Biophysical and functional characterization of immune-related regulatory elements and noncoding variants

免疫相关调节元件和非编码变体的生物物理和功能表征

基本信息

批准号：
10355488
负责人：
TREVOR W SIGGERS
金额：
$ 55.86万
依托单位：
BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-03-16 至 2025-02-28
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10355488
关键词：
Accounting Address Affect Allelic Imbalance Autoimmune Diseases Automobile Driving B-Lymphocytes Binding Binding Sites Biological Assay Biophysical Process Biophysics CISH gene CRISPR/Cas technology Cell Culture Techniques Cell Line Cells Chromatin Complex DNA DNA Binding Data Data Set Disease Disease susceptibility Elements Enhancers Etiology Foundations Gene Expression Gene Expression Regulation Genes Genetic Genetic Transcription Genetic study Genome Genomic approach Goals Human Immune Immune System Diseases Immunological Models Lead Link Maps Mass Spectrum Analysis Measurement Methods Modeling Molecular Mutagenesis Nucleotides Pharmaceutical Preparations Predisposition Proteomics Regulator Genes Regulatory Element Reporter Reporter Genes Resolution Rest Single Nucleotide Polymorphism Stimulus T-Lymphocyte Testing Therapeutic Translating Untranslated RNA Variant base biophysical model causal variant cell type chromatin immunoprecipitation cofactor complex data disease phenotype exhaustion genetic variant genome wide association study in vivo inhibitor therapy macrophage promoter targeted treatment therapeutic target

项目摘要

Project Summary Susceptibility to diverse immune diseases has been associated with genetic differences that affect gene expression. Understanding the mechanisms by which these genetic differences lead to disease has been a central goal of genomic efforts aimed at describing disease mechanisms and identifying targets for therapeutic treatments. While large-scale studies have identified thousands of genetic differences associated with immune diseases, in most cases, it is not known which variants are causal and which are non-causal passenger variants. This is a considerable problem for the many variants that exists in non-coding regions of the genome for which function is difficult to predict. Thus, there is a critical need for the high-throughput experimental approaches to characterize the function and mechanism of the many non-coding variants associated with immune diseases. To tackle this challenge, we will use two complementary high-throughput approaches to study the impact of genetic variants on immune gene expression. We will use MPRAs (Massively Parallel Reporter Assays) to study the impact of genetic variants on gene expression. We will use our recently developed CASCADE (Comprehensive Assessment of Complex Assembly at DNA Elements) approach, in conjunction with mass spectrometry-based studies, to profile the impact of genetic variants on TF- cofactor complex binding. We will use these approaches to characterize (1) the impact of genetic variants on ~30 immune gene regulatory elements, and (2) ~5000 genetic variants found to be associated with immune disease or altered gene expression. Combining these approaches will address both function and biophysical mechanism of genetic variants in a cell- and stimulus-specific manner. Furthermore, as many regulatory cofactors can be inhibited with drugs, characterizing TF- cofactor complexes bound at genetic variants provides an opportunity to identify therapeutics to counteract their effects. Altogether, by integrating complementary, high-throughput approaches that directly account for effects of cell type and cell stimulation, the proposed studies will identify the mechanisms by which non-coding variants affect gene expression and immune diseases. Furthermore, these studies will lay a foundation for translating large-scale genetic studies into therapeutic approaches to treat for immune diseases.

项目概要对多种免疫疾病的易感性与影响的遗传差异有关基因表达。了解这些遗传差异导致疾病的机制一直是基因组工作的核心目标，旨在描述疾病机制和识别治疗的目标。虽然大规模研究已经确定了数千种基因与免疫疾病相关的差异，在大多数情况下，不知道哪些变异是因果乘客变体和非因果乘客变体。这对很多人来说都是一个很大的问题基因组非编码区域中存在的变异，其功能难以预测。因此，迫切需要高通量实验方法来表征该功能以及与免疫疾病相关的许多非编码变异的机制。为了解决这个问题挑战中，我们将使用两种互补的高通量方法来研究遗传的影响免疫基因表达的变异。我们将使用 MPRA（大规模并行报告基因检测）来研究遗传变异对基因表达的影响。我们将使用我们最近开发的 CASCADE（DNA 元素复杂组装的综合评估）方法，结合基于质谱的研究，来分析遗传变异对 TF-的影响辅因子复合物结合。我们将使用这些方法来表征（1）遗传的影响约 30 个免疫基因调控元件的变异，以及 (2) 发现约 5000 个遗传变异与免疫疾病或基因表达改变有关。结合这些方法将解决细胞和刺激特异性遗传变异的功能和生物物理机制方式。此外，由于许多调节辅助因子可以被药物抑制，因此 TF- 与遗传变异结合的辅因子复合物提供了识别治疗方法的机会抵消它们的影响。总而言之，通过整合互补的高通量方法，直接考虑细胞类型和细胞刺激的影响，拟议的研究将确定非编码变异影响基因表达和免疫疾病的机制。此外，这些研究将为大规模遗传学研究转化为基础奠定基础。治疗免疫疾病的治疗方法。