Abstract

BACKGROUND: The occurrence of nonalcoholic fatty liver disease (NAFLD) is closely related to type 2 diabetes, especially in patients with insulin resistance. The purpose of this research was to elucidate the major genes and transcriptional regulation of insulin resistance in the progression of NAFLD.

MATERIAL AND METHODS: We downloaded the gene expression matrix of GSE89632 from Gene Expression Omnibus. Then the principal component analysis was used to identify whether the samples were clustered. Differentially expressed genes were identified by limma R package. Enrichment analysis and protein‑protein interaction network was used to find potential function and screening hub genes. We further used ChIP-seq data from ENCODE to predict the transcriptional regulation of hub genes. Finally, we verified the functions of hub genes with clinical information.

RESULTS: These hub genes were significantly enriched in “response to insulin”, “response to glucose”, and “fat cell differentiation”. ChIP-seq data showed that EGR1 (early growth response gene-1) may play an important role in the transcriptional regulation of SOCS1 (suppressor of cytokine signaling 1), SOCS3 (suppressor of cytokine signaling 3), and Fos gene family in the liver, as the low expression of EGR1 in patients with insulin resistance may promote the occurrence and development of NAFLD. Similarly, correlation analysis showed that EGR1 was positively correlated with the expression of SOCS1, SOCS3, and the genes of Fos gene family, and EGR1 was negatively correlated with the degree of steatosis.

CONCLUSIONS: Newly identified hub genes and their transcriptional regulation may promote understanding of the molecular mechanisms underlying insulin resistance related to the progression of NAFLD and provide a new therapy target and biomarkers.

Keywords: Diabetes Mellitus, Type 2, Early Growth Response Protein 1, Fatty Liver, Insulin Resistance, biomarkers, Disease Progression, Gene Expression Profiling, Insulin, Liver, Non-alcoholic fatty liver disease, Principal Component Analysis, Protein Interaction Maps, Suppressor of Cytokine Signaling 1 Protein, Suppressor of Cytokine Signaling 3 Protein