The coronavirus disease 2019 (COVID-19) pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing global health threat with more than two million infected people since its emergence in late 2019. Detailed knowledge of the molecular biology of the infection is indispensable for understanding of the viral replication, host responses, and disease progression. We provide gene expression profiles of SARS-CoV and SARS-CoV-2 infections in three human cell lines (H1299, Caco-2 and Calu-3 cells), using bulk and single-cell transcriptomics. Small RNA profiling showed strong expression of the immunity and inflammation-associated microRNA miRNA-155 upon infection with both viruses. SARS-CoV-2 elicited approximately two-fold higher stimulation of the interferon response compared to SARS-CoV in the permissive human epithelial cell line Calu-3, and induction of cytokines such as CXCL10 or IL6. Single cell RNA sequencing data showed that canonical interferon stimulated genes such as IFIT2 or OAS2 were broadly induced, whereas interferon beta (IFNB1) and lambda (IFNL1-4) were expressed only in a subset of infected cells. In addition, temporal resolution of transcriptional responses suggested interferon regulatory factors (IRFs) activities precede that of nuclear factor-κB (NF-κB). Lastly, we identified heat shock protein 90 (HSP90) as a protein relevant for the infection. Inhibition of the HSP90 charperone activity by Tanespimycin/17-N-allylamino-17-demethoxygeldanamycin (17-AAG) resulted in a reduction of viral replication, and of TNF and IL1B mRNA levels. In summary, our study established in vitro cell culture models to study SARS-CoV-2 infection and identified HSP90 protein as potential drug target for therapeutic intervention of SARS-CoV-2 infection.

中文翻译：

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SARS-CoV-2感染人类细胞系的单细胞基因大批量和单基因表达谱确定了治疗性干预的分子靶标

由新型严重急性呼吸综合征冠状病毒2（SARS-CoV-2）引起的2019年冠状病毒病（COVID-19）大流行是一种持续的全球健康威胁，自2019年底出现以来已有200万以上的受感染者。详细感染的分子生物学知识对于理解病毒复制，宿主反应和疾病进展必不可少。我们提供了使用大量和单细胞转录组学的三种人类细胞系（H1299，Caco-2和Calu-3细胞）中SARS-CoV和SARS-CoV-2感染的基因表达谱。两种病毒感染后，小RNA谱分析均显示出免疫和与炎症相关的microRNA miRNA-155的强烈表达。与SARS-CoV相比，SARS-CoV-2在允许的人类上皮细胞系Calu-3中引起的干扰素应答刺激程度高出大约两倍，并诱导了诸如CXCL10或IL6的细胞因子。单细胞RNA测序数据表明，典型的干扰素刺激基因（如IFIT2或OAS2）被广泛诱导，而干扰素β（IFNB1）和λ（IFNL1-4）仅在部分感染细胞中表达。此外，转录反应的时间分辨率表明干扰素调节因子（IRF）活性先于核因子-κB（NF-κB）。最后，我们确定了热休克蛋白90（HSP90）作为与感染相关的蛋白。坦西霉素/ 17-N-烯丙基氨基-17-去甲氧基格尔德霉素（17-AAG）抑制HSP90伴侣活性导致病毒复制减少，和TNF和IL1B mRNA水平。总之，我们的研究建立了用于研究SARS-CoV-2感染的体外细胞培养模型，并确定了HSP90蛋白是SARS-CoV-2感染治疗干预的潜在药物靶标。