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过去一年曾酗酒，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、医疗并发症、 据估计，美国每年有近 10% 的酒精消费和澳元具有双胞胎遗传力。 这些性状的全基因组关联研究 (GWAS) 分别鉴定了 380 个。 155 个位点的全基因组显着 SNP 在此修订后的申请中，我们建议使用“基因变体”。 映射到临床影响”方法，将 GWAS 数据与 ATAC-seq 和高分辨率启动子相交叉 重点捕获源自人类诱导多能干细胞 (iPSC) 的 C 神经数据集，以识别 为了优先考虑潜在的效应基因，我们将重点关注那些位于开放染色质中的基因。 增强子表观遗传标记；我们还将根据需要使用 eQTL 资源，我们将验证这些资源。 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 与人类 iPSC 衍生的皮质和多巴胺能神经元以及随后与其他神经元 神经递质系统，如所示，删除含有假定因果关系的基因组邻域 变体以确定其对基因表达的影响，3) 使用来自 4 个生物库的数据来证实 在目标 1 中，我们将扩展功能验证基因与酒精相关表型的关联。 最初通过对 iPSC 衍生的皮层神经元应用类似的方法，初步确定了 43 个位点 衍生的多巴胺能神经元和其他神经元类型，如目标 2a 所示，我们将筛选候选者。 初步发现中确定的基因以及目标 1 中通过敲低或过度表达其确定的基因 在目标 2b 中，我们将使用酒精消耗、偏好、敏感性和耐受性的果蝇模型中的直向同源物。 SNP-CRISPR 在人类 iPSC 衍生神经元中测试是否删除假定的基因组邻域 初步数据或目标 1 中确定的因果变异会影响其靶基因的表达。 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来 通过检查所有假定的效应基因与酒精相关特征的关联来验证它们，进行 下游分析，测试罕见变异效应，并检查全表组关联中的多效性 该项目将鉴定新的遗传变异和相应的效应基因。 酒精相关特征，从而揭示影响酒精发育的生物学途径 研究结果将对诊断、预防和治疗的新方法产生根本性影响。 治疗酗酒和澳元。