Andy B. Chen, Xuhong Yu, Kriti S. Thapa, Hongyu Gao, Jill L Reiter et al.
Although genome-wide association studies (GWAS) have identified loci associated with alcohol consumption and alcohol use disorder (AUD), they do not identify which variants are functional. To approach this, we evaluated the impact of variants in 3’ untranslated regions (3’-UTRs) of genes in loci associated with substance use and neurological disorders using a massively parallel reporter assay (MPRA) in neuroblastoma and microglia cells. Functionally impactful variants explained a higher proportion of heritability of alcohol traits than non-functional variants. We identified genes whose 3’UTR activities are associated with AUD and alcohol consumption by combining variant effects from MPRA with GWAS results. We examined their effects by evaluating gene expression after CRISPR inhibition of neuronal cells and stratifying brain tissue samples by MPRA-derived 3’-UTR activity. A pathway analysis of differentially expressed genes identified inflammation response pathways. These analyses suggest that variation in response to inflammation contributes to the propensity to increase alcohol consumption.
Andy B. Chen, Xuhong Yu, Kriti S. Thapa, Hongyu Gao, Jill L Reiter, Xiaoling Xuei, Andy P. Tsai, Gary E. Landreth, Dongbing Lai, Yue Wang, Tatiana M. Foroud, Jay A. Tischfield, Howard J. Edenberg, Yunlong Liu. Functional 3’-UTR Variants Identify Regulatory Mechanisms Impacting Alcohol Use Disorder and Related Traits. 2024-02-05. https://doi.org/10.1101/2024.01.31.578270
The 24,780-oligo library representing reference and alternative alleles for 13,515 candidate 3′-UTR SNPs was assayed in SV40-immortalized human microglia across six independent transfections. Matched plasmid DNA and poly(A) RNA/cDNA UMI counts were used to quantify allele-specific 3′-UTR reporter activity.
The 24,780-oligo library representing reference and alternative alleles for 13,515 candidate 3′-UTR SNPs was assayed in SH-SY5Y human neuroblastoma cells across six independent transfections. Matched plasmid DNA and poly(A) RNA/cDNA UMI counts were used to quantify allele-specific 3′-UTR reporter activity.
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