Linking Brain and Immune Transcriptomes to Gut-Derived Metabolites in Hepatic Encephalopathy: An Explorative Integrative Multi-Omics Approach.

Abstract

Purpose: Hepatic encephalopathy (HE), one of the more important cerebral complications attributable to acute liver failure and more severe forms, has traditionally been associated with hyperammonemia. However, recent studies implicate gut microbiota-derived metabolites in HE pathogenesis through systemic inflammation and neurotoxicity. Despite this, the integrated molecular mechanisms linking these metabolites to HE remains poorly described. This study addresses this gap by employing a bioinformatics-based systems biology approach to identify interactions between gut metabolites and host genes, thereby identifying novel diagnostic and therapeutic targets.

Methods: Differentially expressed genes (DEGs) from peripheral (GSE184200: CD4⁺ T lymphocytes) and central (GSE57193: fusiform gyrus) tissues of HE patients were analyzed using GEO2R. Genes associated with five gut microbiota-derived metabolites including choline metabolites, lipid metabolites, short-chain fatty acids, tryptophan catabolites, and secondary bile acids were extracted from GeneCards. Overlapping genes between HE-related genes and gut-derived metabolites were then subjected to multi-level enrichment analyses (pathway, phenotype, cell type, and cellular component), and miRNA/drug prediction using Enrichr and ToppGene.

Results: We identified nine hub genes related to gut-systemic interactions and 29 hub genes associated with gut-brain interactions in the context of HE. The most significantly impaired pathways were signaling by interleukin 24 and TP53, as well as oxidative stress, which were affected by gut metabolites and peripheral HE-related genes. Similarly, mitochondrial fatty acid β-oxidation, neuroinflammation, and glutamate tone were significantly altered by gut metabolites and central HE-related genes. Additionally, we predicted 18 miRNAs and 13 potential drugs that target both gut microbiota metabolites and HE.

Conclusion: This study offers the first systems-level framework connecting gut-derived metabolites to HE through gene networks, challenging the ammonia-centric viewpoint. The predicted miRNAs and drugs offer translational potential for precision medicine in HE. Experimental validation of these targets is required to advance therapeutic strategies.