Network pharmacology and molecular docking elucidate potential mechanisms of Eucommia ulmoides in hepatic ischemia-reperfusion injury.

Eucommia ulmoides (EU) and its diverse extracts have demonstrated antioxidative, anti-inflammatory, and cytoprotective properties against hepatic ischemia-reperfusion injury (HIRI). However, the primary constituents of EU and their putative mechanisms remain elusive. This study aims to explore the potential mechanisms of EU in the prevention and treatment of HIRI by employing network pharmacology and molecular docking methodologies. The main components and corresponding protein targets of EU were searched in the literature and TCMSP, and the compound target network was constructed by Cytoscape 3.9.1. Liver ischemia-reperfusion injury targets were searched in OMIM and GeneCards databases. The intersection points of compound targets and disease targets were obtained, and the overlapping targets were imported into the STRING database to construct the PPI network. We further analyzed the targets for GO and KEGG enrichment. Finally, molecular docking studies were performed on the core targets and active compounds. The component-target network unveiled a total of 26 efficacious bioactive compounds corresponding to 207 target proteins. Notably, the top-ranking compounds based on degree centrality were quercetin, ß-sitosterol, and gallic acid. Within the PPI network, the highest degree centrality encompassed RELA, AKT1, TP53. GO and KEGG enrichment analysis elucidated that EU in HIRI primarily engaged in positive regulation of gene expression, positive transcriptional regulation via RNA polymerase II promoter, negative modulation of apoptotic processes, positive regulation of transcription from DNA templates, and drug responsiveness, among other biological processes. Key pathways included cancer pathways, RAGE signaling pathway, lipid metabolism, atherosclerosis, TNF signaling pathway, PI3K-Akt signaling pathway, and apoptotic pathways. Molecular docking analysis revealed robust affinities between quercetin, ß-sitosterol, gallic acid, and RELA, AKT1, TP53, respectively. This study reveals EU exhibits substantial potential in mitigating and treating HIRI through multifaceted targeting and involvement in intricate signaling pathways.

Mitochondrial quality control in hepatic ischemia-reperfusion injury.

Hepatic ischemia-reperfusion injury is a phenomenon in which exacerbating damage of liver cells due to restoration of blood flow following ischemia during liver surgery, especially those involving liver transplantation. Mitochondria, the energy-producing organelles, are crucial for cell survival and apoptosis and have evolved a range of quality control mechanisms to maintain homeostasis in the mitochondrial network in response to various stress conditions. Hepatic ischemia-reperfusion leads to disruption of mitochondrial quality control mechanisms, as evidenced by reduced mitochondrial autophagy, excessive division, reduced fusion, and inhibition of biogenesis. This leads to dysfunction of the mitochondrial network. The accumulation of damaged mitochondria ultimately results in apoptosis of hepatocytes due to the release of apoptotic proteins like cytochrome C. This worsens hepatic ischemia-reperfusion injury. Currently, hepatic ischemia-reperfusion injury protection is being studied using different approaches such as drug pretreatment, stem cells and exosomes, genetic interventions, and mechanical reperfusion, all aimed at targeting mitochondrial quality control mechanisms. This paper aims to provide direction for future research on combating HIRI by reviewing the latest studies that focus on targeting mitochondrial quality control mechanisms.

Chlorogenic Acid Alleviates Hepatic Ischemia-Reperfusion Injury by Inhibiting Oxidative Stress, Inflammation, and Mitochondria-Mediated Apoptosis In Vivo and In Vitro.

Hepatic ischemia-reperfusion injury (HIRI) is the main reason for organ failure following liver surgery; however, its underlying causes are complex, and include oxidative stress, sterile inflammatory, and mitochondrial damage. Unfortunately, treatments for HIRI are based on supportive therapy, and no specific drugs or methods are currently available. Chlorogenic acid (CGA) is a dietary polyphenol with a wide range of pharmacological effects and it has a protective effect on HIRI; however, its specific mechanism remains unclear. In this study, we investigated that CGA pretreatment exerts protective effects against HIRI and the potential underlying mechanisms. We found that CGA pretreatment reduced ALT, AST, MDA, TNF-α, and IL-1ß levels following HIRI, improved SOD and GSH levels, and alleviated pathological liver tissue damage, with the highest CGA dose (100 mg/kg.d) exerted the strongest effect. In addition, we showed that CGA pretreatment significantly decreased the levels of reactive oxygen species following HIRI, inhibited HMGB1 release by decreasing IRF-1 expression, inhibited the expression of HMGB1, TLR-4, MyD88, P-IκB-α, NF-κB P65, and P-P65, and promoted IκB-α degradation. Thus, CGA appears to inhibit oxidative stress and inflammatory responses during HIRI. Furthermore, we found that CGA pretreatment reduced hepatocyte apoptosis following HIRI, alleviated mitochondrial damage, promoted BCL-2 expression, inhibited Bax upregulation, and inhibited cytochrome C release to prevent caspase activation, thereby reducing the expression of the caspase-independent pathway components, ENDOG and AIF. Together, our findings suggest that CGA can protect against HIRI by inhibiting oxidative stress, the HMGB1/TLR-4/NF-κB signaling pathway-mediated inflammatory responses, and mitochondria-mediated apoptosis. Thus, CGA appears to be a promising therapeutic approach for treating HIRI.

Single-Cell Sequencing of Hepatocellular Carcinoma Reveals Cell Interactions and Cell Heterogeneity in the Microenvironment.

BACKGROUND: Hepatocellular carcinoma (HCC) is the main histological subtype of liver cancer, which has the characteristics of poor prognosis and high fatality rate. Single-cell sequencing can provide quantitative and unbiased characterization of cell heterogeneity by analyzing the molecular profile of the whole genome of thousands of single cells. Thus, the purpose of this study was to identify novel prognostic markers for HCC based on single-cell sequencing data. METHODS: Single-cell sequencing of 21 HCC samples and 256 normal liver tissue samples in the GSE124395 dataset was collected from the Gene Expression Omnibus (GEO) database. The quality-controlled cells were grouped by unsupervised cluster analysis and identified the marker genes of each cell cluster. Hereafter, these cell clusters were annotated by singleR and CellMarker according to the expression patterns of the marker genes. Pseudotime analysis was performed to construct the trajectory of cell evolution and to define hub genes in the evolution process. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to explore the potential regulatory mechanism of hub genes in HCC. Next, the differential expression of hub genes and the correlation of the expression of these genes with patients' survival and diagnosis were investigated in The Cancer Genome Atlas (TCGA) database. RESULTS: A total of 9 clusters corresponding to 9 cell types, including NKT cells, hepatocytes, endothelial cells, Kupffer cells, EPCAM+ cells, cancer cells, plasma cells (B cells), immature B cells, and myofibroblasts were identified. We screened 63 key genes related to cell differentiation through trajectory analysis, which were enriched in the process of coagulation. Ultimately, we identified 10 survival-related hub genes in the TCGA database, namely ALDOB, APOC3, APOH, CYP2E1, CYP3A4, GC, HRG, LINC01554, PDK4, and TXN. CONCLUSION: In conclusion, ALDOB, APOC3, APOH, CYP2E1, CYP3A4, GC, HRG, LINC01554, PDK4, and TXN may serve as hub genes in the diagnosis and prognosis for HCC.