Frontiers in molecular biosciences
Integrated transcriptome and single-cell RNA sequencing identifies transient receptor potential channel-related biomarkers in ulcerative colitis
By Bao T, Xie T, Chen J and 4 others.
Abstract
Background
The precise cause of ulcerative colitis (UC) is still unclear. While transient receptor potential (TRP) ion channels are increasingly linked to UC pathophysiology, the comprehensive roles of TRP channel-related genes are not well understood. This study aimed to systematically identify TRP channel-related biomarkers and develop novel diagnostic and therapeutic targets for UC.
Methods
Transcriptomic data were retrieved from the Gene Expression Omnibus (GEO). Machine learning algorithms were applied to select signature genes from the overlap between differentially expressed genes (DEGs) and a curated set of 111 transient receptor potential (TRP) channel-related genes. A diagnostic nomogram incorporating signature genes was constructed, and its performance was assessed by receiver operating characteristic (ROC) curves, calibration plots, and decision curve analysis (DCA). The cellular landscape was characterized using single-cell RNA sequencing (scRNA-seq) combined with pseudotime trajectory inference and cell-cell communication analysis. Key results were further validated in a dextran sulfate sodium (DSS)-induced murine colitis model by flow cytometry, multiplex immunohistochemistry, western blotting, and quantitative real-time PCR.