The Role of HIV-1 Evolution in Neuroadaptation

HIV-1 进化在神经适应中的作用

基本信息

批准号：
8640972
负责人：
Teresa Evering
金额：
$ 19.01万
依托单位：
AARON DIAMOND AIDS RESEARCH CENTER
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-07-01 至 2016-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8640972
关键词：
AIDS Dementia Complex AIDS/HIV problem Adaptive Behaviors Anatomy Antiretroviral drug resistance Appearance Autologous Biological Assay Blood Blood - brain barrier anatomy Brain CCR5 gene Central Nervous System Infections Cerebrospinal Fluid Clinical Cloning Collaborations Cytotoxic T-Lymphocytes Dementia Development Disease Drug resistance Encephalopathies Ensure Evolution Exhibits Generations Genes Genetic Determinism Genetic Recombination Genetic Variation Genome Goals HIV HIV-1 Highly Active Antiretroviral Therapy Immune Immune Targeting Immunity Impaired cognition Impairment In Vitro Incidence Individual Infection Integrase Knowledge Length Letters Literature Measures Methods Minor Morbidity - disease rate Mutation Neuraxis Neurologic Neurotropism Nucleotides Pathogenesis Pathway interactions Patients Pattern Penetration Peptide Hydrolases Pharmaceutical Preparations Phylogenetic Analysis Physiological Plasma Play Polymerase Population Prevalence RNA-Directed DNA Polymerase Reporting Research Research Personnel Risk Role Sampling Severities Site Techniques Vaccines Variant Viral Virus antiretroviral therapy cohort experience improved in vivo innovation mortality mutant neuroadaptation neuropathology neurovirulence novel pol genes pressure public health relevance receptor research study resistance mutation resistant strain sensory neuropathy skills virus tropism

项目摘要

DESCRIPTION (provided by applicant): HIV-1 exhibits numerous strategies to evade host immunity. These strategies include persistence in sanctuary sites, defined as anatomical or privileged cellular sites in which viral replication may continue despite highly active antiretroviral therapy (HAART). The central nervous system (CNS) is an important sanctuary site for HIV-1. Penetration of the CNS by HIV-1 occurs early in infection, and can result in a wide range of pathological and clinical manifestations - all of which contribute significantly to morbidity and mortality. It is therefore important to develop an improved understanding of the adaptive behavior of HIV-1 in the CNS. The overriding goal of the proposed research is to use HIV-1 variants sequenced from cerebrospinal fluid (CSF), to elucidate HIV-1 CNS evolutionary pathways and explore genetic determinants of neuroadaptation through an in-depth, integrated, phylogenetic and functional approach. In order to perform the proposed research, we will use patient samples from the well-characterized CNS HIV Antiretroviral Therapy Effects Research (CHARTER) study. Using standard analysis of clonal sequences and heteroduplex tracking assays (HTA), phylogenetic compartmentalization of contemporaneous intra-patient CNS- and blood-derived viruses has been observed. For this research, we will utilize the single genome amplification (SGA) technique to generate HIV-1 variant sequences. When compared to more conventional sequencing methods, SGA has been shown to decrease taq- induced recombination, template resampling, nucleotide misincorporation and cloning bias and produces a more accurate representation of in-vivo HIV-1 quasispecies. We hypothesize that CNS-specific patterns of evolution observed through longitudinal characterization of HIV-1 envelope (env) and polymerase (pol) reflect attempts by the virus to adapt and persist within the CNS. Furthermore, the use of SGA to generate these variants will provide a more accurate representation of viral quasispecies than currently reported in the literature. Phylogenetic analysis and in-vitro characterization of these variants is expected to reveal novel patterns of CNS-specific evolution and functional consequences of the observed genetic changes. The specific aims of this proposal are therefore: 1) To determine patterns of CNS compartmentalization of HIV-1 env in a cohort of HAART naive individuals 2) To determine patterns of CNS compartmentalization of antiretroviral drug resistance mutations and effects on the HIV-1 pol and env genes in a cohort of HAART experienced individuals, and 3) To determine the functional consequences of genetic variation in SGA-derived HIV-1 env sequences. Understanding adaptive measures undertaken by HIV-1 to persist in viral reservoirs and sanctuary sites are of paramount importance in defining strategies to improve viral suppression and obtain eradication of HIV-1 in the infected host. To our knowledge, current scientific literature contains no application of the novel SGA method to the characterization of HIV-1 variants in the CNS. Importantly, the successful execution of this proposal will allow me to acquire the technical skill and experience necessary to become an innovative and productive independent investigator in translational HIV-1 pathogenesis research. PUBLIC HEALTH RELEVANCE: Infection of the central nervous system (CNS) by the human immunodeficiency virus-1 (HIV-1) can result in a wide range of pathological and clinical manifestations. The widespread use of highly active antiretroviral therapy (HAART) has led to a clear reduction in the incidence of HIV-associated dementia (HAD), one of the most severe manifestations of HIV-1 CNS infection. Despite this decrease, the prevalence of minor HIV-1 associated cognitive impairment appears to be on the rise. Although more subtle, these impairments can be disabling and have been demonstrated to be independently associated with an increased risk for mortality in those with HIV-1. An improved understanding of HIV-1 neuroadaptation will be important for promoting the development of targeted therapies against HIV-1 in this unique sanctuary site.

