Bioinformatic Mapping of HIV-1 Nef Manipulation of T-Cell Activation and Function

描述(申请人提供)：HIV疾病的特征是高水平的CD8+T细胞激活和T细胞功能障碍。尽管是HIV-1感染的显著特征，但人类CD8+T细胞活化变化的基础尚不清楚。HIV-1流行毒株的变异可能是这种变异的原因。我们打算在HIV-1Nef蛋白中定位T细胞激活的病毒遗传决定因素。HIV-1Nef蛋白多次被认为与人类免疫系统的操纵有关。HIV-1Nef具有广泛的功能，下调关键表面受体的表达，如CD4、CD28和MHC，促进病毒进入和释放，直接与信号蛋白相互作用，如T细胞受体近端蛋白，Lck，并诱导IL-2表达。这些站点c 将这些功能传递给Nef位于蛋白质的不同区域--这些区域在不同的HIV-1毒株中顺序不同。NEF在感染早期表达，是CTL免疫逃逸的靶点。感染的CD4+T细胞内HIV-1 Nef活性影响细胞对刺激的反应、细胞因子的分泌模式以及与CD8+T细胞的相互作用。通过这种方式，Nef可能影响CD8+T细胞的激活水平和T细胞的成熟。虽然Nef在体外已经得到了广泛的研究，但在体内Nef序列变异的影响还没有得到很好的研究。我们建议利用先进的生物信息学作图工具，将HIV-1病毒nef序列与T细胞激活水平、T细胞表型和T细胞信号变化联系起来。我们将与加州大学旧金山分校/CFAR核心免疫学实验室和加州大学旧金山分校临床病毒学实验室合作，在220名最近感染HIV-1的成年人中进行这些研究，这些成年人的病程特征很好。我们将使用树形结构的生物统计学方法及其扩展，这些方法非常适合处理高维生物数据类型，如遗传序列和流式细胞术。这一应用的优势包括：可以从特征明确的HIV-1感染成人队列中获得样本；使用先进的生物信息学绘图工具；功能和信号的高维流式细胞术测量；一个高素质的跨学科研究团队；以及研究遗传多样性实体HIV-1的纵向方法。这项工作将促进治疗方法的开发，以提高T细胞反应的有效性，并设计有效的艾滋病毒疫苗。HIV疾病的特征是高水平的CD8+T细胞活化和T细胞功能受损。尽管是HIV-1感染的显著特征，但人类CD8+T细胞活化变化的基础尚不清楚。HIV-1流行毒株的变异可能是这种变异的原因。我们打算在HIV-1Nef蛋白中定位T细胞激活的病毒遗传决定因素。

DESCRIPTION (provided by applicant): HIV disease is characterized by high level CD8+ T cell activation and impairment in T cell function. Despite being the distinguishing characteristic of HIV-1 infection, the basis for the variation in CD8+ T cell activation in humans is not well understood. Variation in circulating strains of HIV-1 may account for this variation. We intend to map viral genetic determinants of T cell activation within the HIV-1 Nef protein. The HIV-1 Nef protein has been repeatedly implicated in manipulation of the human immune system. Adopting a very wide array of functions, HIV-1 Nef down modulates expression of key surface receptors, such as CD4, CD28, and MHC, facilitates viral entry and release, directly interacts with signaling proteins, such as the T cell receptor proximal kinase, Lck, and induce IL-2 expression. The sites c onferring these functions to Nef fall in distinct regions of the protein - regions which vary in sequence across HIV-1 strains. Nef is expressed early in infection, and is a target for CTL immune escape. HIV-1 Nef activity within infected CD4+ T cells influences cellular response to stimuli, cytokine secretion patterns, and interaction with CD8+ T cells. In this way, Nef may influence CD8+ T cell activation levels and T cell maturation. While Nef has been studied extensively in vitro, the impact of Nef sequence variation in vivo has not been well studied. We propose to relate HIV-1 viral nef sequence to T cell activation levels, T cell phenotype, and T cell signaling alterations by use of advanced bioinformatic mapping tools. We will perform these studies in a cohort of 220 recently HIV-1 infected adults with well-characterized disease course and in collaboration with the UCSF/CFAR Core Immunology Laboratory and the UCSF Laboratory of Clinical Virology. We will use tree- structured biostatistical methods and their extensions which are well suited to handling of high-dimensional biological data types, such as genetic sequence and flow cytometry. The strengths of this application include the availability of specimens from a well-characterized cohort of HIV-1 infected adults; the use of advanced bioinformatic mapping tools; high-dimensional flow cytometric measures of function and signaling; a highly qualified inter-disciplinary research team; and a longitudinal approach to study of a genetically diverse entity, HIV-1. This work will facilitate development of therapies to improve the effectiveness of T cell responses and design of an effective HIV vaccine. HIV disease is characterized by high level CD8+ T cell activation and impairment in T cell function. Despite being the distinguishing characteristic of HIV-1 infection, the basis for the variation in CD8+ T cell activation in humans is not well understood. Variation in circulating strains of HIV-1 may account for this variation. We intend to map viral genetic determinants of T cell activation within the HIV-1 Nef protein.