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共表达网络分析确定了对甘油三酯和游离脂肪酸代谢至关重要的枢纽基因,这些基因是小鼠年龄相关血管功能障碍的关键调节因子。

Co-expression network analysis identified hub genes critical to triglyceride and free fatty acid metabolism as key regulators of age-related vascular dysfunction in mice.

作者信息

Li Huimin, Wang Xinhui, Lu Xinyue, Zhu Hongxin, Li Sheng, Duan Shiwei, Zhao Xinzhi, Zhang Fuquan, Alterovitz Gil, Wang Fudi, Li Qiang, Tian Xiao-Li, Xu Mingqing

机构信息

Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China.

Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.

出版信息

Aging (Albany NY). 2019 Sep 12;11(18):7620-7638. doi: 10.18632/aging.102275.

Abstract

Aging has often been linked to age-related vascular disorders. The elucidation of the putative genes and pathways underlying vascular aging likely provides useful insights into vascular diseases at advanced ages. Transcriptional regulatory network analysis is the key to describing genetic interactions between molecular regulators and their target gene transcriptionally changed during vascular aging. A total of 469 differentially expressed genes were parsed into 6 modules. Among the incorporated sample traits, the most significant module related to vascular aging was associated with triglyceride and enriched with biological terms like proteolysis, blood circulation, and circulatory system process. The module associated with triglyceride was preserved in an independent microarray dataset, indicating the robustness of the identified vascular aging-related subnetwork. Additionally, Enpp5, Fez1, Kif1a, F3, H2-Q7, and their interacting miRNAs mmu-miR-449a, mmu-miR-449c, mmu-miR-34c, mmu-miR-34b-5p, mmu-miR-15a, and mmu-let-7, exhibited the most connectivity with external lipid-related traits. Transcriptional alterations of the hub genes Enpp5, Fez1, Kif1a, and F3, and the interacting microRNAs mmu-miR-34c, mmu-miR-34b-5p, mmu-let-7, mmu-miR-449a, and mmu-miR-449c were confirmed. Our findings demonstrate that triglyceride and free fatty acid-related genes are key regulators of age-related vascular dysfunction in mice and show that the hub genes for Enpp5, Fez1, Kif1a, and F3 as well as their interacting miRNAs mmu-miR-34c, mmu-miR-34b-5p, mmu-let-7, mmu-miR-449a, and mmu-miR-449c, could serve as potential biomarkers in vascular aging. The microarray gene expression profiles of aorta samples from 6-month old mice (n=6) and 20-month old mice (n=6) were processed to identify nominal differentially expressed genes. These nominal differentially expressed genes were subjected to a weighted gene co-expression network analysis. A network-driven integrative analysis with microRNAs and transcription factors was performed to define significant modules and underlying regulatory pathways associated with vascular aging, and module preservation test was conducted to validate the age-related modules based on an independent microarray gene expression dataset in mice aorta samples including three 32-week old wild-type mice (around 6-month old) and three 78-week old wild-type mice (around 20-month old). Gene ontology and protein-protein interaction analyses were conducted to determine the hub genes as potential biomarkers in the progress of vascular aging. The hub genes were further validated with quantitative real-time polymerase chain reaction in aorta samples from 20 young (6-month old) mice and 20 old (20-month old) mice.

摘要

衰老常与年龄相关的血管疾病有关。阐明血管衰老潜在的基因和通路可能为老年血管疾病提供有用的见解。转录调控网络分析是描述分子调节因子与其在血管衰老过程中转录变化的靶基因之间遗传相互作用的关键。共469个差异表达基因被解析为6个模块。在纳入的样本特征中,与血管衰老最相关的模块与甘油三酯有关,并富含蛋白水解、血液循环和循环系统过程等生物学术语。与甘油三酯相关的模块在一个独立的微阵列数据集中得以保留,表明所鉴定的血管衰老相关子网的稳健性。此外,Enpp5、Fez1、Kif1a、F3、H2-Q7及其相互作用的微小RNA(mmu-miR-449a、mmu-miR-449c、mmu-miR-34c、mmu-miR-34b-5p、mmu-miR-15a和mmu-let-7)与外部脂质相关特征表现出最强的连通性。枢纽基因Enpp5、Fez1、Kif1a和F3以及相互作用的微小RNA(mmu-miR-34c、mmu-miR-34b-5p、mmu-let-7、mmu-miR-449a和mmu-miR-449c)的转录变化得到了证实。我们的研究结果表明,甘油三酯和游离脂肪酸相关基因是小鼠年龄相关血管功能障碍的关键调节因子,并表明Enpp5、Fez1、Kif1a和F3枢纽基因及其相互作用的微小RNA(mmu-miR-34c、mmu-miR-34b-5p、mmu-let-7、mmu-miR-449a和mmu-miR-449c)可作为血管衰老的潜在生物标志物。对6月龄小鼠(n = 6)和20月龄小鼠(n = 6)主动脉样本的微阵列基因表达谱进行处理,以鉴定名义上差异表达的基因。对这些名义上差异表达的基因进行加权基因共表达网络分析。进行了一项将微小RNA和转录因子纳入的网络驱动综合分析,以定义与血管衰老相关的显著模块和潜在调控通路,并基于小鼠主动脉样本中的一个独立微阵列基因表达数据集进行模块保留测试,该数据集包括三只32周龄野生型小鼠(约6月龄)和三只78周龄野生型小鼠(约20月龄)。进行基因本体和蛋白质-蛋白质相互作用分析,以确定枢纽基因作为血管衰老进程中的潜在生物标志物。通过定量实时聚合酶链反应在20只年轻(6月龄)小鼠和20只年老(20月龄)小鼠的主动脉样本中对枢纽基因进行进一步验证。

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