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

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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.