Discovering new hub genes of dilated cardiomyopathy.

Abstract

Aims: Dilated cardiomyopathy (DCM) has a poor prognosis and exhibits a complex and diverse aetiology and genetic profile. The genes responsible for the pathogenesis of DCM have not been fully identified. The present study aimed to explore new hub genes of DCM by mining the human DCM databases and further by experimental validation.

Methods: Two gene expression profiles of human DCM (GSE9800 and GSE120895) in the Gene Expression Omnibus (GEO) database were analysed to identify the differentially expressed genes (DEGs) (DCM vs. normal) and to obtain the common DEGs (cDEGs, between GSE9800 and GSE120895) using bioinformatic methods. The cDEGs were subjected to Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and the protein-protein interaction (PPI) networks and functional modules were constructed to screen the hub genes. The screened hub genes were identified using the Online Mendelian Inheritance in Man (OMIM) dataset, and their transcription and translation levels were further verified by real-time quantitative PCR (RT-qPCR) and western blotting using doxorubicin (DOX)-treated H9C2 cardiomyocytes that simulate the cellular pathology of DCM, with phosphate-buffered saline (PBS)-treated H9C2 cells as a normal control.

Results: A total of 47 cDEGs were screened out, and 19 DCM-associated hub genes were identified. Among the 19 hub genes, 6 genes (NFKBIB, PSMC4, PSMD3, RAD21, PRNP and STAT2) have not yet been reported as associated with DCM. Among the six genes, NFKBIB and PRNP showed up-regulations, whereas PSMC4, PSMD3 and RAD21 exhibited down-regulations in their mRNA and protein expression levels in DOX-treated H9C2 cardiomyocytes compared with the control H9C2 cells (all P < 0.05). The remaining STAT2 showed a significant up-regulation in its protein expression (P < 0.05), while its mRNA up-regulation did not reach a statistical significance (P = 0.1082).

Conclusions: Six new hub genes of DCM (NFKBIB, PSMC4, PSMD3, RAD21, PRNP and STAT2) were identified by bioinformatic analysis and experimental validation in this study. These hub genes or their products may potentially be new diagnostic biomarkers or therapeutic targets for DCM.