Transcriptomic Exploration Combined With Experimental Validation: Uncovering The Potential Value Of Ammonia Death-Related Biomarkers In Hepatic Ischemia-Reperfusion Injury

Background Hepatic ischemia-reperfusion injury (HIRI) is considered the primary cause of postoperative liver dysfunction and failure. Ammonia-induced cell death, characterized by lysosomal and mitochondrial damage due to ammonia accumulation, may be involved in the pathogenesis of HIRI. Methods The GSE151648 and GSE12720 datasets were obtained from the Gene Expression Omnibus (GEO) database, and 467 AD-related genes were collected from published literature. Differential expression analysis combined with Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify candidate genes and preliminarily explore their potential functions. Subsequently, biomarkers strongly associated with HIRI were identified through protein–protein interaction (PPI) network analysis, machine learning algorithms, and expression validation. Based on these biomarkers, a nomogram was constructed, and Gene Set Enrichment Analysis (GSEA), immune infiltration analysis, and network modeling were performed. Finally, liver tissues from HIRI mouse models were harvested to validate biomarker expression. Results An overlap of 586 differentially expressed genes and 762 key module genes resulted in 39 candidate genes, which were predominantly enriched in inflammatory signaling pathways. Among them, LCP1, SLC16A3, and RGS2 were identified as biomarkers, all of which were significantly upregulated in HIRI samples. The nomogram constructed based on these biomarkers exhibited strong diagnostic performance. Enrichment analysis indicated that the biomarkers were primarily associated with immune-related and metabolic pathways. Consistently, immune cell infiltration and immune functions were elevated in HIRI samples and showed significant correlations with these biomarkers. In addition, the biomarkers were predicted to interact with multiple miRNAs and lncRNAs. Finally, their expression levels in liver tissues from HIRI mouse models were consistent with the transcriptomic dataset results. Conclusion A novel form of cell death characterized by lysosomal and mitochondrial damage—AD—is closely associated with the pathogenesis of HIRI, particularly in relation to immune and metabolic processes. AD related genes LCP1, SLC16A3, and RGS2 have been identified as biomarkers for HIRI. A nomogram constructed using these biomarkers was capable of predicting the likelihood of HIRI occurrence, offering a novel approach for its early diagnosis.These findings advance our understanding of ammonia-induced cell death in HIRI and lay the foundation for future research and therapeutic development. Trial registration : Not applicable