Three-dimensional conformation changes associated with T cell memory and autoimmunity

摘要 自身免疫性疾病是由遗传和环境因素引起的复杂疾病。这个 自身免疫性疾病如1型糖尿病(T1D)的发病机制不是由单细胞类型的 免疫系统。非编码变异在这些疾病中的作用在很大程度上还没有得到充分的研究，但建议 三维染色质结构的变化是可以改变的。早期的工作主要集中在 CD4+T辅助细胞1(Th1)和辅助性T细胞17(Th17)，其次是T调节细胞(Tregs)。最近，T 记忆干细胞(Tscm)已被鉴定，其在自身免疫中的作用才刚刚开始研究。 这些细胞具有干细胞样的自我更新和分化特性。与存储单元(TMEM)不同， 这些细胞寿命很长，提供了延长免疫记忆的来源。因为他们的干细胞状态 以及提供长期记忆的能力，这些细胞对自身免疫、癌症等有重要意义 免疫和免疫疗法，以及免疫系统的重建。在自身免疫的背景下， 意味着这些细胞还提供了自身反应和炎症细胞的储存库，这些细胞可以继续破坏 免疫功能和对慢性病的贡献。我们自己的数据表明，这些细胞富含T1D 献血者与健康对照受试者比较，这可能与疾病风险等位基因有关。整体而言 这项提议的目标是确定二维和三维染色质结构的变化，以区分 CD4+Tscm细胞及其原始祖细胞和衍生细胞的命运，并确定如何改变特定的T1D 通过分析健康对照和T1D受试者的纯细胞群体，有助于疾病的发病机制。 我们将通过对其他自身免疫性疾病的分析来确定与T1D相关的改变是否在其他自身免疫性疾病中普遍存在 来自RA捐赠者的TSCM。我们将确定非编码疾病相关变体在顺式调控中的作用 元素(CRE)可能在这一过程中发挥作用。我们提出将2D和3D染色质体系结构相结合 跨大队列精确确定细胞和疾病特异性基因的靶基因和机制 监管。具体地说，我们将在纯CD4+人群中确定细胞类型特定的染色质结构 利用捕获HIC映射三个关键细胞的调控环与干细胞记忆相关的亚型 在50名健康对照受试者的队列中输入。以确定这些调控循环是否在 在疾病状态下，我们将鉴定T1D特异的染色质结构，以确定TSCM细胞在 长期的炎症和自身反应性。最后，我们将确定染色质体系结构在 通过分析另外50名类风湿关节炎患者的自身免疫TSCM细胞。拟议的研究将 使用创新方法对2D和3D基因组架构进行大规模评估，以确定 使用明确定义的人类队列的特定细胞和疾病的基因调控机制。建议数 研究将促进我们对记忆干细胞在自身免疫中的作用以及 染色质结构上的非编码变体以疾病特有的方式。

ABSTRACT Autoimmune diseases are complex diseases arising from both genetic and environmental factors. The pathogenesis of autoimmune diseases like type 1 diabetes (T1D) is not mediated by a single cell type of the immune system. The role of noncoding variants in these diseases are largely understudied, but suggest that changes in three-dimensional chromatin architecture could be altered. Early work largely focused on the role of CD4+T helper 1 (Th1) and T helper 17 (Th17) cells, followed by T regulatory cells (Tregs). More recently, T memory stem cells (Tscm) were identified and their role in autoimmunity is just beginning to be investigated. These cells possess stem-like properties of self-renewal and differentiation. Unlike memory cells (Tmem), these cells are long-lived, providing a source of prolonged immune memory. Because of their stem cell state and ability to provide long-term memory, these cells have important implications for autoimmunity, cancer immunity and immune therapies, and reconstitution of the immune system. In the context of autoimmunity that means these cells also provide a reservoir of autoreactive and inflammatory cells that can continue disrupt immune function and contribute to chronic disease. Our own data indicate that these cells are enriched in T1D donors compared to healthy control subjects, which may be associated with disease risk alleles. The overall goal of this proposal is to identify two- and three-dimensional chromatin architecture changes that distinguish CD4+ Tscm cells from their naïve progenitor and derived cell fates and determine how changes specific T1D contribute to disease pathogenesis by profiling pure populations of cell from healthy control and T1D subjects. We will determine if T1D-associated change are prevalent in other autoimmune diseases by also profiling Tscms from RA donors. We will determine what role noncoding disease-associated variants at cis-regulatory elements (CREs) might play in this process. We proposed to integrate 2D and 3D chromatin architecture across a large cohort to precisely determine target genes and mechanisms of cell- and disease-specific gene regulation. Specifically, we will identify cell-type specific chromatin architecture in pure populations of CD4+ subtypes related to stem cell memory by employing capture HiC to map regulatory loops across three key cell types in a cohort of 50 healthy control subjects. To determine if these regulatory loops are altered in a diseased state, we will identify T1D-specific chromatin architecture to determine the role of Tscm cells in prolonged inflammation and autoreactivity. Lastly, we will identify chromatin architecture changes common in autoimmune Tscm cells by profiling an addition 50 subjects with rheumatoid arthritis. The proposed study will use innovative approaches to conduct large-scale assessment of 2D and 3D genome architecture to determine cell- and disease-specific gene regulatory mechanisms using a well-defined human cohort. The proposed study will advance our understanding of the role of memory stem cells in autoimmunity and the effects of noncoding variants on chromatin architecture in a disease-specific manner.