Identification of HTRA1, DPT and MXRA5 as potential biomarkers associated with osteoarthritis progression and immune infiltration.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39148085", "kind": "science-record", "revision": 2, "content_hash": "sha256:1c27cefe412dd4fa860cb6232af3bd057df1ee5a3c329a65bf593d3670868f49", "created_at": "2026-11-01T20:29:16Z", "updated_at": "2026-11-01T21:33:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of HTRA1, DPT and MXRA5 as potential biomarkers associated with osteoarthritis progression and immune infiltration.", "doi": "10.1186/s12891-024-07758-7", "pmid": "39148085", "authors": ["Yunchao Sun", "Hui Yang", "Jiaquan Guo", "Jian Du", "Shoujiang Han", "Xinming Yang"], "journal": "BMC musculoskeletal disorders", "year": 2024, "abstract": "BACKGROUND: Our study aimed to identify potential specific biomarkers for osteoarthritis (OA) and assess their relationship with immune infiltration.\nMETHODS: We utilized data from GSE117999, GSE51588, and GSE57218 as training sets, while GSE114007 served as a validation set, all obtained from the GEO database. First, weighted gene co-expression network analysis (WGCNA) and functional enrichment analysis were performed to identify hub modules and potential functions of genes. We subsequently screened for potential OA biomarkers within the differentially expressed genes (DEGs) of the hub module using machine learning methods. The diagnostic accuracy of the candidate genes was validated. Additionally, single gene analysis and ssGSEA was performed. Then, we explored the relationship between biomarkers and immune cells. Lastly, we employed RT-PCR to validate our results.\nRESULTS: WGCNA results suggested that the blue module was the most associated with OA and was functionally associated with extracellular matrix (ECM)-related terms. Our analysis identified ALB, HTRA1, DPT, MXRA5, CILP, MPO, and PLAT as potential biomarkers. Notably, HTRA1, DPT, and MXRA5 consistently exhibited increased expression in OA across both training and validation cohorts, demonstrating robust diagnostic potential. The ssGSEA results revealed that abnormal infiltration of DCs, NK cells, Tfh, Th2, and Treg cells might contribute to OA progression. HTRA1, DPT, and MXRA5 showed significant correlation with immune cell infiltration. The RT-PCR results also confirmed these findings.\nCONCLUSIONS: HTRA1, DPT, and MXRA5 are promising biomarkers for OA. Their overexpression strongly correlates with OA progression and immune cell infiltration.", "claims": [{"id": "claim-method", "statement": "A gene co-expression network was established using the WGCNA R package with normalized expression data for 16,106 genes in the training set [12].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39148085", "locator": "sections[4] \"WGCNA analysis and module selection\" paragraph 2", "quote": "A gene co-expression network was established using the WGCNA R package with normalized expression data for 16,106 genes in the training set [12]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used for analysis in our study are available from GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39148085", "locator": "sections[25] \"Data availability\" paragraph 2", "quote": "The data used for analysis in our study are available from GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "WGCNA identified the blue module as the module most strongly associated with osteoarthritis (R = 0.37, P = 6e-06).", "kind": "quantitative", "target": {"value": 0.37, "unit": "correlation coefficient", "tolerance": null, "source": "As shown in Fig. 1C, the blue module showed the strongest association with OA (R = 0.37, P = 6e-06)."}, "evidence": [{"asset": "source:pmid:39148085", "locator": "sections[13] \"Identification of the key module and enrichment analysis\" paragraph 2", "quote": "As shown in Fig. 1C, the blue module showed the strongest association with OA (R = 0.37, P = 6e-06)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "WGCNA identified the blue module as the module most strongly associated with osteoarthritis (R = 0.37, P = 6e-06).", "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:39148085"], "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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