Investigating possible dilated cardiomyopathy targets via bioinformatic analysis

Abstract

Dilated cardiomyopathy (DCM) is the most common cardiomyopathy associated with heart failure; however, the underlying mechanism remains unclear. Initially, gene expression data of patients with DCM from the GSE4172 and GSE21610 datasets were obtained from the Gene Expression Omnibus website. Differentially expressed genes (DEGs) were analyzed with a false discovery rate < 0.05 and log2 fold change > 1.2. Furthermore, both the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene Set Enrichment Analysis (GSEA) were used to investigate the functional annotations. STRING and Cytoscape tools were used to form the protein-protein interaction (PPI) network and authenticate hub genes. Thereafter, the signature of immune-related genes (IRGs) was selected from the DEGs and data via the IMMPORT website. Hub genes were selected from the differentially expressed IRGs that formed the PPI network. Finally, the receiver-operating characteristic curves of the key genes were measured as biomarkers of DCM. A total of 173 independent DEGs (103 upregulated and 70 downregulated genes) were found in the microarray datasets GSE4172 and GSE21610. KEGG analysis and GSEA indicated that the BMP signaling pathway and apoptosis-related signals have a key effect on DCM development. The 10 hub genes also indicated the key effect of the BMP signaling pathway on DCM. A total of 224 differentially expressed IRGs and 20 featured IRGs were identified. Finally, BMP6, CD69, RUNX2, and SPP1 were identified as possible targets for DCM. Our data suggest a possible molecular regulatory mechanism for DCM therapy. Moreover, BMP6, CD69, RUNX2, and SPP1 may have key effects on the development of DCM.

Keywords: BMP6; CD69; Dilated cardiomyopathy; KEGG; RUNX2; SPP1; gene set enrichment analysis.

Figure 1

Volcanos plot and heatmap of the GSE4172 and GSE21610 datasets. A. Volcano plots of the distribution of differentially expressed genes (DEGs) in each dataset, fold change ≥ 1.2, P < 0.05. B. The expression heatmap of the top 20 upregulated and downregulated DEGs. C, D. The DEGs in GSE4172 and GSE21610 and the Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. E-J. The GSEA analysis of the KEGG pathways significantly enriched in GSE4172 and GSE21610. Screening criteria of selected KEGG pathways: biological functions of pathways, FDR value < 0.25, and p-value < 0.05. ES, Enrichment Score; FDR, False Discovery Rate.

Figure 2

Protein-protein interaction (PPI) networks of the DEGs were constructed based on the STRING database and Cytoscape software. A. PPI network of the DEGs. B. The hub genes were screened by the MCDE from Cytoscape software. C. The hub genes were screened by the cytoHubba from Cytoscape software. D, E. The hub genes in GSE4172 and GSE21610 and the Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis.

Figure 3

Verify the expression level and the prognostic value of key genes. A-D. The expression levels of hub genes (BMP6, CD69, SPP1and RUNX2) in GSE4172 and GSE21610. The p-value was from a Wilcoxon rank-sum test. *P < 0.05. **P < 0.01; ***P < 0.001. The y-axis represents the relative expression value log2 (TPM + 1). E-H. The receiver-operating characteristic curves of the four key genes in dilated cardiomyopathy (DCM).

Figure 4

The differentially expressed immune-related genes and protein-protein interaction PPI network. A. The intersection data of DEGs and immune-related genes (IRGs) were presented. B. The PPI network of the differentially expressed IRGs. C. The top 20 genes with most adjacent nodes among the PPI network were screened by the cytoHubba from Cytoscape software.