Identification of transcriptomic signatures and crucial pathways involved in non-alcoholic steatohepatitis

Abstract

Our study aimed to uncover the crucial genes and functional pathways involved in the development of non-alcoholic steatohepatitis (NASH). Liver transcriptome datasets were integrated with Robust rank aggregation (RRA) method, and transcriptomic signatures for NASH progression and fibrosis severity in NAFLD were developed. The functions of transcriptomic signatures were explored by multiple bioinformatic analyses, and their diagnostic role was also evaluated. RRA analyses of 12 transcriptome datasets comparing NASH with non-alcoholic fatty liver (NAFL) identified 116 abnormally up-regulated genes in NASH patients. RRA analyses of five transcriptome datasets focusing fibrosis severity identified 78 abnormally up-regulated genes in NAFLD patients with advanced fibrosis. The functions of those transcriptomic signatures of NASH development or fibrosis progression were similar, and were both characterized by extracellular matrix (ECM)-related pathways (Adjusted P < 0.05). The transcriptomic signatures could effectively differentiate NASH from NAFL, and could help to identify NAFLD patients with advanced fibrosis. Gene set enrichment analysis and weighted gene co-expression network analysis further validated the key role of ECM-related pathways in NASH development. The top 10 up-regulated genes in NASH patients were SPP1, FBLN5, CHI3L1, CCL20, CD24, FABP4, GPNMB, VCAN, EFEMP1, and CXCL10, and their functions were mainly related to either ECM-related pathways or immunity-related pathways. Single cell RNA-sequencing analyses revealed that those crucial genes were expressed by distinct cells such as hepatocytes, macrophages, and hepatic stellate cells. Transcriptomic signatures related to NASH development and fibrosis severity of NAFLD patients are both characterized by ECM-related pathways, and fibrosis is a main player during NASH progression. This study uncovers some novel key genes involved in NASH progression, which may be promising therapeutic targets.