An experimentally-refined, dynamic gene regulatory network model of T-cell memory

T细胞记忆的实验精炼动态基因调控网络模型 摘要 通过先前接触病原体或接种疫苗而诱导的T细胞记忆可增强对 随后感染了相同的病原体。增强的保护在一定程度上是由克隆扩张推动的，克隆扩张 导致能够识别抗原的T细胞数量增加。此外，记忆性T细胞拥有 一种“快速回忆能力”，使它们能够通过产生细胞因子和其他效应分子来对抗病原体。 在再次暴露的几分钟内(而不是最初暴露的几天内)。我们最近的研究表明， 回忆能力与“快速回忆基因”的增强子和启动子的表观遗传平衡有关 记忆T细胞。重要的是，表观遗传改变的位置与 自身免疫和特应性疾病，表明这一机制对免疫动态平衡很重要。 然而，表观遗传平衡是否以及如何导致快速回忆基因的表达增强仍不清楚。 此外，记忆T细胞会持续一生；然而维持记忆表观基因组的机制-- 几十年来在没有抗原的情况下--都是未知的。我们的初步数据表明，快速召回是 由几个转录因子家族(TF)和数千个假定的DNA调节因子协调 元素。这种复杂性需要系统级的工程方法。因此，这项提议是一项合作 在T细胞生物学家Artem Barski和数学模型师Emily Miraldi的研究小组之间，创造了一种 经过实验验证的记忆免疫反应的基因组规模模型。 目的1.利用单细胞基因组学方法，研究T细胞的基因表达和染色质动态 幼稚和记忆细胞的激活，并构建集成这些数据的数学模型(以及 相关的现有基因组资源)转化为动态的基因调控网络(GRN)。我们的GRN模型将 预测协调快速回忆的分子驱动因素(TF)和调控因素。 目的2.尽管幼稚细胞和记忆细胞中的T细胞激活类似地促进了 我们的数据引导我们假设，最初接触病原体时染色质重塑会发生改变 记忆T细胞中可诱导因子的占有率，这是快速回忆的基础。我们将联合起来 动态转移因子扰动和占位实验，以建立驱动快速回忆的分子相互作用。 目的3.我们将确定记忆T细胞维持表观基因组的机制 快速回忆--跨越人的一生。我们假设构成因子保持表观基因组的平衡 快速回忆。我们提出了动态传递函数微扰实验来揭示这些调节子的身份。 这项研究将有助于揭示T细胞记忆的基本机制，并确定潜在的靶点 操纵免疫记忆反应。因为快速召回是接种疫苗的基础，也是 过敏、哮喘和癌症免疫，这项研究将对人类健康产生广泛影响。

An experimentally-refined, dynamic gene regulatory network model of T-cell memory Summary T cell memory induced by prior exposure to a pathogen or vaccination provides enhanced protection against a subsequent infection with the same pathogen. Enhanced protection is partially driven by clonal expansion, which leads to an increased number of T cells capable of recognizing the antigen. Additionally, memory T cells possess a “rapid recall ability” that allows them to fight pathogens by producing cytokines and other effector molecules within minutes of re-exposure (as opposed to days, upon initial exposure). We recently showed that the rapid recall ability correlates with the epigenetic poising of enhancers and promoters of the “rapid-recall genes” in memory T cells. Importantly, the sites of epigenetic change significantly overlap with the risk loci for autoimmune and atopic disease, suggesting that this mechanism is important for immune homeostasis. However, it is still unclear if and how the epigenetic poising causes enhanced expression of rapid recall genes. Furthermore, memory T cells persist for a lifetime; yet the mechanisms that maintain the memory epigenome – for decades in the absence of antigen – are not known. Our preliminary data suggest that rapid recall is coordinated by several families of transcription factors (TFs) and thousands of putative DNA regulatory elements. This complexity requires a systems-level, engineering approach. Thus, this proposal is a collaboration between the groups of Artem Barski, a T cell biologist, and Emily Miraldi, a mathematical modeler, to create an experimentally validated, genome-scale model of memory immune response. Aim 1. Using single-cell genomics, we will characterize the gene expression and chromatin dynamics of T cell activation in naïve and memory cells and build mathematical models that integrate these data (along with relevant existing genomics resources) into a dynamic gene regulatory network (GRN). Our GRN model will predict the molecular drivers (TFs) and regulatory elements that orchestrate rapid recall. Aim 2. Although T-cell activation in naïve and memory cells similarly promotes nuclear translocation of inducible TFs, our data lead us to hypothesize that chromatin remodeling upon initial pathogen exposure alters the occupancy of inducible TFs in memory T cells and that this is the basis of rapid recall. We will combine dynamic TF perturbation and occupancy experiments to establish the molecular interactions driving rapid recall. Aim 3. We will identify the mechanisms by which memory T cells maintain the epigenome conducive for rapid recall – over the human lifespan. We hypothesize that constitutive TFs maintain the epigenome poised for rapid recall. We propose dynamic TF perturbation experiments to uncover the identities of these regulators. This study will help uncover basic mechanisms of T cell memory and identify potential targets for manipulating immunologic memory responses. Because rapid recall is the basis for vaccination and central to allergy, asthma, and cancer immunity, this study will have a broad impact on human health.