RUI: Transcriptional regulation of host-pathogen viral symbiosis at single-cell resolution

许多病毒感染宿主是终生的。为了做到这一点，病毒必须平衡影响生命周期时间的对立需求。一方面，需要主动复制来制造更多的副本和传播。另一方面，非活性休眠需要避免宿主检测和免疫反应，可以清除病毒。病毒生长的振荡与病毒基因表达的变化有关。受感染的宿主细胞随后通过自身基因表达的变化来应对，扰乱病毒的生命周期。寄主和病原体之间的这种竞争在种群水平上已经得到了很好的研究。然而，该领域的新数据认为，群体中的单个病毒并不是一致行动的。为了平衡活跃复制的风险和非活跃休眠的安全性，亚种群可能表达不同的基因。该项目旨在研究病毒在主动复制和灭活休眠期间如何产生不同的亚群。研究小组获得的数据将由专门为该项目编写代码的本科计算生物学课程进行分析。巴纳德学院（Barnard College）是一所女子文理学院，它将通过与招收代表性不足的少数族裔的现有项目合作，支持这一努力。该项目的综合目标是在病毒学和计算机科学的界面上推进基本问题的知识，同时增加未被充分代表的女性在计算生物学中的参与。人类疱疹病毒-8 （HHV-8）是一种双链DNA病毒，通过建立终身共生感染在宿主体内持续存在。病毒能否持续数年，很大程度上取决于病毒是否有能力关闭转录，使其进入宿主无法检测到的静止潜伏状态。同样重要的是，在细胞压力下自发复制的能力，以及产生新的病毒粒子来补充耗尽的病毒库的能力。虽然已经做了很多工作来了解这种大规模群体中裂解再激活的分子基础，但单细胞分辨率的研究仍然缺乏。初步数据表明，HHV-8在多个亚群中表现出明显的异质性。HHV-8再激活也在一个具有独特宿主转录特征的特定亚群中富集。特异性Aim 1将测试已确定的候选宿主基因对HHV-8再激活的影响。特异性目标2将确定哪些亚群最容易对不同的再激活刺激作出反应。这两个目标都建立在微生物界广泛的文献基础上，展示了在异质种群中下注对冲的转录基础。这些实验的总和将提高我们对控制HHV-8再激活的单细胞转录组的认识。巴纳德学院的生物系正在开设一个新的计算生物学专业。该项目将通过建立一个新的基于课程的本科生研究经验，“计算病毒系统学”，基于所进行的实验做出具体贡献。本课程将整合计算机科学中性别教学研究的策略。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Many viruses infect hosts for a lifetime. In order to do so, viruses must balance opposing needs that affect timing of the life cycle. On one hand, active replication is required to make more copies and propagate. On the other hand, inactive dormancy is required to avoid host detection and immune responses that could clear the virus. These oscillations in viral growth involve changes in viral gene expression. The infected host cell counters with subsequent changes in its own gene expression to perturb the viral life cycle. This competition between host and pathogen has been well studied at the population level. Emerging data in the field, however, argues that individual viruses in a population do not act in unison. To balance the risk of active replication with the safety of inactive dormancy, subpopulations may express different genes. This project aims to study how viruses generate diverse subpopulations during both active replication and inactivate dormancy. Data obtained by a research team will then be analyzed by an undergraduate computational biology class specifically designed to write code for this project. Barnard College, a liberal arts school for women, will support this effort through collaboration with established program cohorts that recruit underrepresented minorities. The integrated goals of the project are to advance knowledge of fundamental questions at the interface of virology and computer science while simultaneously increasing participation of underrepresented women in computational biology.Human herpesvirus-8 (HHV-8) is a double stranded DNA virus that persists in the host by establishing a lifelong symbiotic infection. Persistence over years strongly depends on the ability of the virus to shut down transcription to a quiescent latent state not detectable by the host. Equally important is also the ability to spontaneously replicate in response to cellular stress and generate new virions to replenish a depleted reservoir. While much work has been done to understand the molecular basis of this lytic reactivation in a bulk population, studies at single-cell resolution have been lacking. Preliminary data demonstrates that HHV-8 populations display clear heterogeneity with multiple subpopulations. HHV-8 reactivation is also enriched in one specific subpopulation with a distinct host transcriptional signature. Specific Aim 1 will test the effect of identified candidate host genes on HHV-8 reactivation. Specific Aim 2 will identify which subpopulations respond most readily to different stimuli of reactivation. Both aims build on a wide body of literature in the microbial world demonstrating a transcriptional basis to bet-hedging within a heterogeneous population. The sum of experiments will advance our knowledge of the single-cell transcriptomes that control HHV-8 reactivation. The Department of Biology at Barnard College is establishing a new major in computational biology. This project will specifically contribute through the establishment of a new course-based undergraduate research experience, “Computational ViroSystOmics,” based on the experiments performed. The course will integrate strategies mindful of pedagogical studies of gender in computer science.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.