PXD062696

PXD062696 is an original dataset announced via ProteomeXchange.

Title	Integrative Spatial Proteomics and Single-Cell RNA Sequencing Unveil Molecular Complexity in Rheumatoid Arthritis for Novel Therapeutic Targeting
Description	Understanding the heterogeneity of Rheumatoid Arthritis (RA) and identifying therapeutic targets remain challenging using traditional bulk transcriptomics alone, as it lacks the spatial and protein-level resolution needed to fully capture disease and tissue complexities. In this study, we applied Laser Capture Microdissection (LCM) coupled with mass spectrometry-based proteomics to analyze histopathological niches of the RA synovium, enabling the identification of protein expression profiles of the diseased synovial lining and sublining microenvironments compared to their healthy counterparts. In this respect, key pathogenetic RA proteins like membrane proteins (TYROBP, AOC3, SLC16A3, TCIRG1 and NCEH1), and extracellular matrix (ECM) proteins (PLOD2, OGN and LUM) showed different expression patterns in diseased synovium compartments. To enhance our understanding of cellular dynamics within the dissected regions, we further integrated the proteomic dataset with single-cell RNA sequencing (scRNA-seq) and deduced cell type enrichment including T cells, fibroblasts, NK cells, myeloid cells, B cells and synovial endothelial cells. By combining high-resolution spatial proteomics and transcriptomic analyses, we provide novel insights into the molecular mechanisms driving RA and highlight potential protein targets for therapeutic intervention. This integrative approach offers a more comprehensive view of RA synovial pathology and mitigates the limitations of traditional bulk transcriptomics in target discovery.
HostingRepository	PRIDE
AnnounceDate	2025-06-26
AnnouncementXML	Submission_2025-06-26_11:44:34.025.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fei Wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-07 15:14:09	ID requested
⏵ 1	2025-06-26 11:44:34	announced

10.3390/PROTEOMES13020017;

submitter keyword: Human, Laser capture microdissection, Synovium membrane, LC-MS/MS

Yu Tian
contact affiliation	QTAS, or previously DMPK, Abbvie Bioresearch Center
contact email	yu.tian@abbvie.com
lab head
Fei Wang
contact affiliation	AbbVie Inc.
contact email	wf199209@gmail.com
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/2025/06/PXD062696

PRIDE project URI

• PRIDE
  1. PXD062696
     1. Label: PRIDE project
     2. Name: Integrative Spatial Proteomics and Single-Cell RNA Sequencing Unveil Molecular Complexity in Rheumatoid Arthritis for Novel Therapeutic Targeting