中国组织工程研究 ›› 2022, Vol. 26 ›› Issue (11): 1720-1727.doi: 10.12307/2022.357

• 组织工程相关大数据分析 Big data analysis in tissue engineering • 上一篇    下一篇

基于miRNA-mRNA调控网络股骨头坏死的关键基因筛选与分析

梁学振1,谢国鑫2,李嘉程1,温明韬2,许  波1,李  刚1,3   

  1. 1山东中医药大学第一临床医学院,山东省济南市   250355;2山东中医药大学中医学院,山东省济南市   250355;3山东中医药大学附属医院显微骨科,山东省济南市   250014
  • 收稿日期:2020-11-23 修回日期:2020-11-28 接受日期:2021-03-27 出版日期:2022-04-18 发布日期:2021-12-11
  • 通讯作者: 李刚,博士,教授,主任医师,山东中医药大学第一临床医学院,山东省济南市 250355;山东中医药大学附属医院显微骨科,山东省济南市 250014
  • 作者简介:梁学振,男,1990年生,山东省泰安市人,汉族,2019年山东中医药大学毕业,博士,讲师,主治医师,主要从事中医药防治骨坏死、代谢性骨病的临床与基础研究。
  • 基金资助:
    国家自然科学基金资助项目(82074453),项目负责人:李刚;山东省医药卫生科技发展计划项目(2019WS577),项目负责人:梁学振

Identification and analysis of potential key genes in osteonecrosis of the femoral head based on miRNA-mRNA regulatory network

Liang Xuezhen1, Xie Guoxin2, Li Jiacheng1, Wen Mingtao2, Xu Bo1, Li Gang1, 3   

  1. 1The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong Province, China; 2College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong Province, China; 3Department of Orthopedic Microsurgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, Shandong Province, China
  • Received:2020-11-23 Revised:2020-11-28 Accepted:2021-03-27 Online:2022-04-18 Published:2021-12-11
  • Contact: Li Gang, MD, Professor, Chief physician, The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong Province, China; Department of Orthopedic Microsurgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, Shandong Province, China
  • About author:Liang Xuezhen, MD, Lecturer, Attending physician, The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong Province, China
  • Supported by:
    the National Natural Science Foundation of China, No. 82074453 (to LG); Shandong Provincial Medicine and Health Technology Development Project, No. 2019WS577 (to LXZ)

摘要:

文题释义:
miRNA的调控特点:成熟的miRNA 通过碱基互补配对方式识别靶基因mRNA,发挥降解作用或直接阻断翻译过程。目前已经有>2 000 个miRNA 被证实可在人体表达并参与调控30%的基因。
miRNA的作用特点:大量研究表明miRNA几乎参与疾病发生进展的全过程,包括增殖、凋亡、血管生成以及分化等,在不同类型疾病中通过作用于特定的靶基因mRNA,发挥抑制或促进疾病发生发展的作用。

背景:microRNA (miRNA)被证实参与了股骨头坏死的发生、发展及防治,但其作用机制尚不清楚。
目的:借助GEO数据库,采用生物信息学手段探讨股骨头坏死相关的miRNA-mRNA调控关系对,阐释其潜在的作用机制。
方法:通过GEO数据库下载股骨头坏死相关的miRNA芯片数据集(GSE89587)和mRNA芯片数据集(GSE74089),借助R软件Limma包进行数据差异表达分析,使用miRDB、miRTarbase和TargetScan数据库预测差异表达miRNA调控的潜在下游靶基因,利用Cytoscape构建miRNA-mRNA调控网络,通过R软件clusterProfiler包对靶基因进行GO功能和KEGG通路富集分析,借助STRING数据库构建调控网络中靶基因的蛋白互作网络。
结果与结论:①实验共筛选出23个差异表达的miRNA,其中10个上调(如hsa-miR-4325,hsa-miR-3654),13个下调(如hsa-miR-4680-5p,hsa-miR-4711-3p);②实验共筛选出3 992个差异表达mRNA,其中2 503个上调(如TGFBI,AMTN),1 489个下调(如MSMP、FLJ35424);③利用Targetscan、miRTarBase和miRDB数据库预测出255个同时存在于3个数据库的下游靶基因,整理出10个miRNA(如hsa-miR-3920、hsa-miR-3675-5p)和34个mRNA(如MAPK6、SP1)进行调控网络构建;④GO和KEGG富集分析主要集中在调节mRNA稳定性、转化生长因子β信号通路及自噬等;⑤DDX3X、HNRNPC和SP1作为PPI网络中的枢纽基因,可能是股骨头坏死的关键靶标;⑥实验构建的miRNA-mRNA调控网络在一定程度上阐明了miR-4725-3p可能靶向抑制SP1介导的转化生长因子β信号通路诱发股骨头坏死发病,为股骨头坏死的防治诊疗提供了强有力的数据支撑和研究方向。

