PXD064948-1

PXD064948 is an original dataset announced via ProteomeXchange.

Title	Impact of collagenase treatment on the proteome and transcriptome of human articular chondrocytes
Description	Objective Human primary articular chondrocytes (hPACs) are routinely isolated from articular cartilage and for pre-clinical OA research. Collagenase digest of tissue is an essential step, yet the impact of enzymatic incubation on the phenotype of hPACs is unclear. We aim to delineate this through proteomic and transcriptomic analysis. Design hPACs were isolated from human knee cartilage (N=4) with and without prior fixation. Proteomes were quantified using LC-MS/MS. The Proteome Ruler was employed to estimate protein copy numbers and cell protein masses. Significant differences in protein intensities were determined using paired t-testing and Benjamini-Hochberg correction. Proteomic data were integrated with existing transcriptomes (GSE217871) of hPACs and ground cartilage tissue. Results Collagenase treatment resulted in a 10% increase in protein mass/cell (P=0.06). Seven percent of the proteome (498 proteins) significantly changed (Padj. = 4.5x10-4 - 0.049). Pathway analysis revealed depletion of FOXO signaling terms (FDR = 0.049 – 0.024), and enrichment of ribosomal RNA processing terms (FDR = 0.025 – 2.9x10-11). Transcriptomic anlaysis revealed 3937 differentially expressed genes (P.adj<0.05), of which 97% of differentially-expressed proteins overlapped (R2 =0.83). Propidium iodide staining followed by flow-assisted cell sorting (FACS) (N=3) did not identify significant differences in cell cycle between fixed and unfixed chondrocytes (all P>0.05). Conclusions We identified shifts in the proteome and transcriptome of hPACs following collagenase digest, supporting use of tissue fixation before extracting nucleic acids for analysis. Despite widespread expression changes, hPACs retain their chondrocyte phenotype. These datasets and analyses will serve as a valuable resource for the OA research community.
HostingRepository	PRIDE
AnnounceDate	2025-10-20
AnnouncementXML	Submission_2025-10-19_17:49:12.436.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthias Trost
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-12 09:21:22	ID requested
⏵ 1	2025-10-19 17:49:13	announced

Brumwell A, Raheja S, Cawley W, Birkett-Jones E, Orr SE, Todd C, Deehan DJ, Conlon NJ, Trost M, Rice SJ, A proteomics investigation of primary human articular chondrocyte isolation. Osteoarthr Cartil Open, 7(4):100664(2025) [pubmed]

10.1016/j.ocarto.2025.100664;

submitter keyword: collagenase, chondrocytes, osteoarthritis, transcriptomic, proteomic, phenotype

Matthias Trost
contact affiliation	Laboratory for Biomedical Mass Spectrometry, Newcastle University Biosciences Institute, Newcastle University, England
contact email	matthias.trost@newcastle.ac.uk
lab head
Matthias Trost
contact affiliation	Newcastle University
contact email	matthias.trost@ncl.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD064948
     1. Label: PRIDE project
     2. Name: Impact of collagenase treatment on the proteome and transcriptome of human articular chondrocytes