High Specificity HIV-1 Markers Predictive of Neuro-AIDS

描述(申请人提供)：人类免疫缺陷病毒1型(HIV-1)感染免疫系统、大脑和其他末端器官后的发病机制和疾病进展依赖于病毒进入和在这些间隔内的特定细胞群中复制，这些细胞群通过各种直接和/或间接机制导致细胞功能障碍或死亡。这些病毒与宿主的相互作用可以受到多种因素的调节，包括病毒的结合和进入、宿主细胞的增殖和激活、细胞分化、抗逆转录病毒治疗状态、滥用物质以及病毒和细胞蛋白与长末端重复序列(LTR)的相互作用，以调节病毒的表达。HIV-1的复制能力进一步受到病毒准种进化的影响。研究表明，LTR中自然发生的序列变化通过改变与细胞和病毒反式激活因子的功能相互作用，影响病毒启动子驱动病毒表达的能力。最近的研究表明，HIV-1基因组中的基因改变可能与HIV-1疾病的阶段、神经状态和/或器官划分有关。然而，这些研究中的许多涉及对HAART之前时代的少量患者的临床样本的跨人群分析，而不是来自HAART时代具有足够患者数量的纵向研究。拟议的研究将利用不断扩大的DREXELMED HIV-1感染患者队列进行跨人群和纵向研究，以进行测序和结构/功能分析，以检验工作假设，即LTR和病毒包膜内的结合位点签名可以用作分子标记，以识别更容易发展为晚期疾病的HIV-1感染者，这些疾病可能会因特定的共病，如可卡因或大麻类药物滥用而加剧。这项应用的具体目的是继续：(1)构建HIV-1(B亚型)LTR和Env聚合酶链式反应(PCR)产物来自HIV-1感染的外周血液(PB)的外周血单核细胞(PBMC)的序列数据库和克隆库，纵向收集自具有关于社会和临床人口学的全面临床病史的患者(初始和所有回访)，(2)使用生物信息学工具检测HIV-1gp120或HIV-1 gp41内HIV-1 LTR634个核苷酸中的任何一个处的SNP，以鉴定从PBMC[在选定的情况下，纯化的PB亚群、血浆病毒、CNS组织(NNTC)和其他细胞室]中检测到的LTRs和Env单核苷酸多态(SNPs)和共同选择的SNPs(CsSNPs)，(3)构建平行的聚合酶链式反应产物序列数据库，并定义从美国国家神经-艾滋病组织联合会(NNTC)获得的不同程度的HIV-1相关神经疾病的脑组织中的特定LTR和环境SNPs和csSNPs，以及(4)确定含有特定csSNPs的HIV-1 LTR克隆支持转录和病毒复制研究的能力。 公共卫生相关性：该提案代表了一种重要的创新方法，涉及使用特定的LTR和环境特征序列来预测和跟踪艾滋病毒-1疾病的进展，艾滋病毒相关神经认知障碍的发展，研究药物滥用(可卡因和大麻)对这些过程的影响，并可能帮助指导艾滋病毒疾病的治疗管理。这些研究还将确定HIV-1 LTR和Env内部和之间的共同选择的遗传元件，这些元件与特定细胞类型进入和控制病毒基因表达有关，并可能参与病毒的发病和HIV疾病。

DESCRIPTION (provided by applicant): Pathogenesis and disease progression subsequent to human immunodeficiency virus type 1 (HIV-1) infection of the immune system, brain, and other end organs is dependent on viral entry and replication in specific cell populations within these compartments that cause celular dysfunction or death by a variety of direct and/or indirect mechanisms. These virus-host interactions can be regulated by numerous factors, including viral binding and entry, host cell proliferation and activation, cellular differentiation, antiretroviral therapy status, substances of abuse, and the action of viral and cellular proteins that interface with the long terminal repeat (LTR) and to each other to regulate viral expression. The capacity of HIV-1 to replicate is further affected by the evolution of viral quasispecies. Studies have indicated that naturally-occurring sequence variation within the LTR influences the ability of the viral promoter to drive viral expression by altering functional interactions with cellular and viral trans-activators. Recent studies have suggested the possibility that genetic alterations within the HIV-1 genome may correlate with either the stage of HIV-1 disease, neurologic status, and/or organ compartmentalization. However, many of these studies involved cross population analyses of clinical samples from a small number of patients in the pre-HAART era, rather than from longitudinal studies with sufficient patient numbers in the HAART era. The proposed studies will utilize a continually expanding DREXELMED HIV- 1-infected patient cohort for cross-population and longitudinal studies for sequencing and structure/function analyses to examine the working hypothesis that binding site signatures within the LTR and viral envelope can be used as molecular markers to identify HIV-1-infected individuals more prone to developing advanced stage disease with end-organ involvement that may be exacerbated by specific co-morbidities such as cocaine or cannabinoid abuse The specific aims of this application are to continue to: (1) construct a HIV-1 (subtype B) LTR and Env polymerase chain reaction (PCR) product sequence database and clone bank derived from peripheral blood mononuclear cells (PBMCs) from HIV-1-infected peripheral blood (PB) collected longitudinally from patients with comprehensive clinical histories with respect to social and clinical demographics (initial and all return visits), (2) identify LTR and Env single nucleotide polymorphisms (SNPs) and co-selected SNPs (csSNPs) detected in LTRs derived from PBMCs [and, in selected circumstances, purified PB sub-populations, plasma virus, CNS tissues (NNTC) and other cellular compartments] obtained from a large well studied HIV-1- infected cohort using bioinformatic tools to examine SNPs at any of the 634 nucleotides of the HIV-1 LTR, within the HIV-1 gp120, or within the HIV-1 gp41, (3) construct a parallel PCR product sequence database and define specific LTR and Env SNPs and csSNPs from brain tissues with varying degrees of HIV-1-associated neurologic disorders obtained from the National Neuro-AIDS Tissue Consortium (NNTC)], and (4) determine the ability of HIV-1 LTR clones containing specific csSNPs to support transcription and viral replication studies. PUBLIC HEALTH RELEVANCE: The proposal represents a significant and innovative approach involving the use of specific LTR and Env signature sequences to predict and track HIV-1 disease progression, the development of HIV-associated neurocognitive disorders, study the impact of substance abuse (cocaine and cannabinoids) on these processes, and potentially help guide the therapeutic management of HIV disease. The studies will also identify co-selected genetic elements within and between the HIV-1 LTR and Env that are associated with cell type-specific entry and control of viral gene expression and likely involved in viral pathogenesis and HIV disease.