Ultra-Fast Epigenomic Maps for Monitoring Autoimmunity

改变的基因调控是自身免疫及其治疗的许多方面的基础。致病 自身抗体和免疫复合物最终通过细胞信号转导发挥作用， 影响基因表达。特异性转录因子在驱动免疫细胞命运中的核心作用， 控制基因表达的抗炎和免疫抑制药物-如类固醇， 环孢素A（CsA）和JAK、白细胞介素-1（IL-1）、肿瘤坏死因子（TNF）和B细胞 激活因子（BAFF）-提示了解自身免疫中基因调控的重要性。而 除了简单地观察基因表达的变化，最近的表观基因组学工具使我们有可能 确定基因表达的因果关系，揭示特定的转录因子和调控因子， 驱动不同基因表达程序的元件。然而，现有的实验方法需要10 每个测定需要100万个细胞或更多，并且执行起来复杂且费力。这些限制在很大程度上 使表观基因组分析无法用于包括自身免疫在内的人类疾病的临床研究。 在这里，我们建议开发和应用一种革命性的新方法，称为ATAC-Seq，以绘制开放染色质 全基因组的位点，使自身免疫性疾病患者的表观基因组研究变得容易和快速， 他们对治疗的反应是真实的。我们还将探讨表观遗传学在已知基因型中的作用， Tyk 2、STAT 4和IRF 5等基因存在单核苷酸多态性的SLE患者。最终的结果 将是一组强大的生物标志物和重要的生物学见解自身免疫和炎症 疾病我们研究的长期目标是将ATAC-Seq纳入ACE共享研究议程， ACE研究人员可以将其用作基础科学项目的一部分， ACE临床试验中的检测。

Altered gene regulation underlies many facets of autoimmunity and its treatments. Pathogenic autoantibodies and immune complexes ultimately exert their effects through cellular signal transduction to impact gene expression. The central roles of specific transcription factors in driving immune cell fates, and anti-inflammatory and immunosuppressive drugs that control gene expression - such as steroids, cyclosporine A (CsA), and inhibitors of JAKs, lnterieukin-1 (IL-1), Tumor Necrosis Factor (TNF), and B Cell Activating Factor (BAFF) - suggest the importance of understanding gene regulation in autoimmunity. Rather than simply observing changes in gene expression, recent epigenomic tools have made it possible to determine the causality of gene expression, revealing the specific transcription factors and regulatory elements driving different gene expression programs. However, existing experimental methods require 10 million cells or more per assay, and are complex and laborious to perform. These limitations have largely kept epigenomic analyses out of the reach of the clinical studies of human diseases, including autoimmunity. Here we propose to develop and apply a revolutionary new method called ATAC-Seq to map open chromatin sites genome-wide, to enable facile and rapid epigenomic studies of patients with autoimmune diseases and their response to treatments in real time. We will also explore the role of epigenetics in known genotypes of SLE patients with single nucleotide polymorphisms in genes such as Tyk2, STAT4, and IRF5. The end result will be a set of robust biomarkers and important biological insights into autoimmune and inflammatory diseases. The long term goal of our studies is to include ATAC-Seq in the ACE Shared Research Agenda, where it can be used by ACE investigators as part of their basic science projects, and as a mechanistic assay in ACE clinical trials.