描述（由申请人提供）：HIV-1表现出许多逃避宿主免疫力的策略。这些策略包括在庇护所场所的持久性，该策略定义为解剖或特权的细胞部位，尽管高度活跃的抗逆转录病毒疗法（HAART），病毒复制仍可能继续进行。中枢神经系统（CNS）是HIV-1的重要保护区。 HIV -1的CNS渗透发生在感染的早期，并可能导致广泛的病理和临床表现 - 所有这些表现都对发病率和死亡率产生了重要贡献。因此，重要的是要改善对CNS中HIV-1的适应性行为的理解。拟议的研究的压倒性目标是使用从脑脊液（CSF）测序的HIV-1变体，以阐明HIV-1 CNS进化途径，并通过深入的，整合的，系统发育和功能方法来探索神经适应的遗传决定因素。为了进行拟议的研究，我们将使用特征良好的CNS HIV抗逆转录病毒疗法研究（Charter）研究中的患者样本。使用克隆序列的标准分析和异质动力跟踪测定法（HTA），已经观察到了患者内CNS和血液衍生的病毒的系统发育隔室化。对于这项研究，我们将利用单个基因组扩增（SGA）技术来生成HIV-1变体序列。与更常规的测序方法相比，SGA已被证明可以减少TAQ诱导的重组，模板重采样，核苷酸失位和克隆偏置，并产生更准确的Vivo HIV-1 Quasisspecies。我们假设CNS特异性的进化模式通过HIV-1包膜（ENV）和聚合酶（POL）（POL）（POL）观察到的进化模式反映了病毒在CNS内适应和持续存在的尝试。此外，使用SGA生成这些变体将比文献中当前报道的更准确地表示病毒准菜。这些变体的系统发育分析和体外表征有望揭示CNS特异性进化的新模式和观察到的遗传变化的功能后果。因此，该提案的具体目的是：1）确定HIV-1 ENV在HAART幼稚个体中的CNS隔室化模式2）确定CNS抗逆转录病毒耐药性突变的CNS隔室化模式，并对HIV-1 POL和ENV基因在HAART的队列中经验丰富的个体，以及3）确定SGA衍生的HIV-1 Env序列中遗传变异的功能后果。了解HIV-1在病毒储层和避难所中执行的自适应措施对于确定改善病毒抑制并在感染宿主中消除HIV-1的策略至关重要。据我们所知，当前的科学文献不包含新型SGA方法在中枢神经系统中HIV-1变体的表征中的应用。重要的是，该提案的成功执行将使我能够获得成为转化HIV-1发病机理研究中创新和生产力的独立研究者所必需的技术技能和经验。公共卫生相关性：人类免疫缺陷病毒1（HIV-1）对中枢神经系统（CNS）感染可能导致广泛的病理和临床表现。高度活跃的抗逆转录病毒疗法（HAART）的广泛使用导致HIV相关痴呆症的发生率明显降低，HIV-1 CNS感染是最严重的表现之一。尽管下降了，但次要HIV-1相关的认知障碍的患病率似乎在上升。尽管更微妙，但这些障碍可能是残疾人的，并且已被证明与HIV-1患者的死亡风险增加有关。对HIV-1神经适应的提高的了解对于促进针对HIV-1的靶向疗法在这个独特的避难所中的开发至关重要。

项目成果

期刊论文数量（5）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Drug Resistance Mutation Frequency of Single-Genome Amplification-Derived HIV-1 Polymerase Genomes in the Cerebrospinal Fluid and Plasma of HIV-1-Infected Individuals under Nonsuppressive Therapy.

非抑制治疗下 HIV-1 感染者脑脊液和血浆中单基因组扩增衍生的 HIV-1 聚合酶基因组的耐药突变频率。

DOI：
10.1128/jvi.01824-19
发表时间：
2020
期刊：
Journal of virology
影响因子：
5.4
作者：
StBernard,Leslie;Abolade,Jeremy;Mohri,Hiroshi;Markowitz,Martin;Evering,TeresaH
通讯作者：
Evering,TeresaH

Single genome analysis reveals genetic characteristics of Neuroadaptation across HIV-1 envelope.