Virus-driven human gene misregulation in disease

病毒驱动的人类疾病基因失调

基本信息

批准号：
10388202
负责人：
Matthew Tyson Weirauch
金额：
$ 67.26万
依托单位：
CINCINNATI CHILDRENS HOSP MED CTR
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：
2020-06-15 至 2024-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10388202
关键词：
ATAC-seq Algorithms Alleles Autoimmune Autoimmune Diseases Behavior Binding Biological Assay CRISPR/Cas technology Cause of Death Cell Line Cell Proliferation Cells ChIP-seq Chromatin Chromatin Loop Clustered Regularly Interspaced Short Palindromic Repeats Communities Computer Models Data Data Set Dependence Disease Disease Progression Environment Family Foundations Gene Expression Gene Expression Regulation Genes Genetic Genetic Diseases Genetic Risk Genetic Transcription Genome Growth Factor HIV Health Herpes zoster disease Herpesviridae Herpesviridae Infections Human Human Genome Human Herpesvirus 4 Human Herpesvirus 8 Human Papillomavirus Individual Libraries Link Lupus Malignant Neoplasms Malignant neoplasm of lung Malignant neoplasm of urinary bladder Maps Measures Mission Modeling Molecular Monitor Multiple Sclerosis National Human Genome Research Institute Nature Papillomavirus Pathogenesis Pathogenicity Pathologic Phenotype Physiological Play Process Regulator Genes Reporter Research Resources Role Technology Testing Therapeutic Transfection Update Variant Viral Virus Virus Diseases base chromatin immunoprecipitation computational pipelines computerized tools cytokine data tools disorder risk functional genomics genetic variant genome editing genome-wide genomic data genomic locus human disease insight novel novel strategies novel therapeutics pathogen release factor risk variant tat Protein therapy development transcription factor transcriptome sequencing

项目摘要

ABSTRACT Thousands of genetic variants have been established for hundreds of human diseases. Yet, the vast majority of these diseases remain idiopathic. Interplay between genetics and the environment likely plays a role in many diseases. In particular, hundreds of associations between viral exposure and disease risk have been established. But with rare exceptions, the mechanisms underlying increased disease risk are unknown. We have recently discovered that the Epstein-Barr virus EBNA2 transcriptional co-factor binds up to half of the risk loci associated with seven autoimmune diseases (142 loci in total), with many examples of allele-dependent EBNA2 binding to autoimmune risk variants. We hypothesize that risk allele-dependent binding of viral TFs explains why other viruses cause or influence specific diseases. However, the data required to discover these mechanisms are currently incomplete. Herpesviruses and human papilloma virus play established roles in several human diseases, and their genomes encode many TFs. We will generate the functional genomics datasets needed to discover the roles of these viral TFs (vTFs) in human disease processes. We anticipate discovering multiple causal human disease variants whose mechanisms act in a viral TF and allele- dependent manner, leading to understanding of disease mechanisms and new therapeutic opportunities. Our approach is a generalizable blueprint for global characterization of pathogenic effects on host gene regulation. Aim 1. Create global maps of viral TF-driven human gene regulation. For eight viruses, we will transfect a viral TF into physiologically and pathologically relevant human primary cells and cell lines. We will measure the effect of vTFs on human gene expression by performing RNA-seq in cells with and without vTF transfection. We will monitor the binding of vTFs to the human genome using chromatin immunoprecipitation and calculate the enrichment of each vTF at established risk loci for all human diseases using our RELI algorithm. Aim 2. Uncover the mechanisms and downstream functional impact of viral TF-human genome interactions. We will characterize the mechanisms by which vTFs alter the human regulatory landscape. We will measure the effect of vTFs on human chromatin accessibility (ATAC-seq) and DNA looping (HiChIP-seq). We will use these datasets to construct computational models evaluating disease-relevant mechanisms. We will examine downstream effects of vTF activity on human cell phenotypes by monitoring cell proliferation, cytokine release, and growth factor release subsequent to vTF transfection. Aim 3. Test the allele-dependency of viral TF-provoked human disease mechanisms. We will identify vTF interactions involving human disease risk allele-dependent mechanisms. We will functionally screen for vTF- and disease risk allele-dependent effects on gene regulatory activity using Massively Parallel Reporter Assays. We will interrogate virus-host genomic datasets for allelic behavior using our MARIO computational pipeline. We will validate risk allele-dependent vTF mechanisms using CRISPR-based genome editing.

抽象的已针对数百种人类疾病建立了数千种遗传变异。然而，广阔的大多数这些疾病仍然是特发性的。遗传学和环境之间的相互作用可能发挥作用在许多疾病中。特别是，病毒暴露与疾病风险之间存在数百种关联。已确立的。但除了极少数例外，疾病风险增加的机制尚不清楚。我们有最近发现 Epstein-Barr 病毒 EBNA2 转录辅助因子与多达一半的风险位点结合与 7 种自身免疫性疾病相关（总共 142 个位点），其中有许多等位基因依赖性 EBNA2 的例子与自身免疫风险变异结合。我们假设病毒转录因子的风险等位基因依赖性结合解释了为什么其他病毒会引起或影响特定疾病。然而，发现这些所需的数据目前机制尚不完善。疱疹病毒和人乳头瘤病毒在多种人类疾病，其基因组编码许多转录因子。我们将生成功能基因组学发现这些病毒转录因子（vTF）在人类疾病过程中的作用所需的数据集。我们预计发现多种致病人类疾病变异，其机制作用于病毒 TF 和等位基因依赖的方式，导致对疾病机制的理解和新的治疗机会。我们的该方法是对宿主基因调控的致病效应进行全球表征的通用蓝图。目标 1. 创建病毒 TF 驱动的人类基因调控的全球图谱。对于八种病毒，我们将将病毒 TF 转染到生理和病理相关的人类原代细胞和细胞系中。我们将通过在有和没有 vTF 的细胞中进行 RNA-seq 来测量 vTF 对人类基因表达的影响转染。我们将使用染色质免疫沉淀监测 vTF 与人类基因组的结合并使用我们的 RELI 算法计算每个 vTF 在所有人类疾病的已确定风险位点的富集度。目标2.揭示病毒TF-人类基因组的机制和下游功能影响互动。我们将描述 vTF 改变人类监管环境的机制。我们将测量 vTF 对人类染色质可及性 (ATAC-seq) 和 DNA 循环 (HiChIP-seq) 的影响。我们将使用这些数据集构建评估疾病相关机制的计算模型。我们将通过监测细胞增殖、细胞因子来检查 vTF 活性对人类细胞表型的下游影响 vTF 转染后释放和生长因子释放。目标 3. 测试病毒 TF 引发的人类疾病机制的等位基因依赖性。我们将识别涉及人类疾病风险等位基因依赖性机制的 vTF 相互作用。我们将在功能上使用大规模并行筛选 vTF 和疾病风险等位基因依赖性对基因调控活性的影响记者分析。我们将使用我们的 MARIO 询问病毒宿主基因组数据集的等位基因行为计算管道。我们将使用基于 CRISPR 的基因组验证风险等位基因依赖性 vTF 机制编辑。