3D genome organization of the Ets1-Fli1 locus controls allergic responses

该提案的目标是研究三维（3D）基因组折叠中的扰动如何改变CD 4 + T细胞。 细胞功能，介导过敏性疾病。T细胞身份不仅取决于线性基因组序列， 嵌入了数百万个调控元件，但也有3D染色质架构，协调空间 调节元件与其靶基因的定位。最近我们对 核组织表明，单核苷酸多态性与免疫介导的疾病 可能通过改变3D基因组结构和重组大的基因组区域来影响基因调控 与疾病相关的细胞类型。然而，序列变异、细胞环境、3D基因组之间的联系 在大多数免疫介导的复杂疾病中， 未知我们的目标是确定3D基因组 T细胞中的组织与过敏性疾病有关。我们制定这一目标的基础是四个 意想不到的观察：（A）我们对密集相互作用的多增强子组的算法定义 元素，我们称之为3D集团，揭示了一个含有Ets 1和Fli 1基因的位点， 在T细胞中高度连接。(B)这种独特的3D基因组结构在人类T细胞中是保守的， 具有与2型免疫疾病相关的多种多态性，包括过敏、哮喘和特应性 皮炎(C)我们通过删除一个与基因组同源的非编码序列来产生一种新的小鼠品系。 人类基因组中的过敏相关多态性区域，Ets 1启动子下游约250 kbp。这 基因缺失使T细胞发育完整，但导致CD 4+辅助性T细胞1（Th 1）分化的主要缺陷。 Th 1细胞负责控制细胞内病原体如细菌，并抑制Th 2细胞 对过敏原的反应。因此，由于Ets 1-Fli 1 3D团的遗传修饰，限制了Th 1分化 可能引起过敏反应。(D)我们使用屋尘螨模拟体内2型免疫应答。 在Ets 1-Fli 1 3D团非编码序列缺失的小鼠的肺组织中，我们检测到一种新的表达。 以嗜酸性粒细胞和Th 2显著积聚为特征的过敏反应急剧增加 细胞和Th 1细胞减少。这些未发表的数据为我们提供了令人信服的证据， 工程小鼠品系是理解非编码调控元件和3D 2型免疫疾病中的基因组折叠。然而，详细的细胞和分子机制， Ets 1-Fli 1基因座中的哪种遗传缺失引起明显的过敏反应仍有待了解。 此外，我们的3D集团分析对其他致病性调节节点的可推广性仍然是 接受检查。这项工作是重要的，因为它是有史以来第一次机械调查提供了一个 基因组结构和2型免疫疾病之间的联系。

The goal of this proposal is to study how perturbation in three-dimensional (3D) genome folding alters CD4+ T cell function, mediating allergic disorders. T cell identity depends on not only the linear genome sequence that embeds millions of regulatory elements, but also the 3D chromatin architecture that orchestrates the spatial localization of the regulatory elements with their target genes. Recent advances in our understanding of nuclear organization indicate that single-nucleotide polymorphisms associated with immune-mediated diseases may impact gene regulation through altered 3D genomic structure and reorganization of large genomic regions in the disease relevant cell types. However, the link between sequence variation, cellular context, 3D genome folding, and aberrant gene expression in majority of immune-mediated complex diseases remains largely unknown. Our objective is to determine the molecular processes through which 3D genome organization in T cells is linked to allergic disorders. We formulated this objective based on four unexpected observations: (A) Our algorithmic definition of groups of densely interacting multi-enhancer elements, which we called 3D cliques, revealed that a locus harboring the Ets1 and Fli1 genes is hyperconnected in T cells. (B) This unique 3D genome architecture is conserved in human T cells coinciding with multiple polymorphisms associated to type 2 immune diseases including allergy, asthma, and atopic dermatitis. (C) We generated a novel strain of mice by deleting a non-coding sequence homologous to the allergy-associated polymorphic region in the human genome, ~250kbp downstream of the Ets1 promoter. This genetic deletion left T cell development intact but led to major defects in CD4+ T helper 1 (Th1) differentiation. Th1 cells are responsible for the control of intracellular pathogens such as bacteria and dampen Th2 responses to allergens. Hence, limited Th1 differentiation due to genetic modification of the Ets1-Fli1 3D clique may cause allergic responses. (D) We modeled the type 2 immune responses in vivo using house dust mites. In the lung tissues of mice with a deletion in the non-coding sequence in the Ets1-Fli1 3D clique, we detected a dramatic increase in allergic responses characterized by a significant accumulation of eosinophils and Th2 cells and a reduction in Th1 cells. These unpublished data provide us with compelling evidence that our engineered mouse strain is a model for understanding the role of noncoding regulatory elements and 3D genome folding in type 2 immune diseases. However, detailed cellular and molecular mechanisms through which genetic deletion in the Ets1-Fli1 locus causes overt allergic responses remain to be understood. Moreover, the generalizability of our 3D clique analysis to additional pathogenic regulatory nodes remains to be examined. This work is significant because it is the first-ever mechanistic investigation providing a connection between genome architecture and type 2 immune diseases.