Defining signatures for immune responsiveness by functional systems immunology

描述(由申请人提供)：免疫状态的遗传变异性和个体差异决定了对疫苗接种、感染的反应，并有助于疾病的严重性。人类基因组测序和单倍型图谱的生成现在使人们能够从机制上理解遗传变异如何影响人类免疫反应。然而，多种非遗传因素也相互作用，以维持健康的免疫系统，需要进行复杂的分析，以形成对其对扰动的反应的预测。在这里，我们将使用系统方法和新颖的、高通量和高保真的技术，如多路基因表达、自动化多维流式细胞术和纳米细胞中集成的单细胞分析，以定量评估白细胞功能，最终确定定义个体免疫反应的分子特征。我们将在三个相关研究中解决免疫图谱问题。在研究项目1中，我们将开发流感疫苗反应性的免疫学特征，并确定年龄和功能状态对这些特征的影响。我们将识别能够区分疫苗免疫反应强弱和预测有效反应的基因特征和生物途径。在研究项目2中，我们将调查西尼罗河病毒和丙型肝炎病毒对黄病毒感染的耐药性；通过对分层队列患者反应的分析，我们将建立基因表达、免疫细胞反应和临床结果之间的相关性。在研究项目3中，我们将生成检测连通性并预测免疫系统动态功能反应的数学模型。这一方法将使用多变量统计方法将收集的关于群体和个人的数据联系起来，以整合全队列数据，包括全基因组关联研究和新颖的单细胞分析，以评估与遗传变异相关的免疫反应。我们的功能系统免疫学方法将允许我们定义病毒感染和疫苗接种后的基线人类免疫特征以及与该基线的偏差，目标是确定未来干预的目标，并建立一套预测疫苗接种反应的生物标记物。 项目1：确定流感疫苗接种效率的免疫反应 项目负责人：Shaw，A 项目1描述(申请人提供)：我们物种的遗传多样性决定了一些人会对疫苗产生强烈的体液和细胞免疫反应，而另一些人则不会。随着年龄的增长，保护性免疫的这些差异变得更加严重，反映在老年人因感染而死亡和发病的风险增加。例如，季节性流感的影响在老年年龄组中尤其严重，每年因流感死亡的2万至4万人中有90%发生在65岁以上的个人中。然而，三价灭活流感疫苗的效力低至30%，而面临残疾恶化、住院、跌倒和死亡风险的老年人群中的脆弱群体代表着特别脆弱的人群。该项目建立在我们招募和评估年轻人和老年人流感疫苗反应的经验基础上，以及我们接触到独特的队列--例如虚弱的老年人(包括参与NIH资助的肺炎预防试验的860名养老院老年人的招募队列)和300名30岁以下已接受全基因组基因分型的个人。我们将利用多维流式细胞术和定量基因表达核心，以及项目3的分析方法来开发对流感疫苗成功的先天和适应性免疫反应的细胞和基因表达特征，并将阐明衰老和功能受损状态(如虚弱的老年综合征)对年轻、非虚弱的老年人和虚弱的老年人队列中这些特征的影响。我们获得了300名接受流感疫苗的基因分型个体的遗传信息，这也将有助于将细胞和基因表达数据与疫苗反应的遗传相关性整合在一起。为了更好地理解我们的免疫系统的功能，有必要确定人类的强弱反应背后的基因及其等位基因变异，以及它们的表达模式是如何受到年龄或脆弱的影响的。此外，了解免疫反应的遗传结构可能会确定免疫途径，这些途径可能成为治疗、药物或其他生物治疗的目标，以根据需要增强或抑制免疫反应。 相关性(见说明)：这项提议的目标是确定人类免疫系统中基因表达或细胞功能的模式，这些模式是与预防感染相关的流感疫苗接种反应的“标志”。我们还将评估这些签名在年长或虚弱的个人中是如何改变的，他们通常对疫苗接种不会产生保护性反应，并面临更高的严重流感感染风险。

DESCRIPTION (provided by applicant): The genetic variability and Individual variations in immune status dictate responses to vaccinations, infections, and contribute to disease severity. The sequencing of the human genome and generation of the Haplotype Map now enables a mechanistic understanding of how genetic variation influences human immune responses. Yet manifold non-genetic factors also interact to maintain the healthy immune system, and complex analysis will be required to form predictions for its response to perturbations. Here, we will employ systems approaches and novel, high throughput and high-fidelity technologies such as multiplexed gene expression, automated multidimensional flow cytometry, and integrated single-cell assays in nanowells to quantitatively assess leukocyte function to ultimately identify the molecular signatures defining individual immune responses. We will address immune profiles in three related studies. In Research Project 1, we will develop immunologic signatures of influenza vaccine responsiveness and determine the effect of aging and functional status on these signatures. We will identify gene signatures and biological pathways that can distinguish between strong and weak immune responses to vaccination and that predict effective responses. In Research Project 2, we will investigate resistance to flaviviral infections using West Nile virus, and hepatitis C virus; through analysis of responses in patients from stratified cohorts, we will establish correlations between gene expression, immune cell responses and clinical outcome. In Research Project 3, we will generate mathematical models that detect connectivity and predict dynamic functional responses of the immune system. This approach will link data collected on both populations and individuals using multivariate statistical approaches to integrate cohort-wide data including genome