https://orcid.org/0000-0001-5649-4212(梁学振);https://orcid.org/0000-0002-4587-6650 (李刚) 

中国组织工程研究杂志出版内容重点:组织构建;骨细胞;软骨细胞;细胞培养;成纤维细胞;血管内皮细胞;骨质疏松;组织工程

关键词: 股骨头坏死, GEO数据库, 差异基因, 调控网络, miRNA-mRNA, 基因, 蛋白, 生物信息学

Abstract: BACKGROUND: MicroRNAs (miRNAs) have been confirmed to be involved in the pathogenesis, prevention, and treatment of osteonecrosis of the femoral head. However, the mechanism is not yet elucidated. 
OBJECTIVE: To screen miRNA-mRNA regulatory pairs related to osteonecrosis of the femoral head, to explain its potential mechanism, based on microarray data in the GEO database.
METHODS: The miRNA microarray dataset (GSE89587) and mRNA microarray dataset (GSE74089) were retrieved from NCBI GEO database. Then, we identified the differentially expressed miRNAs and mRNAs for each dataset by the Limma package in R software. Potential downstream targets of these differentially expressed miRNAs were predicted using miRDB, miRTarbase, and TargetScan databases. Based on the relationship among miRNA and mRNA, the miRNA-mRNA regulatory network was visualized using Cytoscape. Next, gene ontology function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of target genes in the regulatory network were carried out by clusterProfiler package in R software. Protein-protein interaction network was constructed by using the Search Tool for the Retrival of Interacting Genes/Protein (STRING) database. 
RESULTS AND CONCLUSION: In total, 23 differentially expressed miRNAs, including 10 upregulated (e.g., hsa-miR-4325, hsa-miR-3654) and 13 downregulated miRNAs (e.g., hsa-miR-4680-5p, hsa-miR-4711-3p), were identified. Totally 3992 differentially expressed mRNAs, including 2503 upregulated (e.g., TGFBI, AMTN) and 1489 downregulated (e.g., MSMP, FLJ35424) mRNAs, were screened by the Limma package in R software. 255 miRNA downstream target genes predicted co-existed in  miRDB, miRTarbase, and TargetScan databases, and 10 miRNAs (e.g., hsa-miR-3920, hsa-miR-3675-5p) and 34 mRNAs (e.g., MAPK6, SP1 ) were sorted out to construct regulatory networks. These screened targets mainly were significantly enriched in the regulation of mRNA stability and transforming growth factor-β signaling pathway and autophagy. DDX3X, HNRNPC, and SP1 were analyzed as the hub genes in protein-protein interactions, which may be the target genes for osteonecrosis of the femoral head. In summary, the miRNA-mRNA regulatory network constructed in this study clarifies that miR-4725-3p may target ONFH by inhibiting SP1-mediated transforming growth factor-β signaling pathway, providing a strong data support and research direction for the prevention and treatment of ONFH.

Key words: osteonecrosis of the femoral head, GEO database, differentially expressed gene, regulatory network, miRNA-mRNA, gene, protein, bioinformatics

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