Methylation Landscapes of Cartilage in Hip Osteoarthritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41496756", "kind": "science-record", "revision": 4, "content_hash": "sha256:fa54b1ab374ef5ecaa847159082387008048dfef182f8f46950295fe129a5584", "created_at": "2026-11-01T20:31:28Z", "updated_at": "2026-11-01T22:57:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Methylation Landscapes of Cartilage in Hip Osteoarthritis.", "doi": "10.1155/genr/5540232", "pmid": "41496756", "authors": ["Ruiyang Jiang", "Maochun Wang", "Guihua Tan", "Jie Lv", "Xiaoyu Jin", "Yuan Liu", "Rui Wu", "Dongquan Shi"], "journal": "Genetics research", "year": 2026, "abstract": "Objective: To elucidate different methylation landscapes between cartilage of femoral neck fracture and preserved and damaged cartilages in hip osteoarthritis (OA).\nMethods: Genome-wide DNA methylation data were acquired from two data sets in GEO database (GSE63106 and GSE63695), which were based on Illumina HumanMethylation450 BeadChip arrays. A total of 63 hip samples were selected for further analysis, including 19 cartilages obtained from patients with femoral neck fracture, 14 preserved cartilages, and 30 damaged cartilages obtained from patients with OA. We identified the differential methylated positions (DMPs) and genes between different cartilage groups.\nResults: There were 116,750 DMPs and 51,200 DMPs identified in preserved and damaged cartilages compared to cartilage in femoral neck fracture, respectively, while there were no signals found between preserved and damaged cartilages. Gene ontology analysis showed that most of differential methylated genes were enriched in extracellular matrix and structure organization, collagen-containing extracellular matrix, and KEGG enrichment highlighted PI3K-AKT and AMPK signaling pathways, which were known to be crucial for the progression of OA. Further construction of protein-protein interaction networks with differential methylated genes elucidated molecular basis of the disease. Three hypermethylated genes (NOTCH1, GREM1, and DYSF) and three hypomethylated genes (HDAC4, S100A10, and RUNX1) were selected to detect the relative expression in different cartilages, and their expression was correlated with the methylation status within the genes.\nConclusion: We demonstrated the differential methylated genes across the whole genome not only on preserved cartilage but also on damaged cartilage during OA. The molecular network highlighted the potential therapy targets which may be involved in the initiation or progression of the disease.", "claims": [{"id": "claim-method", "statement": "DMPs were identified by champ.DMP function in ChAMP R package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41496756", "locator": "sections[4] \"2.2. Identification of DMPs and Gene Enrichment\" paragraph 2", "quote": "DMPs were identified by champ.DMP function in ChAMP R package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated or analyzed during the current study are available in the GEO database (GSE63106 and GSE63695).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41496756", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "The datasets generated or analyzed during the current study are available in the GEO database (GSE63106 and GSE63695)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "There were 116,750 DMPs and 51,200 DMPs identified in preserved and damaged cartilages compared to cartilage in femoral neck fracture, respectively, while there were no signals found between preserved and damaged cartilages.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41496756", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "There were 116,750 DMPs and 51,200 DMPs identified in preserved and damaged cartilages compared to cartilage in femoral neck fracture, respectively, while there were no signals found between preserved and damaged cartilages."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "There were 116,750 DMPs and 51,200 DMPs identified in preserved and damaged cartilages compared to cartilage in femoral neck fracture, respectively, while there were no signals found between preserved and damaged cartilages.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41496756"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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