Expression of immune-related genes and possible regulatory mechanisms in ulcerative colitis

The abnormal immune response may lead to lesions of the intestinal mucosal layer in ulcerative colitis (UC). Immune-related genes (IRGs) are crucial for the immunological reaction in UC. However, the IRGs and their regulatory mechanisms in UC remain incompletely understood. Identification of IRGs in UC is essential for understanding its pathogenesis and developing new targeted therapeutic modalities.

In this study, we combined the R package "SingleR" with manual inspection methods to annotate single-cell RNA-seq data. We then performed differentially expressed genes (DEGs) analysis and pseudo-time analysis. Additionally, we performed weighted gene co-expression network analysis (WGCNA) and identified IRGs in bulk sequencing of UC intestinal tissues. Afterward, GO and KEGG analyses were performed on scRNA and bulk sequencing data. From the Human TFDB database, pertinent regulatory transcription factors (TFs) were found. Using the STRING database, the protein-protein interaction (PPI) network of important TFs was created. Finally, candidate IRGs were validated experimentally by qRT-PCR and immunohistochemistry in colon tissues of DSS-induced UC mouse models.

We verified that the relevant IRGs were highly expressed in T and B cells of UC patients by the single-cell technique. Moreover, analysis of IRGs' regulatory TFs revealed that 11 TFs were associated with the expression of IRGs. Through co-expression analysis and database screening, HNF4A was identified as a key transcription factor among them, and PPI network analysis further indicated its central regulatory role. Immune checkpoint analysis showed significant differences in PVR, ICOS, and CD28 (P < 0.001). Experimental validation confirmed that CD28 was significantly upregulated at both mRNA (P < 0.05) and protein levels (P < 0.001) in DSS-induced colitis mouse models.

Our findings suggest that HNF4A may be associated with T cell activation and potential regulation of CD28 in UC. Importantly, we improved our understanding of the immune landscape in UC inflammatory tissue using scRNA-seq and bulk sequencing data.