生物信息学分析证实肺动脉高压发病机制中潜在的坏死性凋亡基因
西安交通大学医学部基础医学院心血管研究中心, 西安交通大学环境与疾病相关基因教育部重点实验室, 陕西西安 710061
| 摘 要： | 目的：肺动脉高压（Pulmonary artery hypertension, PAH）是一种严重危及生命的肺部疾病，目前尚无有效的治疗药物。坏死性凋亡在PAH的发病机制中起关键作用。因此，我们通过生物信息学和在体实验来研究和验证PAH中潜在的坏死相关基因。方法：首先，我们从Gene Expression Omnibus（GEO）和Kyoto Encyclopedia of genes and Genomes（KEGG）数据库中获取PAH（GSE15197）的微阵列数据和坏死相关基因的数据集；利用生物信息学方法来分析PAH患者肺与健康肺间的差异表达基因；通过富集分析和蛋白-蛋白相互作用分析来筛选关键的枢纽基因。同时，我们进行了模构建和枢纽基因的共表达分析；通过TRRUST网站，我们来解析枢纽基因的关键转录因子。最后我们建立了实验小鼠PAH模型，利用实时荧光定量聚合酶链式反应（qRT-PCR）实验来验证枢纽基因和关键转录因子的表达水平。结果：通过比较健康肺和PAH患者的肺，我们共鉴别出16个与坏死相关的差异表达基因，其中上调基因有10个，下调基因有6个。另外，ClueGO和KEGG富集分析表明，这些与坏死性凋亡相关的差异表达基因参与了一氧化氮生物合成过程、坏死性凋亡细胞死亡、趋化因子的产生和坏死、NOD样受体信号通路的正调控过程。通过cytoHubba，我们获得了7个枢纽基因，包括BAX、XIAP、TLR4、TNF、HSP90AA1、FAS和TNFSF10。qRT-PCR实验结果表明，与正常小鼠相比，实验性PAH小鼠肺中Bax、Tlr4、30tnf、Hsp90aa1、Fas和Tnfsf10的表达显著上调，然而Xiap的表达水平没有显著差异。结论：本研究确定了PAH发病过程中与坏死性凋亡相关的7个重要的枢纽基因，其可作为PAH潜在的治疗靶点，为进一步研究PAH的发病机制及靶向治疗提供了新的思路。 |
| 关 键 词： | 坏死性凋亡; 肺动脉高压; 生物信息学分析; 基因表达综合数据库; 枢纽基因; 转录因子 |
| DOI： | 10.57237/j.life.2024.01.003 |
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收稿日期: 2023-12-07
接受日期: 2024-01-24
在线出版日期: 2024-02-04
Bioinformatics Analysis Confirms Potential Necroptosis Genes in the Pathogenesis of Pulmonary Artery Hypertension
1. Cardiovascular Research Center, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center
2. Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education, Xi’an 710061, China
| Abstract: | Objective: Pulmonary artery hypertension (PAH) is a life-threatening lung disease without effective therapeutic agents. Necroptosis plays a key role in the pathogenesis of PAH. We therefore investigated to identify and validate the potential necroptosis-related genes in PAH by bioinformatics analysis and experiments. Methods: Firstly, the microarray data of PAH (GSE15197) and necroptosis-related genes were obtained from Gene Expression Omnibus (GEO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Then we used the bioinformatics methods to identify the differentially expressed genes (DEGs) between the normal lungs and the lungs of PAH patients and extract the necroptosis-related DEGs. Enrichment analysis and protein-protein interaction (PPI) analysis were performed to screen the hub genes. Module construction and co-expression analysis of hub genes were also conducted. Key transcription factors (TFs) of hub genes were obtained by using the TRRUST website. Finally, the experimental mouse PAH model was performed to verify the expression of hub genes and key TFs by qRT-PCR. Results: A total of 16 necroptosis-related DEGs (10 upregulated genes and 6 downregulated genes) were identified by comparing the normal lungs and the lungs of PAH patients. ClueGO and KEGG enrichment analysis demonstrated these necroptosis-related DEGs were involved in positive regulation of nitric oxide biosynthetic process, programmed necrotic cell death, positive regulation of chemokine production, necroptosis, and NOD-like receptor signaling pathway. 7 hub genes were obtained by cytoHubba, including BAX, XIAP, TLR4, TNF, HSP90AA1, FAS, and TNFSF10. qRT-PCR analysis confirmed that expression of Bax, Tlr4, Tnf, Hsp90aa1, Fas and Tnfsf10 were significantly upregulated, while the expression level of Xiap was not significant in mouse lungs with experimental PAH compared with normal mouse lungs. Conclusion: Our study identified 7 important hub genes related to necroptosis in PAH, which could be used as potential therapeutic targets and provide new insights into further mechanism study for PAH. |
| Keywords: | Necroptosis; Pulmonary Artery Hypertension; Bioinformatics Analysis; Gene Expression Omnibus; Hub Genes; Transcription Factors |
基金
| 1. | 国家自然科学基金项目 (82000072) |
| 2. | 中国博士后科学基金项目 (2020M673425) |
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