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基于生物信息学方法和分子对接技术鉴定骨质疏松症铁死亡相关标志物和潜在治疗化合物。

Identification of osteoporosis ferroptosis-related markers and potential therapeutic compounds based on bioinformatics methods and molecular docking technology.

机构信息

General Hospital of Western Theater Command, Chengdu, China.

Department of Orthopedic Oncology, Shanghai Sixth People's Hospital Affilicated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.

出版信息

BMC Med Genomics. 2024 Apr 22;17(1):99. doi: 10.1186/s12920-024-01872-0.


DOI:10.1186/s12920-024-01872-0
PMID:38650009
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11036634/
Abstract

RESEARCH BACKGROUND AND PURPOSE: Osteoporosis (OP) is one of the most common bone diseases worldwide, characterized by low bone mineral density and susceptibility to pathological fractures, especially in postmenopausal women and elderly men. Ferroptosis is one of the newly discovered forms of cell death regulated by genes in recent years. Many studies have shown that ferroptosis is closely related to many diseases. However, there are few studies on ferroptosis in osteoporosis, and the mechanism of ferroptosis in osteoporosis is still unclear. This study aims to identify biomarkers related to osteoporosis ferroptosis from the GEO (Gene Expression Omnibus) database through bioinformatics technology, and to mine potential therapeutic small molecule compounds through molecular docking technology, trying to provide a basis for the diagnosis and treatment of osteoporosis in the future. MATERIALS AND METHODS: We downloaded the ferroptosis-related gene set from the FerrDb database ( http://www.zhounan.org/ferrdb/index.html ), downloaded the data sets GSE56815 and GSE7429 from the GEO database, and used the R software "limma" package to screen differentially expressed genes (DEGs) from GSE56815, and intersected with the ferroptosis gene set to obtain ferroptosis-related DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed by the R software "clusterProfiler" package. The random forest model was further screened to obtain essential ferroptosis genes. R software "corrplot" package was used for correlation analysis of essential ferroptosis genes, and the Wilcox test was used for significance analysis. The lncRNA-miRNA-mRNA-TF regulatory network was constructed using Cytoscape software. The least absolute shrinkage and selection operator (LASSO) was used to construct a disease diagnosis model, and a Receiver operating characteristic (ROC) curve was drawn to evaluate the diagnostic performance, and then GSE7429 was used to verify the reliability of the diagnosis model. Molecular docking technology was used to screen potential small molecule compounds from the Drugbank database. Finally, a rat osteoporosis model was constructed, and peripheral blood mononuclear cells were extracted for qRT-PCR detection to verify the mRNA expression levels of crucial ferroptosis genes. RESULT: Six DEGs related to ferroptosis were initially screened out. GO function and KEGG pathway enrichment analysis showed that ferroptosis-related DEGs were mainly enriched in signaling pathways such as maintenance of iron ion homeostasis, copper ion binding function, and ferroptosis. The random forest model identified five key ferroptosis genes, including CP, FLT3, HAMP, HMOX1, and SLC2A3. Gene correlation analysis found a relatively low correlation between these five key ferroptosis genes. The lncRNA-miRNA-mRNA-TF regulatory network shows that BAZ1B and STAT3 may also be potential molecules. The ROC curve of the disease diagnosis model shows that the model has a good diagnostic performance. Molecular docking technology screened out three small molecule compounds, including NADH, Midostaurin, and Nintedanib small molecule compounds. qRT-PCR detection confirmed the differential expression of CP, FLT3, HAMP, HMOX1 and SLC2A3 between OP and normal control group. CONCLUSION: This study identified five key ferroptosis genes (CP, FLT3, HAMP, HMOX1, and SLC2A3), they were most likely related to OP ferroptosis. In addition, we found that the small molecule compounds of NADH, Midostaurin, and Nintedanib had good docking scores with these five key ferroptosis genes. These findings may provide new clues for the early diagnosis and treatment of osteoporosis in the future.

