Identification of hub genes through integrated single-cell and microarray transcriptome analysis in osteoarthritic meniscus.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39438957", "kind": "science-record", "revision": 4, "content_hash": "sha256:b031de6e60de5d133ca82cc286782cb51e02b61bd23b809db39cb516c80c2c24", "created_at": "2026-11-01T20:29:42Z", "updated_at": "2026-11-01T22:55:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes through integrated single-cell and microarray transcriptome analysis in osteoarthritic meniscus.", "doi": "10.1186/s13018-024-05175-z", "pmid": "39438957", "authors": ["Yanzhu Shen", "Ruichen Jiang", "Yanjun Huang", "Yuming Wang", "Sizheng Zhan", "Xiangsheng Tang", "Ping Yi"], "journal": "Journal of orthopaedic surgery and research", "year": 2024, "abstract": "BACKGROUND: Osteoarthritis (OA) is marked by the progressive degradation of joint cartilage and subchondral bone. The precise molecular mechanisms driving meniscus deterioration in OA, especially at the single-cell level, remain poorly understood.\nMETHOD: We analyzed two datasets from the GEO database, GSE220243 and GSE98918, focusing on meniscus tissue sequencing data from OA and non-OA patients. The standard Seurat procedure was employed to process single-cell data and identify differentially expressed genes (DEGs). Immune cell infiltration was assessed using the Microenvironment Cell Populations (MCP) counter and CIBERSORT algorithms. For the microarray data, DEGs were identified with the limma package, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using ClusterProfiler. The overlapping DEGs from both datasets were imported into Cytoscape to generate protein-protein interaction (PPI) networks and identify hub genes. Transcription factor (TF) and miRNA interaction networks were analyzed using NetworkAnalyst, and gene-related predictive drugs were enriched through the DSigDB platform.\nRESULT: After quality control, 34,763 cells from the OA patients and 34,145 cells from the healthy controls were analyzed. UMAP identified and SingleR annotated 14 cell clusters. The 10 largest cell clusters were selected for further analysis. The OA group exhibited a notable increase in macrophages and a reduction in cytotoxic lymphocytes and endothelial cells in the meniscus. In GSE98918, 220 DEGs were identified, and the MCODE plug-in in Cytoscape pinpointed a key module containing 12 candidate genes. The MCC methodfiltered the top 20 DEGs in each GSE220243 cluster. Overlapping DEGs from GSE220243 and GSE98918 identified COL1A1, COL3A1, COL5A2, COL6A3, LOX, and VEGFA as significantly decreased in OA, with COL3A1, COL5A2, LOX, and VEGFA upregulated in meniscal chondrocytes. The interaction network highlighted 3 key miRNAs and 13 shared TFs. Ten gene-related predictive drug molecules were identified.\nCONCLUSION: This research highlights crucial genes in the OA meniscus and uncovers their differing regulatory patterns between chondrocytes and non-chondrocytes. These findings enhance our understanding of the molecular mechanisms driving OA pathogenesis and aid in identifying potential drug targets.", "claims": [{"id": "claim-method", "statement": "DEGs between the OA and non-OA group were identified using the limma package [16] (version 3.60.2) according to standard GEO methods.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39438957", "locator": "sections[5] \"Processing of GSE98918 dataset\" paragraph 2", "quote": "DEGs between the OA and non-OA group were identified using the limma package [16] (version 3.60.2) according to standard GEO methods."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data in this study were sourced from the GEO database (http://www.ncbi.nlm.nih.gov/geo/), accessible through IDs GSE98918 and GSE220243.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39438957", "locator": "sections[28] \"Data availability\" paragraph 2", "quote": "All data in this study were sourced from the GEO database (http://www.ncbi.nlm.nih.gov/geo/), accessible through IDs GSE98918 and GSE220243."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The overlapping differentially expressed genes from GSE220243 and GSE98918 identified COL1A1, COL3A1, COL5A2, COL6A3, LOX, and VEGFA as hub genes with significantly decreased expression in OA meniscus.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39438957", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Overlapping DEGs from GSE220243 and GSE98918 identified COL1A1, COL3A1, COL5A2, COL6A3, LOX, and VEGFA as significantly decreased in OA, with COL3A1, COL5A2, LOX, and VEGFA upregulated in meniscal chondrocytes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The overlapping differentially expressed genes from GSE220243 and GSE98918 identified COL1A1, COL3A1, COL5A2, COL6A3, LOX, and VEGFA as hub genes with significantly decreased expression in OA meniscus.", "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:39438957"], "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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GSE220243.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data in this study were sourced from the GEO database (http://www.ncbi.nlm.nih.gov/geo/), accessible through IDs GSE98918 and GSE220243.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM6797148", "GSM6797149", "GSM6797150", "GSM6797151", "GSM6797152", "GSM6797153", "GSM6797154", "GSM6797155", "GSM6797156", "GSM6797157", "GSM6797158", "GSM6797159", "GSM6797160", "GSM6797161", "GSM6797162", "GSM6797163", "GSM6797164", "GSM6797165", "GSM6797166", "GSM6797167", "GSM6797168", "GSM6797169", "GSM6797170", "GSM6797171", "GSM6797172", "GSM6797173"], "sample_count": 26, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "A senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus [Cartilage_Meniscus_scRNAseq]", 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