A systems biology approach to fingerprint HIV immune defense in Elite Controllers

摘要 虽然在干细胞移植后，只有一名患者报告了HIV-1感染的绝育治疗 使用CCR 5 - 32纯合细胞，HIV-1的自发功能性治愈发生在所有感染者的0.3-0.5%中， 人士这些人，被称为精英控制者（EC），保持不可检测的HIV-1复制水平， 缺乏治疗，尽管从他们的血清中反复分离出有复制能力的病毒。在这 通过这种方式，这些人提供了活生生的证据，证明免疫介导的HIV-1感染控制是可能的， 在这些患者中有效的免疫防御机制的鉴定有望 在更广泛的HIV-1患者群体中诱导HIV-1感染的功能性治愈。此前，分析 这种机制主要集中在研究孤立的免疫系统中的单个成分， 然而，现在越来越清楚的是，在这些患者中有效的免疫防御计划是 可能涉及先天性和适应性免疫反应的复杂网络， 分析步骤将需要机械地理解EC中免疫防御的协同网络。 然而，这种免疫控制的整合程序很难用传统的还原论来检测 偏向于特定的预定义分子或研究特定方面的方法 免疫防御系统。在这里，我们将采用多步研究策略来确定 全面的，多系统的免疫防御计划，在EC，并探讨其潜在的功能 机制等在具体目标1中，我们将使用新的高通量技术，如全基因组SNP， 分析和多重mRNA、miRNA和蛋白质表达分析， 鉴定与良种独特相关的特定基因组、转录和蛋白质组学特征 控制者表型这些试验将与多维免疫学试验联合进行。 鉴定选择性观察到的先天性和适应性免疫应答的功能特征的测定 精英控制器（具体目标2）。随后，一些不同的生物计算算法将被 用于检测免疫防御机制各个方面之间的连接，并识别整体， 将基因/蛋白质表达、免疫反应和临床 EC表型的发展;然后将使用尖端的单细胞 分析方法，以确定和表征分子电路最适合和有前途的 治疗操作（具体目标3）。通过全面探讨HIV-1免疫应答在EC中的作用， 与遗传变异和mRNA/miRNA/蛋白质表达谱的关系，并使用这些数据来开发 HIV-1免疫防御的综合模型，拟议的研究将产生前所未有的见解， HIV-1免疫控制的有效机制，并可能导致新的临床策略，以诱导功能性免疫抑制剂。 在更广泛的患者人群中治愈HIV-1。

Abstract While a sterilizing cure of HIV-1 infection has only been reported in a single patient after a stem cell transplant with CCR532 homozygous cells, a spontaneous functional cure of HIV-1 occurs in 0.3-0.5% of all infected persons. These individuals, termed elite controllers (EC), maintain undetectable levels of HIV-1 replication in the absence of treatment, despite the repeated isolation of replication-competent virus from their serum. In this way, these individuals provide living evidence that immune-mediated control of HIV-1 infection is possible, and the identification of effective immune defense mechanisms that are active in these patients holds promise for inducing a functional cure of HIV-1 infection in a broader HIV-1 patient population. Previously, the analysis of such mechanisms has mostly focused on studying individual components of the immune system in an isolated fashion, however, it is now increasingly clear that effective immune defense programs in these patients are likely to involve complex networks of innate and adaptive immune responses and that integrative, iterative analysis steps will be required to mechanistically understand synergistic networks of immune defense in EC. Yet, such integrated programs of immune control can hardly be detected using traditional reductionist approaches that are biased towards specific pre-defined molecules or investigate one specific aspect of immune defense in an isolated fashion. Here, we will employ a multi-step research strategy to identify comprehensive, multi-system programs of immune defense in EC and explore their underlying functional mechanisms. In specific aim 1, we will use novel, high throughput technologies such as genome-wide SNP analysis and multiplexed mRNA, miRNA and protein expression analysis in sorted leukocellular subsets to identify specific genomic, transcriptional and proteomic characteristics uniquely associated with an elite controller phenotype. These assays will be performed in combination with multidimensional immunologic assays to identify functional signatures of innate and adaptive immune responses that are selectively observed in elite controllers (specific aim 2). Subsequently, a number of different biocomputational algorithms will be used to detect connectivity between various aspects of immune defense mechanisms, and identify holistic, integrative and unifying programs that link gene/protein expression, immune responses and clinical development of EC phenotype; these pathways will then be studied in detail using cutting-edge single-cell analysis approaches to identify and characterize the molecular circuits most suitable and promising for therapeutic manipulation (specific aim 3). By comprehensively exploring HIV-1 immune responses in EC in relationship to genetic variation and mRNA/miRNA/protein expression profiles and using this data to develop integrative models of HIV-1 immune defense, the proposed studies will generate unprecedented insights into effective mechanisms of HIV-1 immune control, and may lead to novel clinical strategies to induce a functional cure of HIV-1 in a broader patient population.