Transcriptomics Analysis Identifies the Presence of Upregulated Ribosomal Housekeeping Genes in the Alveolar Macrophages of Patients with Smoking-Induced Chronic Obstructive Pulmonary Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34588774", "kind": "science-record", "revision": 9, "content_hash": "sha256:b0140157461cebc8554084080f86175e28a0c8101b310e941dc5aa5c8830c85f", "created_at": "2026-11-01T15:41:54Z", "updated_at": "2026-11-01T22:47:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomics Analysis Identifies the Presence of Upregulated Ribosomal Housekeeping Genes in the Alveolar Macrophages of Patients with Smoking-Induced Chronic Obstructive Pulmonary Disease.", "doi": "10.2147/COPD.S313252", "pmid": "34588774", "authors": ["Li Han", "Jing Wang", "Xiao-Bin Ji", "Zai-Yan Wang", "Yi Wang", "Li-Yue Zhang", "Hong-Peng Li", "Ze-Ming Zhang", "Qing-Yun Li"], "journal": "International journal of chronic obstructive pulmonary disease", "year": 2021, "abstract": "BACKGROUND AND AIMS: Alveolar macrophages (AM) play a crucial role in the development of chronic obstructive pulmonary disease (COPD). The role that AM plays in the molecular pathways and clinical phenotypes associated with tobacco-related emphysema remain poorly understood. Thus, we investigated the transcriptomic profile of AM in COPD patients with a history of smoking and explored the molecular mechanisms associated with enriched pathways and hub genes.\nMETHODS: Four data sets (GSE2125, GSE8823, GSE13896 and GSE130928) were retrieved from the GEO Database. A total of 203 GEO samples (GSM) were collated for this study. About 125 of these cases were classified as smokers (91 as healthy non-COPD smokers and 34 as COPD smokers). Based on the bioinformatics obtained using the R3.6.1 program, the data were successively adopted for differential genetic expression analysis, enrichment analysis (EA), and then protein-protein interaction analysis (PPI) in a STRING database. Finally, Cytoscape 3.8 software was used to screen the hub genes. A further data analysis was performed using a set of 154 cases, classified as 64 healthy non-smokers and 91 as healthy smokers. The same procedures were used as for the COPD dataset.\nRESULTS: When comparing the data pertaining to COPD-smokers and non-COPD smokers, the top ten genes with the greatest transcriptional differences were found to be NADK, DRAP1, DEDD, NONO, KLHL12, PRKAR1A, ITGAL, GLE1, SLC8A1, SVIL. A GSEA (Gene Set Enrichment Analysis) revealed that these genes manifested an up-regulated ribosomal pathway in contrast with other genes that exhibited an extensive down-regulated pathway. The hub genes were mainly genes encoding ribosomal subunits through PPI. Furthermore, it was found that there is a narrow transcriptional difference between healthy non-smokers and non-COPD smokers and the hub genes identified here are mainly members of the chemokines, including CCL5, CCR5, CXCL9 and CXCL11.\nCONCLUSION: An elevated activity of the ribosome pathway in addition to the increased expression of ribosomal housekeeping genes (also known as hub genes) were identified with COPD-smokers, and these have the potential to cause a wide range of downstream pathogenetic effects. As for the preclinical phase, non-COPD smokers were found to be characterized by enriched pathways of several chemokines in AM.", "claims": [{"id": "claim-method", "statement": "Following the process of the batch effect (Figure 2), analysis and visualization of the differentially expressed genes (DEGs), including a PCA (principal component analysis) chart, heat-map and volcano plot were performed using “means” of the corresponding R package “limma”;", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34588774", "locator": "sections[2] \"Materials and Methods\" paragraph 5", "quote": "Following the process of the batch effect (Figure 2), analysis and visualization of the differentially expressed genes (DEGs), including a PCA (principal component analysis) chart, heat-map and volcano plot were performed using “means” of the corresponding R package “limma”;"}], "state": "complete"}, {"id": "claim-data-access", "statement": "A total of 4 datasets: GSE2125 (n=45), GSE8823 (n=24), GSE13896 (n=88), GSE130928 (n=70), representing a total of 203 cases of GSM, and all on an Affymetrix HG-U133 Plus 2.0 (GPL570 microarray), were obtained (Figure 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34588774", "locator": "sections[2] \"Materials and Methods\" paragraph 2", "quote": "A total of 4 datasets: GSE2125 (n=45), GSE8823 (n=24), GSE13896 (n=88), GSE130928 (n=70), representing a total of 203 cases of GSM, and all on an Affymetrix HG-U133 Plus 2.0 (GPL570 microarray), were obtained (Figure 1)."}], "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:34588774"], "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:GSE130928"], "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:GSE130928"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34588774", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/COPD.S313252", "sha256": 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"licence_read": false}}, {"id": "asset:table:pmid:34588774:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5a4dad66497b7d49ff2df372042ed80d007e990a47f1cf2d5cabd37d293f1137", "bytes": 2071, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#t0001", "version": null, "note": "The Top 10 Genes with Most Significant Difference of Transcription Between Relevant Groups", "structure": {"pmcid": "PMC8473850", "section_index": 5, "section_title": "Differential Gene Expression", "row_count": 21, "column_count": 7}, "table": {"label": "Table 1", "caption": "The Top 10 Genes with Most Significant Difference of Transcription Between Relevant Groups", "rows": [["Group", "Entrez ID", "Symbol", "Description", "Up/Down", "logFC", "Adj.P"], ["The COPD vs non-COPD smokers", "65220", "NADK", "NAD kinase", "Down", "−1.016090856", "1.18E-09"], ["10589", "DRAP1", "DR1 Associated Protein 1", "Down", "−0.70553346", "2.40E-09"], ["9191", "DEDD", "Death Effector Domain Containing", "Down", "−0.834479281", "3.74E-09"], ["4841", "NONO", "Non-POU Domain Containing Octamer Binding", "Down", "−0.751792587", "6.67E-09"], ["59349", "KLHL12", "Kelch Like Family Member 12", "Down", "−0.611660528", "6.67E-09"], ["5573", "PRKAR1A", "Protein Kinase CAMP-Dependent Type I Regulatory Subunit Alpha", "Down", "−0.881787568", "6.67E-09"], ["3683", "ITGAL", "Integrin Subunit Alpha L", "Down", "−0.939391902", "6.67E-09"], ["2733", "GLE1", "GLE1 RNA Export Mediator", "Down", "−0.762754132", "7.34E-09"], ["6546", "SLC8A1", "Solute Carrier Family 8 Member A1", "Down", "−0.860251027", "1.54E-08"], ["6840", "SVIL", "Supervillin", "Down", "−0.839944317", "1.87E-08"], ["The non-COPD smokers vs non-smokers", "227399", "VGLL3", "Vestigial Like Family Member 3", "Down", "−2.194799911", "1.49E-22"], ["226679", "SLC26A11", "Solute Carrier Family 26 Member 11", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE2125", "GSE8823", "GSE13896", "GSE130928"], "resolved_accessions": ["GSE2125", "GSE8823", "GSE13896", "GSE130928"], "statements": ["A total of 4 datasets: GSE2125 (n=45), GSE8823 (n=24), GSE13896 (n=88), GSE130928 (n=70), representing a total of 203 cases of GSM, and all on an Affymetrix HG-U133 Plus 2.0 (GPL570 microarray), were obtained (Figure 1)."], "basis": "The paper names GSE2125, GSE8823, GSE13896, GSE130928 in GEO Database and the accession resolves in the repository. 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