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、免疫组化和免疫学研究表明， 人类脑细胞，特别是骨髓细胞，对HIV-1易感;这些细胞的感染可能 导致神经认知功能障碍和病毒长期持续存在，尽管ART。 在人体中的解剖组织位置中，中枢神经系统（CNS）可以说代表了人体中最重要的解剖组织位置。 很难接近和评估病毒感染和持续性。最近取得了重大进展， 使用新的下一代测序方法来定义病毒库， 单基因组或单细胞分辨率的序列分析。使用这些技术，可以分析 病毒物种在中枢神经系统的进化动力学非常详细，并获得罕见的洞察到潜在的 机制和途径，影响HIV-1水库建立和持久性的中枢神经系统。这里我们 提出一个合作的跨学科研究项目，涉及具有互补经验的研究人员 在神经学、神经病理学、病毒学、计算建模和HIV-1患者的临床护理方面取得进展 目前的理解中枢神经系统作为一个解剖网站的长期持久的复制能力 HIV-1在具体目标1中，我们将利用来自以下患者的配对CSF和血浆样本的独特收集： 随访的未经治疗的HIV-1患者，以评估系统发育相关性和相关病毒 来自CNS的病毒序列与替代解剖学隔室之间的群体基因组学;这些 这些研究将有助于追踪ART前长期病毒库的播种和建立。 在具体目标2中，我们将使用来自ART治疗的HIV-1患者的尸检材料，这些患者在死亡时具有抑制的病毒血症 分析分离的前病毒的频率、克隆性、染色体定位和复制能力， 分选的CNS细胞，特别是来自骨髓实质小胶质细胞、来自骨髓血管周围巨噬细胞和 星形胶质细胞总之，这些研究将使我们能够深入地描述HIV-1储存库细胞的动力学特征。 CNS，并可能为未来旨在根除和治愈HIV-1的临床策略提供信息。

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.