Identification and validation of immune-related genes in osteoarthritic synovial fibroblasts.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38571590", "kind": "science-record", "revision": 5, "content_hash": "sha256:4f45318a38d718c58a333281bc908a560dd56b40f1b4f4051d980fc7984c444f", "created_at": "2026-11-01T19:20:32Z", "updated_at": "2026-11-01T22:54:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of immune-related genes in osteoarthritic synovial fibroblasts.", "doi": "10.1016/j.heliyon.2024.e28330", "pmid": "38571590", "authors": ["Yaduan Dai", "Lin Chen", "Zhan Zhang", "Xueyong Liu"], "journal": "Heliyon", "year": 2024, "abstract": "Objective: OA was generally considered as a non-inflammatory disease dominated by articular cartilage degeneration. However, the role of synovitis in OA pathogenesis has received increasing attention. Recent studies support that OA patients have a pro-inflammatory/catabolic synovial environment similar to RA patients, promoting the occurrence and development of OA. Therefore, we investigated the co-immune-related genes and pathways of OA and RA to explore whether part of the pathogenesis of RA synovitis can be used to explain OA synovitis.\nMethods: Data of GSE29746 and GSE12021 were downloaded from the Gene Expression Omnibus (GEO) database. Compared with control group, differentially expressed genes (DEGs) of OA and RA groups were screened separately by R software, Venny website was used to screen co-DEGs. Metascape was used to screen the common enriched terms and pathways between OA and RA. STRING website and Cytoscape software were used to map protein-protein interaction (PPI) networks and screen co-hub genes. GSE29746 was selected as the test dataset, and GSE12021 as the validation dataset for validate the co-hub genes. The results were validated by western blotting (WB) and real-time quantitative polymerase chain reaction (qPCR) of clinical synovial samples.\nResults: We identified 573 OA-related DEGs, 148 RA-related DEGs, and 52 co-DEGs, revealing 14 common enriched terms, most of which were related to immune inflammation. IL7R was the only upregulated co-hub gene between OA and RA in the PPI network, consistent with the validation dataset. IL7R was highly expressed in clinical osteoarthritic synovial samples (P < 0.001).\nConclusion: Our findings suggested that IL7R is a critical co-DEG in OA and RA and confirmed the involvement of immune inflammation in disease pathogenesis. Furthermore, it confirms the role of IL7R in synovial inflammation in RA and OA synovitis and provides evidence for further investigation of OA immune inflammation.", "claims": [{"id": "claim-method", "statement": "The limma, dplyr, and Tibble R packages were used for differentially expressed gene (DEG) screening, with a threshold of P < 0.05 and |log2 fold change (FC)| > 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38571590", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "The limma, dplyr, and Tibble R packages were used for differentially expressed gene (DEG) screening, with a threshold of P < 0.05 and |log2 fold change (FC)| > 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available from public databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38571590", "locator": "sections[21] \"Data availability\" paragraph 2", "quote": "The data that support the findings of this study are available from public databases."}], "state": "complete"}, {"id": "claim-target-result", "statement": "IL7R was the only upregulated co-hub gene between OA and RA in the PPI network, consistent with the validation dataset.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38571590", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "IL7R was the only upregulated co-hub gene between OA and RA in the PPI network, consistent with the validation dataset."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "IL7R was the only upregulated co-hub gene between OA and RA in the PPI network, consistent with the validation dataset.", "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:38571590"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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The results were validated by western blotting (WB) and real-time quantitative polymerase c"], "order_basis": "paper_text_order:1222", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["time quantitative polymerase chain reaction (qPCR) of clinical synovial samples. Results: We i", "ment; ⑥ No palpable warmth of synovium [24]. qPCR-based mRNA analysis of co-hub genes Total RN", "cription Kit (TaKaRa Bio, Kusatsu, Japan). 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