High Precision System Analysis of Infant Immune Responses

婴儿免疫反应的高精度系统分析

• 批准号: 10267402
• 负责人: Octavio Ramilo
• 金额: $ 125.84万
• 依托单位: RESEARCH INST NATIONWIDE CHILDREN'S HOSP
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-18 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10267402
• 关键词: ATAC-seq; Adult; Affect; Age-Months; Antibody Response; Antigens; Bacterial Infections; Biological Assay; Blood; Blood Volume; Blood specimen; Cause of Death; Cells; Characteristics; Child; Chromatin; Clinical; Code; Communicable Diseases; Competence; Complex; Custom; Cytometry; Data; Data Set; Development; Disease; Dose; Flow Cytometry; Foundations; Future; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Genes; Genetic Transcription; Genomics; Goals; Human; Hybrids; Immune; Immune response; Immune system; Immunity; Immunization Programs; Immunogenomics; Immunophenotyping; Infant; Infant Health; Infection; Intervention; Knowledge; Life; Maps; Molecular; Molecular Profiling; Morbidity - disease rate; Pathway interactions; Peripheral Blood Mononuclear Cell; Phenotype; Population; Protein Isoforms; Regulation; Resolution; Sample Size; Sampling; Shapes; Systems Analysis; Systems Biology; Technology; Time; Transcript; Untranslated RNA; Vaccination; Vaccines; Work; age related; analysis pipeline; analytical tool; base; bioinformatics tool; cell type; cohort; design; epigenome; epigenomics; experience; flexibility; genomic signature; high risk; immune function; imprint; innovation; innovative technologies; insight; longitudinal analysis; mortality; neutralizing antibody; response; single molecule real time sequencing; tool; transcriptome; transcriptome sequencing; transcriptomics

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.

项目摘要 这个项目旨在克服我们对早期婴儿免疫力理解的局限性 通过纵向基因组和细胞研究免疫发展和主要反应， 两个月的常规疫苗。婴儿和幼儿更容易受到侵袭性感染， 由于保护性免疫反应能力总体下降，包括疫苗， 需要在几个月内施用多剂量以获得足够的长期保护。而 免疫接种计划大大降低了全球由感染引起的发病率和死亡率， 传染病仍然是婴儿和幼儿死亡的最常见原因。的 造成这种脆弱性的细胞、分子和基因机制基本上是未知的。史以来 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缺陷病毒的转录组学、表观基因组学和功能特征， 细胞群然而，这些研究受到难以获得来自临床样本的限制。 婴儿，许多基因组技术用于小体积样品的不相容性，以及缺乏 生物信息学工具，用于整合和解释互补但复杂的数据集。这项建议会 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 在开发用于人血源性免疫细胞（PBMC）的免疫基因组学检测方面的专业知识。 具体而言，我们建议对i）2个月、6个月和12个月婴儿的PBMC进行纵向分析，以确定 免疫发育的基线细胞、表型和基因组特征（Aim 1），和ii）在关键时间 在两个月的常规疫苗接种过程中， 与对疫苗的初次免疫应答相关的特征（Aim 2）。我们将采用创新的 我们开发的免疫基因组分析和分析管道（iPAP）允许我们提取最大的 转录组学（RNA-seq）、表观基因组学（ATAC-seq）、异甲酸（SMRT-seq）、细胞计数（50参数流式细胞术 细胞术）和免疫表型（CyTOF）信息，并整合 这些独特的数据集，对相关的细胞和基因组特征有着无与伦比的深入了解， 免疫发育和疫苗反应性。我们的方法是公正的，多方面的，高度 技术驱动，结合了许多最前沿的基因组和定量细胞技术 我们在将这些技术应用于人类婴儿免疫细胞方面拥有丰富的经验。为配合 为了实现RFA的目标，该项目将产生一个来自婴儿的综合数据集， 确定与免疫发育和原发性免疫缺陷相关的基本机制和途径 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 为婴儿诱导更有效的保护性免疫反应。

项目成果

Differences in SARS-CoV-2 Clinical Manifestations and Disease Severity in Children and Adolescents by Infecting Variant.

• DOI: 10.3201/eid2811.220577
• 发表时间: 2022-11
• 期刊: Emerging infectious diseases
• 影响因子: 11.8

Host transcriptional signatures as predictive markers of infection in children.

宿主转录特征作为儿童感染的预测标记。

• DOI: 10.1097/qco.0000000000000750
• 发表时间: 2021-10-01
• 期刊: Current opinion in infectious diseases
• 影响因子: 3.9
• 作者: Mejias A;Cohen S;Glowinski R;Ramilo O
• 通讯作者: Ramilo O

Characteristics of CD4+ T cells which transfer murine AIDS (MAIDS).

传播小鼠艾滋病 (MAIDS) 的 CD4 T 细胞的特征。

• DOI: 10.1006/cimm.1994.1191
• 发表时间: 1994
• 期刊: Cellular immunology
• 影响因子: 4.3
• 作者: Donaldson,LA;Cheng,R;Savage,SM;Sopori,ML
• 通讯作者: Sopori,ML

SARS-CoV-2 spreads through cell-to-cell transmission.

• DOI: 10.1073/pnas.2111400119
• 发表时间: 2022-01-04
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1
• 作者: Zeng C;Evans JP;King T;Zheng YM;Oltz EM;Whelan SPJ;Saif LJ;Peeples ME;Liu SL
• 通讯作者: Liu SL

Young infants display heterogeneous serological responses and extensive but reversible transcriptional changes following initial immunizations.

年幼的婴儿在初次免疫后表现出异质的血清学反应和广泛但可逆的转录变化。

• DOI: 10.1038/s41467-023-43758-2
• 发表时间: 2023-12-02
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Nouri, Nima;Cao, Raquel Giacomelli;Bunsow, Eleonora;Nehar-Belaid, Djamel;Marches, Radu;Xu, Zhaohui;Smith, Bennett;Heinonen, Santtu;Mertz, Sara;Leber, Amy;Smits, Gaby;van der Klis, Fiona;Mejias, Asuncion;Banchereau, Jacques;Pascual, Virginia;Ramilo, Octavio
• 通讯作者: Ramilo, Octavio