High Precision System Analysis of Infant Immune Responses

项目总结 这个项目试图克服目前我们对婴儿早期免疫的理解上的限制 通过纵向基因组和细胞研究免疫发展和主要反应 常规的两个月疫苗。婴幼儿更容易受到侵袭性感染。 成年人由于保护性免疫反应能力的总体下降，包括对疫苗的免疫，这 需要在几个月内多次服用，以获得足够的长期保护。而当 免疫接种计划极大地降低了由感染引起的全球发病率和死亡率 仍然，传染病是婴幼儿最常见的死亡原因。这个 造成这一漏洞的细胞、分子和基因组机制在很大程度上尚不清楚。永远不会 基因组学和系统生物学中更强大的工具为解决这些知识提供了令人兴奋的机会 通过详细分析婴儿免疫的转录、表观基因组和功能特征发现差距 细胞群。然而，这类研究受到从临床样本获取的困难的限制。 婴儿，许多基因组技术用于小体积样本的不相容，以及缺乏 生物信息学工具，用于整合和解释免费但复杂的数据集。这项提议将 利用我们研究婴儿免疫反应的经验，我们接触婴儿群体的机会，以及我们的 在开发用于人类血源性免疫细胞(PBMCs)的免疫基因组分析方面的专业知识。 具体地说，我们建议对出生2个月、6个月和12个月的婴儿的PBMC进行纵向分析，以建立 免疫发展的基线细胞、表型和基因组特征(目标1)和关键时刻 在两个月的常规疫苗接种过程中进行积分，以确定细胞、表型和基因组 与疫苗的主要免疫反应相关的特征(目标2)。我们将使用一种创新的 我们开发的免疫基因组图谱和分析流水线(IPAP)允许我们最大限度地提取 转录(RNA-seq)、表观基因组(atac-seq)、异构体(Smrt-seq)、细胞学(50参数Flow 细胞学)和免疫表型(CyTOF)信息从单个婴儿血液样本中提取，并整合 这些独特的数据集为深入了解相关的细胞和基因组签名提供了无与伦比的深度 免疫发展和疫苗反应性。我们的方法是不偏不倚的、多方面的和高度 技术驱动，结合了许多最尖端的基因组和基于定量细胞的技术 凭借我们在将这些技术应用于人类婴儿免疫细胞方面的深厚经验。符合 此RFA的目标，该项目将从婴儿中产生一个全面的数据集，可用于 确定与免疫发育和初级免疫相关的基本机制和途径 对疫苗的反应，并将为未来旨在设计新干预措施的研究奠定基础 为婴儿诱导更有效和保护性的免疫反应。

PROJECT SUMMARY This project seeks to surmount current limitations in our understanding of early infant immunity through longitudinal genomic and cellular studies of immune development and primary responses to routine two-month vaccines. Infants and young children are more susceptible to invasive infections than adults owing to overall reduced competency of protective immune responses, including to vaccines, which require administration of multiple doses over several months for adequate long-term protection. While immunization programs have dramatically decreased the global morbidity and mortality caused by infections, it remains that infectious diseases are the most frequent cause of death in infants and young children. The cellular, molecular and genomic mechanisms that contribute to this vulnerability are largely unknown. Ever more powerful tools in genomics and systems biology offer exciting opportunities to resolve these knowledge gaps through detailed analysis of the transcriptomic, epigenomic and functional signatures of infant immune cell populations. However, such studies have been limited by the difficulty in accessing clinical samples from infants, the incompatibility of many genomic technologies for use in small-volume samples, and the lack of bioinformatic tools for integrating and interpreting complimentary yet complex datasets. This proposal will capitalize on our experience studying the infant immune response, our access to infant populations, and our expertise in developing immunogenomic assays for use in human blood-derived immune cells (PBMCs). Specifically, we propose a longitudinal analysis of PBMCs from infants i) at 2, 6 and 12 months, to establish the baseline cellular, phenotypic and genomic signatures of immune development (Aim 1), and ii) at key time points over the course of routine two-month vaccinations, to identify the cellular, phenotypic and genomic signatures associated with primary immune responses to vaccines (Aim 2). We will use an innovative immunogenomic Profiling and Analysis Pipeline (iPAP) we developed that allows us to extract maximal transcriptomic (RNA-seq), epigenomic (ATAC-seq), isoformic (SMRT-seq), cytometric (50-parameter flow cytometry) and immunophenotypic (CyTOF) information from a single infant blood sample, and to integrate these distinct datasets for unparalleled depth of insight into the correlated cellular and genomic signatures of immune development and vaccine responsiveness. Our approach is unbiased, multifaceted and highly technology-driven, combining many of the most cutting-edge genomic and quantitative cell-based technologies with our deep experience in applying these technologies for use in human infant immune cells. In line with the goals of this RFA, this project will yield a comprehensive dataset from infants that can be used to identify fundamental mechanisms and pathways associated with immune development and primary responses to vaccines, and will set the stage for future studies aimed at designing new interventions that induce more potent and protective immune responses for young infants.