Functional consequences of intergenic autoimmune disease risk variants

基因间自身免疫性疾病风险变异的功能后果

• 批准号: 10655161
• 负责人: F. Yesim Demirci
• 金额: $ 88.36万
• 依托单位: HOSPITAL FOR SPECIAL SURGERY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-03-03 至 2028-02-29
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10655161
• 关键词: ATAC-seq; Alleles; Autoimmune Diseases; B-Lymphocytes; Binding; Binding Proteins; Biological; Biological Assay; CRISPR/Cas technology; Cell Line; Cell surface; Cells; Chromatin; Chromosomes; Code; Complex; Computing Methodologies; Data; Data Set; Disease; Electrophoretic Mobility Shift Assay; Elements; Enhancers; Experimental Designs; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genome; Heritability; Human; Human Cell Line; Immune; Immune system; Individual; Interferon Type I; Interferon alpha; Knock-out; Knowledge; Lead; Lupus; Macrophage; Measures; Mediating; Memory B-Lymphocyte; Messenger RNA; Methods; Modeling; Morbidity - disease rate; Outcome; Pathogenesis; Pathogenicity; Pathway interactions; Patients; Pattern; Phenotype; Plasmids; Production; Proteins; RNA analysis; Regulatory Element; Reporter; Reporting; Risk; Role; Site; Small Interfering RNA; System; Systemic Lupus Erythematosus; TLR7 gene; Testing; Transfection; Untranslated RNA; Variant; Viral Genes; candidate identification; cell type; cytokine; disorder risk; experimental study; genetic variant; genome editing; genome wide association study; immunopathology; in silico; ineffective therapies; knock-down; mRNA Expression; monocyte; mortality; new therapeutic target; novel; risk variant; transcription factor; transcriptome sequencing

ABSTRACT Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease characterized by high morbidity and mortality, and largely ineffective treatments. SLE is genetically complex with strong familial aggregation and high heritability. Most of the risk alleles for SLE are not protein-coding sequence changes, suggesting that a significant portion of disease risk is mediated by regulatory variants in the noncoding genome. At a recently identified intergenic SLE risk locus on chromosome 12q12, our in silico analyses implicate the risk variants as eQTLs that impact transcription of genes in multiple biological pathways that contribute to SLE immunopathology, including type I interferon (IFN) and anti-viral genes. This intergenic SLE risk locus is enriched in regulatory elements and resides adjacent to several long non-coding RNA (lncRNA) genes. In this proposal, we outline a comprehensive set of mechanistic and functional experiments to understand the role of the 12q12 risk locus in human immune cells. We hypothesize that several variants within cis-regulatory elements at the 12q12 locus alter the expression of adjacent lncRNAs, which in turn exert cis and trans effects on immune system genes resulting in increased SLE risk. An alternate hypothesis is that the 12q12 locus could be a long-range enhancer for nearby protein- coding and/or non-coding genes. These hypotheses are not mutually exclusive, and our experimental design will detect each possibility. In Aim 1, we will determine the overall impact of the intergenic 12q12 locus on gene regulation in primary immune cells and selected cell lines. Integrative analyses will be used to infer lncRNA influences on mRNA networks. Candidate lncRNAs from these analyses will be knocked down with siRNAs to confirm their function. In Aim 2, we will identify causal cis-regulatory elements in the intergenic 12q12 region. We will use complementary methods to identify likely regulatory elements, and putative causal elements will be knocked out in cell lines to confirm function and reversion to a non-risk cellular phenotype. We expect to find that the intergenic 12q12 locus influences the expression of adjacent lncRNAs and/or neighboring protein-coding or non-coding genes in a cell type-specific manner, resulting in simultaneous modulation of multiple biological pathways involved in SLE pathogenesis. This knowledge could suggest novel therapeutic targets for SLE that would influence multiple pathogenic pathways. This represents a novel mechanism of disease in SLE and provides an illustration of how intergenic risk variants can function in complex disease pathogenesis.

抽象的 全身性红斑狼疮（SLE）是一种多系统自身免疫性疾病，其特征是发病率高和 死亡率，在很大程度上无效的治疗方法。 SLE在遗传上很复杂，家族聚集很强，高 遗传力。 SLE的大多数风险等位基因不是蛋白质编码序列的变化，这表明显着 疾病风险的一部分是由非编码基因组中的调节变异介导的。在最近确定的 基因间SLE风险基因座上的染色体12q12，我们的硅中分析意味着风险变体是eqtls 在多种生物学途径中的基因的影响转录，导致SLE免疫病理学，包括 I型干扰素（IFN）和抗病毒基因。这个基因间SLE风险基因座丰富了调节元素和 驻留在几个长的非编码RNA（LNCRNA）基因附近。在此提案中，我们概述了一个全面的 一组机械和功能实验，以了解12q12风险基因座在人免疫中的作用 细胞。我们假设12q12基因座的顺式调节元素内的几种变体改变了表达式 相邻的lncrNA，进而对免疫系统基因施加顺序和反式影响，导致增加 SLE风险。另一种假设是12q12基因座可能是附近蛋白质的远程增强子 编码和/或非编码基因。这些假设不是相互排斥的，我们的实验设计将 检测每种可能性。在AIM 1中，我们将确定基因间12q12基因座对基因的总体影响 原代免疫细胞和选定细胞系中的调节。集成分析将用于推断lncRNA 对mRNA网络的影响。这些分析中的候选LNCRNA将被sirnas击倒 确认其功能。在AIM 2中，我们将确定基因间12q12区域中的因果关系调节元件。 我们将使用互补方法来识别可能的调节元素，并且假定的因果因素将是 在细胞系中撞倒以确认功能并重新转换为非风险的细胞表型。我们希望找到 基因间12q12基因座影响相邻lncRNA和/或相邻蛋白质编码或 以细胞类型特异性方式进行非编码基因，从而同时调节多个生物学 涉及SLE发病机理的途径。这些知识可以暗示SLE的新型治疗靶标 会影响多种致病途径。这代表了SLE和 提供了基因间风险变异在复杂疾病发病机理中如何发挥作用的说明。