Identification of Key Endoplasmic Reticulum Stress-Related Genes in Non-Alcoholic Fatty Liver Disease

Abstract

Background: Endoplasmic reticulum stress (ERS) is involved in the etiology of non-alcoholic fatty liver disease (NAFLD). Thus, the current study was designed to identify key ERS-associated genes in NAFLD. Methods: RNA-Seq data of NAFLD and controls were sourced from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in NAFLD and controls were identified by limma. By overlapping DEGs and ERS-related genes, ERS-related DEGs were identified. The function of ERS-related DEGs was characterized by clusterProfiler. Next, the protein–protein interaction (PPI) network was created using the Cytoscape software and the STRING database to identify key ERS-related genes in NAFLD. Furthermore, the correlations among key ERS-related genes were calculated. Results: A total of 8965 DEGs were identified between NAFLD and controls in the GSE126848 dataset. After overlapping these DEGs and ERS-related genes, 20 genes were identified as ERS-related DEGs in NAFLD. Functional analysis revealed that the genes mainly participated in ER-related functions, such as the ER–nucleus signaling pathway, regulation of ERS response, and protein processing in ER. The PPI network revealed the interactions among 17 ERS-related DEGs, including ERN1, ATF6, and EIF2S1 as the key genes. The expressions of ERN1, ATF6, and EIF2S1 were significantly down-regulated in NAFLD and were strongly positively correlated with each other. Further, the expression of ERN1 and ATFA6 was also similar in the GSE89632 datasets. Conclusion: The present study identified ERN1, ATF6, and EIF2S1 as key ERS-related genes in NAFLD. These findings may provide a molecular basis for the role of ERS in NAFLD.