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

• 批准号: 10417585
• 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
• 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/10417585
• 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; obesity-associated asthma; pathogen; promoter; single cell sequencing; single-cell RNA sequencing; stem cells; tissue repair; tool; transcription factor; 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; obesity-associated asthma; pathogen; promoter; single cell sequencing; single-cell RNA sequencing; stem cells; tissue repair; tool; transcription factor

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.

项目摘要 第1组，第2和3个先天淋巴样细胞（ILC1，ILC2和ILC3）是免疫效应细胞，有助于组织 体内平衡和主持人防御几乎所有类别的病原体，但它们的失调也起着关键作用 在癌症，肥胖，哮喘和结肠炎等流行疾病中。转录因子（TF）网络 最近已经确定了不同ILC组不同组的发展和功能。但是如何 染色质可及性景观和3维（3D）基因组结构决定了发展， ILC的稳态和效应子功能在很大程度上是未知的。因此，该提议的总体目标是 揭示3D基因组和表观遗传结构如何调节每个ILC子集的发展 以及过敏性气道炎症的发展。现在，转录的良好 阻遏物ID2确定ILC谱系的承诺和身份。因此，ID2的表达现在为 被认为是老鼠和人类所有ILC子集的标志。我们的初步数据表明ID2表达 通过特定的远程DNA相互作用环在特定的远端中控制，而不是ILC1（而不是ILC2或ILC3）控制的 顺式调节元件（顺式RE）和ID2启动子。此外，我们表明这些启动子的消融 - 小鼠中的顺式相互作用导致多个组织中的ILC1显着降低，而发育和发育和 ILC2和ILC3的功能没有改变。因此，我们的发现首次表明ID2表达是 由ID2启动子和远端顺式REOP在ILC-SUBSET中的远程DNA相互作用循环调节 具体方式。此外，这表明烧毁这些顺式 - RE是生成遗传工具的有力策略 在原本完整的免疫系统的背景下研究每个ILC子集的作用。然而染色质是如何 可访问性景观和3D基因组架构在ILC2和ILC3中专门确定ID2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型遗传工具，单一的遗传工具 细胞测序技术和HIC以阐明染色质折叠和可及性如何确定 ILC2和ILC3的开发和功能通过ID2表达的调节。在AIM 3中，我们将利用 这些调节机制的特异性研究在过敏性气道炎症过程中研究ILC2的功能 在原本完整的免疫系统的背景下。总的来说，这些研究将回答长期存在的 如何控制ID2表达以驱动ILC命运的问题。而且，它将产生3D的地图集 每个ILC子集的基因组景观， 那 将使我们能够确定未知的非编码监管区域 对于通过识别而言，对于功能和开发ILC1，ILC2和ILC3至关重要。 每个ILC子集中的特定调节机制，我们创建了新型的小鼠遗传工具来研究 在原本完整的免疫系统的背景下，每组ILC的功能可能揭开新颖性 炎症性疾病期间靶向ILC的治疗方法。