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

Ets1-Fli1 基因座的 3D 基因组组织控制过敏反应

基本信息

批准号：
10654172
负责人：
Jorge Henao-Mejia
金额：
$ 77.22万
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-07-10 至 2028-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10654172
关键词：
3-Dimensional Address Algorithms Allergens Allergic Allergic Disease Architecture Asthma Atopic Dermatitis Bacteria CD4 Positive T Lymphocytes Cell physiology Cells Chromatin Competence Complex Control Locus Data Defect Disease ETS1 gene Elements Endowment Engineering Etiology FLI1 gene Flow Cytometry Gene Expression Gene Expression Regulation Genes Genetic Genetic Enhancer Element Genetic Polymorphism Genome Genomic Segment Genomics Goals Heritability Human Human Genome Hypersensitivity Immune Immune System Diseases Immune response Investigation Left Link Lung Mediating Modeling Modification Molecular Mouse Strains Mus Nuclear Nucleotides Pathogenicity Phenotype Play Population Process Public Health Pyroglyphidae Regulatory Element Role Sequence Homologs Single Nucleotide Polymorphism Structure Structure of parenchyma of lung T cell differentiation T-Cell Development T-Lymphocyte Testing Th2 Cells Untranslated RNA Variant Work allergic response cell type eosinophil experimental study genome wide association study in vivo multiple omics novel pathogen promoter response risk variant superresolution microscopy

项目摘要

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.

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 CD4+ T 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，还嵌入了协调空间的 3D 染色质架构调节元件及其靶基因的定位。我们的理解的最新进展核组织表明单核苷酸多态性与免疫介导的疾病相关可能通过改变 3D 基因组结构和重组大基因组区域来影响基因调控在疾病相关的细胞类型中。然而，序列变异、细胞背景、3D 基因组之间的联系大多数免疫介导的复杂疾病中的折叠和异常基因表达在很大程度上仍然存在未知。我们的目标是确定 3D 基因组的分子过程 T 细胞的组织与过敏性疾病有关。我们根据四个方面制定了这一目标意外的观察结果：（A）我们对密集相互作用的多增强子组的算法定义我们称之为 3D 派系的元素揭示了包含 Ets1 和 Fli1 基因的基因座 T 细胞中超连接。 (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) 我们通过删除与人类基因组中与过敏相关的多态性区域，位于 Ets1 启动子下游约 250kbp。这基因缺失使 T 细胞发育完整，但导致 CD4+ T 辅助细胞 1 (Th1) 分化出现重大缺陷。 Th1 细胞负责控制细菌等细胞内病原体并抑制 Th2 对过敏原的反应。因此，由于 Ets1-Fli1 3D 团的基因修饰，Th1 分化受到限制可能会引起过敏反应。 (D) 我们使用屋尘螨模拟了体内 2 型免疫反应。在 Ets1-Fli1 3D 团非编码序列缺失的小鼠肺组织中，我们检测到以嗜酸性粒细胞和 Th2 显着积累为特征的过敏反应急剧增加细胞和 Th1 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，表明我们的工程小鼠品系是了解非编码调控元件和 3D 作用的模型 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 Ets1-Fli1 基因座中的哪种基因缺失会导致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调控节点的普遍性仍有待提高。被检查。这项工作意义重大，因为这是有史以来第一次提供机制研究基因组结构与 2 型免疫疾病之间的联系。