3-Dimensional genomic architecture in innate lymphoid cells and allergic inflammation

先天淋巴细胞和过敏性炎症的三维基因组结构

基本信息

批准号：
10650334
负责人：
Jorge Henao-Mejia
金额：
$ 64.53万
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-06-20 至 2027-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10650334
关键词：
3-Dimensional Ablation Address Allergens Allergic Allergic inflammation Architecture Asthma Atlases Binding Bone Marrow CD4 Positive T Lymphocytes Cell Lineage Cell Maintenance Chromatin Colitis DNA Data Data Set Defect Development Disease Distal Effector Cell Enhancers Epigenetic Process Fetal Liver Genetic Genetic Transcription Genome Genomic Segment Genomics Goals Homeostasis Host Defense Human Immune Immune response Immune system Inflammatory Innate Immune System Lung Lymphoid Cell Malignant Neoplasms Metabolic Mouse Strains Mus Names Nucleic Acid Regulatory Sequences Obesity Pathology Play Population Process Regulation Regulatory Element Role Specificity Technology Testing Time Tissues Transcription Repressor Untranslated RNA allergic airway inflammation allergic response chromosome conformation capture histone modification mouse genetics mouse model novel novel therapeutic intervention pathogen promoter single cell sequencing single-cell RNA sequencing stem cells tissue repair tool transcription factor

项目摘要

PROJECT SUMMARY Group 1, 2, and 3 innate lymphoid cells (ILC1, ILC2, and ILC3) are immune effector cells that contribute to tissue homeostasis and host defense against nearly all classes of pathogens, but their dysregulation also play key roles in prevalent diseases such as cancer, obesity, asthma, and colitis. The transcription factor (TF) networks that control the development and functions of the different groups of ILC have recently been identified. Yet how the chromatin accessibility landscape and the 3-dimensional (3D) genome architecture determine the development, homeostasis, and effector functions of ILC is largely unknown. Thus, the overarching goal of this proposal is to uncover how the 3D genomic and epigenetic architecture regulate the development of each ILC subset and to the development of allergic airway inflammation. It is now well-stablished that the transcriptional repressor Id2 determines the commitment and identity of the ILC lineage. As such, Id2 expression is now considered a hallmark of all ILC subsets in mice and humans. Our preliminary data indicates that Id2 expression is controlled in ILC1, but not ILC2 or ILC3, by specific long-range DNA interacting loops between specific distal cis-regulatory elements (cis-RE) and the Id2 promoter. Moreover, we showed that ablation of these promoter- cis-RE interactions in mice leads to a dramatic reduction in ILC1 in multiple tissues, while the development and functions of ILC2 and ILC3 were unaltered. Thus, our findings indicate for the first time that Id2 expression is regulated by long-range DNA interacting loops between the Id2 promoter and distal cis-RE in an ILC-subset specific manner. Moreover, it indicates that ablating these cis-RE is a powerful strategy to generate genetic tools to study the roles of each ILC subset in the context of an otherwise intact immune system. Yet how the chromatin accessibility landscape and the 3D genomic architecture determines Id2 expression specifically in ILC2 and ILC3 remains unknown. Thus, in aims 1 and 2 of this project, we will use novel genetic tools that we generated, single cell sequencing technologies, and HiC to elucidate how chromatin folding and accessibility determine the development and functions of ILC2 and ILC3 through the regulation of Id2 expression. In aim 3, we will exploit the specificity of these regulatory mechanisms to study the functions of ILC2 during allergic airway inflammation in the context of an otherwise intact immune system. Collectively, these studies will answer the long-standing question of how Id2 expression is controlled to drive the ILC fate. Moreover, it will generate an atlas of the 3D genomic landscape of each ILC subset, which that will allow us to identify unknown non-coding regulatory regions are critical for the function and development ILC1, ILC2, and ILC3.Importantly, through the identification of specific regulatory mechanisms in each ILC subset, we have created novel mouse genetic tools to study the functions of each group of ILC in the context of an otherwise intact immune system, which might unveil novel therapeutic approaches to target ILC during inflammatory disorders.

项目概要第 1、2 和 3 组先天淋巴细胞（ILC1、ILC2 和 ILC3）是对组织有贡献的免疫效应细胞体内平衡和宿主对几乎所有类别病原体的防御，但它们的失调也发挥着关键作用癌症、肥胖、哮喘和结肠炎等常见疾病。转录因子 (TF) 网络最近已经确定了 ILC 不同群体的发育和功能控制。然而如何染色质可及性景观和 3 维 (3D) 基因组结构决定了发展， ILC 的稳态和效应器功能在很大程度上是未知的。因此，该提案的总体目标是揭示 3D 基因组和表观遗传结构如何调节每个 ILC 子集的发育以及过敏性气道炎症的发展。现在已经确定转录阻遏蛋白 Id2 决定 ILC 谱系的承诺和身份。因此，Id2 表达式现在是被认为是小鼠和人类所有 ILC 亚群的标志。我们的初步数据表明Id2表达受 ILC1 控制，但不受 ILC2 或 ILC3 控制，通过特定远端之间的特定长程 DNA 相互作用环进行控制。顺式调控元件 (cis-RE) 和 Id2 启动子。此外，我们表明这些启动子的消融- 小鼠中的 cis-RE 相互作用导致多个组织中 ILC1 的急剧减少，而发育和 ILC2和ILC3的功能没有改变。因此，我们的研究结果首次表明 Id2 表达是由 ILC 子集中 Id2 启动子和远端 cis-RE 之间的长程 DNA 相互作用环调节具体方式。此外，它表明消除这些 cis-RE 是生成遗传工具的强大策略研究每个 ILC 子集在完整的免疫系统中的作用。然而染色质如何可及性景观和 3D 基因组结构决定了 ILC2 和 ILC3 中 Id2 的表达仍然未知。因此，在该项目的目标 1 和 2 中，我们将使用我们生成的新颖的遗传工具，单一细胞测序技术和 HiC 来阐明染色质折叠和可及性如何决定通过调节 Id2 表达来调节 ILC2 和 ILC3 的发育和功能。在目标 3 中，我们将利用这些调节机制的特异性来研究ILC2在过敏性气道炎症期间的功能在免疫系统完好无损的情况下。总的来说，这些研究将回答长期存在的问题如何控制 Id2 表达以驱动 ILC 命运的问题。此外，它还会生成 3D 地图集每个 ILC 子集的基因组景观，那将使我们能够识别未知的非编码监管区域对于 ILC1、ILC2 和 ILC3 的功能和发育至关重要。重要的是，通过识别每个 ILC 子集的特定调节机制，我们创建了新型小鼠遗传工具来研究在免疫系统完整的情况下，每组 ILC 的功能可能会揭示新的功能炎症性疾病期间针对 ILC 的治疗方法。