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Connecting AMD SNPs to Functions Using Allele-specific Interactions

使用等位基因特异性相互作用将 AMD SNP 连接到功能

基本信息

批准号：
10322157
负责人：
Jiang Qian
金额：
$ 47.19万
依托单位：
JOHNS HOPKINS UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-01-01 至 2025-11-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10322157
关键词：
ATAC-seq Affect Affinity Age related macular degeneration Alleles American Atrophic Base Pairing Binding Binding Proteins Binding Sites Biochemical Bioinformatics Biological Biological Assay Blindness CRISPR interference Cell Differentiation process Cell physiology Cells Chromatin Clustered Regularly Interspaced Short Palindromic Repeats DNA DNA Binding DNA Probes DNA-Binding Proteins DNA-Protein Interaction Data Development Disease ES Cell Line Effectiveness Elderly Electrophoretic Mobility Shift Assay Engineering Functional disorder Gene Expression Genetic Diseases Genetic Risk Genetic Transcription Genetic study Genome Goals Human Immunoprecipitation In Vitro Individual Interferometry Investigation Knowledge Lead Length Luciferases Maps Molecular Neurodegenerative Disorders Phenotype Photoreceptors Population Predisposition Protein Analysis Protein Array Protein Microchips Proteins Proteome Public Health Quantitative Trait Loci RNA-Binding Proteins Reporter Research Resources Retina Retinal Pigments Risk Role Series Single Nucleotide Polymorphism Site Specificity Stress Structure of retinal pigment epithelium Surveys Technology Testing Transcriptional Regulation Transposase Untranslated RNA Validation XCL1 gene base behavioral response bevacizumab cell behavior cell type chromatin immunoprecipitation complement system disorder risk effective therapy genetic risk factor genetic variant genome editing genome wide association study genomic locus high risk high throughput screening human embryonic stem cell human stem cells insight interest loss of function neovascular novel novel therapeutics predictive test risk variant screening stressor success transcription factor treatment strategy

项目摘要

PROJECT SUMMARY. Age-related Macular Degeneration (AMD) is a retinal neurodegenerative disease that is a major cause of vision loss among the elderly worldwide. Although anti-VEGF treatments can be effective in the treatment of the neovascular (“wet”) form of the disease, there are no proven and approved treatments for the more common atrophic (“dry”) form of the disease. Greater understanding of the genetics and disease mechanisms underlying AMD has the potential to aid in the development of more effective treatment strategies. Genomewide association studies (GWAS) have identified a large number of single nucleotide polymorphisms (SNPs) that are associated with increased risk of AMD. Although these GWAS studies have led to increased interest in the role of the complement system in AMD, the molecular mechanisms by which AMD risk alleles lead to increased risk for the disease are poorly understood. Understanding AMD risk SNPs is particularly challenging because most of them occur in non-coding regions of the genome. As one approach to this problem, expression quantitative trait loci (eQTLs) studies can identify SNPs that are likely to modulate downstream gene expression. However, eQTLs do not provide information on SNP-binding proteins. Determining intersecting GWAS SNPs with transcription factor (TF) binding sites by chromosomal immunoprecipitation sequencing (ChIP-seq) is another useful approach to identify functional SNPs and their interacting TFs, but this approach requires a priori knowledge of the relevant TFs. In this application, using an approach that has not, to our knowledge, been previously applied to AMD research, we propose to implement a Proteome-Wide Analysis of disease-associated SNPs (PWAS) study of non-protein coding region SNPs to identify allele-specific protein-DNA interactions and alteration of regulatory activity in AMD. The rationale for this approach is our hypothesis that functional AMD-related DNA SNPs likely execute their function via allele-specific interactions with specific proteins. We will survey the entire human TF and RNA-binding protein repertoires with SNP-carrying DNA probes using a protein array-based approach in which greater than 1,700 human transcription factors (TFs)/DNA binding proteins can be simultaneously surveyed for each probe. Identified allele-specific protein-DNA interactions will be prioritized using a series of bioinformatics analyses and validated using human retinal pigment epithelial (RPE) and photoreceptor (PR) cells differentiated from human stem cells. In Aim 1 we will identify TFs that show differential binding to allele-specific AMD-associated SNPs. Aim 2 will biochemically characterize and prioritize the TFs identified in Aim 1. Aim 3 will functionally characterize the identified AMD-SNP allele-specific protein interactions in AMD-relevant cell types, and explore how they affect cell behavior and response to AMD-related stressors. Taken together, we hope that these studies will provide new therapeutically relevant insights in the mechanisms underlying the development and progression of AMD.

项目总结。