Comparative Retroviral Epigenomics

摘要 尽管抗逆转录病毒疗法(ART)的开发取得了成功，但人们期待已久的艾滋病毒治疗方法仍然没有 被发现了。病毒整合到全身组织的DNA中，并在 艺术学院。接受抗逆转录病毒治疗的人不能停止服药，因为在大多数情况下，病毒会 当艺术停止时，简单地反弹。找到治愈方法的一种方法是通过携带 病毒的潜伏期过长，使被感染的细胞可能被ART或宿主免疫系统杀死。表观遗传 机制被认为在逆转录病毒潜伏期中起重要作用，但对表观遗传学知之甚少。 与艾滋病毒潜伏宿主相关的标志物。令人惊讶的是，SIV发表的文章甚至更少，其中 接触组织的途径和感染的时间线得到了更好的表征和控制。虽然SIV感染了 猕猴是人类感染艾滋病毒的模型，目前还不知道SIV和艾滋病毒 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 对于潜伏期，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和含有 HIV感染者在ART期间和停止ART后的抑制性表观遗传学标志 感染SIV的猕猴。此外，我将使用这些参数来评估与 ART停止后，外周T细胞和脑中的储存库、细胞相关RNA和病毒反弹， 这是一种特征不佳的储藏组织。这些研究将使我得出压抑的作用 表观遗传标记在前病毒潜伏期中发挥作用，以及这些机制是否在组织和物种之间有所不同。 重要的是，这个项目将支持我作为一名具有临床专业知识的独立研究员的发展。 逆转录病毒表观遗传学和比较研究。拟议的培训将使我有机会参加审判。 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，以及 我希望从事的比较研究将需要对研究设计和统计方法的理解 数据分析。最后，这个项目将建立在我在比较医学、逆转录病毒学和 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(NHP)程序和NHP动物福利4)艾滋病毒研究的道德行为和5) 专业发展，包括专业精神、建立协作和报告研究结果。 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。这项建议的基础是 以前NIH资助的研究和补充了目前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.