Gene circuits programming IL-17 production in innate lymphocytes

描述与细胞谱系分化相关的基因转录动力学可以在三个连续过程上建模：第一，负责开启与分化状态相关的基因的转录因子（TF）的活性的快速和短暂发作;第二，与直接前体状态或替代细胞命运选择相关的基因的抑制;第三，与分化状态相关的基因的持久诱导。与免疫基因组计划（ImmGen）联合产生的成熟先天γδTCR+胸腺细胞亚群的转录组纲要的初稿与该模型相匹配，并预测具有共享功能但在独特解剖位置起作用的其他先天淋巴细胞（ILC）由具有主题共性的调控网络控制。为了揭示指定关键先天免疫功能的基因调控网络，我们建议测试控制γδT细胞（Tγδ17）产生先天IL-17的预测调控模块。IL-17家族细胞因子已成为导致人类自身免疫性疾病的炎症反应的中心效应物。虽然广泛研究了适应性T细胞产生IL-17的规则，但如何调节来自特化ILC亚群的IL-17产生是未知的。Tγδ17细胞是细菌感染期间IL-17的主要来源，并且其产生IL-17的能力在胸腺中被编程。控制编程的基因调控网络是未知的。一旦发现负责Tγδ17分化的结构蓝图，可以用作理解所有效应ILC发育的指导。先天性T效应细胞谱系分化的全面理解可以通过三种相互关联的方法来实现：第一，鉴定定义分化的Tγ δ 17状态的TF的初始波和其中初始编程明显的祖细胞;第三，从基因调控网络的顶点扰动网络（基因KO小鼠和病原体攻击），然后进行影响分析以确定网络内基因模块的功能互连性。功能 通过对Tγδ17细胞命运调控网络中主要基因节点的分析，发现了5种重要的转录因子：SOX 13、SOX 4、RORγt、TCF 1和LEF 1，其中只有RORγt是已知的。Sox 13或Sox 4缺陷的小鼠Tγδ17分化受损。缺乏TCF 1的小鼠产生具有IL-17高产量的T细胞，而LEF 1表达是双相的，被排除在IL-17先天效应物之外。因此，这五种TF构成了先天性IL-17产生的核心调节因子，并且它们嵌入其他ILC效应器程序中，支持共同的基因网络蓝图产生ILC效应器的预测，并且理解它们相互关联的功能将是炎症性疾病的潜在靶向免疫治疗的核心。

DESCRIPTION (provided by applicant): Gene transcription dynamics associated with cell lineage differentiation can be modeled on three sequential processes: First, a rapid and transient onset of activities of transcription factors (TFs) responsible for turning on genes associated with differentiated states; second, suppression of genes associated with the immediate precursor state or alternate cell fate choice; and third, long lasting induction of gene associated with differentiated states. The first draft of a compendium of transcriptomes of maturing innate γδTCR+ thymocyte subsets produced in conjunction with the Immunological Genome Project (ImmGen) matches the model and predicts that other innate lymphoid cells (ILCs) with shared function, but acting at unique anatomical locations, are controlled by regulatory networks with thematic commonality. To uncover the gene regulatory networks that specify critical innate immune function we propose to test the predicted regulatory modules controlling innate IL-17 production from γδT cells (Tγδ17). IL-17 family of cytokines has emerged as the central effectors of inflammatory responses contributing to autoimmune disorders in humans. While the rules for IL-17 production by adaptive T cells are extensively studied how IL-17 production from specialized ILC subsets is regulated is unknown. Tγδ17 cells are the primary source of IL-17 during bacterial infection and its capacity for IL-17 production is programmed in the thymus. The gene regulatory network controlling the programming was unknown. The architectural blueprint responsible for Tγδ17 differentiation, once discovered, can be used as a guide to understand all effector ILC development. A comprehensive understanding of innate T effector lineage differentiation can be accomplished by three interconnected approaches: First, identification of the initial wave of TFs that define differentiated Tγδ17 state and the progenitors in which the initial programming is evident; second, a systematic mapping of TF regulator occupancy of target Tγδ17 genes; and third, perturbation of the network (gene KO mice and pathogen challenge) from the apex of the gene regulatory network followed by impact analyses to determine functional interconnectivity of gene modules within the network. Functional characterization of the primary gene nodes in the regulatory network specifying Tγδ17 cell fate has so far revealed five essential transcription factors (TFs): SOX13, SOX4, RORγt, TCF1 and LEF1, of which only one, RORγt, was previously identified. Mice deficient in Sox13 or Sox4 have impaired Tγδ17 differentiation. Mice lacking TCF1 generate T cells with hyper-production of IL-17 while LEF1 expression is biphasic, excluded from IL-17 innate effectors. The five TFs therefore constitute the core regulators of innate IL-17 production and they are embedded in other ILC effector programs, supporting the prediction that a common gene network blueprint generates ILC effectors and understanding their interconnected function will be central to potential targeted immunotherapies of inflammatory disorders.