Exploring the Intervention Mechanism of Effective-Component Combination of Bufei Yishen Formula III for Airway Epithelial Barrier Injury: A miRNA-mRNA Regulatory Network Analysis.
{"title":"Exploring the Intervention Mechanism of Effective-Component Combination of Bufei Yishen Formula III for Airway Epithelial Barrier Injury: A miRNA-mRNA Regulatory Network Analysis.","authors":"Chunlei Liu, Changyuan Yue, Xiaoxiang Xing, Lidong Huang, Yanxin Wei, Peng Zhao, Jiansheng Li, Qingzhou Guan","doi":"10.2147/JIR.S529587","DOIUrl":null,"url":null,"abstract":"<p><strong>Objective: </strong>To investigate the mechanism by which the effective-component combination of Bufei Yishen formula III (ECC-BYF III) ameliorates airway epithelial barrier injury in chronic obstructive pulmonary disease (COPD) through miRNA-mRNA regulatory networks.</p><p><strong>Methods: </strong>Differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs) were identified using the edgeR algorithm. The target genes of DEmiRNAs were predicted using four online databases. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis based on the hypergeometric distribution model was performed for DEmRNAs and the predicted target genes, respectively. DEmiRNAs and their corresponding target genes that were regulated by ECC-BYF III were subsequently identified. The reliability of these miRNAs and target genes was validated using independent datasets, qRT-PCR in human bronchial airway epithelial cells (BEAS-2B), COPD rat models, and molecular docking.</p><p><strong>Results: </strong>Compared with the control group, 2997 DEmRNAs and 4 DEmiRNAs were identified in the model group (edgeR, <i>P</i><0.05). A total of 2430 target genes of the DEmiRNAs were predicted, and the miRNA-mRNA regulatory network was constructed. Pathway enrichment analysis revealed that DEmRNAs were enriched in 96 pathways and target genes in 112 pathways, with 53 overlapping pathways (<i>P</i><0.05). ECC-BYF III treatment reversed the expression of 13 miRNA-mRNA pairs. Further screening and validation in COPD rat models and BEAS-2B cells identified two miRNAs and five regulated hub genes (ESM1, RNF44, BCL2L1, ADAM19, and SMYD5). The reliability of these hub genes was further confirmed by independent datasets (GSE173896 and GSE11906) and molecular docking.</p><p><strong>Conclusion: </strong>ECC-BYF III may alleviate airway epithelial barrier injury in COPD by regulating the hsa-miR-3685-ESM1 and hsa-miR-3936-RNF44/BCL2L1/ADAM19/SMYD5 networks.</p>","PeriodicalId":16107,"journal":{"name":"Journal of Inflammation Research","volume":"18 ","pages":"12145-12167"},"PeriodicalIF":4.1000,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12417688/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Inflammation Research","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.2147/JIR.S529587","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"IMMUNOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Objective: To investigate the mechanism by which the effective-component combination of Bufei Yishen formula III (ECC-BYF III) ameliorates airway epithelial barrier injury in chronic obstructive pulmonary disease (COPD) through miRNA-mRNA regulatory networks.
Methods: Differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs) were identified using the edgeR algorithm. The target genes of DEmiRNAs were predicted using four online databases. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis based on the hypergeometric distribution model was performed for DEmRNAs and the predicted target genes, respectively. DEmiRNAs and their corresponding target genes that were regulated by ECC-BYF III were subsequently identified. The reliability of these miRNAs and target genes was validated using independent datasets, qRT-PCR in human bronchial airway epithelial cells (BEAS-2B), COPD rat models, and molecular docking.
Results: Compared with the control group, 2997 DEmRNAs and 4 DEmiRNAs were identified in the model group (edgeR, P<0.05). A total of 2430 target genes of the DEmiRNAs were predicted, and the miRNA-mRNA regulatory network was constructed. Pathway enrichment analysis revealed that DEmRNAs were enriched in 96 pathways and target genes in 112 pathways, with 53 overlapping pathways (P<0.05). ECC-BYF III treatment reversed the expression of 13 miRNA-mRNA pairs. Further screening and validation in COPD rat models and BEAS-2B cells identified two miRNAs and five regulated hub genes (ESM1, RNF44, BCL2L1, ADAM19, and SMYD5). The reliability of these hub genes was further confirmed by independent datasets (GSE173896 and GSE11906) and molecular docking.
Conclusion: ECC-BYF III may alleviate airway epithelial barrier injury in COPD by regulating the hsa-miR-3685-ESM1 and hsa-miR-3936-RNF44/BCL2L1/ADAM19/SMYD5 networks.
期刊介绍：
An international, peer-reviewed, open access, online journal that welcomes laboratory and clinical findings on the molecular basis, cell biology and pharmacology of inflammation.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
