PXD023708-2

PXD023708 is an original dataset announced via ProteomeXchange.

Title	Proteomics profiling of human synovial fluid suggests global increased protein interplay in early-osteoarthritis (OA) and lost in late-stage OA
Description	The underlying molecular mechanisms in osteoarthritis (OA) development are largely unknown. This study explores the proteome and the pairwise interplay of proteins on a global level in synovial fluid from patients with late-stage knee OA (arthroplasty), early knee OA (arthroscopy due to degenerative meniscal tear) and from deceased controls without knee OA. Synovial fluid samples were analyzed using state-of-the-art mass spectrometry with data-independent acquisition. The differential expression of the proteins detected was clustered and evaluated with data mining strategies and a multilevel model. Group-specific slopes of associations were estimated between expressions of each pair of identified proteins to assess the co-expression (i.e. interplay) between the proteins in each group. More proteins were increased in early-OA vs controls than late-stage OA vs controls. For most of these proteins, the fold changes between late-stage OA vs controls and early stage OA vs controls were remarkably similar suggesting potential involvement in the OA process. Further, for the first time this study illustrated distinct patterns in protein co-expression suggesting that the global interplay between the protein machinery is increased in early-OA and lost in late-stage OA. Further efforts should probably focus on earlier stages of the disease than previously considered.
HostingRepository	PRIDE
AnnounceDate	2022-01-27
AnnouncementXML	Submission_2022-01-30_13:32:29.218.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Neserin Ali
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; deaminated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-20 08:14:46	ID requested
1	2022-01-27 10:13:07	announced
⏵ 2	2022-01-30 13:32:30	announced	2022-01-30: Updated publication reference for PubMed record(s): 35074580.
3	2024-10-22 05:31:01	announced	2024-10-22: Updated project metadata.

Ali N, Turkiewicz A, Hughes V, Folkesson E, Tj, ö, rnstand J, Neuman P, Ö, nnerfjord P, Englund M, Proteomics Profiling of Human Synovial Fluid Suggests Increased Protein Interplay in Early-Osteoarthritis (OA) That Is Lost in Late-Stage OA. Mol Cell Proteomics, 21(3):100200(2022) [pubmed]

submitter keyword: Osteoarthritis, DIA, Synovial fluid

Neserin Ali
contact affiliation	Lund University
contact email	neserin.ali@med.lu.se
lab head
Neserin Ali
contact affiliation	Lund University
contact email	neserin.ali@med.lu.se
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/2022/01/PXD023708

PRIDE project URI

• PRIDE
  1. PXD023708
     1. Label: PRIDE project
     2. Name: Proteomics profiling of human synovial fluid suggests global increased protein interplay in early-osteoarthritis (OA) and lost in late-stage OA