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Zhang C, Yang H, Xu Q, Liu M, Chao X, Chen J, Zhou B, Liu Y. Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in Pigs. Biomolecules 2023; 13:1381. [PMID: 37759782 PMCID: PMC10526945 DOI: 10.3390/biom13091381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Copy number variation (CNV) represents a significant reservoir of genetic diversity within the genome and exhibits a strong association with economically valuable traits in livestock. The manifestation of aggressive behavior in pigs has detrimental effects on production efficiency, immune competency, and meat quality. Nevertheless, the impact of CNV on the aggressive behavior of pigs remains elusive. In this investigation, we employed an integrated analysis of genome and transcriptome data to investigate the interplay between CNV, gene expression changes, and indicators of aggressive behavior in weaned pigs. Specifically, a subset of pigs comprising the most aggressive pigs (MAP, n = 12) and the least aggressive pigs (LAP, n = 11) was purposefully selected from a herd of 500 weaned pigs following a mixing procedure based on their composite aggressive score (CAS). Subsequently, we thoroughly analyzed copy number variation regions (CNVRs) across the entire genome using next-generation sequencing techniques, ultimately revealing the presence of 6869 CNVRs. Using genome-wide association study (GWAS) analysis and evaluating variance-stabilizing transformation (VST) values, we successfully identified distinct CNVRs that distinguished the MAP and LAP counterparts. Among the prioritized CNVRs, CNVR-4962 (designated as the top-ranked p-value and VST value, No. 1) was located within the Solute Carrier Organic Anion Transporter Family Member 3A1 (SLCO3A1) gene. The results of our analyses indicated a significantly higher (p < 0.05) copy number of SLCO3A1 in the MAP compared to the LAP. Furthermore, this increased copy number exhibited a positive correlation with the CAS of the pigs (p < 0.05). Furthermore, we integrated genomic data with transcriptomic data from the temporal lobe to facilitate the examination of expression quantitative trait loci (eQTL). Importantly, these observations were consistent with the mRNA expression pattern of SLCO3A1 in the temporal lobe of both MAP and LAP (p < 0.05). Consequently, our findings strongly suggest that CNVs affecting SLCO3A1 may influence gene expression through a dosage effect. These results highlight the potential of SLCO3A1 as a candidate gene associated with aggressive traits in pig breeding programs.
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Affiliation(s)
| | | | | | | | | | | | - Bo Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (H.Y.); (Q.X.); (M.L.); (X.C.); (J.C.)
| | - Yang Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (H.Y.); (Q.X.); (M.L.); (X.C.); (J.C.)
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2
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Chenoweth MJ, Lerman C, Knight J, Tyndale RF. A Genome-Wide Association Study of Nausea Incidence in Varenicline-Treated Cigarette Smokers. Nicotine Tob Res 2021; 23:1805-1809. [PMID: 33713409 DOI: 10.1093/ntr/ntab044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/11/2021] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Varenicline is the most efficacious smoking cessation treatment; however, long-term cessation rates tend to be <25%. Nausea, the most common side effect of varenicline, observed in ~28% of individuals treated, peaks early following treatment initiation and reduces cessation success. Genetic variation influences treatment response, however genetic contributors to individual differences in side effects are less understood. METHODS We conducted a genome-wide association study of nausea incidence at 1 week following the initiation of varenicline treatment (corresponding to the target quit date) in 189 cigarette smokers of European ancestry (NCT01314001). Additive genetic models examining the likelihood of experiencing any versus no nausea controlled for population substructure, age, and sex. Variants with minor allele frequencies (MAF)≥10% were considered. RESULTS Fifty-seven (30.2%) out of 189 participants reported nausea. The top variant associated with nausea was rs1568209 (odds ratio [OR] = 2.61 for A vs. G allele; 95% confidence interval [CI] = 1.65,4.15; p = 2.1e-7; MAF = 48.7%), mapping to the SLCO3A1 drug transporter gene on chromosome 15. In the same trial, rs1568209 was not associated with nausea in either the nicotine patch (p = .56; n = 181) or placebo (p = .59; n = 174) arms. In varenicline-treated smokers, the incidence of nausea was higher in females (44.6%; n = 74) versus males (20.9%; n = 115) (p = .001), however there was no evidence of a difference in the influence of rs1568209 on nausea between the sexes (p for sex*genotype interaction = .36). Future studies in larger samples are required to test the robustness of this finding. CONCLUSIONS Variation in SLCO3A1 may influence the risk for developing nausea in varenicline-treated smokers, which may alter adherence and cessation. IMPLICATIONS Varenicline-associated nausea reduces adherence and limits cessation success. Previous candidate gene association studies showed genetic factors influence nausea on varenicline. This pilot genome-wide investigation of nausea, the most common side effect associated with varenicline treatment and an important cause of treatment discontinuation, suggests the potential involvement of common variation in the SLCO3A1 drug transporter gene.
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Affiliation(s)
- Meghan J Chenoweth
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Caryn Lerman
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jo Knight
- Data Science Institute and Lancaster University Medical School, Lancaster, UK.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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Zhang W, Venkataraghavan S, Hetmanski JB, Leslie EJ, Marazita ML, Feingold E, Weinberg SM, Ruczinski I, Taub MA, Scott AF, Ray D, Beaty TH. Detecting Gene-Environment Interaction for Maternal Exposures Using Case-Parent Trios Ascertained Through a Case With Non-Syndromic Orofacial Cleft. Front Cell Dev Biol 2021; 9:621018. [PMID: 33937227 PMCID: PMC8085423 DOI: 10.3389/fcell.2021.621018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Two large studies of case-parent trios ascertained through a proband with a non-syndromic orofacial cleft (OFC, which includes cleft lip and palate, cleft lip alone, or cleft palate alone) were used to test for possible gene-environment (G × E) interaction between genome-wide markers (both observed and imputed) and self-reported maternal exposure to smoking, alcohol consumption, and multivitamin supplementation during pregnancy. The parent studies were as follows: GENEVA, which included 1,939 case-parent trios recruited largely through treatment centers in Europe, the United States, and Asia, and 1,443 case-parent trios from the Pittsburgh Orofacial Cleft Study (POFC) also ascertained through a proband with an OFC including three major racial/ethnic groups (European, Asian, and Latin American). Exposure rates to these environmental risk factors (maternal smoking, alcohol consumption, and multivitamin supplementation) varied across studies and among racial/ethnic groups, creating substantial differences in power to detect G × E interaction, but the trio design should minimize spurious results due to population stratification. The GENEVA and POFC studies were analyzed separately, and a meta-analysis was conducted across both studies to test for G × E interaction using the 2 df test of gene and G × E interaction and the 1 df test for G × E interaction alone. The 2 df test confirmed effects for several recognized risk genes, suggesting modest G × E effects. This analysis did reveal suggestive evidence for G × Vitamin interaction for CASP9 on 1p36 located about 3 Mb from PAX7, a recognized risk gene. Several regions gave suggestive evidence of G × E interaction in the 1 df test. For example, for G × Smoking interaction, the 1 df test suggested markers in MUSK on 9q31.3 from meta-analysis. Markers near SLCO3A1 also showed suggestive evidence in the 1 df test for G × Alcohol interaction, and rs41117 near RETREG1 (a.k.a. FAM134B) also gave suggestive significance in the meta-analysis of the 1 df test for G × Vitamin interaction. While it remains quite difficult to obtain definitive evidence for G × E interaction in genome-wide studies, perhaps due to small effect sizes of individual genes combined with low exposure rates, this analysis of two large case-parent trio studies argues for considering possible G × E interaction in any comprehensive study of complex and heterogeneous disorders such as OFC.
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Affiliation(s)
- Wanying Zhang
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Sowmya Venkataraghavan
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, United States
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ingo Ruczinski
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Margaret A. Taub
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Alan F. Scott
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Debashree Ray
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Terri H. Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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Thorpe HHA, Talhat MA, Khokhar JY. High genes: Genetic underpinnings of cannabis use phenotypes. Prog Neuropsychopharmacol Biol Psychiatry 2021; 106:110164. [PMID: 33152387 DOI: 10.1016/j.pnpbp.2020.110164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/25/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022]
Abstract
Cannabis is one of the most widely used substances across the globe and its use has a substantial heritable component. However, the heritability of cannabis use varies according to substance use phenotype, suggesting that a unique profile of gene variants may contribute to the different stages of use, such as age of use onset, lifetime use, cannabis use disorder, and withdrawal and craving during abstinence. Herein, we review a subset of genes identified by candidate gene, family-based linkage, and genome-wide association studies related to these cannabis use phenotypes. We also describe their relationships with other substances, and their functions at the neurobiological, cognitive, and behavioral levels to hypothesize the role of these genes in cannabis use risk. Delineating genetic risk factors in the various stages of cannabis use will provide insight into the biological mechanisms related to cannabis use and highlight points of intervention prior to and following the development of dependence, as well as identify targets to aid drug development for treating problematic cannabis use.
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Affiliation(s)
- Hayley H A Thorpe
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | | | - Jibran Y Khokhar
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada.
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5
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Shi X, Han X, Cao Y, Li C, Cao Y. ZCCHC14 regulates proliferation and invasion of non-small cell lung cancer through the MAPK-P38 signalling pathway. J Cell Mol Med 2020; 25:1406-1414. [PMID: 33345444 PMCID: PMC7875900 DOI: 10.1111/jcmm.16223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 01/07/2023] Open
Abstract
ZCCHC14 is a CCHC‐type zinc finger protein which is expressed in tissues in human and mouse. The function of ZCCHC14 in tumours remains unclear. In this research, we explored the expression, function and related molecular mechanisms of ZCCHC14 in human non–small cell lung cancer (NSCLC). Immunochemistry staining showed that ZCCHC14 was low‐expressed or absent in NSCLC tissues. In NSCLC patients, the low expression of ZCCHC14 in tumour tissues was significantly correlated with TNM stage, differentiation degree and adverse clinical outcome (P < .05). The proliferation and invasion ability of cancer cells transfected with ZCCHC14 CRISPR/Ca9 KO plasmids was significantly enhanced (P < .05). Immunoblotting analysis indicated that the expression of p‐P38, cyclinD1 and MMP7 were significantly up‐regulated after disabling ZCCHC14 (P < .05). We used MAPK‐P38 pathway inhibitor doramapimod (BIRB 796) to inhibit P38 signalling pathway activity and determined that the agent significantly disrupted the function of ZCCHC14 and hindered the proliferation and invasion of the tumour. The finding revealed that ZCCHC14 can regulate proliferation and invasion of NSCLC through the P38 pathway. ZCCHC14 plays a crucial regulatory role in the development of NSCLC and may become a zinc finger target for clinical treatment.
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Affiliation(s)
- Xiuying Shi
- Department of Immunology, The College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xu Han
- Department of Pathology, The College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Yu Cao
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Cheng Li
- Department of Immunology, The College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Yaming Cao
- Department of Immunology, The College of Basic Medical Sciences, China Medical University, Shenyang, China
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Prom-Wormley EC, Ebejer J, Dick DM, Bowers MS. The genetic epidemiology of substance use disorder: A review. Drug Alcohol Depend 2017; 180:241-259. [PMID: 28938182 PMCID: PMC5911369 DOI: 10.1016/j.drugalcdep.2017.06.040] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND Substance use disorder (SUD) remains a significant public health issue. A greater understanding of how genes and environment interact to regulate phenotypes comprising SUD will facilitate directed treatments and prevention. METHODS The literature studying the neurobiological correlates of SUD with a focus on the genetic and environmental influences underlying these mechanisms was reviewed. Results from twin/family, human genetic association, gene-environment interaction, epigenetic literature, phenome-wide association studies are summarized for alcohol, nicotine, cannabinoids, cocaine, and opioids. RESULTS There are substantial genetic influences on SUD that are expected to influence multiple neurotransmission pathways, and these influences are particularly important within the dopaminergic system. Genetic influences involved in other aspects of SUD etiology including drug processing and metabolism are also identified. Studies of gene-environment interaction emphasize the importance of environmental context in SUD. Epigenetic studies indicate drug-specific changes in gene expression as well as differences in gene expression related to the use of multiple substances. Further, gene expression is expected to differ by stage of SUD such as substance initiation versus chronic substance use. While a substantial literature has developed for alcohol and nicotine use disorders, there is comparatively less information for other commonly abused substances. CONCLUSIONS A better understanding of genetically-mediated mechanisms involved in the neurobiology of SUD provides increased opportunity to develop behavioral and biologically based treatment and prevention of SUD.
