Epigenome-Guided Causal Variant Discovery and Mechanisms

表观基因组引导的因果变异发现和机制

基本信息

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
项目类别：
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

项目摘要

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.

项目摘要全身性红斑狼疮（SLE）是一种原型自身免疫性疾病，其特征是失调干扰反应和对细胞抗原的自我耐受性丧失，这导致炎症过程最终导致系统性的最终器官损坏。尽管进行了数十年的研究，但基本机制驱动SLE的发病机理仍然不完全理解。全基因组关联研究（GWAS）已经确定了100多个携带数百个SNP的SLE风险单倍型，功能不明在疾病发作和进展中。区分因果与非毒物SNP，从而翻译遗传对可行的临床知识的知识一直是实验室，效率低下且资源密集的任务。我们的实验室已经开发了一种新方法来加快因果变体发现过程鉴定风险单倍型上可能因果变异的表观基因组。我们通过识别表观遗传来做到这一点通过芯片测量的中毒和活性增强子中SNP（“ HQTLS”）的Allic不平衡的足迹测序。我们的方法能够在连锁disequilbirium和提供了先验的证据，表明假定的因果变体通过识别等位基因失衡而起作用组蛋白标记的大小。我们还使用3D染色质拓扑数据来构建分子接线图相互作用的增强子和包含HQTL的启动子。由于这些数据利用表观基因组不同特定细胞和细胞状态中的轮廓提供了有关哪些细胞过程的重要上下文信息 EPIQTL在确定方面最重要。 R01 AR073606的此重新提交旨在1）表观基因组引导的方法，以鉴定来自原代B细胞的静息和刺激依赖性HQTL； 2）验证并确认具有大规模正交归因于HQTL的等位基因特异性转录调节平行记者测定； 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和染色质的HQTL调节网络中包含的基因构象捕获（3C）。我们相信该项目将我们定位在因果变体的前沿识别和风险单倍型功能表征，将有助于更好地理解人SLE和相关自身免疫性疾病的基因型和表型之间的联系。