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

T细胞记忆的实验精炼的动态基因调控网络模型 总结 由先前暴露于病原体或疫苗接种诱导的T细胞记忆提供增强的针对免疫缺陷的保护。 随后感染同一病原体。增强的保护部分是由克隆扩张驱动的， 导致能够识别抗原的T细胞数量增加。此外，记忆T细胞具有 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 在再暴露的几分钟内（而不是最初暴露后的几天）。我们最近发现快速回忆 与记忆T细胞中“快速回忆基因”的增强子和启动子的表观遗传平衡相关。 重要的是，表观遗传改变的位点与自身免疫性和特应性的风险位点显著重叠。 疾病，这表明这种机制对人类健康很重要。然而，目前还不清楚是否以及如何 表观遗传平衡导致快速回忆基因的表达增强。此外，记忆T细胞持续存在， 然而，维持记忆表观基因组的机制-几十年-尚不清楚。我们 初步数据表明，快速回忆是由几个转录因子家族协调的， 数以千计的DNA调控元件这种复杂性需要系统级的工程方法。 因此，这个提议是T细胞生物学家阿尔特姆巴斯基和艾米丽米拉尔迪小组之间的合作， 一个数学模型，创建实验验证，记忆免疫反应的基因组规模的模型 在异质性T细胞群体中。 目标1.利用单细胞基因组学，我们将描述T细胞的基因表达和染色质动力学， 激活在幼稚和记忆细胞，并建立数学模型，整合这些数据（沿着与 相关的现有基因组学资源）整合到动态基因调控网络（GRN）中。我们的GRN模型 预测快速回忆的分子驱动因素（TF）和调控因素。 目标2.虽然幼稚细胞和记忆细胞中的T细胞活化类似地促进细胞核转位， 我们的数据使我们假设，在初始病原体暴露时染色质重塑改变了 记忆T细胞中可诱导的TF的占据，这是快速回忆的基础。我们将联合收割机 动态TF扰动和占用实验，以建立驱动快速回忆的分子相互作用。 目标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-在人的一生中。我们假设组成型转录因子维持表观基因组， 快速回忆我们提出了动态TF扰动实验来揭示这些监管机构的身份。 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回忆是疫苗接种的基础， 过敏，哮喘和癌症免疫，这项研究将对人类健康产生广泛的影响。

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 rapid recall 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 human health. 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– 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 experimentally validated, genome-scale models of memory immune responses across heterogeneous T cell populations. 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.