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

项目摘要 第1、2和3组先天性淋巴样细胞（ILC 1、ILC 2和ILC 3）是免疫效应细胞，有助于组织 体内平衡和宿主防御几乎所有种类的病原体，但它们的失调也发挥关键作用 癌症、肥胖症、哮喘和结肠炎等流行病中。转录因子（TF）网络， 控制ILC的不同群体的发展和功能最近已经被确定。然而， 染色质可及性景观和三维（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，本提案的总体目标是 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。现在已经很好地确定， 阻遏物Id 2决定ILC谱系的定型和身份。因此，Id 2表达式现在是 被认为是小鼠和人类中所有ILC亚群的标志。我们的初步数据表明，Id 2表达 在ILC 1中，而不是ILC 2或ILC 3中，由特异性远端DNA之间的特异性长距离DNA相互作用环控制 顺式调控元件（cis-RE）和Id 2启动子。此外，我们发现，这些启动子的切除- 小鼠中的顺式RE相互作用导致多种组织中ILC 1的急剧减少，而发育和 ILC 2和ILC 3的功能没有改变。因此，我们的研究结果首次表明，Id 2的表达， 受ILC亚群中Id 2启动子和远端cis-RE之间的长距离DNA相互作用环调控 具体方式。此外，这表明切除这些顺式RE是产生遗传工具的有力策略 研究每个ILC亚群在完整免疫系统中的作用。然而， 可及性景观和3D基因组结构决定了Id 2在ILC 2和ILC 3中的表达 仍然未知。因此，在本项目的目标1和目标2中，我们将使用我们生成的新颖的遗传工具， 细胞测序技术和HiC，以阐明染色质折叠和可及性如何决定细胞的功能。 ILC 2和ILC 3通过调节Id 2表达而发育和发挥功能。在目标3中，我们将利用 这些调节机制的特异性，以研究ILC 2在过敏性气道炎症中的功能 在免疫系统完整的情况下。总的来说，这些研究将回答长期存在的 Id 2的表达是如何被控制以驱动ILC命运的问题。此外，它还将生成3D地图集 每个ILC子集的基因组景观， 的 将使我们能够识别未知的非编码调控区域 对ILC 1、ILC 2和ILC 3的功能和发育至关重要。 在每个ILC亚群中的特定调控机制，我们已经创造了新的小鼠遗传工具来研究 在其他完整的免疫系统中，每组ILC的功能可能揭示新的 在炎症性疾病期间靶向ILC的治疗方法。

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.