Interaction of Biochemical Processes between Chronic Obstructive Pulmonary Disease (COPD), Pulmonary Arterial Hypertension (PAH), and Coronavirus Disease 2019 (COVID-19).

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37216361", "kind": "science-record", "revision": 4, "content_hash": "sha256:d48533db6cc6cdd3973dc6c5ad1b6dc8ae33217dad6e946e0a4a6e7cf61afcd7", "created_at": "2026-11-01T19:01:55Z", "updated_at": "2026-11-01T22:51:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Interaction of Biochemical Processes between Chronic Obstructive Pulmonary Disease (COPD), Pulmonary Arterial Hypertension (PAH), and Coronavirus Disease 2019 (COVID-19).", "doi": "10.33073/pjm-2023-015", "pmid": "37216361", "authors": ["Zhe Tian", "Lilan Cen"], "journal": "Polish journal of microbiology", "year": 2023, "abstract": "Both pulmonary arterial hypertension (PAH) and chronic obstructive pulmonary disease (COPD) are risk factors for coronavirus disease 2019 (COVID-19). Patients with lung injury and altered pulmonary vascular anatomy or function are more susceptible to infections. The purpose of the study is to ascertain whether individuals with COPD or PAH are affected synergistically by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Data sources for the construction of a protein-protein interaction (PPI) network and the identification of differentially expressed genes (DEGs) included three RNA-seq datasets from the GEO database (GSE147507, GSE106986, and GSE15197). Then, relationships between miRNAs, common DEGs, and transcription factor (TF) genes were discovered. Functional analysis using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and other databases, as well as the forecasting of antiviral medications for COPD and PAH patients infected with SARS-CoV-2, were also performed. Eleven common DEGs were found in the three datasets, and their biological functions were primarily enriched in the control of protein modification processes, particularly phosphorylation. Growth factor receptor binding reflects molecular function. KEGG analysis indicated that co-DEGs mainly activate Ras, and PI3K-Akt signaling pathways and act on focal adhesions. NFKB1 interacted with HSA-miR-942 in the TF-miRNA-DEGs synergistic regulatory network. Acetaminophen is considered an effective drug candidate. There are some connections between COPD and PAH and the development of COVID-19. This research could aid in developing COVID-19 vaccines and medication candidates that would work well as COVID-19 therapies.", "claims": [{"id": "claim-method", "statement": "The data were loaded into R software (version 3.6.3) and ran the DESeq2 package (15) for standardized visualization and differential analysis. The sample groups were compared using the GEO query and limma R programs in GEO2R, and all DEGs were chosen based on padj < 0.05 and |log FC| > 1. The intersection of the DEGs from the three datasets was taken to find co-DEGs, the ggplot2 package in R language (version 3.6.3) was loaded, and a Veen diagram was created.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37216361", "locator": "sections[5] \"Finding co-DEGs and identifying DEGs in COVID-19, COPD, and PAH\" paragraph 2", "quote": "The data were loaded into R software (version 3.6.3) and ran the DESeq2 package (15) for standardized visualization and differential analysis. The sample groups were compared using the GEO query and limma R programs in GEO2R, and all DEGs were chosen based on padj < 0.05 and |log FC| > 1. The intersection of the DEGs from the three datasets was taken to find co-DEGs, the ggplot2 package in R language (version 3.6.3) was loaded, and a Veen diagram was created."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Availability of data and material: The data used to support this study is available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37216361", "locator": "sections[18] \"fn-group\" paragraph 1", "quote": "Availability of data and material: The data used to support this study is available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using DESeq2 and GEO2R/limma on three GEO datasets, the study identified 11 common DEGs shared by COVID-19, COPD, and PAH.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37216361", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data sources for the construction of a protein-protein interaction (PPI) network and the identification of differentially expressed genes (DEGs) included three RNA-seq datasets from the GEO database (GSE147507, GSE106986, and GSE15197)."}, {"asset": "source:pmid:37216361", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Eleven common DEGs were found in the three datasets, and their biological functions were primarily enriched in the control of protein modification processes, particularly phosphorylation."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using DESeq2 and GEO2R/limma on three GEO datasets, the study identified 11 common DEGs shared by COVID-19, COPD, and PAH.", "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:37216361"], "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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