ldentify potential feature genes and immune cell infiltration of HIRI based on branched-chain amino acid-related genes by machine learning and experimental validation

抄録

Background: Branched-chain amino acid metabolism is involved in the pathogenesis of various liver diseases. In this study, we investigate the potential role of branched-chain amino acid metabolism-related genes in the pathogenesis of hepatic ischemia reperfusion (HIRI). Methods: The gene Expression profiles of HIRI were obtained from the Gene Expression Omnibu database. To determine the differential expression of branched-chain amino acid metabolism-related genes between HIRI and normal tissues. Then, the GO and KEGG analyses were performed, and the protein-protein interaction network was constructed. Next, the random forest and LASSO algorithms were used to screen hub genes, and machine learning techniques were used to build diagnostic models. immunoinfiltration was analyzed in both HIRI patients and controls and the ceRNA network was established. Finally, quantitative real-time PCR was used to verify the expression of hub gene. Results: Based on data set GSE23649, three central DEGs (SLC7A5, SLC1A5, SLC43A2) were determined by the intersection of three machine learning algorithms and used to establish a nomogram that yielded a high predictive performance (area under the curve 0.733−0.922). In the external GSE15480 dataset, AUC value for three key genes is as high as 1.000. Further analysis of nomogram, decision curve and calibration curve also confirme the predictive efficacy of diagnosis. GSEA and GSVA suggest that these three marker genes were involved in multiple pathways associated with HIRI progression. Immunoinfiltration analysis suggest that the proportion of macrophages, neutrophils, aDCs, Treg, and Th1 cells in HIRI group is higher than that in control group, with statistical significance(P<0.05). The ceRNA network demonstrates the complex regulatory relationships among the three hub genes and these mRNA levels were further confirmed in mouse HIRI liver samples. Conclusions: Our study have provided a comprehensive understanding of the association between branched-chain amino acid and HIRI, may provide potential target for HIRI treatment and diagnosis. And provide new insights into the mechanisms of HIRI. Graphical Abstract: