Kriti S Thapa1, Andy B Chen2, Dongbing Lai2, Xiaoling Xuei2, Leah Wetherill2, Jay A Tischfield3, Yunlong Liu2, Howard J Edenberg1,2. 1. From the, Department of Biochemistry and Molecular Biology, (KST, HJE), Indiana University School of Medicine, Indianapolis, Indiana. 2. Department of Medical and Molecular Genetics, (ABC, DL, XX, LW, YL, HJE), Indiana University School of Medicine, Indianapolis, Indiana. 3. Department of Genetics, (JAT), Rutgers University, Piscataway, New Jersey.
Abstract
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.
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.
Authors: Lucia A Hindorff; Praveen Sethupathy; Heather A Junkins; Erin M Ramos; Jayashri P Mehta; Francis S Collins; Teri A Manolio Journal: Proc Natl Acad Sci U S A Date: 2009-05-27 Impact factor: 11.205
Authors: R Varon; C Vissinga; M Platzer; K M Cerosaletti; K H Chrzanowska; K Saar; G Beckmann; E Seemanová; P R Cooper; N J Nowak; M Stumm; C M Weemaes; R A Gatti; R K Wilson; M Digweed; A Rosenthal; K Sperling; P Concannon; A Reis Journal: Cell Date: 1998-05-01 Impact factor: 41.582
Authors: Yeunkum Lee; Ji Soo Lee; Kea Joo Lee; R Scott Turner; Hyang-Sook Hoe; Daniel T S Pak Journal: Neuropharmacology Date: 2017-03-01 Impact factor: 5.250
Authors: J-C Lambert; B Grenier-Boley; D Harold; D Zelenika; V Chouraki; Y Kamatani; K Sleegers; M A Ikram; M Hiltunen; C Reitz; I Mateo; T Feulner; M Bullido; D Galimberti; L Concari; V Alvarez; R Sims; A Gerrish; J Chapman; C Deniz-Naranjo; V Solfrizzi; S Sorbi; B Arosio; G Spalletta; G Siciliano; J Epelbaum; D Hannequin; J-F Dartigues; C Tzourio; C Berr; E M C Schrijvers; R Rogers; G Tosto; F Pasquier; K Bettens; C Van Cauwenberghe; L Fratiglioni; C Graff; M Delepine; R Ferri; C A Reynolds; L Lannfelt; M Ingelsson; J A Prince; C Chillotti; A Pilotto; D Seripa; A Boland; M Mancuso; P Bossù; G Annoni; B Nacmias; P Bosco; F Panza; F Sanchez-Garcia; M Del Zompo; E Coto; M Owen; M O'Donovan; F Valdivieso; P Caffarra; P Caffara; E Scarpini; O Combarros; L Buée; D Campion; H Soininen; M Breteler; M Riemenschneider; C Van Broeckhoven; A Alpérovitch; M Lathrop; D-A Trégouët; J Williams; P Amouyel Journal: Mol Psychiatry Date: 2012-03-20 Impact factor: 15.992
Authors: Henry R Kranzler; Hang Zhou; Rachel L Kember; Rachel Vickers Smith; Amy C Justice; Scott Damrauer; Philip S Tsao; Derek Klarin; Aris Baras; Jeffrey Reid; John Overton; Daniel J Rader; Zhongshan Cheng; Janet P Tate; William C Becker; John Concato; Ke Xu; Renato Polimanti; Hongyu Zhao; Joel Gelernter Journal: Nat Commun Date: 2019-04-02 Impact factor: 14.919
Authors: Ji Soo Lee; Yeunkum Lee; Emily A André; Kea Joo Lee; Thien Nguyen; Yang Feng; Nuo Jia; Brent T Harris; Mark P Burns; Daniel T S Pak Journal: PLoS One Date: 2019-07-15 Impact factor: 3.240