系统鉴定与分析新型冠状病毒感染心肌细胞内的A-to-I RNA编辑事件

Systematic Identification and Analysis of A-to-I RNA Editing Events in SARS-CoV-2-infected Cardiomyocytes

严重急性呼吸综合征冠状病毒2(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)感染增加了心肌损伤的风险,其致病分子机制还不是很清楚。本文比较了SARS-CoV-2感染心肌细胞(感染组)与未感染病毒心肌细胞(对照组)中RNA编辑的变化,以期从RNA编辑角度了解SARS-CoV-2感染对心肌细胞的影响。首先,从GEO数据库中下载SARS-CoV-2感染的人诱导多能干细胞衍生的心肌细胞(human induced pluripotent stem cell-derived cardiomyocyte,hiPSC-CM)的原始测序数据(GSE150392);然后,用SPRINT软件识别RNA编辑位点(RNAediting site,RES),比较感染组和对照组心肌细胞编辑水平的变化;最后,对编辑位点进行分析和注释,并进行相关基因的功能分析。结果显示,总共检测到约92899个碱基替换位点,其中87670个被鉴定为A-to-I RES,这些A-to-I编辑位点发生在Alu区域上的有78978个;A-to-I编辑位点倾向于成簇分布,主要分布在内含子、基因间区等区域;与对照组相比,感染组中编辑水平显著上调的A-to-I RES有102个,显著下调的有94个,这些含有显著差异RES的基因参与的病毒感染相关的GO(Gene Ontology)生物学过程主要富集于病毒过程、病毒生命周期和响应病毒感染的防御等,并且其KEGG(kyoto Encyclopedia of Genes and Genomes)功能通路也富集在病毒感染等方面,而筛选的含有高质量A-to-I RES、组间编辑水平存在显著差异的11个基因的功能则富集于内吞、细胞因子-细胞因子受体相互作用、蛋白酶体、烟酸和烟酰胺代谢以及铁死亡等方面。本研究结果表明,SARS-CoV-2感染影响了心肌细胞中A-to-I的RNA编辑,这类RNA编辑事件的发生体现了宿主心肌细胞对病毒感染的一种响应机制。

Novel coronavirus(SARS-CoV-2)infection increases the risk of myocardial injury,and the molecular mechanisms of pathogenesis remain to be elucidated.Herein,the changes of RNA editing in SARSCoV-2 infected cardiomyocytes(infection group)and uninfected cardiomyocytes(mock group)were compared to explore the effects of the viral infection on cardiomyocytes from the perspective of RNA editing.RNA-seq data(GSE150392)of SARS-CoV-2 infection of human induced pluripotent stem cell-derived cardiomyocytes(hiPSC-CMs)was downloaded from the GEO database,and RNA editing sites(RESs)were identified using SPRINT software.The changes in editing levels of cardiomyocytes in the infection and mock groups were compared,editing sites were annotated,and relevant functional analyses were performed.A total of about 92899 base substitutions were detected,of which 87670 were identified as A-to-I RESs,and 78978 Bioof these A-to-I editing sites were found to appear in the Alu regions.A-to-I editing sites tend to be distributed in clusters,mainly in regions such as introns and intergenic regions.By screening the differential RESs between the infection and mock groups in A-to-I editing,it was found that 102 of the significantly differential RESs are up-regulated and 94 are down-regulated in editing level.These genes with significant differences in RES are involved in the biological processes of viral infection related GO(Gene Ontology),which are mainly enriched in viral process,virus life cycle,and defense response to virus,et al.,and their Kyoto Encyclopedia of Genes and Genomes(KEGG)functional pathways are also mainly related to viral infection.In contrast,the 11 screened genes with high-quality A-to-I RESs and significant differences in editing levels between groups are enriched in endocytosis,cytokine-cytokine receptor interaction,proteosome,nicotinate and nicotinamide metabolism,and ferroptosis,et al..The results showed that SARS-CoV-2 infection affects A-to-I RNA editing in cardiac myocytes,and the occurrence of such RNA editing events is a response of host cardiac myocytes to the viral infection.