Role of Top1 and 3D Genome structure in SARS-CoV-2 infection [Hi-C]

The ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Targeting these pathways might therefore be a viable therapeutic strategy. Previously, we have reported that chromatin factors such as Topoisomerase I (Top1) play key roles in controlling the induction of inflammatory gene expression programs. Here, by using multidimensional epigenetic, transcriptional, in vitro and in vivo analyses, we show that Topoisomerase 1 (Top1) inhibition in infected cells and animals suppresses lethal inflammation induced by SARS-CoV-2. To study alterations in genome structure after SARS-CoV-2 infection, we performed Hi-C on SARS-CoV-2 infected A549-ACE2 cells at 0,8 and 24 hours post infection. Experiment was done in biological duplicate. Each biological replicate was sequenced with 4 technical replicates. To study the impact of Top1 on the inflammatory response to SARS-CoV-2, we knocked-down TOP1 expression using siRNA in A549-ACE2 cells. Cells were then left uninfected or infected with SARS-CoV-2. Cells that were not treated with siRNA (no siRNA) or scrambled siRNA (siSCR) were used as controls. The experiment was done in triplicate.

由严重急性呼吸综合征冠状病毒2（Severe Acute Respiratory Syndrome Coronavirus 2，SARS-CoV-2）引发的持续全球大流行，目前正影响着全球数百万民众的生命健康。多项大型回顾性研究显示，炎性细胞因子与促炎因子水平升高，与疾病严重程度加剧及死亡率上升均显著相关，因此靶向此类通路或为可行的治疗策略。此前本团队已有研究报道，诸如拓扑异构酶I（Topoisomerase I，Top1）这类染色质因子，在调控炎性基因表达程序的诱导过程中发挥关键作用。本研究通过多维度表观遗传组学、转录组学、体外及体内实验分析，证实感染细胞与动物体内的拓扑异构酶1（Topoisomerase 1，Top1）抑制可有效缓解SARS-CoV-2诱导的致死性炎症反应。为探究SARS-CoV-2感染后宿主基因组结构的改变，我们对感染病毒的A549-ACE2细胞分别于感染后0、8及24小时开展Hi-C测序实验。该实验设置2次生物学重复，每个生物学重复均进行4次技术重复测序。为探究Top1对SARS-CoV-2感染炎症应答的影响，我们通过siRNA敲低A549-ACE2细胞中TOP1的基因表达水平。随后将细胞分为未感染组与SARS-CoV-2感染组，同时设置未转染siRNA（无siRNA）及转染无序siRNA（siSCR）的细胞作为对照。该实验设置3次生物学重复。