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

Li, Zhongchen; Hao, Jiheng; Chen, Kun; Jiang, Qunlong; Wang, Peijian; Xing, Xiaohui; Wang, Jiyue; Zhang, Yinjiang; Xiao, Yi; Zhang, Liyong

doi:10.18632/aging.202943

Cited by 3 publications

(3 citation statements)

References 40 publications

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“…RNA-seq data has been used to analyze the underlying mechanism of carotid atherosclerosis (CAS). Differential and functional enrichment analysis of sequencing data from CAS patients and control group showed that inflammation and immune response were the potential pathogenesis of CAS, and significant DEGs CCR5 , NPY , and NPY5R were potential therapeutic targets of CAS ( Li et al, 2021 ). The method is also often used to study cancer therapeutic targets.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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“…Studies have shown that inhibiting NF-κB phosphorylation significantly reduces the inflammatory response and improves AS. [51,52] However, there are some limitations to network pharmacology. When we use network pharmacology to study the efficacy of active ingredients in prescription decoctions, the method simply superimposes the chemical constituents of single herbs.…”

Section: Discussionmentioning

confidence: 99%

“…Studies have shown that inhibiting NF-κB phosphorylation significantly reduces the inflammatory response and improves AS. [51,52]…”

Section: Discussionmentioning

confidence: 99%

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

Li,

Zhang,

Zhao

et al. 2023

Medicine

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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.

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Shared Molecular Mechanisms Between Primary open angle glaucoma and Atherosclerosis via Integrated Bioinformatic Analysis

Sun

Liu

Zhang

2023

Preprint

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This study aims to explore the shared hub genes and molecular mechanisms between primary open angle glaucoma (POAG) and atherosclerosis (AS) through integrated bioinformatic analysis. Data were downloaded from the Gene Expression Omnibus database. Ninety-two common genes were identified through the differentially expressed genes (DEGs) analysis and Weighted Gene Co-Expression Network Analysis (WGCNA) between POAG and AS. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the common genes were enriched in oxidative stress and inflammatory response. Then, through the protein-protein interaction (PPI) network and ROC curve analysis, four shared hub genes were identified and the Gene Set Enrichment Analysis (GSEA) indicated these were all highly enriched in inflammatory and immune response. In addition, eight miRNAs and six transcription factors (TFs) were predicted to be key miRNAs and TFs. Finally, the Comparative Toxicogenomics Database identified twenty potential small-molecule drugs. This study revealed shared hub genes and molecular mechanisms between POAG and AS. Oxidative stress, the inflammatory and immune response may be a common contributor to POAG and AS. These common hub genes and molecular mechanisms may offer promising clues for further experimental studies.

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

Cited by 3 publications

References 40 publications

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

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

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

Shared Molecular Mechanisms Between Primary open angle glaucoma and Atherosclerosis via Integrated Bioinformatic Analysis

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