Identification of differentially expressed genes, associated functional terms pathways, and candidate diagnostic biomarkers in inflammatory bowel diseases by bioinformatics analysis

Abstract

Inflammatory bowel diseases (IBDs), including ulcerative colitis (UC) and Crohn's disease (CD), are chronic inflammatory disorders caused by genetic influences, the immune system and environmental factors. However, the underlying pathogenesis of IBDs and the pivotal molecular interactions remain to be fully elucidated. The aim of the present study was to identify genetic signatures in patients with IBDs and elucidate the potential molecular mechanisms underlying IBD subtypes. The gene expression profiles of the GSE75214 datasets were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified in UC and CD patients compared with controls using the GEO2R tool. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of DEGs were performed using DAVID. Furthermore, protein-protein interaction (PPI) networks of the DEGs were constructed using Cytoscape software. Subsequently, significant modules were selected and the hub genes were identified. In the GO and KEGG pathway analysis, the top enriched pathways in UC and CD included Staphylococcus aureus infection, rheumatoid arthritis, complement and coagulation cascades, PI3K/Akt signaling pathway and osteoclast differentiation. In addition, the GO terms in the category biological process significantly enriched by these genes were inflammatory response, immune response, leukocyte migration, cell adhesion, response to molecules of bacterial origin and extracellular matrix (ECM) organization. However, several other biological processes (GO terms) and pathways (e.g., 'chemotaxis', 'collagen catabolic process' and 'ECM-receptor interaction') exhibited significant differences between the two subtypes of IBD. The top 10 hub genes were identified from the PPI network using respective DEGs. Of note, the hub genes G protein subunit gamma 11 (GNG11), G protein subunit beta 4 (GNB4), Angiotensinogen (AGT), Phosphoinositide-3-kinase regulatory subunit 3 (PIK3R3) and C-C motif chemokine receptor 7 (CCR7) are disease-specific and may be used as biomarkers for differentiating UC from CD. Furthermore, module analysis further confirmed that common significant pathways involved in the pathogenesis of IBD subtypes were associated with chemokine-induced inflammation, innate immunity, adapted immunity and infectious microbes. In conclusion, the present study identified DEGs, key target genes, functional pathways and enrichment analysis of IBDs, enhancing the understanding of the pathogenesis of IBDs and also advancing the clarification of the underlying molecular mechanisms of UC and CD. Furthermore, these results may provide potential molecular targets and diagnostic biomarkers for UC and CD.

Keywords: Crohn's disease; bioinformatics analysis; differentially expressed genes; hub genes; inflammatory bowel disease; module analysis; protein-protein interaction network; ulcerative colitis.

Figure 1.

Venn diagrams illustrating the number of (A) upregulated and (B) downregulated genes in UC and CD. The intersection represents the DEGs shared between the two groups. UC, ulcerative colitis; CD, Crohn's disease; DEG, differentially expressed gene.

Figure 2.

GO and KEGG pathway functional enrichment analysis of significant DEGs in (A) the ulcerative colitis group and in (B) the Crohn's disease group (top 10 GO terms of biological processes and functional pathways). The vertical axis represents the GO term or KEGG pathway terms significantly enriched by the DEGs; the horizontal axis indicates the negative Log10 (P-value). GO, Gene Ontology; DEG, differentially expressed gene.

Figure 3.

The top module of the protein-protein interaction network of the differentially expressed genes for UC vs. controls. (A) The top module of UC. (B) The enriched pathways of the top module for UC. UC, ulcerative colitis.

Figure 4.

The top module of the protein-protein interaction network of the differentially expressed genes for CD vs. controls. (A) The top module of CD. (B) The enriched pathways of the top module for CD. CD, Crohn's disease.

Figure 5.

The top module of the protein-protein interaction network of the overlapping DEGs between ulcerative colitis and Crohn's disease. (A) The top module of the overlapping DEGs. (B) Overview chart with functional groups including specific terms for the genes involved in the top module. The percentage of terms per groups is presented. (C) Functional distribution of Gene Ontology (GO) terms in the category biological process for the genes involved in the top module. The bars represent the number of genes associated with the biological functions. The percentage of genes per term is presented as a bar label. **P<0.01; the numbers on the x-axis indicate the number of genes associated with biological functions. DEG, differentially expressed gene.

Figure 6.

Functional distribution of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway terms for the top module of the protein-protein interaction network of the overlapping differentially expressed genes between ulcerative colitis and Crohn's disease. (A) Overview chart with functional groups including pathway terms for the genes involved in the top module. The percentage of terms per groups is presented. (B) KEGG pathway terms for the genes involved in the top module. The bars represent the number of genes associated with KEGG pathway terms. The percentage of genes per term is presented as a bar label **P<0.01; the numbers on the x-axis indicate the number of genes associated with the biological pathways.