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

 描述（由申请人提供）：虽然在使用CCR 5D32纯合细胞进行干细胞移植后，仅在单个患者中报告了HIV-1感染的绝育治愈，但在所有感染者中，HIV-1的自发功能性治愈发生在0.3-0.5%中。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，在没有治疗的情况下，尽管从他们的血清中重复分离的复制能力的病毒。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，并且在这些患者中活跃的有效免疫防御机制的鉴定有望在更广泛的HIV-1患者人群中诱导HIV-1感染的功能性治愈。以前，这种机制的分析主要集中在孤立地研究免疫系统的各个组成部分，然而，现在越来越清楚的是，这些患者的有效免疫防御计划可能涉及先天性和适应性免疫反应的复杂网络，并且需要综合的迭代分析步骤来机械地理解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使用传统的还原主义方法来检测，这些方法偏向于特定的预定义分子或以孤立的方式研究免疫防御的一个特定方面。在这里，我们将采用多步骤的研究策略，以确定全面的，多系统的免疫防御计划，在EC和探索其潜在的功能机制。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和miRNA表达分析，在分类的白细胞亚群中结合多维免疫学检测，以确定有效的先天性和适应性HIV-1免疫应答的分子特征。使用生物计算算法，我们将能够检测免疫防御机制的各个方面之间的连接，并确定连接基因表达，免疫反应和EC表型的临床发展的程序。在具体目标2中，我们将通过测试其在替代自然史HIV-1患者队列中的预测能力来验证这些识别的免疫控制模式;这些研究将允许识别一组经验证的免疫防御参数，这些参数可以显着影响HIV- 1疾病的结局，并可能代表干预方法的可能目标。通过调查，验证和机制探索EC中HIV-1免疫反应与遗传变异和mRNA/miRNA表达谱的关系，拟议的研究将对HIV-1免疫控制的有效机制产生前所未有的见解，并可能导致新的临床策略，在更广泛的患者人群中诱导HIV-1的功能性治愈。

 DESCRIPTION (provided by applicant): While a sterilizing cure of HIV-1 infection has only been reported in a single patient after a stem cell transplant with CCR5D32 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 th 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, yet, 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 and miRNA expression analysis in sorted leukocellular subsets in combination with multidimensional immunologic assays to identify molecular signatures that define effective innate and adaptive HIV-1 immune responses in EC. Using biocomputational algorithms, we will be able to detect connectivity between various aspects of immune defense mechanisms, and identify programs that link gene expression, immune responses and clinical development of EC phenotype. In Specific Aim 2, we will validate these identified patterns of immune control by testing their predictive power in alternative natural-history HIV-1 patient cohorts; these studies will allow to identify a set of validated immune defense parameters that can significantly influence HIV- 1 disease outcome, and may represent possible targets for interventional approaches. By investigating, validating and mechanistically exploring HIV-1 immune responses in EC in relationship to genetic variation and mRNA/miRNA expression profiles, 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.