Nasal RNA response to respiratory viral infections

项目摘要 呼吸道病毒如SARS-CoV-2和流感是引起季节性疾病的常见病原体， 可以达到大流行的程度。人类对这些病毒的早期反应是在鼻腔中， 鼻咽部定义疾病轨迹的生物标志物对于选择治疗和 监督决策。我们假设鼻咽部tRNA谱可以用来预测症状 呼吸道病毒感染导致的严重程度。我们将应用我们新开发的RNA测序技术 探索人类分子特征和导致疾病轨迹的因素。这些配置文件可以 包括宿主tRNA的组成，片段化模式，和上转录组的修饰。 呼吸道目标1将对鼻咽样本进行tRNA测序，以确定感染特征 使用记录有SARS-CoV-2、甲型流感和B型流感的库鼻咽拭子， 感染.结合已知的患者结局，我们将分析鼻咽拭子中的tRNA特征 并绘制出鼻tRNA谱与病毒感染严重程度之间的关系。由于鼻咽部 该区域充满了免疫细胞，包括对抗病毒感染的秘密RNA酶，我们将量化 核糖核酸酶活性，并将这些结果与tRNA签名相关联。目标2将开发以下的qPCR测定： 基于tRNA的生物标志物。我们开发了一种优化鼻咽样本引物设计的算法 基于tRNA测序结果。我们的方法还检测tRNA修饰分数的变化。我们将 进一步开发该检测试剂盒，使其能够应用于鼻咽拭子样本，以进行快速、常规和 经济的tRNA生物标志物分析。这些结果将扩大我们对人类tRNA谱如何被 呼吸道病毒病理学的生物标志物。

PROJECT SUMMARY Respiratory viruses such as SARS-CoV-2 and influenza are common pathogens that cause seasonal illness and can reach pandemic proportions. The early human response to these viruses are in the nasal cavity and nasopharyngeal regions. Defining biomarkers of disease trajectory is important for opting for treatment and monitoring decisions. We hypothesize that the nasopharyngeal tRNA profiles can be used to predict symptom severity resulting from respiratory virus infection. We will apply our newly developed RNA sequencing technology to explore the human molecular signatures and factors that contribute to disease trajectory. These profiles can include the host tRNA composition, fragmentation patterns, and epitranscriptomic modification in the upper respiratory tract. Aim 1 will perform tRNA sequencing of nasopharyngeal samples to identify infection signatures of host tRNA using banked nasopharyngeal swabs with documented SARS-CoV-2, influenza A, and influenza B infections. Together with known patient outcomes, we will dissect tRNA signatures in nasopharyngeal swabs and map the relationship between nasal tRNA profiles and viral infection severity. Since the nasopharyngeal region is highly populated with immune cells, including secret RNases to counter viral infections, we will quantify the ribonuclease activity and associate these results with tRNA signatures. Aim 2 will develop qPCR assays of tRNA-based biomarkers. We developed an algorithm that optimizes primer design for nasopharyngeal samples based on tRNA sequencing results. Our approach also detects changes in tRNA modification fractions. We will further develop this assay to enable its implementation to nasopharyngeal swab samples for rapid, routine and economic tRNA biomarker analysis. These results will expand our insights on how human tRNA profiles can be biomarkers for the pathology of respiratory viruses in general.