Identification of Functional Genetic Variants Associated With Alcohol Dependence and Related Phenotypes Using a High-Throughput Assay.
3′Untranslated Regions
Alcohol Dependence
GWAS
Gene Expression
Neuronal Cells
Journal
Alcoholism, clinical and experimental research
ISSN: 1530-0277
Titre abrégé: Alcohol Clin Exp Res
Pays: England
ID NLM: 7707242
Informations de publication
Date de publication:
12 2020
12 2020
Historique:
received:
30
04
2020
accepted:
20
10
2020
pubmed:
30
10
2020
medline:
30
9
2021
entrez:
29
10
2020
Statut:
ppublish
Résumé
Genome-wide association studies (GWAS) of alcohol dependence (AD) and related phenotypes have identified multiple loci, but the functional variants underlying the loci have in most cases not been identified. Noncoding variants can influence phenotype by affecting gene expression; for example, variants in the 3' untranslated regions (3'UTR) can affect gene expression posttranscriptionally. We adapted a high-throughput assay known as PASSPORT-seq (parallel assessment of polymorphisms in miRNA target sites by sequencing) to identify among variants associated with AD and related phenotypes those that cause differential expression in neuronal cell lines. Based upon meta-analyses of alcohol-related traits in African American and European Americans in the Collaborative Study on the Genetics of Alcoholism, we tested 296 single nucleotide polymorphisms (SNPs with meta-analysis p values ≤ 0.001) that were located in 3'UTRs. We identified 60 SNPs that affected gene expression (false discovery rate [FDR] < 0.05) in SH-SY5Y cells and 92 that affected expression in SK-N-BE(2) cells. Among these, 30 SNPs altered RNA levels in the same direction in both cell lines. Many of these SNPs reside in the binding sites of miRNAs and RNA-binding proteins and are expression quantitative trait loci of genes including KIF6,FRMD4A,CADM2,ADD2,PLK2, and GAS7. The SNPs identified in the PASSPORT-seq assay are functional variants that might affect the risk for AD and related phenotypes. Our study provides insights into gene regulation in AD and demonstrates the value of PASSPORT-seq as a tool to screen genetic variants in GWAS loci for one potential mechanism of action.
Sections du résumé
BACKGROUND
Genome-wide association studies (GWAS) of alcohol dependence (AD) and related phenotypes have identified multiple loci, but the functional variants underlying the loci have in most cases not been identified. Noncoding variants can influence phenotype by affecting gene expression; for example, variants in the 3' untranslated regions (3'UTR) can affect gene expression posttranscriptionally.
METHODS
We adapted a high-throughput assay known as PASSPORT-seq (parallel assessment of polymorphisms in miRNA target sites by sequencing) to identify among variants associated with AD and related phenotypes those that cause differential expression in neuronal cell lines. Based upon meta-analyses of alcohol-related traits in African American and European Americans in the Collaborative Study on the Genetics of Alcoholism, we tested 296 single nucleotide polymorphisms (SNPs with meta-analysis p values ≤ 0.001) that were located in 3'UTRs.
RESULTS
We identified 60 SNPs that affected gene expression (false discovery rate [FDR] < 0.05) in SH-SY5Y cells and 92 that affected expression in SK-N-BE(2) cells. Among these, 30 SNPs altered RNA levels in the same direction in both cell lines. Many of these SNPs reside in the binding sites of miRNAs and RNA-binding proteins and are expression quantitative trait loci of genes including KIF6,FRMD4A,CADM2,ADD2,PLK2, and GAS7.
CONCLUSION
The SNPs identified in the PASSPORT-seq assay are functional variants that might affect the risk for AD and related phenotypes. Our study provides insights into gene regulation in AD and demonstrates the value of PASSPORT-seq as a tool to screen genetic variants in GWAS loci for one potential mechanism of action.
Identifiants
pubmed: 33119910
doi: 10.1111/acer.14492
pmc: PMC7725989
mid: NIHMS1640903
doi:
Substances chimiques
3' Untranslated Regions
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
2494-2518Subventions
Organisme : NIAAA NIH HHS
ID : U10 AA008401
Pays : United States
Informations de copyright
© 2020 by the Research Society on Alcoholism.
