Integrated transcriptome and single-cell RNA sequencing identifies transient receptor potential channel-related biomarkers in ulcerative colitis.

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.

RESULTS

Five TRP channel-related feature genes (IL-1β, PIK3R3, ADCY3, ADCY7, and TRPV1) were identified. In UC, IL-1β, PIK3R3, ADCY3, and ADCY7 were notably upregulated, while TRPV1 was markedly downregulated. The nomogram, utilizing these five feature genes, exhibited outstanding discriminatory capability (AUC = 0.993) and provided enhanced net clinical benefit. scRNA-seq analysis identified B and plasma cells as the most significantly expanded pathogenic population, exhibiting acquired bidirectional crosstalk with epithelial cells in UC. Pseudotime trajectory analysis revealed that IL-1β and PIK3R3 were mainly concentrated during the initial developmental phases of B and plasma cells. In the DSS-induced colitis model, there was a notable increase in B-cell infiltration, accompanied by significant upregulation of IL-1β and Pik3r3 at both protein and mRNA levels, with confirmed colocalization with Cd19+ B cells.

CONCLUSION

This study identified five TRP channel-related biomarkers and created a high-performance diagnostic nomogram for UC. The study underscores the pivotal role of B and plasma cells, identifying IL-1β and PIK3R3 as early-activated genes in pathogenic B-cell responses, thus offering new diagnostic biomarkers and therapeutic targets for UC.