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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：
10614380
负责人：
Matthew Tyson Weirauch
金额：
$ 65.95万
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 2025-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10614380
关键词：
Algorithms Alleles Autoimmune Autoimmune Diseases BZLF1 gene 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 Reapplication Regulator Genes Reporter Research Resources Role Technology Testing Therapeutic Transfection Update Variant Viral Virus Virus Diseases chromatin immunoprecipitation cofactor 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.

摘要