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.

项目概要系统性红斑狼疮 (SLE) 是一种典型的自身免疫性疾病，其特征是免疫调节失调干扰素反应和对细胞抗原的自我耐受性丧失，导致炎症过程最终导致系统性终末器官损伤，尽管经过数十年的研究，其潜在机制仍不清楚。 SLE 发病机制的驱动因素仍不完全清楚。已鉴定出超过 100 个 SLE 风险单倍型，携带数百个功能重要性未知的 SNP 区分因果 SNP 和非因果 SNP，从而转化遗传。将知识转化为可操作的临床知识一直是一项费力、低效且资源密集的任务。我们的实验室开发了一种新方法来加快因果变异发现过程，我们使用表观基因组来识别风险单倍型的可能因果变异我们通过识别表观遗传变异来做到这一点。通过 ChIP 测量的稳定增强子和活性增强子中 SNP（“hQTL”）等位基因不平衡的足迹我们的方法能够识别连锁不平衡背景下的因果变异。通过识别等位基因不平衡，提供了推定因果变异具有功能性的先验证据我们还使用 3D 染色质拓扑数据来构建分子接线图。包含 hQTL 的相互作用的增强子和启动子，因为这些数据利用了不同的表观基因组。特定细胞和细胞状态的概况提供了有关细胞过程的重要上下文信息 epiQTL 在调节中最重要。R01 AR073606 的重新提交旨在 1) 使用表观基因组引导方法从原代 B 细胞中识别静息和刺激依赖性 hQTL；2) 验证并使用正交大规模确认归因于 hQTL 的等位基因特异性转录调控平行报告分析；3) 确定 hQTL 如何改变基因表达和 3D 染色质组织使用多重定量 PCR 和染色质分析 hQTL 调控网络中包含的基因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，并将有助于更好地理解人类系统性红斑狼疮和相关自身免疫性疾病基因型和表型之间的联系。