腹主动脉瘤特异性ceRNA调控网络的筛选与构建
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1.遵义医科大学附属医院 普通外科,贵州 遵义 563000;2.遵义市第一人民医院/遵义医科大学第三附属医院 2. 乳甲中心 3. 心脏血管外科, 贵州 遵义 563000;3.四川大学华西医院 血管外科, 四川 成都 610043

作者简介:

霍金龙,遵义医科大学附属医院/遵义市第一人民医院(遵义医科大学第三附属医院)主治医师,主要从事肝胆、甲状腺、血管疾病方面的研究。

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Screening and construction of abdominal aortic aneurysm specific ceRNA regulatory network
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1.Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China;2.Department of Breast and Thyroid Surgery 3. Department of Cardiovascular surgery, the First People's Hospital of Zunyi/the Third Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China;3.Department of Vascular Surgery, West China Hospital, Sichuan University, Chengdu 610043, China

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    摘要:

    背景与目的 腹主动脉瘤(AAA)是一种在老年患者中发病率及病死率均较高的疾病。目前基于内源性竞争RNA(ceRNA)网络在AAA发病机制中的作用不明。本研究通过筛选和构建AAA特异性的长链非编码RNA(lncRNA)-微小RNA(miRNA)-mRNA的ceRNA网络,以期揭示ceRNA网络在AAA形成与发展中的作用。方法 首先通过基因表达数据库(GEO)筛选数据集,寻找AAA与正常腹主动脉组织的差异lncRNA及差异mRNA;利用Lasso回归从差异RNA中筛选疾病特征性基因;运用软件Starbase寻找与差异lncRNA和特异性mRNA共同结合的miRNA,利用Cytoscape软件构建lncRNA-miRNA-mRNA的ceRNA网络,使用Cytoscape中的cytohubba模块进一步筛选核心ceRNA网络。结果 筛选获得GSE7084和GSE57691两个数据集,获得差异mRNA 114个,差异lncRNA 13个;利用Lasso回归从差异mRNA中获得17个特异性的mRNA;结果显示,lncRNA HCP5-miR27-FOSB被认为可能是导致AAA发生发展最为关键的ceRNA网络。结论 所构建的ceRNA网络可能参与AAA的形成及发展,但该结果需开展后续研究进一步探明和验证。

    Abstract:

    Background and Aims Abdominal aortic aneurysm (AAA) is a disease with high morbidity and mortality in elderly patients. The actions of endogenous competing RNA (ceRNA) networks in the underlying pathogenesis of AAA are unclear at present. Therefore, this study was conducted to investigate the role of ceRNA network in the formation and development of AAA through screening and establishing the AAA-specific long non-coding RNA (lncRNA)-microRNA (miRNA)-mRNA ceRNA network.Methods Firstly, the data set was screened in gene expression database (GEO), and the differentially expressed lncRNAs and mRNAs between AAA and normal abdominal aorta tissues were identified. Lasso regression was used to screen the disease characteristic genes from differentially expressed RNAs. Starbase software was used to search for miRNAs that combined with differentially expressed lncRNAs and specific mRNAs, and Cytoscape software was used to construct the lncRNA-miRNA-mRNA ceRNA network. The cytohubba module in Cytoscape was used to further screen the core ceRNA network.Results Two data sets GSE7084 and GSE57691 were screened, and 144 differentially expressed mRNAs and 13 differentially expressed lncRNAs were obtained. Seventeen specific mRNAs were obtained from differentially expressed mRNAs by Lasso regression. lncRNA HCP5-miR27-FOSB was considered be the most critical ceRNA network for the occurrence and development of AAA.Conclusion The constructed ceRNA network may be involved in the formation and development of AAA. However, this result still needs to be further investigated and verified by subsequent studies.

    表 2 AAA的17个特异性基因诊断模型Table 2 17 specific gene diagnostic models of AAA
    图1 AAA与AA差异基因筛选(图1A中绿色表示下调基因,红色为上调基因,黑色无差异基因;图1B中红色为上调基因,蓝色为下调基因) A:AAA与AA差异基因火山图;B:AAA与AA差异基因热图Fig.1 Identification of the differentially expressed genes between AAA and AA (green color represents down-regulated genes, the red color represents up-regulated genes, and black color represents no difference genes in figure 1A; red color represents the up-regulated genes and blue color represents the down-regulated genes in figure 1B) A: Volcano map of differentially expressed genes between AAA and AA; B: Heat map of differentially expressed genes between AAA and AA
    图2 差异基因富集分析(颜色越红代表差异越显著,形状越大表示在该分子功能上富集越显著) A:GO分析;B:KEGG分析Fig.2 Enrichment analysis of the differentially expressed genes (the redder the color, the more significant the difference, and the larger the shape, the more significant of enrichment in the molecular function) A: GO analysis; B: KEGG analysis
    图3 惩罚因素选择的交叉验证Fig.3 Cross-validation for the choice of penalty factors
    图4 基因诊断模型相关ceRNA网络构建及关键ceRNA网络分析(红色代表上调的基因,蓝色代表下调基因,绿色圆形为miRNA;方形为lncRNA,三角形为mRNA) A:AAA特异性基因诊断模型参与的ceRNA网络;B:AAA关键ceRNA网络Fig.4 Establishment of ceRNA network involved in AAA-specific gene diagnosis model and analysis of key ceRNA network (red representing up-regulated genes, blue representing down-regulated genes, and green circles representing miRNAs; the square shapes representing lncRNAs, and the triangle representing mRNAs) A: The ceRNA network involved in AAA-specific gene diagnosis model; B: The key ceRNA network in AAA
    表 1 差异lncRNA列表Table 1 List of DElncRNAs
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霍金龙,吴浪,赵纪春,郭又铭,瞿锐,赵礼金.腹主动脉瘤特异性ceRNA调控网络的筛选与构建[J].中国普通外科杂志,2022,31(12):1653-1659.
DOI:10.7659/j. issn.1005-6947.2022.12.013

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  • 收稿日期:2022-09-11
  • 最后修改日期:2022-11-02
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  • 在线发布日期: 2023-01-08