Localizing functional variants in SLE susceptibility genes

描述(由申请人提供)：系统性红斑狼疮(SLE或狼疮)是一种复杂的自身免疫性疾病，其特征是由致病性自身抗体产生引起的广泛的临床表现。系统性红斑狼疮对妇女和某些族裔群体的影响不成比例。与欧洲裔美国人相比，亚洲人、非裔美国人和西班牙裔人的SLE患病率高3-5倍，临床表现更严重。遗传因素强烈影响狼疮的发生和发展，全基因组关联研究(GWAS)已经确定了40多个与SLE易感性相关的遗传因素，其中大部分来自具有欧洲血统的个人。为了了解导致系统性红斑狼疮疾病亚型的生物学机制，描述负责GWAS关联信号的功能变异是至关重要的。然而，准确地描述功能变体一直是一个主要的挑战，因为来自GWA的相关变体通常是实际功能变体所在的单倍型的“标签”。我们的研究团队已经获得了所需的经验、专业知识、资源和基础设施，以加快发现和表征这些信号背后的因果变量。我们已经成功地确定了ITGAM基因中的因果变异及其功能后果。我们建议研究四个SLE易感基因，IFIH1、ETS1、IKZF1和PRDM1，这些基因与多种自身免疫性疾病的易感性有关，表明它们在自身免疫中发挥更广泛的作用。我们的主要目标是定义这些基因中的功能变异，并解释它们与SLE及其临床亚型的因果关系。在目标1中，我们将整合我们来自具有1000个基因组的多种族队列的基因分型和测序数据，同时利用不同种群之间的遗传差异。这些分析将确定我们候选基因中最有可能的功能变异，并阐明SLE临床亚型的遗传和临床异质性。在目标2中，我们将预测和验证候选变体的功能效应。我们将首先从ENCODE数据中识别功能元件，包括蛋白质编码序列、转录调节区、伴随的染色质状态、表观遗传标记和eQTL信号。生物信息学和分子建模将指导在原代和培养细胞中的后续实验，以验证候选细胞的功能效应 基因表达和蛋白质功能的变异。进行这项提议的大部分数据和样本已经提供给我们。凭借我们的综合研究战略、积累的专业知识、良好的记录、可用的生物材料、资源和基础设施，我们有很强的潜力成功完成这一项目。我们期望这个项目能够识别与SLE相关的功能变异，并确定它们在相关生物通路中的作用，从而阐明狼疮的发病机制。最终，该项目可能为未来对受这些基因影响的系统性红斑狼疮和其他自身免疫性疾病的治疗干预提供基础。

DESCRIPTION (provided by applicant): Systemic lupus erythematosus (SLE or lupus) is a complex autoimmune disease characterized by a broad spectrum of clinical manifestations that arise from pathogenic autoantibody production. SLE disproportionately affects women and certain ethnic groups. Asians, African-Americans, and Hispanics show 3-5 fold higher prevalence and more severe clinical manifestations of SLE compared to European-Americans. Genetic factors strongly influence lupus development and progression, and genome-wide association studies (GWAS) have identified over 40 genetic associations for SLE susceptibility, mostly from the individuals with European ancestry. In order to understand the biological mechanisms that lead to disease sub-phenotypes in SLE, it is crucial to delineate the functional variants responsible for GWAS association signals. However, precisely delineating functional variants has been a major challenge, since associated variants from GWAS are often ''tags'' for haplotypes on which the actual functional variants reside. Our research team has acquired the experience, expertise, resources and infrastructure necessary to move beyond GWAS to accelerate discovery and characterization of the causal variants underlying these signals. We have successfully identified causal variants and their functional consequences in the ITGAM gene. We propose studying four SLE-susceptibility genes, IFIH1, ETS1, IKZF1, and PRDM1, that have been implicated in susceptibility to multiple autoimmune diseases, suggesting their broader roles in autoimmunity. Our primary goals are to define functional variants in these genes and explain their causal relationships with SLE and its clinical sub-phenotypes. In Aim 1 we will integrate our genotype and sequencing data from multi-ethnic cohorts with 1000 Genomes, while leveraging genetic differences between populations. These analyses will identify the most likely functional variants from our candidate genes, and elucidate genetic and clinical heterogeneity with SLE clinical sub-phenotypes. In Aim 2 we will predict and validate functional effects for candidate variants. We will first identify functional elements from ENCODE data, including protein coding sequence, transcriptional regulatory regions, attendant chromatin states, epigenetic marks, and eQTL signals. Bioinformatics and molecular modeling will guide follow-up experiments in primary and cultured cells to validate the functional effects of candidate variants on gene expression and protein function. Most of the data and samples for conducting this proposal are already available to us. With our integrated research strategy, cumulative expertise, strong track record, available biomaterials, resources and infrastructure, we have strong potential to successfully complete this project. We expect that this project will identify SLE-associated functional variants and define their effects on relevant biological pathways in order to elucidate the pathogenic mechanisms of lupus. Ultimately, this project could provide a basis for future therapeutic interventions for SLE and other autoimmune diseases influenced by these genes.