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

描述（由申请方提供）：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未得到很好的理解。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-1 Nef蛋白中绘制T细胞活化的病毒遗传决定因素。HIV-1 Nef蛋白已多次涉及操纵人类免疫系统。HIV-1 Nef具有广泛的功能，下调关键表面受体（如CD4、CD28和MHC）的表达，促进病毒进入和释放，直接与信号蛋白（如T细胞受体近端激酶Lck）相互作用，并诱导IL-2表达。网站C 赋予Nef这些功能的基因位于蛋白质的不同区域，这些区域在HIV-1毒株中的序列不同。Nef在感染早期表达，并且是CTL免疫逃逸的靶标。感染的CD4 + T细胞内的HIV-1 Nef活性影响细胞对刺激的反应、细胞因子分泌模式以及与CD8 + T细胞的相互作用。通过这种方式，Nef可以影响CD8 + T细胞活化水平和T细胞成熟。虽然Nef已经在体外进行了广泛的研究，但Nef序列变异在体内的影响还没有得到很好的研究。我们建议通过使用先进的生物信息学作图工具，将HIV-1病毒nef序列与T细胞活化水平、T细胞表型和T细胞信号改变联系起来。我们将与UCSF/CFAR核心免疫学实验室和UCSF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。我们将使用树结构的生物统计方法及其扩展，这些方法非常适合处理高维生物数据类型，如基因序列和流式细胞术。该应用程序的优势包括来自HIV-1感染成年人的良好特征队列的标本的可用性;使用先进的生物信息学映射工具;功能和信号的高维流式细胞术测量;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。这项工作将有助于开发治疗方法，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未得到很好的理解。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-1 Nef蛋白中绘制T细胞活化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.