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基于生物信息学的卵巢癌相关脂代谢潜在靶点和小分子药物的筛选。

Screening of potential targets and small-molecule drugs related to lipid metabolism in ovarian cancer based on bioinformatics.

机构信息

Department of Gynecology, The Second Affiliated Hospital of Kunming Medical University, NO.374 Dianmian Rd. Kunming, Yunnan, 650000, China.

Department of Gynecology, The Second Affiliated Hospital of Kunming Medical University, NO.374 Dianmian Rd. Kunming, Yunnan, 650000, China.

出版信息

Biochem Biophys Res Commun. 2024 Nov 12;733:150673. doi: 10.1016/j.bbrc.2024.150673. Epub 2024 Sep 11.


DOI:10.1016/j.bbrc.2024.150673
PMID:39293329
Abstract

BACKGROUND: about 70 % of ovarian cancer (OC) patients with postoperative chemotherapy relapse within 2-3 years due to drug resistance and metastasis, and the 5-year survival rate is only about 30 %. Lipid metabolism plays an important role in OC. We try to explore the potential targets and drugs related to lipid metabolism to provide clues for the treatment of OC. METHODS: the gene expression profiles of OC and normal ovarian tissue samples were obtained from the cancer genome atlas (TCGA) and genotype-tissue expression databases (GTEx). The differentially expressed genes (DEGs) were analyzed. Lipid metabolism related genes (LMRGs) were downloaded from MSigDB database. The DEGs related to lipid metabolism in OC was obtained by intersection. And gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses were performed. The protein-protein interaction (PPI) network of lipid metabolism related DEGs was constructed, and seven algorithms were used to screen core potential target genes. Its expression in OC and prognostic ability were analyzed by Univariate Cox. Cmap database mining OC lipid metabolism related potential small-molecular drugs and docking. CCK8, scratch assay, transwell test and free fatty acid (FFA) assay, fluorescence detection of cellular fatty acid uptake, and the reactivity assay of CPT1A were used to detect the biological effects of drugs on OC cell.Rreverse transcription PCR(RT-qPCR) and WesternBlot were performed to measure the expression of core targets. RESULTS: 437 DEGs related to lipid metabolism of OC were screened. GO and KEGG analysis showed that these DEGs were lipid metabolism, fatty acid metabolism, sphingolipid metabolism, PPAR signal pathway and so on. The PPI network based on lipid metabolism DEGs consists of 301 nodes and 1107 interaction pairs, and 6 core target genes were screened. ROC curve analysis showed that all of the 6 genes could predict the prognosis of OC. Three small molecular drugs Cephaeline, AZD8055 and GSK-1059615 were found by cmap and molecular docking showed that they all had good binding ability to target gene. Cephaeline has the strongest inhibitory effect on SKOV3 cells of OC, and could significantly inhibit cell migration and invasion regulate the mRNA and protein expression of some targets, and inhibit lipid metabolism process in ovarian cancer cells. CONCLUSION: six OC potential genes related to lipid metabolism were identified and verified, which can be used as potential biomarkers and therapeutic targets to evaluate the prognostic risk of OC patients. In addition, three small-molecular drugs that may be effective in the treatment of OC were unearthed, among which Cephaeline has the most potential. We speculate that Cephaeline may target six genes to inhibit progression of OC by affecting lipid metabolism.

摘要

背景:约 70%的卵巢癌(OC)患者在术后化疗后 2-3 年内因耐药和转移而复发,5 年生存率仅约 30%。脂质代谢在 OC 中起着重要作用。我们试图探索与脂质代谢相关的潜在靶点和药物,为 OC 的治疗提供线索。

方法:从癌症基因组图谱(TCGA)和基因型组织表达数据库(GTEx)中获得 OC 和正常卵巢组织样本的基因表达谱。分析差异表达基因(DEGs)。从 MSigDB 数据库下载脂质代谢相关基因(LMRGs)。通过交集获得 OC 中与脂质代谢相关的 DEGs。并进行基因本体(GO)和京都基因与基因组百科全书(KEGG)分析。构建脂质代谢相关 DEGs 的蛋白质-蛋白质相互作用(PPI)网络,并用七种算法筛选核心潜在靶基因。通过单变量 Cox 分析其在 OC 中的表达和预后能力。Cmap 数据库挖掘 OC 脂质代谢相关潜在小分子药物并进行对接。CCK8、划痕实验、Transwell 实验和游离脂肪酸(FFA)测定、细胞脂肪酸摄取的荧光检测和 CPT1A 的反应性测定,检测药物对 OC 细胞的生物学效应。逆转录 PCR(RT-qPCR)和 WesternBlot 用于测量核心靶标基因的表达。

结果:筛选出 437 个与 OC 脂质代谢相关的 DEGs。GO 和 KEGG 分析表明,这些 DEGs 参与脂质代谢、脂肪酸代谢、鞘脂代谢、PPAR 信号通路等。基于脂质代谢 DEGs 的 PPI 网络由 301 个节点和 1107 个相互作用对组成,筛选出 6 个核心靶基因。ROC 曲线分析表明,这 6 个基因均能预测 OC 的预后。通过 cmap 发现 Cephaeline、AZD8055 和 GSK-1059615 三种小分子药物,分子对接显示它们均与靶基因具有良好的结合能力。Cephaeline 对 OC 的 SKOV3 细胞具有最强的抑制作用,可显著抑制细胞迁移和侵袭,调节部分靶基因的 mRNA 和蛋白表达,并抑制卵巢癌细胞中的脂质代谢过程。

结论:鉴定和验证了与 OC 脂质代谢相关的 6 个潜在基因,可作为评估 OC 患者预后风险的潜在生物标志物和治疗靶点。此外,还挖掘了三种可能对 OC 治疗有效的小分子药物,其中 Cephaeline 最具潜力。我们推测 Cephaeline 可能通过影响脂质代谢,靶向 6 个基因抑制 OC 的进展。

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