High-Definition Characterization of the Persistence and Perturbation of the HIV Reservoir: Project 2

摘要 大量的临床、神经病理学、免疫组织化学和免疫学研究表明 人类脑细胞，特别是髓系细胞，对HIV-1易感；感染这些细胞可能 导致神经认知功能障碍和病毒的长期持续，尽管抗逆转录病毒治疗。然而，在所有人中， 人体的解剖组织位置，中枢神经系统(CNS)可以说代表了 很难访问和评估病毒感染和持久性。最近，取得了重大进展。 在使用新的下一代测序方法定义病毒库方面取得了进展，经常允许病毒 单基因组或单细胞分辨率的序列分析。使用这些技术，就有可能分析 非常详细的CNS中病毒物种的进化动态，并获得对潜在的罕见的洞察 影响HIV-1病毒在中枢神经系统中建立和持续的机制和途径。在这里，我们 提出一个合作的、跨学科的研究项目，让具有互补经验的研究人员参与 在神经学、神经病理学、病毒学、计算建模和临床护理方面取得进展 目前对中枢神经系统作为具有复制能力的长期持续存在的解剖部位的理解 HIV-1。在具体目标1中，我们将利用独特的配对脑脊液和血浆样本收集来自 对未经治疗的HIV-1患者进行纵向跟踪，以评估系统发育关联和相关病毒 来自中枢神经系统的病毒序列和不同的解剖区段之间的群体基因组学；这些 研究将有助于跟踪抗逆转录病毒治疗前的播种和建立持久的病毒库。 在特定目标2中，我们将使用经抗逆转录病毒治疗的hiv-1患者死亡时病毒血症抑制的尸检材料。 目的：分析从中国分离的前病毒的频率、克隆性、染色体位置和复制能力 分离的CNS细胞，特别是从髓系血管周围巨噬细胞和髓系实质小胶质细胞中分离出来的CNS细胞 星形胶质细胞。综上所述，这些研究将使人们能够深入描述HIV-1储藏细胞的动力学 CNS，并可能为未来旨在根除和治愈HIV-1的临床战略提供信息。

Abstract A considerable number of clinical, neuropathological, immunohistochemical and immunological studies suggest that human brain cells, in particular those of myeloid origin, are susceptible to HIV-1; infection of these cells may contribute to neurocognitive dysfunction and viral long-term persistence despite ART. However, among all anatomical tissue locations in the human body, the central nervous system (CNS) arguably represents the most difficult one to access and to evaluate for viral infection and persistence. Recently, significant progress has been made in defining viral reservoirs using novel next-generation sequencing approaches, frequently allowing viral sequence profiling at single-genome or single-cell resolution. Using such technologies, it is possible to profile the evolutionary dynamics of viral species in the CNS in great detail, and to obtain rare insight into the underlying mechanisms and pathways that influence HIV-1 reservoir establishment and persistence in the CNS. Here, we propose a collaborative, interdisciplinary research project involving investigators with complementary experience in neurology, neuropathology, virology, computational modeling and clinical care of HIV-1 patients to advance the current understanding of the CNS as an anatomical site for long-term persistence of replication-competent HIV-1. In specific aim 1, we will leverage a unique collection of paired CSF and plasma samples from longitudinally-followed, untreated HIV-1 patients to evaluate phylogenetic associations and interrelated viral population genomics between viral sequences from the CNS and alternative anatomical compartments; these studies will be instrumental for tracking the seeding and establishment of long-lasting viral reservoirs pre-ART. In specific aim 2, we will use autopsy material from ART-treated HIV-1 patients with suppressed viremia at death to profile the frequency, clonality, chromosomal location and replication competence of proviruses isolated from sorted CNS cells, in particular from myeloid parenchymal microglia, from myeloid perivascular macrophages and astrocytes. Together, these studies will allow for a deep characterization of HIV-1 reservoir cell dynamics in the CNS, and may be informative for future clinical strategies aiming at HIV-1 eradication and cure.