摘要

研究背景与目的:骨质疏松症(OP)是全球最常见的骨骼疾病之一,其特征是骨密度低且易发生病理性骨折,尤其是绝经后妇女和老年男性。铁死亡是近年来新发现的一种受基因调控的细胞死亡形式。许多研究表明,铁死亡与许多疾病密切相关。然而,关于骨质疏松症中铁死亡的研究较少,其机制尚不清楚。本研究旨在通过生物信息学技术从 GEO(基因表达综合数据库)数据库中鉴定与骨质疏松症铁死亡相关的生物标志物,并通过分子对接技术挖掘潜在的治疗性小分子化合物,试图为未来骨质疏松症的诊断和治疗提供依据。

材料和方法:我们从 FerrDb 数据库(http://www.zhounan.org/ferrdb/index.html)下载铁死亡相关基因集,从 GEO 数据库下载数据集 GSE56815 和 GSE7429,使用 R 软件“limma”包筛选 GSE56815 中的差异表达基因(DEGs),并与铁死亡基因集进行交集,获得铁死亡相关 DEGs。使用 R 软件“clusterProfiler”包进行基因本体论(GO)和京都基因与基因组百科全书(KEGG)分析。进一步通过随机森林模型筛选出关键的铁死亡基因。使用 R 软件“corrplot”包进行关键铁死亡基因的相关性分析,并使用 Wilcox 检验进行显著性分析。使用 Cytoscape 软件构建 lncRNA-miRNA-mRNA-TF 调控网络。使用最小绝对收缩和选择算子(LASSO)构建疾病诊断模型,并绘制接收者操作特征(ROC)曲线评估诊断性能,然后使用 GSE7429 验证诊断模型的可靠性。使用 Drugbank 数据库的分子对接技术筛选潜在的小分子化合物。最后,构建大鼠骨质疏松症模型,提取外周血单核细胞进行 qRT-PCR 检测,验证关键铁死亡基因的 mRNA 表达水平。

结果:初步筛选出与铁死亡相关的 6 个 DEGs。GO 功能和 KEGG 通路富集分析表明,铁死亡相关 DEGs主要富集在维持铁离子稳态、铜离子结合功能和铁死亡等信号通路中。随机森林模型鉴定出 5 个关键铁死亡基因,包括 CP、FLT3、HAMP、HMOX1 和 SLC2A3。基因相关性分析发现这 5 个关键铁死亡基因之间相关性较低。lncRNA-miRNA-mRNA-TF 调控网络表明,BAZ1B 和 STAT3 也可能是潜在的分子。疾病诊断模型的 ROC 曲线表明该模型具有良好的诊断性能。分子对接技术筛选出 NADH、Midostaurin 和 Nintedanib 三种小分子化合物。qRT-PCR 检测证实 CP、FLT3、HAMP、HMOX1 和 SLC2A3 在 OP 组和正常对照组之间存在差异表达。

结论:本研究鉴定出 5 个关键铁死亡基因(CP、FLT3、HAMP、HMOX1 和 SLC2A3),它们可能与 OP 铁死亡有关。此外,我们发现 NADH、Midostaurin 和 Nintedanib 小分子化合物与这 5 个关键铁死亡基因的结合评分较好。这些发现可能为未来骨质疏松症的早期诊断和治疗提供新的线索。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/254752191e7c/12920_2024_1872_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/7debaf72cd9f/12920_2024_1872_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/b05ddcdcde1d/12920_2024_1872_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/c04f0c3411f5/12920_2024_1872_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/2b6c27aff5e4/12920_2024_1872_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/254752191e7c/12920_2024_1872_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/7debaf72cd9f/12920_2024_1872_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/b05ddcdcde1d/12920_2024_1872_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/c04f0c3411f5/12920_2024_1872_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/2b6c27aff5e4/12920_2024_1872_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b5b4/11036634/254752191e7c/12920_2024_1872_Fig7_HTML.jpg

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本文引用的文献

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