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去年酗酒，5.6%的人符合去年的标准 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%酒精消费和AUD具有估计的双胞胎遗传力 分别为43%和49%。这些性状的全基因组关联研究（GWAS）已经确定了380个 在155个基因座中存在全基因组显著的SNPs。在这个修改后的申请中，我们建议使用“基因变体”， 映射到临床影响”的方法，将GWAS数据与ATAC-seq和高分辨率启动子交叉， 来自人类诱导多能干细胞（iPSC）的聚焦Capture C神经元数据集， 潜在的效应基因为了优先考虑SNP，我们将重点关注那些位于开放染色质中的SNP， 增强子表观遗传标记;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人：1）在建立的酒精行为影响的果蝇模型中，2）最初 与人iPSC衍生的皮质和多巴胺能神经元以及随后与其他神经元的神经元进行比较。 神经递质系统，如所示，删除基因组附近窝藏一个假定的因果关系， 变异，以确定其对基因表达的影响，和3）从4个生物库的数据，以证实 功能验证的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衍生的皮质神经元的43个基因座的初步集合，最初通过对iPSC应用类似的方法- 衍生的多巴胺能神经元和其它神经元类型。在目标2a中，我们将筛选候选人 在初步发现中鉴定的基因和在Aim 1中通过敲低或过表达其 在酒精消耗、偏好、敏感性和耐受性的果蝇模型中的直系同源物。在目标2b中，我们将使用 SNP-CRISPR在人类iPSC衍生的神经元中的表达，以测试是否删除了推定的iPSC基因的基因组邻域。 来自初步数据的致病变体或在目标1中鉴定的那些影响其靶基因的表达。在 目标3，我们将使用来自欧洲和非洲血统个体的阵列和外显子组序列数据， 通过检查所有假定的效应基因与酒精相关性状的关联来验证它们， 下游分析，测试罕见变异效应，并检查全表型关联中的多效性 问题研究该项目将确定新的遗传变异和相应的效应基因，有助于 酒精相关的性状，从而阐明影响发展的生物学途径， 性状研究结果将对新的诊断、预防和治疗方法产生重要影响。 酗酒和澳元的治疗。