Epigenomics of SLE

描述（申请人提供）：系统性红斑狼疮（SLE）是一种慢性全身性自身免疫性疾病。非裔美国妇女受到不成比例的影响，病因被认为是遗传和环境因素的结合。其自然病程通常包括多种器官系统受累和伴有耀斑的慢性病程。多项研究表明，单核细胞功能在SLE中是异常的，这是重要的，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，从而由于其异常功能而产生级联效应。巨噬细胞形成动脉粥样硬化性疾病的初始病变，与SLE的主要死亡原因相关，巨噬细胞浸润到肾脏中与发病率和死亡率增加特别相关。这些形成了SLE单核细胞研究的基本原理。我们特别假设SLE疾病过程驱动单核细胞中改变的表观基因组，这有助于疾病的延续和终末器官表现。表达潜力的改变可能导致异常单核细胞迁移或炎症介质表达。对常见无害刺激（如病毒）的病理反应可能是表观基因组改变的结果。这项提案将检查SLE单核细胞的表观遗传景观，并开始确定与改变组蛋白修饰相关的途径。将通过ChIP-Seq检查两个相对的组蛋白标记，H3 K4 me 2和H3 K27 me 3。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乙酰化改变。对具有改变的组蛋白修饰的基因集的网络分析证明了生物相关性的节点，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，组织特异性反义RNA的TNF 1基因的上游，这是与结合的转录抑制。将检查长的mRNA样非编码RNA，并使用S9.6的新型ChIP-Seq方法来探索潜在调控RNA的结构。S9.6抗体将用于鉴定DNA：RNA杂交结构，并将用于过滤生物信息学鉴定的非编码RNA。本申请的主要目标之一是开始过渡到对表观基因组的改变的机械检查。我们假设疾病本身驱动了表观基因组的大部分改变，然而，同一SLE队列的现有SNP数据库将用于检查与改变的组蛋白修饰的潜在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样品的基础。这项建议将检查表观基因组在系统性红斑狼疮和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化提供一个新的范例。

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.