Comparative Retroviral Epigenomics

摘要 尽管抗逆转录病毒疗法（ART）的成功发展，人们期待已久的艾滋病毒治愈方法仍然没有实现。 被发现病毒整合到全身组织的DNA中， 接受抗逆转录病毒治疗的人不能停止用药，因为在大多数情况下，病毒会 只是在停止抗逆转录病毒疗法后反弹找到治疗方法的一种方法是通过将 病毒的潜伏期，使受感染的细胞可能被杀死的艺术或宿主免疫系统。后生 机制被认为在逆转录病毒潜伏期中起重要作用，但对表观遗传学机制知之甚少。 与HIV潜伏库相关的标志物。令人惊讶的是，关于SIV的报道甚至更少， 更好地表征和控制了对组织的接近和感染的时间线。虽然SIV感染 猕猴作为人类艾滋病病毒感染的模型，目前还不知道是否SIV和HIV 表观遗传学有任何相似之处。开发针对HIV表观遗传机制的成功疗法 潜伏期，我们必须首先确定这些机制，以及动物模型是否适合测试它们。 拟议的项目将描述位于开放染色质中的前病毒的比例， HIV感染者在ART期间和ART停止后的抑制性表观遗传标记， SIV感染的猕猴。此外，我将使用这些参数来评估与大小的关联 外周T细胞和脑中ART停止后的储库、细胞相关RNA和病毒反弹， 这是一种表征不佳的储库组织。这些研究将使我得出结论，什么作用压抑 表观遗传标记在前病毒潜伏期中起作用，以及这些机制在组织和物种之间是否不同。 重要的是，这个项目将支持我的发展，作为一个独立的研究人员与专业知识，在临床 逆转录病毒表观遗传学和比较研究。拟议的培训将使我接触到审判 设计和分析方法，包括生物统计学和生物信息学。这些方法对我的 职业发展，因为我们现在严重依赖下一代测序技术， 我希望进行的比较研究需要了解研究设计的统计方法， 数据分析最后，这个项目将建立在我的背景比较医学，逆转录病毒学， 表观遗传学我将接受1）临床表观遗传学技术2）生物统计学和生物信息学3）非 人类灵长类动物（NHP）程序和NHP动物福利4）HIV研究的道德行为和5） 专业发展，包括研究、建立合作和报告研究结果。 我的指导团队在所有拟议的培训领域都有出色的记录，包括逆转录病毒学， 表观遗传学、生物统计学、生物信息学和非人灵长类SIV研究。该提案基于 以前NIH资助的研究和补充目前NIH资助的项目。

Abstract Despite the successful development of antiretroviral therapies (ART), the long-awaited cure for HIV has still not been discovered. The virus integrates into DNA of tissues throughout the body and becomes latent after institution of ART. Persons receiving ART cannot discontinue their medications, as in most cases the virus will simply rebound upon ART cessation. One approach to finding a cure is to eliminate the reservoir by bringing the virus out of latency so that infected cells might be killed by ART or the host immune system. Epigenetic mechanisms are believed to play an important role in retroviral latency, yet little is known about the epigenetic markers associated with the latent reservoir for HIV. Surprisingly, even less has been published for SIV, where access to tissues and time lines of infection are better characterized and controlled. While SIV-infected macaques serve as a model for human HIV infection, there is no knowledge of whether SIV and HIV epigenetics have any similarity. To develop successful therapeutics that target epigenetic mechanisms of HIV latency, we must first identify these mechanisms and whether animal models will be suitable to test them. The proposed project will characterize the proportion of proviruses located in open chromatin and containing repressive epigenetic marks both during ART and after discontinuation of ART in HIV-infected humans and SIV-infected macaques. Further, I will use these parameters to evaluate the association with the size of the reservoir, cell-associated RNA, and viral rebound after ART cessation in both peripheral T cells and brain, which is a poorly characterized reservoir tissue. These studies will allow me to conclude what role repressive epigenetic marks play in proviral latency, and whether these mechanisms differ between tissues, and species. Importantly, this project will support my development as an independent researcher with expertise in clinical retroviral epigenetics and comparative research. The proposed training will provide me with exposure to trial design and analysis methods, including biostatistics and bioinformatics. These methods are critical to my career development, as we are now heavily reliant on next-generation sequencing technologies, and the comparative studies I wish to pursue will require an understanding of statistical methods for study design and data analysis. Finally, this project will build upon my background in comparative medicine, retrovirology, and epigenetics. I will receive training in 1) clinical epigenetics techniques 2) biostatistics and bioinformatics 3) non- human primate (NHP) procedures and NHP animal welfare 4) ethical conduct of HIV research and 5) professional development, including grantsmanship, building collaborations, and reporting research findings. My mentoring team includes an excellent track records in all proposed areas of training, including retrovirology, epigenetics, biostatistics, bioinformatics, and non-human primate SIV research. This proposal builds upon previous NIH funded research and complements current NIH funded projects.