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pmid:32598336
Potential Molecular Mechanisms and Drugs for Aconitine-Induced Cardiotoxicity in Zebrafish through RNA Sequencing and Bioinformatics Analysis.
Mingzhu Wang · Yanan Shi · Lei Yao · Qiang Li · Youhua Wang · Deyu Fu
Medical science monitor : international medical journal of experimental and clinical research · 2020 doi:10.12659/MSM.924092
Paper
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Experiment
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Data
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Analysis
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Execution
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Complete file
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However, the molecular mechanism of AC-induced cardiotoxicity remains unclear, there is little direct evidence for therapeutic targets and drugs of AC-induced cardiotoxicity. MATERIAL AND METHODS Zebrafish were exposed to AC to evaluate cardiotoxicity by calculating the heart rates and observing the changes of cardiac and vascular structure. RNA-seq (RNA sequencing) and bioinformatics analysis were used to obtain differentially expressed genes (DEGs). The anti-AC cardiotoxicity compound was identified via connectivity map (CMAP) analysis and molecular docking. RESULTS AC-induced cardiotoxicity in zebrafish predominantly included arrhythmias, extended sinus venous and bulbus arteriosus (SV-BA) distance, and larger pericardial edema aera. A total of 1380 DEGs were identified by RNA-seq and bioinformatics analysis. cyclin-dependent kinase-1 (CDK1) was screened as the hub gene and the most potential therapeutic target due to its significant downregulation in cardiotoxicity based on protein-protein interaction (PPI) and drug-gene interaction (DGIdb) network analysis. Cell cycle signal pathway was the most significant pathways identified in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Furthermore, the expression of CDK1 was validated in the Gene Expression Omnibus (GEO) database GSE71906, GSE65705, and GSE95140. Finally, heptaminol was identified as a novel anti-AC cardiotoxicity compound via CMAP analysis and molecular docking. CONCLUSIONS Totally, hub genes and key pathways identified in this study can aid in the understanding of the molecular changes in AC-induced cardiotoxicity. 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"resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE65705 not downloaded", "asset:data:geo:GSE65705 licence not read", "asset:data:geo:GSE71906 not downloaded", "asset:data:geo:GSE71906 licence not read", "asset:data:geo:GSE95140 not downloaded", "asset:data:geo:GSE95140 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE71906", "GSE65705", "GSE95140"], "resolved_accessions": ["GSE71906", "GSE65705", "GSE95140"], "statements": ["The dataset GSE71906 that is the gene expression matrix of myocardial infarction heart tissue in mouse (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71906) was screened from the GEO database"], "basis": "The paper names GSE71906, GSE65705, GSE95140 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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