wide association studies and novel single-cell analyses to assess immune responsiveness in relationship to genetic variation. Our functional systems immunology approach will allow us to define baseline human immune signatures following viral infection and vaccination along with deviations from this baseline, with the goal of identifying future targets for intervention and establishing sets of biomarkers that predict responses to vaccination PROJECT 1: Immune Responses Defining Efficiency of Influenza Vaccination Project Leader: Shaw, A PROJECT 1 DESCRIPTION (provided by applicant): The genetic variability of our species dictates that some individuals will develop strong humoral and cellular immune responses to vaccines whereas others do not. With aging, these differences in protective immunity become even more severe, reflected in the increased risk for death and morbidity from infections in older individuals. For example, the impact of seasonal influenza is particularly acute in the geriatric age group, with 90% of the 20 to 40 thousand annual deaths attributed to influenza occurring in individuals over the age of 65. However, the efficacy of the trivalent inactivated influenza vaccine is as low as 30%, and the frail subset of elderly individuals who are at risk for worsened disability, hospitalization, falls and death, represent a particularly vulnerable population. This project builds on our experience recruiting and evaluating influenza vaccine response in young and older individuals, and our access to unique cohorts-such as frail elderly individuals (including a recruited cohort of 860 nursing home elders participating in an NIH-funded trial of pneumonia prevention) and a group of 300 individuals under the age of 30 already subjected to genome wide genotyping. We will utilize the Multidimensional Flow Cytometry and Quantitative Gene Expression Cores, and the analytic methods of Project 3 to develop cellular and gene expression signatures of a successful innate and adaptive immune response to influenza vaccination, and will elucidate the impact of aging and impaired functional status (such as the geriatric syndrome of frailty) on these signatures in cohorts of young, non-frail older, and frail older individuals. Our access to genetic information on 300 genotyped individuals receiving influenza vaccine will also facilitate the integration of cellular and gene expression data with genetic correlates of vaccine response. Identifying the genes and their allelic variations in humans that underlie robust or weak responses, and how their expression patterns are affected by age or frailty is a necessity for a greater understanding of the function of our immune system. Moreover, understanding the genetic architecture of immune responses is likely to identify immune pathways that could be targets of therapies, drugs or other biological treatments to enhance or suppress immune responses as needed. RELEVANCE (See instructions): The goal of this proposal is to identify patterns of gene expression or cell function in the human immune system that are "signatures" of a response to influenza vaccination that is associated with protection from infection. We will also evaluate how these signatures are altered in older or frail individuals, who usually do not generate protective responses to vaccination and are at increased risk for severe influenza infection.