Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders

Xi Rao, Kriti S. Thapa, Andy B. Chen, Hai Lin, Hongyu Gao, Jill Reiter, Katherine A. Hargreaves, Joseph Ipe, Dongbing Lai, Xiaoling Xuei, Yue Wang, Hongmei Gu, Manav Kapoor, Sean P. Farris, Jay Tischfield, Tatiana Foroud, Alison M. Goate, Todd Skaar, R. Dayne Mayfield, Howard EdenbergYunlong Liu

Research output: Contribution to journalArticle

Abstract

Genome-wide association studies (GWAS) of complex traits, such as alcohol use disorders (AUD), usually identify variants in non-coding regions and cannot by themselves distinguish whether the associated variants are functional or in linkage disequilibrium with the functional variants. Transcriptome studies can identify genes whose expression differs between alcoholics and controls. To test which variants associated with AUD may cause expression differences, we integrated data from deep RNA-seq and GWAS of four postmortem brain regions from 30 subjects with AUD and 30 controls to analyze allele-specific expression (ASE). We identified 88 genes with differential ASE in subjects with AUD compared to controls. Next, to test one potential mechanism contributing to the differential ASE, we analyzed single nucleotide polymorphisms (SNPs) in the 3′ untranslated regions (3′UTR) of these genes. Of the 88 genes with differential ASE, 61 genes contained 437 SNPs in the 3′UTR with at least one heterozygote among the subjects studied. Using a modified PASSPORT-seq (parallel assessment of polymorphisms in miRNA target-sites by sequencing) assay, we identified 25 SNPs that affected RNA levels in a consistent manner in two neuroblastoma cell lines, SH-SY5Y and SK-N-BE(2). Many of these SNPs are in binding sites of miRNAs and RNA-binding proteins, indicating that these SNPs are likely causal variants of AUD-associated differential ASE. In sum, we demonstrate that a combination of computational and experimental approaches provides a powerful strategy to uncover functionally relevant variants associated with the risk for AUD.

Original languageEnglish (US)
JournalMolecular Psychiatry
DOIs
StateAccepted/In press - Jan 1 2019

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Alleles
Single Nucleotide Polymorphism
Alcohols
Genome-Wide Association Study
3' Untranslated Regions
MicroRNAs
RNA
Genes
Gene Expression
RNA-Binding Proteins
Linkage Disequilibrium
Alcoholics
Heterozygote
Neuroblastoma
Transcriptome
Binding Sites
Cell Line
Brain

ASJC Scopus subject areas

  • Molecular Biology
  • Psychiatry and Mental health
  • Cellular and Molecular Neuroscience

Cite this

Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders. / Rao, Xi; Thapa, Kriti S.; Chen, Andy B.; Lin, Hai; Gao, Hongyu; Reiter, Jill; Hargreaves, Katherine A.; Ipe, Joseph; Lai, Dongbing; Xuei, Xiaoling; Wang, Yue; Gu, Hongmei; Kapoor, Manav; Farris, Sean P.; Tischfield, Jay; Foroud, Tatiana; Goate, Alison M.; Skaar, Todd; Mayfield, R. Dayne; Edenberg, Howard; Liu, Yunlong.

In: Molecular Psychiatry, 01.01.2019.

