Screening and identification of differentially expressed miRNA and mRNA for intervertebral disc degeneration on bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41354850", "kind": "science-record", "revision": 4, "content_hash": "sha256:0135f8c755fb80e58c14cbaf09f2063f83c5c2fe9c338347bcb1e697fbb84d7a", "created_at": "2026-11-01T20:31:22Z", "updated_at": "2026-11-01T22:57:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and identification of differentially expressed miRNA and mRNA for intervertebral disc degeneration on bioinformatics.", "doi": "10.1186/s40001-025-03630-z", "pmid": "41354850", "authors": ["Jing Yan", "Yi Gao", "Rui Chen", "Shuo Miao", "Yuting Gong", "Yuning Zhu", "Quan Zhou"], "journal": "European journal of medical research", "year": 2025, "abstract": "BACKGROUND: Intervertebral disc degeneration (IDD), characterized by multifaceted pathological mechanisms, presents substantial therapeutic challenges. Globally, over 50% of individuals experience IDD-related low back pain (LBP), a debilitating condition associated with high recurrence rates and profound socioeconomic burdens. Current clinical strategies demonstrate limited efficacy in halting IDD progression, underscoring the critical need for targeted therapies.\nMETHODS: We analyzed the gene expression data of IDD mRNA and miRNA in the GEO database. Subsequently, the mRNA was screened for differentially expressed genes (DEGs) using R language. Immediately after that, we conducted a screening analysis of DEGs on miRNAs, and then used Venn diagrams to obtain hub genes by taking the intersection of DEGs. Then, the function of the hub genes is enriched through miRDB. Then, the downstream target genes of miRNA hub genes are predicted through miRDB to construct the possible miRNA-mRNA regulatory network. Finally, we collected clinical nucleus pulposus (NP) tissues and constructed the degeneration models of nucleus pulposus cells (NPCs) and IDD in rats to verify the expression of mRNA DEGs and miRNA hub genes.\nRESULTS: We obtained a total of 29 differentially expressed genes from the GSE34095 and GSE70362 mRNA gene data sets, such as ERBB2 and POSTN. Five hub genes (hsa-miR-4741, hsa-miR-5100, hsa-miR-4306, hsa-miR-3158-5p, and hsa-miR-508-5p) were obtained from GSE63492 and GSE116726. It is functionally related to cell death, differentiation, transmembrane transport and tumorigenesis. Finally, we identified the following miRNA-mRNA regulatory networks: hsa-miR-508-5p-DRP2, hsa-miR-3158-ERBB2, hsa-miR-4306-POSTN and hsa-miR-5100-CAPRIN1. Subsequently, we verified our above findings using clinical IDD samples, senescent nucleus pulposus cell models, and IDD rat models.\nCONCLUSIONS: These findings offer new insights into the occurrence and development of IDD and provide certain reference value for the subsequent diagnosis and treatment of IDD.", "claims": [{"id": "claim-method", "statement": "We used the “limma” package to screen the DEGs of mRNA and miRNA gene data sets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41354850", "locator": "sections[4] \"Microarray data analysis\" paragraph 2", "quote": "We used the “limma” package to screen the DEGs of mRNA and miRNA gene data sets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41354850", "locator": "sections[31] \"notes\" paragraph 1", "quote": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:41354850"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE116726"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE116726"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41354850", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40001-025-03630-z", "sha256": 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CONCLUSIONS: These findings offer ne"], "order_basis": "paper_text_order:1241", "id": "assay:1"}, {"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": ["We used the “limma” package to screen the DEGs of mRNA and miRNA gene data sets."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}