tRNA-derived RNA Fragments and their Role in Nasal SARS-CoV-2 Infection

严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)是一种新出现的致病病毒，它的传播不仅导致了2019年冠状病毒病(新冠肺炎)的大流行，也导致了经济衰退。为了从战略上开发针对SARS-CoV-2的抗病毒疗法，迫切需要在确定宿主如何应对SARS-CoV-2的机制方面做出重点努力。非编码RNA(NcRNAs)贡献了98%的人类转录产物，是治疗病毒感染的有前途的靶点。利用ncRNAs作为有希望的治疗靶点的一个有效例子是miR122抑制剂RG-101单剂量抑制丙型肝炎病毒(HCV)。因此，研究ncRNA对新出现病毒的反应可能为开发有效的治疗干预措施提供一条捷径。我们最近发现，在SARS-CoV-2鼻拭子样本中，受影响最大的小核糖核糖核酸(SncRNAs)属于tRNA衍生RNA片段(TRFs)，这是一个新发现的ncRNA家族。我们还发现SARS-CoV-2诱导的TRF不太可能是降解副产物，但受到严格调控的分子和鼻腔呼吸道上皮细胞(AECs)可以概括SARS-CoV-2诱导的TRF。与肝炎病毒和呼吸道合胞病毒(RSV)诱导的TRFs相比，SARS-CoV-2诱导的TRFs具有许多特征。鉴于TRF在其他病毒感染中的新作用，包括我们对其在RSV感染中的前病毒作用的早期观察，以及我们的初步数据证实SARS-CoV-2诱导的TRF在调节病毒RNA合成方面具有重要作用，我们假设SARS-CoV-2诱导的TRF在SARS-CoV-2感染中也具有重要的功能。我们将通过1)表征TRF特征和2)研究TRF是否影响SARS-CoV-2复制和相关的宿主反应来解决这一假说。UTMB是BSL4加尔维斯顿国家实验室(GNL)的所在地，该实验室是我国应对新出现传染病的主要资源。GNL于2020年1月底获得了首个SARS-CoV-19样本，目前正在进行基础、动物、临床试验和流行病学等各方面的研究。我们与合作者王田博士进行了持续的合作，他是研究宿主对BSL3RNA病毒反应的专家。她的实验室已经建立了一套纯化SARS-CoV-2感染病毒的方案。我们最近一直在合作建立AEC模型，以研究宿主与SARS-CoV-2之间的相互作用。该项目的结果不仅为确定SARS-CoV-2复制和致病相关的分子机制提供了可能，而且对开发SARS-CoV-2潜在的疾病生物标志物和治疗策略具有重要的指导意义。总之，我们团队的总体目标是为设计新型抗病毒药物提供与ncRNAs相关的信息。

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an emerging pathogenic virus, has resulted in not only the coronavirus disease 2019 (COVID-19) pandemic, but also economic recession. To strategically develop antiviral therapies against SARS-CoV-2, a focused effort in identifying mechanisms on how the host responds to SARS-CoV-2 is urgently needed. Non-coding RNAs (ncRNAs) contribute to 98% of human transcriptional products and are promising therapeutic targets against viral infections. One effective example for utilizing ncRNAs as promising therapeutic targets is that miR122 inhibitor RG-101 suppresses the hepatitis C virus (HCV) with a single dose. Therefore, studying the ncRNA responses for emerging viruses may provide a shortcut to developing effective therapeutic interventions. We recently discovered that the most impacted small ncRNAs (sncRNAs) by SARS-CoV-2 in nasal swab samples belong to tRNA-derived RNA Fragments (tRFs), a recently discovered ncRNA family. We also found that SARS-CoV-2-induced tRFs are unlikely to be degradation byproducts, but tightly regulated molecules, and nasal airway epithelial cells (AECs) can recapitulate tRF induction by SARS-CoV-2. Compared with tRFs induced by hepatitis viruses and respiratory syncytial virus (RSV), SARS-CoV-2-induced tRFs share several features with them. Given the emerging roles of tRFs in other viral infections, including our early observation on their proviral role in RSV infection and our preliminary data validating a SARS-CoV-2-induced tRF being important in regulating viral RNA synthesis, we hypothesize that SARS-CoV-2-induced tRFs are also functionally important to SARS-CoV-2 infection. We will address the hypothesis by 1) characterizing tRF signatures, and 2) investigating whether tRFs affect SARS-CoV-2 replication and associated host responses. UTMB is the home of the BSL4 Galveston National Laboratory (GNL), a leading resource for our national response to emerging infectious diseases. The GNL obtained the first sample of SARS- CoV-19 at the end of January of 2020, and is currently conducting research on all fronts; basic, animal, clinical trials, and epidemiological. We have an ongoing collaboration with co-investigator Dr. Tian Wang, who is an expert in studying host responses to BSL3 RNA viruses. Her laboratory has established a protocol to purify SARS-CoV-2 for the infection. We recently have been working together on AEC models to study the interaction between host and SARS-CoV-2. The results of this project will not only provide the potential to determine the molecular mechanisms associated with the replication and pathogenesis of SARS-CoV-2, but also are highly instructive for the development of potential disease biomarkers and therapeutic strategies for SARS-CoV-2. In conclusion, the overall goal of our team is to provide ncRNAs-related information for designing novel antiviral drugs.