Epigenomics of SLE

描述（由申请人提供）：系统性红斑狼疮（SLE）是一种慢性系统性自身免疫性疾病。非裔美国妇女受到的影响尤为严重，其病因被认为是遗传和环境因素的结合。典型的自然病程包括不同的器官系统受累和慢性病程，不时发作。多项研究表明，单核细胞功能在SLE中是异常的，这一点很重要，因为单核细胞可以作为分化的巨噬细胞在组织中持续存在，并形成适应性反应，从而由于其功能异常而产生一系列效应。巨噬细胞形成动脉粥样硬化疾病的初始病变，与SLE的主要死亡原因有关，巨噬细胞浸润肾脏与发病率和死亡率增加特别相关。这些构成了研究SLE单核细胞的基本原理。我们特别假设SLE疾病过程驱动单核细胞表观基因组的改变，这有助于疾病的延续和终末器官表现。表达潜能的改变可能导致单核细胞异常迁移或炎症介质表达。对常见的无害刺激（如病毒）的病理反应可能是表观基因组改变的结果。本提案将研究SLE单核细胞的表观遗传景观，并开始确定与组蛋白修饰改变相关的途径。ChIP-Seq将检测两个相反的组蛋白标记H3K4me2和H3K27me3。我们有初步的数据表明，与对照组相比，SLE患者单核细胞中的H4乙酰化发生了改变。组蛋白修饰改变的基因组的网络分析显示了生物学相关的节点，包括已知的炎症途径。第二个表观遗传特征，非编码rna，将在探索性的基础上进行检查。初步数据表明，TNF1基因上游存在组织特异性反义RNA，与转录抑制因子的结合有关。我们将研究长mrna样非编码rna，并使用一种新的ChIP-Seq方法，使用S9.6来探索潜在的调控rna的结构。S9.6抗体将用于鉴定DNA:RNA杂交结构，并用于过滤生物信息学鉴定的非编码RNA。该应用的主要目标之一是开始过渡到表观基因组改变的机制检查。我们假设疾病本身驱动了大部分表观基因组的改变，然而，同一SLE队列的现有SNP数据库将用于检查与组蛋白修饰改变的潜在SNP关联。对RNA-Seq和ChIP- Seq数据的SNP分析将允许对对照进行等位基因特异性定量，作为SLE样本的基础。本提案将检查SLE的表观基因组，并开始检查潜在的原因和后果。总的来说，这些方法将进一步加深我们对SLE的理解，并可能为理解自身免疫性疾病的慢性性提供一个新的范例。公共卫生相关性：本应用旨在了解白细胞、单核细胞如何在系统性红斑狼疮（SLE）的疾病影响下发展新功能。该项目将定义SLE导致的基因组状态的变化，并描述导致这些变化的生理过程。这些研究对于我们的免疫系统如何被先前的经验所塑造，并可能导致SLE的新疗法具有广泛的意义。

DESCRIPTION (provided by applicant): Systemic lupus erythematosus (SLE) is a chronic systemic autoimmune disease. African American women are disproportionately affected and the etiology is believed to be a combination of genetic and environmental factors. The natural history typically includes diverse organ system involvement and a chronic course punctuated by flares. Multiple studies have demonstrated that monocyte function is aberrant in SLE and this is significant because monocytes can persist in tissues as differentiated macrophages and mold adaptive responses, thus producing a cascade of effects as a consequence of their aberrant function. Macrophages form the initial lesion in atheromatous disease, associated with the major cause of death in SLE and macrophage infiltration into the kidney is specifically associated with increased morbidity and mortality. These form the rationale for the study of SLE monocytes. We specifically hypothesize that the SLE disease process drives an altered epigenome in monocytes and this contributes to disease perpetuation and end organ manifestations. An altered potential for expression could lead to aberrant monocyte migration or inflammatory mediator expression. Pathologic responses to common innocuous stimuli, such as viruses could ensue as a result of an altered epigenome. This proposal will examine the epigenetic landscape of SLE monocytes and begin to identify pathways that are associated with altered histone modifications. Two opposing histone marks will be examined by ChIP-Seq, H3K4me2 and H3K27me3. We have preliminary data demonstrating altered H4 acetylation in SLE patient monocytes compared to controls. Network analysis of the gene set with altered histone modifications demonstrated nodes of biological relevance, including known inflammatory pathways. A second epigenetic feature, non-coding RNAs, will be examined on an exploratory basis. Preliminary data demonstrate tissue-specific antisense RNA upstream of the TNF1 gene which is associated with binding of a transcriptional repressor. Long mRNA-like non-coding RNAs will be examined and a novel ChIP-Seq approach, using S9.6, used to explore the structure of the potential regulatory RNAs. The S9.6 antibody will be used to identify DNA:RNA hybrid structures and this will be used to filter the non-coding RNAs identified bioinformatically. One of the major goals of this application is to begin to transition to a mechanistic examination of the alterations to the epigenome. We hypothesize that the disease itself drives most of the alterations to the epigenome, however, an existing SNP database on the same SLE cohort will be used to examine potential SNP associations with altered histone modifications. SNP analysis on RNA-Seq and ChIP- Seq data will allow allele-specific quantitation on controls, as a foundation for the SLE samples. This proposal will examine the epigenome in SLE and begin to examine potential causes and consequences. Collectively, these approaches will further our understanding of SLE and may develop a new paradigm for the understanding of the chronicity of autoimmune disease in general. Public Health Relevance: This application seeks to understand how white cells, monocytes, develop new functions as a result of disease effects in systemic lupus erythematosus (SLE). This project will define changes in the status of the genome as a result of SLE and characterize the physiologic processes that led to the changes. These studies have broad implications for how our immune system could be molded by prior experiences and could lead to novel therapies for SLE.