Identification of Key Genes Associated With Epithelial Barrier Dysfunction by Comprehensive Analysis and Experimental Validation

BACKGROUND: Epithelial barrier dysfunction is a pivotal feature of asthma, and it also commonly occurs in other inflammatory conditions such as atopic dermatitis (AD) and ulcerative colitis (UC). However, the core regulatory mechanisms underlying epithelial barrier dysfunction-especially whether shared mechanisms exist across these diseases-remain unclear. METHODS: Gene expression profiles of patients with asthma, AD, and UC were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified using the limma package. Common DEGs among the three diseases were identified via a Venn diagram, followed by correlation analysis with junction molecules to screen for key genes. Interaction networks (protein-protein, transcription factor-gene, miRNA-gene, chemical-gene) of the key genes were constructed, and their correlations with asthma clinical features [Asthma Control Questionnaire (ACQ) score, Inhaled Corticosteroid (ICS) dose, lung function parameters] were analyzed. The effects of the key genes on epithelial barrier function were assessed in airway, epidermal, and intestinal epithelial cells. RESULTS: A total of eight common DEGs exhibited consistent upregulation in the epithelial tissues of patients with asthma, AD, and UC. Four key genes-CDC7, PXDN, TCN1, and TIMP1-were identified; they were upregulated in the epithelium of all three diseases, significantly elevated in IL-13-stimulated airway epithelial cells, and negatively correlated with junction molecules that were downregulated in the three diseases. Furthermore, the expression of these key genes was associated with the severity of asthma. Correlation analysis between key gene expression and asthma clinical features revealed that PXDN expression was significantly negatively correlated with the lung function parameter FEV1 (forced expiratory volume in 1 s), while TCN1 expression showed a significant negative correlation with FEV1/FVC (forced expiratory volume in 1 s/forced vital capacity). Chemical-gene interaction analysis revealed that benzo[a]pyrene could induce the expression of these four key genes. Subsequent experiments confirmed that stimulation of airway epithelial cells with benzo[a]pyrene significantly upregulated the expression of these key genes. Finally, targeting these key molecules was found to alleviate the IL-13-induced reduction in CLDN1 expression in airway epithelial cells. In in vitro collagen-coated transwell assays, knocking down either CDC7 or TCN1 significantly attenuated IL-13-induced epithelial barrier disruption in airway, epidermal, and intestinal epithelia. CONCLUSION: Our findings confirm that targeting CDC7 and TCN1 facilitates the improvement of barrier function in airway epithelial cells, epidermal keratinocytes, and intestinal epithelial cells in vitro, thereby providing promising therapeutic targets for diseases characterized by epithelial barrier dysfunction.