Identification and Validation of CDKN1A and HDAC1 as Senescence-Related Hub Genes in Chronic Obstructive Pulmonary Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35975032", "kind": "science-record", "revision": 4, "content_hash": "sha256:9b44d92a6443f57fc4854a9616e74a4dfa663b54d79c4c180b379e218c869f22", "created_at": "2026-11-01T18:15:06Z", "updated_at": "2026-11-01T22:07:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Validation of CDKN1A and HDAC1 as Senescence-Related Hub Genes in Chronic Obstructive Pulmonary Disease.", "doi": "10.2147/COPD.S374684", "pmid": "35975032", "authors": ["Jie Yang", "Meng-Yu Zhang", "Yi-Ming Du", "Xiu-Li Ji", "Yi-Qing Qu"], "journal": "International journal of chronic obstructive pulmonary disease", "year": 2022, "abstract": "Purpose: Cellular senescence participates in the occurrence and development of chronic obstructive pulmonary disease (COPD). This study aimed to identify senescence-related hub genes and explore effective diagnostic markers and therapeutic targets for COPD.\nMethods: The microarray data from the GSE38974 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The overlapping genes between genes from the GSE38974 dataset and CellAge database were considered differentially expressed senescence-related genes (DESRGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using R software. Protein-protein interaction (PPI), miRNA-mRNA network, and competitive endogenous RNA (ceRNA) network were constructed and visualized by Cytoscape software. GSE100281 and GSE103174 datasets were employed to validate the expression and diagnostic value of hub genes. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to measure the mRNA levels of hub genes in peripheral blood mononuclear cells (PBMCs) from COPD and control samples.\nResults: A total of 23 DESRGs were identified between COPD samples and healthy controls. Enrichment analysis revealed that DESRGs were mainly related to apoptosis and senescence. Moreover, four hub genes and two key clusters were acquired by Cytohubba and MCODE plugin, respectively. CDKN1A and HDAC1 were verified as final hub genes based on GSE100281 and GSE103174 datasets validation. The mRNA expression level of CDKN1A was negatively related to forced expiratory volume in 1 second/forced vital capacity (FEV1/FVC), and HDAC1 expression had the opposite correlation. Finally, an HDAC1-based ceRNA network, including 6 miRNAs and 11 lncRNAs, was constructed.\nConclusion: We identified two senescence-related hub genes, CDKN1A and HDAC1, which may be effective biomarkers for COPD diagnosis and treatment. An HDAC1-related ceRNA network was constructed to clarify the role of senescence in COPD pathogenesis.", "claims": [{"id": "claim-data-access", "statement": "The datasets analyzed in this paper can be found in the GEO database. Senescence-related genes are downloaded from the CellAge database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35975032", "locator": "sections[24] \"Data Sharing Statement\" paragraph 2", "quote": "The datasets analyzed in this paper can be found in the GEO database. Senescence-related genes are downloaded from the CellAge database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 23 differentially expressed senescence-related genes were identified between COPD samples and healthy controls, with CDKN1A and HDAC1 verified as final hub genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35975032", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 23 DESRGs were identified between COPD samples and healthy controls."}, {"asset": "source:pmid:35975032", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "CDKN1A and HDAC1 were verified as final hub genes based on GSE100281 and GSE103174 datasets validation."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A total of 23 differentially expressed senescence-related genes were identified between COPD samples and healthy controls, with CDKN1A and HDAC1 verified as final hub genes.", "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:35975032"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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