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

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.

项目总结 第1、2和3组固有淋巴样细胞(ILC1、ILC2和ILC3)是对组织有贡献的免疫效应细胞 动态平衡和寄主防御几乎所有种类的病原体，但它们的失调也起着关键作用。 在癌症、肥胖症、哮喘和结肠炎等流行疾病中。转录因子(TF)网络 最近确定了控制国际法委员会不同群体的发展和职能。然而，这是如何 染色质可及性景观和三维(3D)基因组结构决定了发育， 内稳态，ILC的效应器功能在很大程度上是未知的。因此，这项提案的首要目标是 揭示3D基因组和表观遗传结构如何调节每个ILC亚集的发育 以及过敏性呼吸道炎症的发展。现在已经很好地确定了转录 抑制子Id2决定了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 在ILC1中，但不是ILC2或ILC3中，由特定末端之间的特定远程DNA相互作用环控制 顺式调控元件(cis-RE)和Id2启动子。此外，我们还表明，这些启动子的消融- 在小鼠体内，顺式-稀土的相互作用导致多种组织中ILC1的显著减少，而发育和 ILC2和ILC3的功能没有改变。因此，我们的发现第一次表明Id2的表达是 受ILC亚群中Id2启动子和远端顺-RE之间的长程DNA相互作用环调控 具体的方式。此外，它还表明，去除这些顺式稀土是产生遗传工具的一种强有力的策略 研究每个ILC亚集在一个原本完整的免疫系统中的作用。然而染色质是如何 可访问性景观和3D基因组结构决定了ID2在ILC2和ILC3中的具体表达 仍然不为人知。因此，在这个项目的目标1和2中，我们将使用我们产生的新的遗传工具，单个 细胞测序技术，以及HIC，以阐明染色质折叠和可及性如何决定 ILC2和ILC3在Id2表达调控中的发育和功能在目标3中，我们将利用 这些调节机制在研究ILC2在过敏性呼吸道炎症中作用的特异性 在其他方面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。此外，它还将生成3D地图集 每个ILC子集的基因组图谱，其中 那 将使我们能够识别未知的非编码调控区域 对于ILC1、ILC2和ILC3的功能和发展至关重要。重要的是，通过识别 在每个ILC亚群中特定的调节机制，我们创造了新的小鼠遗传工具来研究 每一组ILC在原本完整的免疫系统的背景下的功能，这可能揭示出新的 炎症性疾病期间靶向ILC的治疗方法。