Transcriptome analysis reveals the impact of NETs activation on airway epithelial cell EMT and inflammation in bronchiolitis obliterans.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37932341", "kind": "science-record", "revision": 5, "content_hash": "sha256:65e1ac0cd5aed1275d80a74d5d0288fea10cb27d40897ac5cff9a4923ec53142", "created_at": "2026-11-01T19:02:49Z", "updated_at": "2026-11-01T22:53:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome analysis reveals the impact of NETs activation on airway epithelial cell EMT and inflammation in bronchiolitis obliterans.", "doi": "10.1038/s41598-023-45617-y", "pmid": "37932341", "authors": ["Zhongji Wu", "Xiaowen Chen", "Shangzhi Wu", "Zhenwei Liu", "Hongwei Li", "Kailin Mai", "Yinghui Peng", "Haidi Zhang", "Xiaodie Zhang", "Zhaocong Zheng", "Zian Fu", "Dehui Chen"], "journal": "Scientific reports", "year": 2023, "abstract": "Bronchiolitis obliterans (BO) is a chronic airway disease that was often indicated by the pathological presentation of narrowed and irreversible airways. However, the molecular mechanisms of BO pathogenesis remain unknown. Although neutrophil extracellular traps (NETs) can contribute to inflammatory disorders, their involvement in BO is unclear. This study aims to identify potential signaling pathways in BO by exploring the correlations between NETs and BO. GSE52761 and GSE137169 datasets were downloaded from gene expression omnibus (GEO) database. A series of bioinformatics analyses such as differential expression analysis, gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and gene set enrichment analysis (GSEA) were performed on GSE52761 and GSE137169 datasets to identify BO potential signaling pathways. Two different types of BO mouse models were constructed to verify NETs involvements in BO. Additional experiments and bioinformatics analysis using human small airway epithelial cells (SAECs) were also performed to further elucidate differential genes enrichment with their respective signaling pathways in BO. Our study identified 115 differentially expressed genes (DEGs) that were found up-regulated in BO. Pathway enrichment analysis revealed that these genes were primarily involved in inflammatory signaling processes. Besides, we found that neutrophil extracellular traps (NETs) were formed and activated during BO. Our western blot analysis on lung tissue from BO mice further confirmed NETs activation in BO, where neutrophil elastase (NE) and myeloperoxidase (MPO) expression were found significantly elevated. Transcriptomic and bioinformatics analysis of NETs treated-SAECs also revealed that NETs-DEGs were primarily associated through inflammatory and epithelial-to-mesenchymal transition (EMT) -related pathways. Our study provides novel clues towards the understanding of BO pathogenesis, in which NETs contribute to BO pathogenesis through the activation of inflammatory and EMT associated pathways. The completion of our study will provide the basis for potential novel therapeutic targets in BO treatment.", "claims": [{"id": "claim-method", "statement": "We used the R package limma to obtain DEGs between the BO and control groups from the GSE52761 and GSE137169 datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37932341", "locator": "sections[8] \"Data processing and differentially expressed genes identification\" paragraph 2", "quote": "We used the R package limma to obtain DEGs between the BO and control groups from the GSE52761 and GSE137169 datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. These data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52761. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137169. The raw RNA sequencing data of SAECs have been uploaded to the GEO database, and readers can access the dataset by entering a Reviewer token after the following website (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232805. Reviewer token: idgvasqibhwnzoz).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37932341", "locator": "sections[37] \"Data availability\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. These data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52761. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137169. The raw RNA sequencing data of SAECs have been uploaded to the GEO database, and readers can access the dataset by entering a Reviewer token after the following website (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232805. 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Pathway enrichment analysis revealed that these genes were primarily involved in inflammatory signaling processes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 115 differentially expressed genes that were found up-regulated in BO, with pathway enrichment primarily involving inflammatory signaling processes.", "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:37932341"], "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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