Mechanism of effective-component compatibility of Bufei Yishen formula Ⅲ in COPD and identification of hub genes

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a prevalent respiratory disease characterized by airflow limitation, with genetic factors playing a crucial role in its pathogenesis. Effective-component compatibility of Bufei Yishen formula Ⅲ (ECC-BYF Ⅲ) has been shown to effectively ameliorate COPD symptoms; however, its underlying molecular mechanism remains elusive. PURPOSE: To investigate the intervention mechanism of ECC-BYF Ⅲ on COPD and identify hub genes. METHODS: Using the GSEA method, which retains all gene information, and exhibits robustness under small-sample conditions as well as high statistical power, COPD-related pathways were identified. Among the genes contained in those pathways, hub genes were identified by protein-protein interaction (PPI) network analysis, cytoHubba algorithm, etc. The reliability of the identified hub genes was validated by independent datasets, qRT-PCR in rats with COPD, HUVEC and MH-S cells, molecular docking, molecular dynamics simulations (MD), and surface plasmon resonance (SPR). RESULTS: Compared with COPD rats, ECC-BYF Ⅲ could ameliorate pathological changes and improve lung function. Then, utilizing the RNA-seq data from COPD rats, 106 disease related pathways were identified in the COPD group when contrasted with the control group (FDR < 0.05), of which 72 pathways were reversed after ECC-BYF Ⅲ intervention. Of the 3081 genes in those reversal pathways, 395 genes were differentially dysregulated in the COPD rat samples as opposed to the control samples (FDR < 0.05). Then, six genes (Gsk3b, Ctnnb1, Pten, Met, Pik3r3, and Erbb2) were identified by PPI network analysis, cytoHubba algorithm, and GeneCards database. Two hub genes (Ctnnb1 and Pik3r3) were well confirmed in independent datasets, the COPD rat model, HUVEC and MH-S cells, molecular docking, MD, and SPR. CONCLUSION: Two COPD hub genes were identified, and their regulation by ECC-BYF Ⅲ was demonstrated. Our results might provide a basis for the study of the mechanism of COPD, and its prevention and treatment guided by traditional Chinese medicine.