Drug Repositioning of Inflammatory Bowel Disease Based on Co-Target Gene Expression Signature of Glucocorticoid Receptor and TET2

Abstract

The glucocorticoid receptor (GR) and ten-eleven translocation 2 (TET2), respectively, play a crucial role in regulating immunity and inflammation, and GR interacts with TET2. However, their synergetic roles in inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), remain unclear. This study aimed to investigate the co-target gene signatures of GR and TET2 in IBD and provide potential therapeutic interventions for IBD. By integrating public data, we identified 179 GR- and TET2-targeted differentially expressed genes (DEGs) in CD and 401 in UC. These genes were found to be closely associated with immunometabolism, inflammatory responses, and cell stress pathways. In vitro inflammatory cellular models were constructed using LPS-treated HT29 and HCT116 cells, respectively. Drug repositioning based on the co-target gene signatures of GR and TET2 derived from transcriptomic data of UC, CD, and the in vitro model was performed using the Connectivity Map (CMap). BMS-536924 emerged as a top therapeutic candidate, and its validation experiment within the in vitro inflammatory model confirmed its efficacy in mitigating the LPS-induced inflammatory response. This study sheds light on the pathogenesis of IBD from a new perspective and may accelerate the development of novel therapeutic agents for inflammatory diseases including IBD.

Keywords: GR; IBD; TET2; drug repositioning; in vitro inflammatory model.

Figure 1

Assessment of the role of GR and TET2 regulation in IBD. (A) Split violin plot revealing the expressional differences of the 17 biomarkers between IBD and HC. (B) Correlating GR and TET2 separately with the 17 markers in mRNA level. (C) Box plot showing the comparison of 22 kinds of immune cells between IBD and HC. (D) Correlating the differentially infiltrated immune cells with the four markers upon the threshold of p < 0.05. (E) ROC curves of the four markers. * p < 0.05; ** p < 0.01; **** p < 0.0001; ns, not significant.

Figure 2

Identification of DEGs associated with UC and CD. (A) Volcano plot of DEGs in the colon tissue between UC and HC. (B) Volcano plot of DEGs in the colon tissue between CD and HC. (C) Heatmap revealing the expression pattern of common and distinct DEGs between groups.

Figure 3

Functional enrichments for IBD signatures around GR and TET2. Top slimmed GO terms for the (A) GR- and TET2-related UC DEGs and (B) GR- and TET2-related CD DEGs upon the threshold of q < 0.05. Top MSigDB hallmark-pathway enrichments for the (C) GR- and TET2-related UC DEGs and (D) GR- and TET2-related CD DEGs upon the threshold of q < 0.05. CSEA testing results of the (E) GR- and TET2-related UC DEGs and (F) GR- and TET2-related CD DEGs. The x-axis indicates the cell types derived from the intestinal tissue and blood. Dots represent the intestine cell types annotated by 23 general classifications descending by order of significance. The dashed line is the significant threshold with FDR < 0.05.

Figure 4

Comparative transcriptome analyses of two in vitro inflammatory cell models. GSEA revealing the overrepresented pathways in overall gene expression of (A) HCT116 cells and (B) HT29 cells after LPS stimulation. (C) RRHO analysis results for comparing expression patterns across the two cell models. (D) Venn diagram showing the overlapping genes between specific three gene sets. (E) KEGG pathway enrichments for the overlapping genes.

Figure 5

Identification and validation of potential therapeutic compounds. (A) The description of top 10 promising small molecules for IBD treatment. (B) The chemical structure of the top-ranked BMS-536924. (C) The cytotoxicity of BMS-536924 on HT29 cells by CCK8 assay. The effects of BMS-536924 treatment on the expression of proinflammatory cytokines (D) IL-6 and (E) TNF-α in LPS-induced HT29 cells. Values are expressed as the means ± SD; n = 4 in each group. ### p < 0.001 vs. the NC group. ** p < 0.01, *** p < 0.001, and **** p < 0.0001 vs. the LPS group.