Identification of potential biomarkers associated with cellular senescence in benign prostatic hyperplasia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41286044", "kind": "science-record", "revision": 3, "content_hash": "sha256:5858fce1884ae10fdf3cd8fc93bec30ed536ea70b86904b30d636e9266b81320", "created_at": "2026-11-01T20:31:19Z", "updated_at": "2026-11-01T22:15:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential biomarkers associated with cellular senescence in benign prostatic hyperplasia.", "doi": "10.1038/s41598-025-25734-6", "pmid": "41286044", "authors": ["Lei Zhou", "Xiao Zhong", "Dan Hu", "Guoqian Hu", "Chao Li", "Shuo Tan", "Wei Xiong", "Lan Li", "Jin Tang"], "journal": "Scientific reports", "year": 2025, "abstract": "Benign prostatic hyperplasia (BPH) is a prevalent condition among aging men, characterized by prostate enlargement and urinary symptoms. Despite its common occurrence, the molecular mechanisms, particularly those related to cellular senescence, are not well understood. This study aims to pinpoint and analyze cellular senescence-related differentially expressed genes (CSRDEGs) in BPH. We integrated data from GEO datasets GSE119195 and GSE7307, addressing batch effects to ensure data reliability. Differential gene expression analysis revealed key CSRDEGs, which were further analyzed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, highlighting their involvement in significant biological processes and pathways such as inflammation, cell cycle regulation, and extracellular matrix organization. Protein-protein interaction networks were constructed, and hub genes, including IGF1, SOX2, ID1, WNT2, LGALS3, and KL, were determined and analyzed for their diagnostic potential through receiver operating characteristic curve analysis. Regulatory network analyses of these hub genes exhibited intricate mRNA-miRNA and mRNA-TF interactions, providing insights into post-transcriptional and transcriptional regulation mechanisms. Our findings underscore the crucial role of cellular senescence in BPH pathogenesis and propose novel biomarkers and therapeutic targets. This study enhances our understanding of BPH at the molecular level, offering a foundation for future research aimed at improving diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "Group comparisons were conducted using the Wilcoxon Rank Sum Test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41286044", "locator": "sections[14] \"Statistical analysis\" paragraph 2", "quote": "Group comparisons were conducted using the Wilcoxon Rank Sum Test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data will be made available upon reasonable request. For inquiries regarding the data from this study, please contact Jin Tang at ajin530@139.com.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41286044", "locator": "sections[28] \"Data availability\" paragraph 2", "quote": "Data will be made available upon reasonable request. For inquiries regarding the data from this study, please contact Jin Tang at ajin530@139.com."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We determined key hub genes, including IGF1, SOX2, ID1, WNT2, LGALS3, and KL, which play pivotal roles in cellular senescence and have potential as diagnostic biomarkers.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41286044", "locator": "sections[24] \"Discussion\" paragraph 3", "quote": "We determined key hub genes, including IGF1, SOX2, ID1, WNT2, LGALS3, and KL, which play pivotal roles in cellular senescence and have potential as diagnostic biomarkers."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We determined key hub genes, including IGF1, SOX2, ID1, WNT2, LGALS3, and KL, which play pivotal roles in cellular senescence and have potential as diagnostic biomarkers.", "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:41286044"], "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:GSE119195"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE119195"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41286044", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-25734-6", "sha256": "sha256:1eee71660d3f2c9d0cea85b13d9a4941ae9adfc4f4d0b323188ae6c19c9ad3d1", "bytes": 44483, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-25734-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12644519", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE119195", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119195", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE119195", "version": null, "note": "Data will be made available upon reasonable request. For inquiries regarding the data from this study, please contact Jin Tang at ajin530@139.com.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data will be made available upon reasonable request. For inquiries regarding the data from this study, please contact Jin Tang at ajin530@139.com.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3360636", "GSM3360637", "GSM3360638", "GSM3360639", "GSM3360640", "GSM3360641", "GSM3360642", "GSM3360643"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Expression data from benign prostatic hyperplasia samples and normal controls", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE7307", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7307", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7307", "version": null, "note": "Data will be made available upon reasonable request. For inquiries regarding the data from this study, please contact Jin Tang at ajin530@139.com.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data will be made available upon reasonable request. 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