Research output: Contribution to journalArticle

Rao, X, Thapa, KS, Chen, AB, Lin, H, Gao, H, Reiter, J, Hargreaves, KA, Ipe, J, Lai, D, Xuei, X, Wang, Y, Gu, H, Kapoor, M, Farris, SP, Tischfield, J, Foroud, T, Goate, AM, Skaar, T, Mayfield, RD, Edenberg, H & Liu, Y 2019, 'Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders', Molecular Psychiatry. https://doi.org/10.1038/s41380-019-0508-z
Rao, Xi ; Thapa, Kriti S. ; Chen, Andy B. ; Lin, Hai ; Gao, Hongyu ; Reiter, Jill ; Hargreaves, Katherine A. ; Ipe, Joseph ; Lai, Dongbing ; Xuei, Xiaoling ; Wang, Yue ; Gu, Hongmei ; Kapoor, Manav ; Farris, Sean P. ; Tischfield, Jay ; Foroud, Tatiana ; Goate, Alison M. ; Skaar, Todd ; Mayfield, R. Dayne ; Edenberg, Howard ; Liu, Yunlong. / Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders. In: Molecular Psychiatry. 2019.
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abstract = "Genome-wide association studies (GWAS) of complex traits, such as alcohol use disorders (AUD), usually identify variants in non-coding regions and cannot by themselves distinguish whether the associated variants are functional or in linkage disequilibrium with the functional variants. Transcriptome studies can identify genes whose expression differs between alcoholics and controls. To test which variants associated with AUD may cause expression differences, we integrated data from deep RNA-seq and GWAS of four postmortem brain regions from 30 subjects with AUD and 30 controls to analyze allele-specific expression (ASE). We identified 88 genes with differential ASE in subjects with AUD compared to controls. Next, to test one potential mechanism contributing to the differential ASE, we analyzed single nucleotide polymorphisms (SNPs) in the 3′ untranslated regions (3′UTR) of these genes. Of the 88 genes with differential ASE, 61 genes contained 437 SNPs in the 3′UTR with at least one heterozygote among the subjects studied. Using a modified PASSPORT-seq (parallel assessment of polymorphisms in miRNA target-sites by sequencing) assay, we identified 25 SNPs that affected RNA levels in a consistent manner in two neuroblastoma cell lines, SH-SY5Y and SK-N-BE(2). Many of these SNPs are in binding sites of miRNAs and RNA-binding proteins, indicating that these SNPs are likely causal variants of AUD-associated differential ASE. In sum, we demonstrate that a combination of computational and experimental approaches provides a powerful strategy to uncover functionally relevant variants associated with the risk for AUD.",
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AU - Rao, Xi

AU - Thapa, Kriti S.

AU - Chen, Andy B.

AU - Lin, Hai

AU - Gao, Hongyu

AU - Reiter, Jill

AU - Hargreaves, Katherine A.

AU - Ipe, Joseph

AU - Lai, Dongbing

AU - Xuei, Xiaoling

AU - Wang, Yue

AU - Gu, Hongmei

AU - Kapoor, Manav

AU - Farris, Sean P.

AU - Tischfield, Jay

AU - Foroud, Tatiana

AU - Goate, Alison M.

AU - Skaar, Todd

AU - Mayfield, R. Dayne

AU - Edenberg, Howard

AU - Liu, Yunlong

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Genome-wide association studies (GWAS) of complex traits, such as alcohol use disorders (AUD), usually identify variants in non-coding regions and cannot by themselves distinguish whether the associated variants are functional or in linkage disequilibrium with the functional variants. Transcriptome studies can identify genes whose expression differs between alcoholics and controls. To test which variants associated with AUD may cause expression differences, we integrated data from deep RNA-seq and GWAS of four postmortem brain regions from 30 subjects with AUD and 30 controls to analyze allele-specific expression (ASE). We identified 88 genes with differential ASE in subjects with AUD compared to controls. Next, to test one potential mechanism contributing to the differential ASE, we analyzed single nucleotide polymorphisms (SNPs) in the 3′ untranslated regions (3′UTR) of these genes. Of the 88 genes with differential ASE, 61 genes contained 437 SNPs in the 3′UTR with at least one heterozygote among the subjects studied. Using a modified PASSPORT-seq (parallel assessment of polymorphisms in miRNA target-sites by sequencing) assay, we identified 25 SNPs that affected RNA levels in a consistent manner in two neuroblastoma cell lines, SH-SY5Y and SK-N-BE(2). Many of these SNPs are in binding sites of miRNAs and RNA-binding proteins, indicating that these SNPs are likely causal variants of AUD-associated differential ASE. In sum, we demonstrate that a combination of computational and experimental approaches provides a powerful strategy to uncover functionally relevant variants associated with the risk for AUD.

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