Exploration of the core pathway of inflammatory bowel disease complicated with metabolic fatty liver and two-sample Mendelian randomization study of the causal relationships behind the disease

Abstract

Background: Inflammatory bowel disease (IBD) is often associated with complex extraintestinal manifestations. The incidence of nonalcoholic fatty liver disease (NAFLD) in IBD populations is increasing yearly. However, the mechanism of interaction between NAFLD and IBD is not clear. Consequently, this study aimed to explore the common genetic characteristics of IBD and NAFLD and identify potential therapeutic targets.

Materials and methods: Gene chip datasets for IBD and NAFLD were obtained from the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was performed to identify modules in those datasets related to IBD and NAFLD. ClueGO was used for biological analysis of the shared genes between IBD and NAFLD. Based on the Human MicroRNA Disease Database (HMDD), microRNAs (miRNAs) common to NAFLD and IBD were obtained. Potential target genes for the miRNAs were predicted using the miRTarbase, miRDB, and TargetScan databases. Two-sample Mendelian randomization (MR) and two-way MR were used to explore the causal relationship between Interleukin-17 (IL-17) and the risk of IBD and NAFLD using data from GWAS retrieved from an open database.

Results: Through WGCNA, gene modules of interest were identified. GO enrichment analysis using ClueGO suggested that the abnormal secretion of chemokines may be a common pathophysiological feature of IBD and NAFLD, and that the IL-17-related pathway may be a common key pathway for the pathological changes that occur in IBD and NAFLD. The core differentially expressed genes (DEGs) in IBD and NAFLD were identified and included COL1A1, LUM, CCL22, CCL2, THBS2, COL1A2, MMP9, and CXCL8. Another cohort was used for validation. Finally, analysis of the miRNAs identified potential therapeutic targets. The MR results suggested that although there was no causal relationship between IBD and NAFLD, there were causal relationships between IL-17 and IBD and NAFLD.

Conclusion: We established a comorbid model to explain the potential mechanism of IBD with NAFLD and identified the chemokine-related pathway mediated by cytokine IL-17 as the core pathway in IBD with NAFLD, in which miRNA also plays a role and thus provides potential therapeutic targets.

Keywords: IL-17; chemokine; inflammatory bowel disease; nonalcoholic fatty liver disease; therapy.

Figure 1

Weighted gene co-expression network analysis (WGCNA). (A) Cluster tree of the IBD co-expressed genes. (B) Cluster tree of the NAFLD co-expressed genes. (C) Module–feature relationships in IBD. Each cell contains the corresponding correlation and p-value. (D) Module–feature relationships in NAFLD. Each cell contains the corresponding correlation and p-value. IBD, Inflammatory bowel disease; NAFLD, Nonalcoholic fatty liver disease.

Figure 2

ClueGO enrichment analysis. (A) Interactive network of GO terms groups generated by the Cytoscape plugin ClueGO, and (B) proportion of each GO terms group in the total. GO, gene ontology. **p<0.05.

Figure 3

ClueGO enrichment analysis. (A) Interactive network of KEGG terms groups generated by the Cytoscape plugin ClueGO, and (B) proportion of each KEGG terms group in the total. KEGG, Kyoto Encyclopedia of Genes and Genomes. **p<0.05.

Figure 4

PPI network. (A–C) Clusters 1–3 obtained from the black module of IBD, (D–F) Clusters 1–3 obtained from the blue modules in patients with NAFLD. PPI, Protein–protein network; IBD, inflammatory bowel disease; NAFLD, nonalcoholic fatty liver disease.

Figure 5

Biological process analysis of GO enrichment. (A–C) GO biological process analysis of three gene clusters in IBD, (D–F) GO biological process analysis of three NAFLD gene clusters. GO, gene ontology; IBD, inflammatory bowel disease; NAFLD, nonalcoholic fatty liver disease. **p<0.05.

Figure 6

Biological process analysis of KEGG enrichment. (A–C) KEGG enrichment analysis of three gene clusters in IBD. KEGG enrichment analysis of three gene clusters of (D–F) in NAFLD. KEGG: Kyoto Encyclopedia of Genes and Genomes; IBD, inflammatory bowel disease; NAFLD, nonalcoholic fatty liver disease. **p<0.05.

Figure 7

Identification of the common DEGs and ClueGO enrichment analysis. (A) Venn diagrams of the upregulated and downregulated genes in IBD and NAFLD, (B) Interaction network of KEGG terms generated by the Cytoscape plugin ClueGO and the proportion of KEGG terms in the total. KEGG: Kyoto Encyclopedia of Genes and Genomes; IBD, inflammatory bowel disease; NAFLD, nonalcoholic fatty liver disease. **p<0.05.

Figure 8

Interaction network of KEGG terms generated by the Cytoscape plugin ClueGO and the proportion of KEGG terms in the total. GO, Gene ontology; IBD, inflammatory bowel disease; NAFLD, nonalcoholic fatty liver disease. **p<0.05.

Figure 9

PPI network and core gene network. (A) PPI network; (B) Core gene network and ranking.

Figure 10

GO and KEGG enrichment analysis. (A) GO enrichment analysis (BP), (B) KEGG enrichment analysis.

Figure 11

Gene expression of each group at different stages of IBD progression. (A) GSE89632 gene expression, (B) GSE130970 gene expression, (C) GSE179285 gene expression. ***:p< 0.001, **:p<0.01, *:p<0.05, ns:p>0.05.

Figure 12

(A) GO functional enrichment analysis of nine common miRNAs. The box shows the chemokine-mediated signaling pathway. (B) Venn diagrams of the miRNA target genes predicted from the miRTarbase, miRDB, and TargetScan databases. (C) miRNA–mRNA network of MiRNAs and microRNAs.

Figure 13

Associations with IBD and NAFLD. NAFLD is associated with IL-17F. IBD is associated with IL-17A and IL-17B, and IL-17A and IL-17F are bidirectionally correlated. There is no causal relationship between IBD and NAFLD.