Disease and Race Specific Single-cell Epigenetic Mechanisms in Human SLE

项目摘要 系统性红斑狼疮（SLE）是一种典型的自身免疫性疾病，其特征是 干扰素应答和对细胞抗原自身耐受性的丧失，导致炎症过程， 最终导致系统性终末器官损伤。欧洲人和欧洲人之间存在着惊人的遗传和临床差异。 美国（EA）和非洲裔美国人（AA）SLE患者，导致他们的诊断，管理差异 和结果。尽管经过数十年的研究和100多个风险位点的确定， SLE的发病机制及其种族差异仍不完全清楚。我们的实验室联合了 由哈佛大学的JasonRistrostro博士领导的研究小组评估和理解了表观遗传调控是如何在 特定的细胞类型有助于疾病和种族特异性SLE发病机制。我们用sci-ATAC-seq （转座酶可及染色质的单细胞索引测定），在 Estrostro实验室，以评估疾病和种族特异性差异的全基因组染色质可及性 (CA)在来自冷冻保存的外周血单核细胞的细胞亚型中。将这些数据与 基因分型数据使我们能够鉴定在CA区域富集的等位基因不平衡变体（caQTL）， 提示这些变体在调节CA中的机制作用。我们在EA SLE中进行的初步数据 和健康对照表明，我们能够定义多个主要的PBMC细胞亚群， CA和caQTL的差异可区分SLE患者和对照组。我们现在提出一个扩大的 这项研究不仅将在更大的样本中评估疾病特异性CA和caQTL的改变， 种族特异性改变将单细胞转录组数据和临床数据与CA和caQTL数据整合 将有助于SLE相关CA差异的功能解释。我们的目标AR 077434 重新提交的目的是1）定义细胞类型特异性染色质可及性差异，以识别两种疾病- 特异性和种族特异性的改变; 2）鉴定细胞类型和种族特异性的caQTL， SLE病例和对照之间CA的差异;和3）定义CA之间的机制关系， caQTL，基因表达架构，在顺式共可及性网络的背景下。我们相信这 该项目使我们处于领先地位，以开发一个精确的表观遗传路线图，将遗传变异与 作为SLE疾病特异性机制的基础的有害细胞和临床表型及其 显著的种族差异

PROJECT SUMMARY Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterized by dysregulated interferon responses and loss of self-tolerance to cellular antigens that result in inflammatory processes that ultimately lead to systemic end-organ damage. Striking genetic and clinical differences exist between European American (EA) and African American (AA) SLE patients that result in disparities in their diagnoses, management and outcomes. Despite decades of research and over 100 risk loci identified, the underlying mechanisms driving the pathogenesis of SLE and its racial disparities remain incompletely understood. Our lab has joined forces with the team led by Jason Buenrostro, PhD, at Harvard to evaluate and understand how epigenetic regulation in specific cell types contributes to both disease- and race-specific SLE pathogenesis. We use a sci-ATAC-seq (single cell indexing assay for transposase-accessible chromatin), method developed and optimized in the Buenrostro laboratory, to assess disease- and race-specific differences in genome-wide chromatin accessibility (CA) in cell subtypes from cryopreserved peripheral blood mononuclear cells. Integrating these data with genotyping data allows us to identify allelically imbalanced variants that are enriched in regions of CA (caQTLs), suggesting a mechanistic role for these variants in regulating CA. Our preliminary data conducted in EA SLE and healthy controls demonstrate that we are able to define multiple major PBMC cell subsets, and that extensive differential CA and caQTLs discriminate between SLE case and control subjects. We now propose an expanded study that will not only evaluate disease-specific CA and caQTL alterations in a much larger sample, but also race-specific alterations. Integrating single-cell transcriptomic data and clinical data with CA and caQTL data will facilitate the functional interpretation of SLE relevant CA differences. Our goals for this AR077434 resubmission are to 1) define cell type-specific differences in chromatin accessibility that identify both disease- specific and race-specific alterations; 2) identify cell type and race-specific caQTLs that associate with differences in CA between SLE cases and controls; and 3) define the mechanistic relationships between CA, caQTLs, gene expression architectures, within the context of cis co-accessibility networks. We believe this project positions us at the leading edge to develop a precise epigenetic roadmap connecting genetic variation to deleterious cellular and clinical phenotypes that underlie the disease-specific mechanisms of SLE and its remarkable race-specific disparities.