Identification of tryptophan metabolism-related biomarkers for nonalcoholic fatty liver disease through network analysis.

Abstract

Background: Increasing evidence demonstrate that tryptophan metabolism is closely related to the development of NAFLD. This study aimed to identify the specific biomarkers of NAFLD associated with tryptophan metabolism and researched its function mechanism.

Methods: We downloaded RNA-sequencing data of NAFLD from GSE89632 and GSE24807 and got tryptophan metabolism-related genes (TMRGs) from MsigDB database. R package Limma and WGCNA were used to identify TMRGs-DEGs and GO, KEGG, cytoscape were used to analyse and visualize the data. Immune cell infiltration analysis was used to explore immune mechanism of NAFLD and the biomarkers. We also validated extended levels of biomarkers.

Results: We identified 375 differentially genes of NAFLD and got 85 TMRGs-DEGs overlapped. GO/KEGG analysis revealed TMRGs-DEGs mainly enriched in triglyceride and cholesterol metabolism. ROC curves identified CCL20 (AUC=0.917), CD160 (AUC=0.933) and CYP7A1 (AUC=1) were biomarkers of NAFLD. Immune infiltration analysis showed significant difference of 10 immune cells and dendritic cells activated and mast cells activated were highly positive correlated with NAFLD. CCL20, CD160 and CYP7A1 were highly correlated with macrophages M2, neutrophils and mast cells activated, respectively. 27 TMRGs correlated with hub genes, and GSEA demonstrated their function in tryptophan and lysine-containing metabolic process. We obtained 41 therapeutic drugs corresponding to 2 hub genes and identified 4 drugs co-targeting CCL20 and CYP7A1. Finally, the three hub genes were validated in our mouse model.

Conclusions: CCL20, CD160 and CYP7A1 are tryptophan metabolism-related biomarkers of NAFLD, related to glycerol ester and cholesterol metabolism. And finally we screened 4 compounds co-targeted CCL29 and CYP7A1 to provide potential experimental drugs for NAFLD.