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Proteomics and acetylated proteomics of cartilage degeneration in osteoarthritis

ABSTRACT: In this project, the rat model of osteoarthritis (OA) induced by ACLT+DMM+MCLT was used as the research object, and the proteomics and acetylated proteomics analysis of cartilage tissue were focused. Proteins were extracted by liquid nitrogen grinding and specific lysate, digested by enzyme, and enriched by acetylated peptide immunoprecipitation. The Orbitrap Exploris 480 mass spectrometer was used to detect the differentially expressed proteins and acetylation modification sites in DIA mode. Combined analysis showed that 853 proteins were jointly identified in the two omics, and the up-regulated proteins and acetylation modifications were significantly enriched in the ECM-receptor interaction pathway. Acetylation changes of key proteins such as Fn1, Tnc, and Itgb1 drove cartilage matrix remodeling. Simultaneous down-regulation inhibited energy metabolism-related pathways. Through the integrated analysis of the two omics, this study reveals the molecular mechanism of the key pathways of non-histone acetylation reprogramming in OA, and provides the core basis for the targeted intervention of OA at the protein level and modification level.

ORGANISM(S): Rattus Rattus

SUBMITTER: Wenpeng Xie

PROVIDER: PXD073041 | iProX | Tue Jan 13 00:00:00 GMT 2026

REPOSITORIES: iProX

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Project description:Osteoarthritis (OA) is an age-related degenerative musculoskeletal disease characterised by loss of articular cartilage, synovitis, abnormal bone proliferation and subchondral bone sclerosis. The underlying pathogenesis of OA is yet to be fully elucidated with no OA specific biomarkers in clinical use. Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) allow identification of the global metabolome and proteome respectively. During this study, ex-vivo equine cartilage explants (n=5) were incubated in TNF-α/IL-1β supplemented culture media for 8 days, with media removed and replaced at 2, 5 and 8 days. Acetonitrile metabolite extractions of 8 day cartilage explants and media samples at all time points underwent 1H NMR metabolic analysis with media samples also undergoing MS proteomic analysis. Within the cartilage, metabolites glucose and lysine were elevated following TNF-α/IL-1β treatment whilst adenosine, alanine, betaine, creatine, myo-inositol and uridine levels decreased. Within the culture media, four, four and six metabolites were identified as being differentially abundant between control and treatment groups for 1-2 day, 3-5 day and 6-8 day time points respectively. Culture media proteomics identified 154, 138 and 72 proteins differentially abundant, with > 2 fold change, between control and treatment groups for 1-2 day, 3-5 day and 6-8 day time points respectively. Nine potential novel OA neopeptides were elevated in treated media. This is the first study to use a multi ‘omics’ approach to simultaneously investigate the metabolomic profile of ex-vivo cartilage and metabolomic/proteomic profiles of culture media using the TNF-α/IL-1β ex-vivo OA cartilage model. This study has identified a panel of metabolites, proteins and extracellular matrix derived neopeptides which are differentially abundant during an early phase of the OA model which may provide further information on underlying disease pathogenesis, allow potential translation for clinical markers and possible novel therapeutic targets.

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Proteomics and acetylated proteomics of cartilage degeneration in osteoarthritis

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