基于网络药理学和生物信息学的天然虾青素抗肾透明细胞癌的治疗机制

[Therapeutic mechanism of natural astaxanthin against renal clear cell carcinoma based on network pharmacology and bioinformatics].

作者信息

Gao J, Yang D, Cao R, Pan X, Xia J

机构信息

Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical College, Bengbu 233030, China.

Department of Laboratory Medicine, Second People's Hospital of Lianyungang, Lianyungang 222000, China.

出版信息

Nan Fang Yi Ke Da Xue Xue Bao. 2021 Dec 20;41(12):1763-1772. doi: 10.12122/j.issn.1673-4254.2021.12.02.

DOI:10.12122/j.issn.1673-4254.2021.12.02

PMID:35012906

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8752422/

Abstract

OBJECTIVE

To explore the molecular mechanism by which natural astaxanthin (AST) inhibits renal clear cell carcinoma (KIRC) based on network pharmacology and bioinformatics.

METHODS

PharmMapper database was used to retrieve the targets of natural astaxanthin, and TCGA database was used to identify the differentially expressed genes (DEGs) in KIRC and adjacent tissues. The target genes of AST was analyzed using Cytoscape software to construct the "drug-target" network diagram. The visual protein-protein interaction (PPI) network was constructed using String database, and GO enrichment analysis of the core targets was performed. Single gene bioinformatics was performed to verify the screened core target of AST, namely placental growth factor (PGF). The effect of natural AST on the viability of KIRC cells was tested using CCK-8 method, and the binding between natural AST and PGF was assessed with molecular docking technology. The effect of natural AST on the mRNA and protein expression of the target genes was analyzed using RT-qPCR and Western blotting.

RESULTS

We identified 278 candidate targets of AST, 1081 KIRC-related targets, and 7 core targets involved in the therapeutic mechanism of AST against KIRC. Among these 7 core targets, PGF showed significantly upregulated expression in KIRC ( < 0.001) in correlation with a poor prognosis (HR=1.37, =0.043). Molecular docking showed that the binding energy of AST and PGF was -5.43 kcal/mol. CCK-8 assay showed that AST at the concentration of 50 μmol/L was capable of inhibiting the proliferation of KIRC cells, and a higher concentration resulted in a stronger inhibitory effect. The results of RT-qPCR and Western blotting showed that AST treatment significantly reduced the expression of PGF at both the mRNA and protein levels in KIRC cells.

CONCLUSION

Natural AST can suppress the proliferation of KIRC and inhibit the expression of PGF in the cells.

摘要

目的

基于网络药理学和生物信息学探讨天然虾青素（AST）抑制肾透明细胞癌（KIRC）的分子机制。

方法

利用PharmMapper数据库检索天然虾青素的靶点，使用TCGA数据库鉴定KIRC及癌旁组织中的差异表达基因（DEG）。利用Cytoscape软件分析AST的靶基因，构建“药物-靶点”网络图。使用String数据库构建可视化蛋白质-蛋白质相互作用（PPI）网络，并对核心靶点进行基因本体（GO）富集分析。进行单基因生物信息学分析以验证筛选出的AST核心靶点，即胎盘生长因子（PGF）。采用CCK-8法检测天然AST对KIRC细胞活力的影响，并运用分子对接技术评估天然AST与PGF之间的结合情况。使用RT-qPCR和蛋白质印迹法分析天然AST对靶基因mRNA和蛋白质表达的影响。

结果

我们鉴定出278个AST候选靶点、1081个KIRC相关靶点以及7个参与AST治疗KIRC机制的核心靶点。在这7个核心靶点中，PGF在KIRC中表达显著上调（<0.001），且与预后不良相关（HR=1.37，=0.043）。分子对接显示AST与PGF的结合能为-5.43 kcal/mol。CCK-8实验表明，50 μmol/L的AST能够抑制KIRC细胞的增殖，且浓度越高抑制作用越强。RT-qPCR和蛋白质印迹法结果显示，AST处理显著降低了KIRC细胞中PGF在mRNA和蛋白质水平的表达。