Analysis of the polarization states of the alveolar macrophages in chronic obstructive pulmonary disease samples based on miRNA-mRNA network signatures.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34532470", "kind": "science-record", "revision": 9, "content_hash": "sha256:95a1695042c313448f474ae067cd819cd69c2ad39bd8aad9f46050c12befd6f4", "created_at": "2026-11-01T15:41:52Z", "updated_at": "2026-11-01T22:47:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of the polarization states of the alveolar macrophages in chronic obstructive pulmonary disease samples based on miRNA-mRNA network signatures.", "doi": "10.21037/atm-21-3815", "pmid": "34532470", "authors": ["Wen Shen", "Shukun Wang", "Ruili Wang", "Yang Zhang", "Hong Tian", "Xiaolei Yang", "Wei Wei"], "journal": "Annals of translational medicine", "year": 2021, "abstract": "BACKGROUND: Multiple gene expression studies have been performed to investigate the biomarkers of chronic obstructive pulmonary disease (COPD). However, few studies have related COPD to macrophage cells.\nMETHODS: The gene expression levels of clinical samples of COPD smokers (COPD; n=6), healthy smokers (Smoke; n=11), and never smokers (Never; n=4) were downloaded from the Gene Expression Omnibus (GEO) repository of GSE124180. The expression levels of messenger RNAs (mRNAs) and microRNAs (miRNAs) in macrophage cells of M0 (n=7), M1 (n=7), and M2 (n=7) were downloaded from the GEO repository of GSE46903 and GSE51307. Differentially expressed (DE) mRNAs (DEmRNAs) were identified by edgeR and GEO2R, with an adjusted P value <0.05 and |log2fold change (FC)| ≥1 chosen as the cut-off threshold. The potential target genes of miRNA were identified using miRanda (v3.3a) and TargetScan (v6.0) with default settings. Gene Ontology (GO) and Reactome pathway analyses were performed.\nRESULTS: The composition of macrophages was quite different between COPD, Never, and Smoke samples. The proportion of M1 cells was lower than that of M0 and M2 cells in Smokers and COPD samples. Most of the genes specifically up-regulated in M1 are related to inflammation/immunity. The expression levels of miR-30a-5p, miR-200c-3p, miR-20b-5p, miR-199b-5p, and miR-301b-3p in M1 macrophages were all lower than that of M0. Their expression levels in M2 macrophages compared with M1 varied, with higher expression in miR-30a-5p, miR-20b-5p, and lower expression in miR-200c-3p, and miR-301b-3p. The mRNAs of the fms related receptor tyrosine kinase 1 (FLT1), cardiotrophin like cytokine factor 1 (CLCF1), phosphodiesterase 4D (PDE4D), coagulation factor III, and tissue factor (F3) were dysregulated in COPD and macrophage cells.\nCONCLUSIONS: The present study mined the miRNA-mRNA signature which might play an essential role in COPD and macrophage polarization.", "claims": [{"id": "claim-method", "statement": "The Student’s t-test was used for comparisons between two groups, and analysis of variance (ANOVA) for three groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34532470", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "The Student’s t-test was used for comparisons between two groups, and analysis of variance (ANOVA) for three groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression levels of clinical samples of COPD patients (COPD, n=6), healthy smokers (Smoke, n=11), and never smokers (Never, n=4) were downloaded as the verification dataset from the Sequence Read Archive (SRA) with the accession number of PRJNA510951 [Gene Expression Omnibus (GEO) repository: GSE124180] (32).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34532470", "locator": "sections[3] \"Retrieval and process of public data\" paragraph 2", "quote": "The gene expression levels of clinical samples of COPD patients (COPD, n=6), healthy smokers (Smoke, n=11), and never smokers (Never, n=4) were downloaded as the verification dataset from the Sequence Read Archive (SRA) with the accession number of PRJNA510951 [Gene Expression Omnibus (GEO) repository: GSE124180] (32)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34532470"], "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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