OJIA have not been explored. This study represents the first detailed longitudinal characterization investigation of EV proteome in newly diagnosed OJIA patients. Fourty-five OJIA patients were recruited at disease onset and followed up for 24 months, and protein expression profiling was carried out by liquid chromatography-tandem mass spectrometry in EVs isolated from plasma (PL) and synovial fluid (SF) samples. Because joints are the main targets of clinical manifestations, we first searched for EV-prots potentially implicated in disease development by comparing the EV-proteome of SF (SF_OJIA) vs paired PL (PL_OJIA). We identified a subset of 83 proteins significantly (FDR < 0.01) differentially expressed (31 up- and 52 downregulated) in EVs from SF compared to PL and 33 EV-prots exclusively present in SF samples. Pathway analysis revealed EV-prot enrichment in processes related to cartilage/bone metabolism and inflammation suggesting their role in OJIA joint pathogenesis and potential value as early biomarkers of disease development. Comparative analysis of the SF_OJIA and PL_OJIA EV-proteomic profiles was then carried out respect to the PL of 24 age/gender-matched control children (PL_CTR) to identify early disease-specific proteins. Significant up- and down-regulation of 110 and 92 EV-prots, respectively, were observed in PL_OJIA compared to PL_CTR samples, and 294 EV-prots were found exclusively present, effectively differentiating new-onset OJIA patients from control children. EV-prots were significantly associatd to biological processes related to innate immunity, antigen processing and presentation, and cytoskeleton organization. Importantly, a subset of 76 EV-prots displayed consensual regulation in, and 77 exclusively expressed EV-prots were shared by, PL and SF from patients respect to CTR, potentially representing a disease-associated signature measurable at both the systemic and local levels with diagnostic potential. Finally, we runned WGCNA on the SF- and PL-derived EV-prot datasets to search for EV-prot clusters associated to clinical parameters, such as ANA positivity, disease relapse, polyarticular extension, and iridocyclitis development occurring within the 2 years of follow-up, and we identified 9 and 7 EV-prot modules in SF and PL samples, respectively, able to stratify OJIA patients in distinct subgroups with different disease course. These data provide mechanistic insights into OJIA pathophysiology and an important contribution in the search of new candidate biomarkers for the disease.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:52:10.679.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martina Bartolucci
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-02 19:00:24	ID requested
1	2023-07-05 06:23:50	announced
2	2023-11-14 07:03:27	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:52:11	announced	2024-10-22: Updated project metadata.

10.3389/FIMMU.2023.1134747;

submitter keyword: proteomics, mass spectrometry,OJIA, extracellular vesicles, plasma, synovial fluid

Andrea Petretto
contact affiliation	IRCCS Istituto G Gaslini
contact email	a.petretto@gmail.com
lab head
Martina Bartolucci
contact affiliation	IRCCS Gaslini
contact email	smartibartolucci@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD039166
     1. Label: PRIDE project
     2. Name: Proteomic profiling of Extracellular Vesicles in synovial fluid and plasma from Oligoarticular Juvenile Idiopathic Arthritis patients reveals novel immunopathogenic biomarkers