Identifying critical modules and biomarkers of intervertebral disc degeneration by using weighted gene co-expression network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39430414", "kind": "science-record", "revision": 4, "content_hash": "sha256:ab0ebb65fc5c7933a9f335488edd10cd51e7353ea409ee8e0e0f0c8b35bbcf93", "created_at": "2026-11-01T20:29:40Z", "updated_at": "2026-11-01T22:55:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying critical modules and biomarkers of intervertebral disc degeneration by using weighted gene co-expression network.", "doi": "10.1002/jsp2.70004", "pmid": "39430414", "authors": ["Daqian Zhou", "Tao Liu", "Yongliang Mei", "Jiale Lv", "Kang Cheng", "Weiye Cai", "Silong Gao", "Daru Guo", "Xianping Xie", "Zongchao Liu"], "journal": "JOR spine", "year": 2024, "abstract": "Background: Intervertebral disc degeneration (IVDD) is an age-related orthopedic degenerative disease characterized by recurrent episodes of lower back pain, the pathogenesis of which is not fully understood. This study aimed to identify key biomarkers of IVDD and its causes.\nMethods: We acquired three gene expression profiles from the Gene Expression Omnibus (GEO) database, GSE56081, GSE124272, and GSE153761, and used limma fast differential analysis to identify differentially expressed genes (DEGs) between normal and IVDD samples after removing batch effects. We applied weighted gene co-expression network (WGCNA) to identify the key modular genes in GSE124272 and intersected these with DEGs. Next, A protein-protein interaction network (PPI) was constructed, and Cytoscape was used to identify the Top 10 hub genes. Functional enrichment analyses were performed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Three key genes were validated using Western Blot (WB) and qRT-PCR. Additionally, we predicted miRNAs involved in hub gene co-regulation and analyzed miRNA microarray data from GSE116726 to identify four differentially expressed miRNAs.\nResults: We identified 10 hub genes using bioinformatics analysis, gene function enrichment analysis revealed that they were primarily enriched in pathways, such as the TNF signaling pathway. We chose JUNB, SOCS3, and CEBPB as hub genes and used WB and qRT-PCR to confirm their expression. All three genes were overexpressed in the IVDD model group compared to the control group. Furthermore, we identified four miRNAs involved in the co-regulation of the hub genes using miRNet prediction: mir-191-5p, mir-20a-5p, mir-155-5p, and mir-124-3p. Using limma difference analysis, we discovered that mir-191-5p, mir-20a-5p, and mir-155-5p were all down-regulated and expressed in IVDD samples, but mir-124-3p showed no significant change.\nConclusion: JUNB, SOCS3, and CEBPB were identified as key genes in IVDD, regulated by specific miRNAs, providing potential biomarkers for early diagnosis and therapeutic targets.", "claims": [{"id": "claim-method", "statement": "To obtain an integrated dataset, we used the Limma rapid differential analysis method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39430414", "locator": "sections[17] \"Identification of DEGs\" paragraph 2", "quote": "To obtain an integrated dataset, we used the Limma rapid differential analysis method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39430414", "locator": "sections[32] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In this step, we successfully identified 496 DEGs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39430414", "locator": "sections[17] \"Identification of DEGs\" paragraph 2", "quote": "In this step, we successfully identified 496 DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In this step, we successfully identified 496 DEGs.", "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:39430414"], "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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Three key genes were validated using Western Blot (WB) and qRT-PCR. Additionally, we predicted"], "order_basis": "paper_text_order:1078", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["in hub gene co-regulation and analyzed miRNA microarray data from GSE116726 to identify four differe"], "order_basis": "paper_text_order:1197", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["intervertebral disc tissue and lentivirally transfected to carry the SV40 gene. We bought LPS from A"], "order_basis": "paper_text_order:2405", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ed. Cell culture and LPS treatment NPCs were cultured in DMEM containing 10% FBS and 1% antibiotics,"], "order_basis": "paper_text_order:2998", "id": "assay:4"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["in the pathogenesis of IVDD. Cell stress and apoptosis: Genes such as SOD2, DAPK1, and BCL6 are ass", "se to oxidative stress and the regulation of apoptosis, which are important in the survival and dea", "in IVDD. Experimental validation results The CCK8 assay showed significant changes in NP cell", "tment. Cell viability was assessed using the CCK8 assay. *p <0.05 compared to the control grou"], "order_basis": "paper_text_order:7656", "id": "assay:5"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["To obtain an integrated dataset, we used the Limma rapid differential analysis method."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}