文章摘要

基于转录调控网络识别老年期抑郁症的诊断标志物

作者: 1邓志芳, 1刘珏, 2肖晗, 2高雯琪
1 华中科技大学同济医学院附属武汉市中心医院药学部,武汉 430022
2 华中科技大学同济医学院附属武汉儿童医院(武汉市妇幼保健院),妇女儿童健康研究所,武汉 430015
通讯: 高雯琪 Email: gwq1103@ctgu.edu.cn
DOI: 10.3978/j.issn.2095-6959.2022.08.025
基金: 国家自然科学基金(81903592);武汉市临床医学科研项目(WX20C15);武汉市黄鹤英才-优秀青年人才项目。

摘要

目的:老年抑郁障碍的自杀和血管性痴呆等风险较高,本研究基于基因转录调控网络,整合并利用生物信息学分析,探索老年期抑郁症(geriatric depression,GD)的诊断生物标志物。方法:从公共数据库Gene Expression Omnibus(GEO)中下载基因表达谱数据集GSE76826。R软件鉴定GD与健康对照样本两组之间的差异表达基因(differentially expressed genes,DEGs)。基于DAVID数据库对DEGs进行基因本体论(Gene Ontology,GO)功能注释、京都基因和基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)通路富集分析。STRING在线生物信息学工具对DEGs进行调控网络分析并构建蛋白质-蛋白质相互作用(protein-protein interaction,PPI)网络,Cytoscape软件筛选枢纽基因。之后,采用pROC软件包进行受试者工作特征(receiver operating characteristic,ROC)曲线分析,筛选转录因子以获得诊断生物标志物。结果:与健康对照相比,GD样本中共鉴定出1 411个DEGs。DEGs构建的PPI中共识别出4个关键模块。KEGG通路富集分析结果显示:DEGs在纤毛运动、抗菌体液反应、O-glycan加工、黏膜免疫反应、碳水化合物跨膜转运活动、激素生物合成、神经递质生物合成以及药物代谢酶P450通路中富集。从Cytoscape构建的PPI网络中获取15个转录因子,ROC分析表明转录因子LMO2和CEBPB对GD具有较高的诊断效能。结论:通过对公共数据集GSE76826的整合分析,获取可能成为GD潜在诊断生物标志物的转录因子,为深入了解GD的早期诊断提供新的视角。
关键词: 转录调控网络;差异表达基因;老年期抑郁症;诊断

Identification of diagnostic markers for geriatric depression based on transcriptional regulatory network

Authors: 1DENG Zhifang, 1LIU Jue, 2XIAO Han, 2GAO Wenqi
1 Department of Pharmacy, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430022, China
2 Institute of Maternal and Child Health, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University & Technology, Wuhan 430015, China

CorrespondingAuthor: GAO Wenqi Email: gwq1103@ctgu.edu.cn

DOI: 10.3978/j.issn.2095-6959.2022.08.025

Foundation: This work was supported by the National Natural Science Foundation (81903592), Wuhan Clinical Medical Research Project (WX20C15), and Wuhan Yellow Crane Talent, Outstanding Young Talents Program, China.

Abstract

Objective: Geriatric depression (GD) is associated with higher risk of suicide and vascular dementia. The present study aims to explored diagnostic biomarkers of depression in the elderly based on gene transcriptional regulation network. Methods: The gene expression profile dataset GSE76826 was downloaded from Gene Expression Omnibus (GEO). R software was used to identify differentially expressed genes (DEGs) between GD and healthy controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were carried out based on DAVID database. The STRING online bioinformatics tool performed regulatory network analysis of DEGs and constructed protein-protein interaction (PPI) networks. Cytoscape software was used to identify hub genes and search for transcription factor. pROC software package performed receiver operating characteristic (ROC) curve analysis to screen transcription factors for diagnostic biomarkers. Results: Compared with healthy controls, a total of 1 411 DEGs were differentially expressed in the GD samples. Four key modules were identified from the PPI constructed by DEGs. KEGG pathway enrichment analysis showed that DEGs were enrichment in cilium movement, antimicrobial humoral response, O-glycan processing, mucosal immune response, Myocardial transmembrane transporter activity, hormone biosynthetic process, neurotransmitter biosynthetic process, and drug metabolism-cytochrome P450 pathway. Fifteen transcription factors were obtained from the PPI network constructed by Cytoscape. ROC analysis revealeded that transcription factors LMO2 and CEBPB had high diagnostic efficiencies. Conclusion: Through integrated analysis of dataset GSE76826, transcription factors that may be potential diagnostic biomarkers of GD were obtained, which provides a new perspective for understanding the early diagnosis of GD.

Keywords: transcriptional regulatory network; differentially expressed genes; geriatric depression; diagnose

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