Epigenome-Guided Causal Variant Discovery and Mechanisms

表观基因组引导的因果变异发现和机制

• 批准号: 10158442
• 负责人: Patrick M Gaffney
• 金额: $ 64.11万
• 依托单位: OKLAHOMA MEDICAL RESEARCH FOUNDATION
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-05-06 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10158442
• 关键词: 3-Dimensional; Address; Agonist; Alleles; Allelic Imbalance; Antigen-Antibody Complex; Antigens; Autoantibodies; Autoantigens; Autoimmune Diseases; Automobile Driving; B-Cell Antigen Receptor; B-Lymphocytes; Bioinformatics; Biological Assay; Blood donor; CD40 Ligand; Cell Line; Cell physiology; Cells; ChIP-seq; Chromatin; Chromatin Loop; Complement; Complex; Control Groups; DNA Resequencing; Data; Databases; Disease; Disease Progression; Enhancers; Epigenetic Process; Exhibits; Exposure to; Gene Expression; Gene Structure; Genes; Genetic; Genetic Diseases; Genetic Predisposition to Disease; Genetic Research; Genetic Risk; Genetic Translation; Genomic Segment; Genotype; Haplotypes; Histones; Human; Human Herpesvirus 4; Imiquimod; Immune System Diseases; Immune Tolerance; Immunoglobulin M; Inflammatory; Influentials; Interferons; Knowledge; Laboratories; Lead; Linkage Disequilibrium; Maps; Measures; Messenger RNA; Methods; Molecular; Onset of illness; Organ; Pathogenesis; Pathway interactions; Phenotype; Positioning Attribute; Precision Medicine Initiative; Process; Production; Publishing; Quantitative Trait Loci; Regulation; Reporter; Reproducibility; Research; Resources; Rest; Risk; Sampling; Scanning; Self Tolerance; Stimulus; Systemic Lupus Erythematosus; TLR7 gene; Technology; Testing; Transcriptional Regulation; Translating; Variant; case control; causal variant; chromatin modification; chromosome conformation capture; clinically actionable; crosslink; disorder risk; epigenome; experimental study; gene expression variation; genetic variant; genome wide association study; genome-wide; innovation; novel strategies; promoter; response; risk variant; transcriptome sequencing

PROJECT SUMMARY Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterized by dysregulated interferon responses and loss of self-tolerance to cellular antigens, which result in inflammatory processes that ultimately lead to systemic end-organ damage. Despite decades of research, the underlying mechanisms driving the pathogenesis of SLE remain incompletely understood. Genome-wide association studies (GWAS) have identified over 100 SLE risk haplotypes carrying hundreds of SNPs with unknown functional importance in disease onset and progression. Distinguishing causal from non-causal SNPs, and thus translating genetic knowledge into actionable clinical knowledge has been a laborious, inefficient, and resource-intensive task. Our laboratory has developed a new approach to expedite the causal variant discovery process where we use the epigenome to identify likely causal variants on risk haplotypes. We do this by identifying epigenetic footprints of allelic imbalance at SNPs (“hQTLs”) in poised and active enhancers measured by ChIP- sequencing. Our approach is able to identify causal variants in the context of linkage disequilibrium and provides a priori evidence that the putative causal variant is functional by identifying allelic imbalance in the magnitude of histone marks. We also use 3D chromatin topology data to construct a molecular wiring diagram of interacting enhancers and promoters that contain hQTLs. Since these data leverage the epigenome distinct profiles in specific cells and cell states provide important contextual information about what cellular processes the epiQTL is most important in regulating. This resubmission of R01 AR073606 aims to 1) use an epigenome-guided approach to identify resting and stimulus-dependent hQTLs from primary B cells; 2) validate and confirm the allele-specific transcriptional regulation attributed to hQTLs using an orthogonal massively parallel reporter assay; and 3) determine how hQTLs modify gene expression and 3D chromatin organization of genes contained within regulatory networks of hQTLs using multiplex quantitative PCR and chromatin conformation capture (3C). We believe this project positions us at the leading edge of causal variant identification and risk haplotype functional characterization and will contribute to a better understanding of the connection between genotype and phenotype for human SLE and related autoimmune diseases.

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，这导致炎性过程， 最终导致系统性终末器官损伤。尽管经过几十年的研究， 驱动SLE的发病机制仍不完全清楚。全基因组关联研究（GWAS） 已经鉴定了超过100种SLE风险单倍型，携带数百种功能重要性未知的SNP 疾病的发生和发展。区分因果和非因果SNP，从而将遗传 将知识转化为可操作的临床知识是一项费力、低效和资源密集的任务。 我们的实验室已经开发出一种新的方法来加快因果变异发现过程， 表观基因组，以确定风险单倍型可能的因果变异。我们通过鉴定表观遗传 通过ChIP测量的平衡和活性增强子中SNP（“hQTL”）处等位基因不平衡的足迹， 测序我们的方法能够在连锁不平衡的背景下识别因果变异， 提供了一个先验的证据，即假定的因果变异是功能性的，通过鉴定等位基因的不平衡， 组蛋白标记的大小。我们还使用3D染色质拓扑数据来构建分子布线图 相互作用的增强子和含有hQTL的启动子。由于这些数据利用了表观基因组独特的 特定细胞和细胞状态中的概况提供了关于哪些细胞过程 epiQTL在调控中是最重要的。R 01 AR 073606的重新提交旨在1）使用 表观基因组引导的方法来鉴定来自原代B细胞的静息和刺激依赖性hQTL; 2）验证 并利用正交大规模实验验证了hQTL的等位基因特异性转录调控作用 平行报告基因分析; 3）确定hQTL如何修饰基因表达和3D染色质组织 使用多重定量PCR和染色质 构象捕获（3C）。我们相信这个项目使我们处于因果变异的前沿 识别和风险单倍型功能表征，并将有助于更好地了解 SLE与相关自身免疫性疾病基因型和表型的关系