Abstract
BACKGROUND: Super-enhancers (SEs) are implicated in the regulation of the onset and progression of Crohn's disease (CD). However, the precise mechanisms remain unclear. This study aims to investigate the diagnostic potential and molecular mechanisms of SE-related genes (SERGs) as biomarkers for CD from a transcriptomics perspective. METHODS: Data on CD and SERGs were retrieved from public databases. Differential expression analysis, the Maximal Clique Centrality algorithm, and two machine learning methods were applied, complemented by receiver operating characteristic analysis and expression level assessment to identify biomarkers and construct a nomogram for evaluating their diagnostic value. Enrichment and immune infiltration analyses were performed subsequently. Unsupervised clustering categorized CD samples into distinct subtypes based on the biomarkers, and functional and immune microenvironmental differences among these subtypes were examined. Immunohistochemical experiments confirmed the elevated protein expression of hub genes in colonic tissues from patients with CD relative to healthy controls (P < 0.05). RESULTS: PAQR5, IFITM3, PSMB8, and IRF1, were identified as biomarkers for CD, demonstrating robust diagnostic performance, with area under curve (AUC) values of 0.988, 0.973, 0.959, and 0.940, respectively. When integrated into a nomogram, the AUC reached 0.991. Except for PAQR5, the other three genes showed significantly higher expression in CD samples, a trend confirmed clinically by immunohistochemical experiments. These biomarkers were involved in areas such as immune regulation, cell biology, and sensory perception. Immunoassays further elucidated the specific infiltration patterns of different immune cells in CD and highlighted the importance of these biomarkers in regulating immune cell functions. Additionally, we classified the CD samples into two subtypes, with the biomarkers exhibiting significant expression differences between the subtypes. These two subtypes possessed distinct immune microenvironments, with the biomarkers showing moderate correlation with the differential immune cells between the subtypes. CONCLUSION: PAQR5, IFITM3, PSMB8, and IRF1 serve as biomarkers for CD, offering substantial diagnostic and immune regulatory value. These biomarkers differentiate CD into two subtypes, providing insights for personalized therapeutic strategies.