Références
Nat Commun. 2019 Apr 2;10(1):1499
pubmed: 30940813
Front Genet. 2018 Jun 15;9:219
pubmed: 29963077
Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7
pubmed: 19474294
PLoS One. 2019 Jul 15;14(7):e0219691
pubmed: 31306446
Addiction. 1999 Sep;94(9):1361-70
pubmed: 10615721
Nucleic Acids Res. 2014 Jan;42(Database issue):D86-91
pubmed: 24163105
Mol Psychiatry. 2013 Apr;18(4):461-70
pubmed: 22430674
Alcohol Res Health. 2002;26(3):214-8
pubmed: 12875050
Cell. 1998 May 1;93(3):467-76
pubmed: 9590180
Neuropharmacology. 2017 May 1;117:387-400
pubmed: 28257888
Mol Psychiatry. 2014 Jan;19(1):41-9
pubmed: 24166409
Mol Psychiatry. 2019 Sep 2;:
pubmed: 31477794
Curr Psychiatry Rep. 2019 Feb 7;21(2):10
pubmed: 30729322
Addict Biol. 2020 Mar;25(2):e12800
pubmed: 31270906
Alcohol Clin Exp Res. 2015 Aug;39(8):1312-27
pubmed: 26110981
J Neurosci. 2019 Mar 27;39(13):2562-2572
pubmed: 30718321
Ann N Y Acad Sci. 2013 Apr;1282:39-70
pubmed: 23170934
Hum Genet. 2012 Jun;131(6):1009-21
pubmed: 22006218
Genes Brain Behav. 2019 Jul;18(6):e12579
pubmed: 31090166
Nat Neurosci. 2018 Sep;21(9):1161-1170
pubmed: 30150663
Am J Med Genet. 1998 May 8;81(3):207-15
pubmed: 9603606
Nat Neurosci. 2018 Dec;21(12):1656-1669
pubmed: 30482948
Mol Psychiatry. 2017 Oct;22(10):1376-1384
pubmed: 28937693
J Neurochem. 2007 Jul;102(1):141-52
pubmed: 17442057
Nat Neurosci. 2020 Jul;23(7):809-818
pubmed: 32451486
Biol Psychiatry. 2019 Sep 1;86(5):365-376
pubmed: 31151762
Nature. 2017 Oct 11;550(7675):204-213
pubmed: 29022597
Alcohol Clin Exp Res. 2018 Dec;42(12):2281-2297
pubmed: 30320893
J Neurochem. 2012 Aug;122(4):834-43
pubmed: 22671569
BMC Genomics. 2011 Feb 21;12:124
pubmed: 21338521
Alzheimer Dis Assoc Disord. 2015 Apr-Jun;29(2):169-72
pubmed: 24384746
Lancet Psychiatry. 2018 Dec;5(12):987-1012
pubmed: 30392731
Transl Psychiatry. 2016 Mar 29;6:e769
pubmed: 27023175
Hum Mol Genet. 2009 Oct 1;18(19):3553-66
pubmed: 19578180
Methods Mol Biol. 2008;419:93-108
pubmed: 18369977
Nucleic Acids Res. 2019 Jan 8;47(D1):D853-D858
pubmed: 30407534
Eur J Med Genet. 2016 Jan;59(1):26-31
pubmed: 26723519
Science. 2012 Sep 7;337(6099):1190-5
pubmed: 22955828
Genes Brain Behav. 2019 Jul;18(6):e12580
pubmed: 31099175
Genome Res. 2017 Mar;27(3):491-499
pubmed: 28100584
J Neurol Neurosurg Psychiatry. 2020 Feb;91(2):126-131
pubmed: 31776209
Nature. 2013 Dec 12;504(7479):315-8
pubmed: 24336289
Nat Rev Gastroenterol Hepatol. 2013 Aug;10(8):487-94
pubmed: 23712313
J Biol Chem. 2010 Jan 22;285(4):2807-22
pubmed: 19889641
J Stud Alcohol. 1994 Mar;55(2):149-58
pubmed: 8189735
PLoS Genet. 2018 Nov 26;14(11):e1007817
pubmed: 30475797
Elife. 2015 Aug 12;4:
pubmed: 26267216