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。的 自身免疫性疾病如1型糖尿病（T1D）的发病机制不是由单个细胞类型介导的， 免疫系统非编码变异在这些疾病中的作用在很大程度上尚未得到充分研究，但表明， 可以改变三维染色质结构的变化。早期的工作主要集中在 CD4+辅助性T细胞1（Th1）和辅助性T细胞17（Th17），然后是调节性T细胞（Th）。最近，T 记忆干细胞（Tscm）被鉴定，并且它们在自身免疫中的作用刚刚开始被研究。 这些细胞具有干细胞样的自我更新和分化特性。与存储器单元（T）不同， 这些细胞是长寿的，提供了延长免疫记忆的来源。因为他们的干细胞状态 和提供长期记忆的能力，这些细胞对自身免疫，癌症 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， 意味着这些细胞也提供了自身反应和炎症细胞的储存库， 免疫功能，并有助于慢性疾病。我们自己的数据表明，这些细胞富含T1D 与健康对照受试者相比，这可能与疾病风险等位基因相关。整体 该提案的目标是确定二维和三维染色质结构的变化， CD4+ Tscm细胞从其幼稚祖细胞和衍生细胞的命运，并确定如何改变特定的T1D 通过分析来自健康对照和T1D受试者的纯细胞群，有助于疾病发病机制。 我们还将通过分析T1D相关改变在其他自身免疫性疾病中是否普遍存在， 来自RA供体的TSCMS。我们将确定非编码疾病相关变异在顺式调控中的作用， 在这个过程中，克雷斯元素可能发挥作用。我们提出了整合2D和3D染色质结构 在一个大的队列中精确地确定靶基因和细胞和疾病特异性基因的机制， 调控具体来说，我们将在纯的CD4+细胞群中鉴定细胞类型特异性染色质结构。 通过使用捕获HiC来映射跨三个关键细胞的调节环， 在50名健康对照受试者的队列中。为了确定这些调节环是否在一个 疾病状态下，我们将确定T1D特异性染色质结构，以确定Tscm细胞的作用， 延长炎症和自身反应性。最后，我们将确定常见的染色质结构变化， 通过对另外50名患有类风湿性关节炎的受试者进行谱分析来检测自身免疫性Tscm细胞。拟定的研究将 使用创新方法对2D和3D基因组结构进行大规模评估，以确定 细胞和疾病特异性基因调控机制使用一个明确的人类队列。拟议 这项研究将促进我们对记忆干细胞在自身免疫中的作用以及 非编码变异对染色质结构的影响。

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.