Integrated RNA-seq and scRNA-seq to explore the biological mechanisms of mitophagy-related genes in ulcerative colitis

Abstract

Mitophagy’s role in ulcerative colitis (UC) is not fully understood. This study explores mitophagy’s impact on UC and aims to create a diagnostic model. The transcriptomic datasets of patients with UC and healthy controls were obtained from the Gene Expression Omnibus database. The mitophagy-related differentially expressed genes (MRDEGs) and hub genes were identified by weighted gene co-expression network and protein-protein interaction (PPI) network analysis. Networks of mRNA-miRNA and mRNA-TF were established to detect pertinent mechanisms. CIBERSORT was used to evaluate association between immune cells with hub genes. A diagnostic model was developed utilizing logistic regression. Single-cell RNA sequencing was used to characterize the expression of hub genes in specific cell clusters and the results of the differential analysis were annotated with the hub genes identified in the logistic model. Finally, a mice model of colitis was established, and the results were verified using qRT-PCR and western blot. The study identified 28 MRDEGs and 20 hub genes. A significant link was found between immune cell infiltration and hub genes, highlighting mitophagy’s interaction with the immune response. A diagnostic model with 13 potential markers was developed, achieving high accuracy. Single-cell RNA sequencing delineated key cell types and confirmed varied hub gene expression, with validation through RT-qPCR and western blot. These findings not only deepens our understanding of mitochondrial autophagy in UC but also establishe a robust diagnostic model through interdisciplinary approaches, laying the groundwork for the development of targeted diagnostic and therapeutic strategies that warrant further research for clinical application.