Leveraging GWAS Findings to Map Variants and Identify Novel Effector Genes for Alcohol-Related Traits

利用 GWAS 研究结果绘制变异图谱并识别酒精相关特征的新效应基因

• 批准号: 10657933
• 负责人: Struan F A Grant
• 金额: $ 64.63万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-01 至 2028-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10657933
• 关键词: 3-Dimensional; ATAC-seq; Address; Adult; Affect; African ancestry; Alcohol abuse; Alcohol consumption; Alcohols; Behavioral; Biological; Biological Models; Biological Process; CRISPR/Cas technology; Candidate Disease Gene; Cells; Cessation of life; Chromatin; Chromosome Mapping; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Data; Data Set; Development; Diagnosis; Diagnostic; Drosophila genus; Drosophila melanogaster; Electronic Health Record; Elements; Enhancers; Epigenetic Process; European ancestry; Gene Expression; Genes; Genetic; Genomics; Heavy Drinking; Heritability; Hi-C; Human; Individual; Induced pluripotent stem cell derived neurons; Laboratories; Latino; Light; Link; Maps; Measures; Medical; Meta-Analysis; Methods; Modeling; Molecular Genetics; Neighborhoods; Neurons; Neurotransmitters; Orthologous Gene; Pathway Analysis; Pathway interactions; Phenotype; Population; Prevention; Public Health; Regulatory Element; Reporting; Resolution; Resources; Sampling; Single Nucleotide Polymorphism; System; Testing; Therapeutic; Time; Twin Multiple Birth; Untranslated RNA; Variant; Veterans; alcohol behavior; alcohol effect; alcohol related gene; alcohol use disorder; binge drinking; biobank; candidate identification; causal variant; comorbidity; data integration; dopaminergic neuron; exome; fly; genetic architecture; genetic manipulation; genetic variant; genome wide association study; genome-wide; induced pluripotent stem cell; innovation; knock-down; novel; novel strategies; overexpression; phenome; pleiotropism; preference; programs; promoter; psychosocial; rare variant; risk variant; trait; transcriptome sequencing

More than one-quarter of U.S. adults report past-year binge drinking and 5.6% meet criteria for a past-year alcohol use disorder (AUD). These traits are associated with psychosocial disruption, medical co-morbidities, and nearly 10% of all U.S. deaths annually. Alcohol consumption and AUD have an estimated twin heritability of 43% and 49%, respectively. Genome-wide association studies (GWAS) of these traits have identified 380 genome-wide significant SNPs in 155 loci. In this revised application, we propose to use a “variant to gene mapping to clinical impact” approach, intersecting GWAS data with ATAC-seq and high-resolution promoter- focused Capture C neuronal datasets derived from human induced pluripotent stem cells (iPSCs) to identify potential effector genes. To prioritize SNPs, we will focus on those residing in open chromatin and with enhancer epigenetic marks; we will also use eQTL resources, as needed. We will validate these and newly identified candidates in three ways: 1) in established Drosophila models of alcohol behavioral effects, 2) initially with human iPSC-derived cortical and dopaminergic neurons and subsequently with neurons of other neurotransmitter systems, as indicated, to delete the genomic neighborhood harboring a putative causal variant to determine its effects on the gene's expression, and 3) with data from 4 biobanks to corroborate the association of the functionally validated genes with alcohol-related phenotypes. In Aim 1, we will expand our preliminary set of 43 loci from iPSC-derived cortical neurons, initially by applying similar methods to iPSC- derived dopaminergic neurons and other neuronal types, as indicated. In Aim 2a, we will screen candidate genes identified in preliminary findings and those identified in Aim 1 by knocking down or over-expressing their orthologs in fly models of alcohol consumption, preference, sensitivity, and tolerance. In Aim 2b, we will use SNP-CRISPR in human iPSC-derived neurons to test whether deleting the genomic neighborhood of putative causal variants from preliminary data or those identified in Aim 1 affects expression of their target gene(s). In Aim 3, we will use array and exome sequence data from both European- and African-ancestry individuals to validate all putative effector genes by examining their association with alcohol-related traits, conducting downstream analyses, testing rare variant effects, and examining pleiotropy in phenome-wide association studies. This project will identify novel genetic variants and the corresponding effector genes that contribute to alcohol-related traits, thereby shedding light on the biological pathways that influence the development of the traits. Study results will have fundamental implications for novel approaches to the diagnosis, prevention, and treatment of heavy drinking and AUD.

超过四分之一的美国成年人报告在过去一年中酗酒，5.6%的人符合过去一年的标准 酒精使用障碍(AUD)。这些特征与心理社会混乱、医学共病、 占美国每年死亡人数的近10%。据估计，饮酒和AUD具有孪生遗传性 分别为43%和49%。对这些性状的全基因组关联研究(GWAS)已经确定了380个 155个基因座的全基因组显著SNPs。在这个修改后的申请中，我们建议使用一种“基因的变体” 映射到临床影响“的方法，将Gwas数据与ATAC-SEQ和高分辨率启动子- 从人诱导多能干细胞(IPSCs)获得的聚焦捕获C神经元数据集用于鉴定 潜在的效应基因。为了确定SNPs的优先顺序，我们将重点关注那些存在于开放染色质和 增强表观遗传标记；我们还将根据需要使用eQTL资源。我们将验证这些和新的 通过三种方式确定候选者：1)在已建立的酒精行为影响的果蝇模型中，2)最初 与人IPSC来源的皮质和多巴胺能神经元以及随后与其他 神经递质系统，如图所示，删除含有推定原因的基因组邻域 变种以确定其对基因表达的影响，以及3)使用来自4个生物库的数据来证实 功能验证基因与酒精相关表型的关联。在目标1中，我们将扩大我们的 来自IPSC皮质神经元的43个基因座的初步设置，最初是通过对IPSC应用类似的方法- 衍生的多巴胺能神经元和其他神经元类型，如图所示。在目标2a中，我们将筛选候选人 在初步发现中确定的基因和在目标1中通过敲除或过度表达其基因而确定的基因 果蝇模型中的酒精消耗量、偏好、敏感性和耐受性的同源基因。在目标2b中，我们将使用 SNP-CRISPR在人IPSC来源神经元中检测是否删除假定的基因组邻域 初步数据的因果变异或AIM 1中确定的变异会影响其目标基因的表达(S)。在……里面 目标3，我们将使用来自欧洲和非洲血统的个体的阵列和外显子组序列数据来 通过检查它们与酒精相关特征的关联来验证所有假定的效应基因，进行 下游分析，测试罕见的变异效应，并检查表型范围内的多效性 学习。该项目将识别新的遗传变异和相应的效应基因，这些基因有助于 与酒精相关的特征，从而揭示了影响酒精发育的生物途径 特征。研究结果将对新的诊断、预防和治疗方法具有重要意义。 酗酒和AUD的治疗。