Identification of a liver fibrosis and disease progression-related transcriptome signature in non-alcoholic fatty liver disease

Abstract

Non-alcoholic fatty liver disease (NAFLD)-related liver fibrosis is closely associated with long-term outcomes of patients. This study aimed to establish a transcriptome signature to distinguish NAFLD patients with mild or advanced fibrosis and to monitor disease progression. Using least absolute shrinkage selection operator regression, we identified a signature of 11 hub genes by performing differential gene expression analysis in six bulk transcriptome profiles in the Gene Expression Omnibus database from liver fibrosis patients with different etiologies. Patients with NAFLD were classified using the 11-hub gene signature. Integrated analysis of signaling pathway enrichment, gene set enrichment, nearest template prediction, infiltration by hepatic stellate cells (HSCs) and pseudotime trajectories was performed on three bulk and one single-cell transcriptomes from NAFLD patients. Molecular features were compared between high-risk and low-risk groups, and associations were explored between hub gene signature expression and activation of HSCs. It was found that the high-risk group was characterized by advanced fibrosis stage, elevated risk for hepatocellular carcinoma, more significant infiltration by activated HSCs, as well as enrichment in signaling pathways related to fibrogenesis and NAFLD progression. Moreover, the 11-hub gene signature at the single-cell transcriptome level correlated with HSCs activation. In vitro experiments were conducted to evaluate the expression levels of hub genes, and IL6 was found to be up-regulated in activated LX-2 cells showing lipid accumulation. Our findings suggest that the 11-hub gene signature can help identify fibrosis stage in patients with NAFLD and detect disease progression. We also suggest that the role of IL6 in HSC activation deserves more investigation in the context of NAFLD.