This study combines microarray technology with comprehensive bioinformatics analysis to explore the possible pathogenesis and biomarkers of Crohn's disease. After comparing the gene expression levels of the Crohn's disease group and the control group, we predicted 74 possible EDGs for Crohn's disease. WGCNA shows that the characteristic genes in the blue module are significantly related to Crohn’s disease. By intersecting the genes in the blue module with DEGs, 32 CGs were obtained. To further evaluate the diagnostic value of these CGs, five hub genes (CDH17, CSF1R, CXCL10, CXCL9 and COL3A1) were identified according to the degree of nodes in the PPI network, and a prediction model of Crohn's disease risk based on HUB genes was established. The ROC curve indicates that the model has good prediction accuracy. Meanwhile, this study predicted that 3 miRNAs (hsa-miR-29a-3p, hsa-miR-29b-3p, hsa-miR-29c-3p) and 2 TFs(TCF4, HINFP) might be involved in the pathogenesis of Crohn's disease.
Hub genes have received wide attention as possible targets of potential drug action. In this study, 5 hub genes (CXCL9, CXCL10, CSF1R, CDH17, COL3A1) may play an important role in the pathogenesis of Crohn’s disease. C-X-C motif chemokine ligand 9 (CXCL9) belongs to the T cell chemoattractant in the CXC chemokine family. It is involved in the growth, movement and activation of immune and inflammatory cells, as well as the chemotaxis of activated T cells(22). A study by Elia et al. showed that the recruitment of monocytes and granulocytes by CXCL9 plays an important role in maintaining the inflammatory state of ulcerative colitis(23). A recent study(24) suggests that CXCL9 overexpression may be related to the inflammatory state of Crohn’s disease, which is the same as our findings. CXC motif chemokine ligand 10 (CXCL10) is induced by interferon γ to stimulate the secretion of monocytes, fibroblasts, natural killer cells, endothelial cells and dendritic cells(25). It mainly binds specifically to Th1 cells to chemoattract inflammatory factors, and mediate the migration and aggregation of immune cells(26). This research suggests that CXCL10 is significantly expressed at lower levels in Crohn's disease tissues. It is worth noting that the expression of CXCL10 in the diseased tissues of patients who fail to respond to treatment of Crohn’s disease with monoclonal antibodies against tumor necrosis factor-α (TNFα) is elevated(27). Therefore, the high expression of CXCL10 may be related to the drug resistance mechanism of Crohn's disease. The protein encoded by colony stimulating factor 1 receptor (CSF1R) is the colony stimulating factor 1 receptor, which regulates the proliferation, differentiation and function of macrophages(28). Previous studies confirmed that CSF1R was highly expressed in inflammatory bowel disease, which is consistent with our research results(29, 30). Zapata-Velandia et al. speculated that CSF1R may be a susceptibility gene for Crohn's disease(31). The latest research shows that patients with inflammatory bowel disease may benefit from CSF1R inhibitors(32). Cadherin-17(CDH17) is a calcium-dependent transmembrane glycoprotein involved in cell-to-cell adhesion in the intestinal epithelium(33). Currently, CDH17 has been confirmed as a diagnostic marker for gastrointestinal adenocarcinoma(34, 35). However, whether the expression of CDH17 is related to Crohn's disease has not been reported. Fortunately, a previous study demonstrated that CDH17 is involved in pathways associated with antigen presentation and immune response(36). This is also reflected in the results of this study. Therefore, CDH17 may be a potential marker of Crohn's disease. Collagen type III alpha 1 chain (COL3A1) encodes a type of fibrous collagen that is widely found in expandable connective tissues such as the skin, gastrointestinal tract and vascular system(37). Chokr et al. found that COL3A1 is involved in intestinal fibrosis leading to the progression of Crohn's disease(38). Therefore, COL3A1 may be a therapeutic target to delay the progression of Crohn's disease.
To date, the relationship between hsa-miR-29a-3p, hsa-miR-29b-3p, hsa-miR-29c-3p and inflammatory bowel disease has not been reported. Notably, hsa-miR-29a-3p and hsa-miR-29b-3p are considered to be important predictors of miRNA in osteoarthritis(39). Moniri et al. speculated that hsa-miR-29b-3p and hsa-miR-29c-3p might play an important role in wound healing(40). The circulating base level of hsa-miR-29b-3p was significantly associated with metastasis and prognosis of colorectal cancer(41, 42). In addition, circulating hsa-miR-29c-3p can be used as a miRNA to predict acute cell rejection after cardiac transplantation(43).
Crohn's disease has been associated with reduced expression of the transcription factor T cell factor 4 (TCF4) in the Wnt signaling pathway in several studies(44–46). Histone nuclear factor P (HINFP) is a transcription factor that regulates the expression of the histone H4 gene and plays an important role in normal cell cycle control and proliferation(47). This study suggests that HINFP may be involved in the pathogenesis of Crohn's disease.
This study provides a reasonable prediction of possible biomarkers for Crohn's disease. However, there are still shortcomings in this study; for example, the above research results have not been further verified in this study. It is well known that inflammatory cell infiltration and abnormal activation of immune pathways are the pathological features of Crohn's disease. It is necessary to further explore the relationship between the biomarkers predicted in this study and the immune characteristics of Crohn's disease.