Bioinformatics analysis of vascular RNA-seq data revealed hub genes and pathways in a novel Tibetan minipig atherosclerosis model induced by a high fat/cholesterol diet
Bioinformatics analysis of vascular RNA-seq data revealed hub genes and pathways in a novel Tibetan minipig atherosclerosis model induced by a high fat/cholesterol diet
复制标题
血管RNA-seq数据的生物信息学分析揭示了高脂肪/胆固醇饮食诱导的新型西藏小型猪动脉粥样硬化模型中的中心基因和通路
DOI：
10.1186/s12944-020-01222-w
复制
发表时间：
2020-03-25
影响因子：
4.5
通讯作者：
Chen, Minli
中科院分区：
文献类型：
--
作者：
Pan, Yongming;Yu, Chen;Chen, Minli
动脉粥样硬化是心血管事件的主要诱因，但其分子机制尚不清楚。动脉粥样硬化的动物模型可以为深入了解动脉粥样硬化的病因、病理生理学和并发症提供宝贵的工具。利用人颈动脉粥样硬化数据库（GSEA 43292）和RT-PCR方法对鉴定的基因进行验证。结果研究结果表明，饲喂24周HFC日粮后，小型猪表现出明显的血脂异常、氧化应激、炎症反应、动脉粥样硬化斑块，低密度脂蛋白（LDL）和白细胞募集增加。我们的RNA-seq结果显示，在动脉粥样硬化/NC组中有1716个DEGs，其中1468个基因上调，248个基因下调。DEGs的功能富集分析显示，HFC饮食引起的改变与血管免疫炎症反应、脂质代谢和肌肉收缩有关，表明HFC饮食引起的高胆固醇血症可以激活先天和适应性免疫反应，驱动动脉粥样硬化的发展。此外，我们从主要的PPI网络中确定了四个模块，它们与细胞趋化性、髓系白细胞活化、细胞因子产生和淋巴细胞活化有关。共发现TNF、PTPRC、ITGB2、ITGAM、VCAM1、CXCR4、TYROBP、TLR4、LCP2、C5AR1、CD86、MMP9、PTPN6、C3、CXCL10等15个枢纽基因和NF-ĸB1、SPI1两个转录因子（TF）。这些结果与人类颈动脉斑块的表达模式一致，并经RT-PCR验证。
BackgroundAtherosclerosis is a major contributor to cardiovascular events, however, its molecular mechanism remains poorly known. Animal models of atherosclerosis can be a valuable tool to provide insights into the etiology, pathophysiology, and complications of atherosclerosis. In particular, Tibetan minipigs are a feasible model for studying diet-related metabolic and atherosclerotic diseases.MethodsWe used vascular transcriptomics to identify differentially expressed genes (DEGs) in high fat/cholesterol (HFC) diet-fed Tibetan minipig atherosclerosis models, analyzed the DEGs gene ontology (GO) terms, pathways and protein-protein interactions (PPI) networks, and identified hub genes and key modules using molecular complex detection (MCODE), Centiscape and CytoHubba plugin. The identified genes were validated using the human carotid atherosclerosis database (GSEA 43292) and RT-PCR methods.ResultsOur results showed that minipigs displayed obvious dyslipidemia, oxidative stress, inflammatory response, atherosclerotic plaques, as well as increased low-density lipoprotein (LDL) and leukocyte recruitment after 24 weeks of HFC diet feeding compared to those under a regular diet. Our RNA-seq results revealed 1716 DEGs in the atherosclerotic/NC group, of which 1468 genes were up-regulated and 248 genes were down-regulated. Functional enrichment analysis of DEGs showed that the HFC diet-induced changes are related to vascular immune-inflammatory responses, lipid metabolism and muscle contraction, indicating that hypercholesterolemia caused by HFC diet can activate innate and adaptive immune responses to drive atherosclerosis development. Furthermore, we identified four modules from the major PPI network, which are implicated in cell chemotaxis, myeloid leukocyte activation, cytokine production, and lymphocyte activation. Fifteen hub genes were discovered, including TNF, PTPRC, ITGB2, ITGAM, VCAM1, CXCR4, TYROBP, TLR4, LCP2, C5AR1, CD86, MMP9, PTPN6, C3, and CXCL10, as well as two transcription factors (TF), i.e. NF-ĸB1 and SPI1. These results are consistent with the expression patterns in human carotid plaque and were validated by RT-PCR.ConclusionsThe identified DEGs and their enriched pathways provide references for the development and progression mechanism of Tibetan minipig atherosclerosis model induced by the HFC diet.