Identification of key pathways and genes in carotid atherosclerosis through bioinformatics analysis of RNA-seq data

Exploring the mechanism of Erchen decoction in the treatment of atherosclerosis based on network pharmacology and molecular docking

BACKGROUND

Atherosclerosis (AS) is the cause of most cardiovascular diseases and imposes a huge economic burden on society. Erchen decoction (ECD) is an effective formula for treating AS, but its therapeutic mechanism remains unclear. This study will explore the mechanism of ECD mechanism for treating AS using network pharmacology and molecular docking.

METHODS

We searched ECD chemical composition information and related targets via Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform and SwissTargetPrediction databases, and gene names correction was performed using the UniProt database. AS-related targets were retrieved from OMIM, GeneCards, and DrugBank databases, and Venny 2.1 were used for intersection analysis. Protein-protein interaction network was constructed by the STRING database, and an interactive network of the drug-component-target-disease was drawn using the Cytoscape 3.9.0 software. Gene ontology and Kyoto Gene and Genome Encyclopedia enrichment analysis were performed by the DAVID database, and molecular docking validation of vital active ingredients and action targets of ECD was performed using AutoDock Vina software.

RESULTS

The 127 active components of ECD act on AS by regulating 231 targets and 151 pathways. The 6 core components are quercetin, polyporenic acid C, 18α-hydroxyglycyrrhetic acid, glyuranolide, 3beta-hydroxychloroxy-24-methylene-8-lanostene-21-oic acid, and obacunone. They may regulate AS by regulating core target genes, such as JUN, SRC, AKT1, PTGS2, ESR1, AR, MAPK1, MAPK3, and RELA, and acting on multiple vital pathways, such as AGE-RAGE signaling pathway in diabetic complications, Lipid and AS, and Fluid shear stress and AS. Molecular docking showed that the selected target protein had good binding activity to the active ingredient.

CONCLUSIONS

ECD has the characteristics of multi-components, multi-targets and multi-pathways in the treatment of AS. The results provide a theoretical basis for the clinical application of ECD and its mechanism.

New Insights Into the Persistent Effects of Acute Exposure to AFB1 on Rat Liver

Aflatoxin B₁ (AFB₁) has mutagenesis, carcinogenesis and teratogenesis effects and mainly found in food crops and their processed foods. AFB₁ exposure can cause acute or chronic liver poisoning, but there were few studies on the persistent effects of acute AFB₁ exposure on the liver. In this study, rat liver injury models were established 2 and 7 days after single exposure to high and low doses of AFB₁. The persistent effects of AFB₁ single acute exposure (ASAE) on rat liver were analyzed from the phenotypic and genetic levels. The results showed that compared with the control group, liver function indexes, MDA content in liver and the number of apoptotic hepatocytes in model groups increased to the highest on the 2nd day after ASAE (p < 0.001). However, the changes of liver coefficient were most significant on the 7th day after ASAE (p < 0.01). The results of liver pathology showed that the liver injury was not alleviated and the activities of antioxidant enzymes GSH-Px and SOD were the lowest on the 7th day (p < 0.001). RNA-Seq results indicated that there were 236, 33, 679, and 78 significantly differentially expressed genes (DEGs) in the model groups (LA-2d, LA-7d, HA-2d, HA-7d) compared with the control group. Among them, the Gtse1 gene related to the proliferation, differentiation and metastasis of liver cancer cells, the Lama5 and Fabp4 gene related to the inflammatory response were significantly DEGs in the four model groups, and the differential expression of the immune system-related Bcl6 gene increased with the prolonged observation time after ASAE. In conclusion, ASAE can cause persistent liver damage in rats. The persistently affected genes Lama5, Gtse1, Fabp4, and Bcl6 possess the potential to be therapeutic targets for liver disease induced by AFB₁.