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Affiliation(s)
- Elizabeth C Prom-Wormley
- Dvision of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, PO Box 980212, Richmond, VA 23298-0212, USA.
| | - Jane Ebejer
- School of Cognitive Behavioural and Social Sciences, University of New England, Armidale, NSW 2350, Australia
| | - Danielle M Dick
- Department of Psychology, Virginia Commonwealth University, PO Box 842509, Richmond, VA 23284-2509, USA
| | - M Scott Bowers
- Faulk Center for Molecular Therapeutics, Biomedical Engeneering, Northwestern University, Evanston, IL 60201, USA
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7
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Pedram P, Zhai G, Gulliver W, Zhang H, Sun G. Two novel candidate genes identified in adults from the Newfoundland population with addictive tendencies towards food. Appetite 2017; 115:71-79. [DOI: 10.1016/j.appet.2017.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 12/06/2016] [Accepted: 01/06/2017] [Indexed: 02/06/2023]
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8
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Langevin SM, Eliot M, Butler RA, Cheong A, Zhang X, McClean MD, Koestler DC, Kelsey KT. CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma. Clin Epigenetics 2015; 7:125. [PMID: 26635906 PMCID: PMC4668652 DOI: 10.1186/s13148-015-0160-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/01/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND There are currently no screening tests in routine use for oral and pharyngeal cancer beyond visual inspection and palpation, which are provided on an opportunistic basis, indicating a need for development of novel methods for early detection, particularly in high-risk populations. We sought to address this need through comprehensive interrogation of CpG island methylation in oral rinse samples. METHODS We used the Infinium HumanMethylation450 BeadArray to interrogate DNA methylation in oral rinse samples collected from 154 patients with incident oral or pharyngeal carcinoma prior to treatment and 72 cancer-free control subjects. Subjects were randomly allocated to either a training or a testing set. For each subject, average methylation was calculated for each CpG island represented on the array. We applied a semi-supervised recursively partitioned mixture model to the CpG island methylation data to identify a classifier for prediction of case status in the training set. We then applied the resultant classifier to the testing set for validation and to assess the predictive accuracy. RESULTS We identified a methylation classifier comprised of 22 CpG islands, which predicted oral and pharyngeal carcinoma with a high degree of accuracy (AUC = 0.92, 95 % CI 0.86, 0.98). CONCLUSIONS This novel methylation panel is a strong predictor of oral and pharyngeal carcinoma case status in oral rinse samples and may have utility in early detection and post-treatment follow-up.
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Affiliation(s)
- Scott M Langevin
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, ML0056, Cincinnati, OH 45267 USA
| | - Melissa Eliot
- Department of Epidemiology, Brown University, Providence, RI USA
| | - Rondi A Butler
- Department of Epidemiology, Brown University, Providence, RI USA
| | - Agnes Cheong
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA USA
| | - Xiang Zhang
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, ML0056, Cincinnati, OH 45267 USA
| | - Michael D McClean
- Department of Environmental Health, Boston University School of Public Health, Boston, MA USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KA USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI USA ; Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Box G-E3, Providence, RI 02912 USA
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9
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Palmer RHC, McGeary JE, Heath AC, Keller MC, Brick LA, Knopik VS. Shared additive genetic influences on DSM-IV criteria for alcohol dependence in subjects of European ancestry. Addiction 2015; 110. [PMID: 26211938 PMCID: PMC4644467 DOI: 10.1111/add.13070] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND AND AIMS Genetic studies of alcohol dependence (AD) have identified several candidate loci and genes, but most observed effects are small and difficult to reproduce. A plausible explanation for inconsistent findings may be a violation of the assumption that genetic factors contributing to each of the seven DSM-IV criteria point to a single underlying dimension of risk. Given that recent twin studies suggest that the genetic architecture of AD is complex and probably involves multiple discrete genetic factors, the current study employed common single nucleotide polymorphisms in two multivariate genetic models to examine the assumption that the genetic risk underlying DSM-IV AD is unitary. DESIGN, SETTING, PARTICIPANTS, MEASUREMENTS AD symptoms and genome-wide single nucleotide polymorphism (SNP) data from 2596 individuals of European descent from the Study of Addiction: Genetics and Environment were analyzed using genomic-relatedness-matrix restricted maximum likelihood. DSM-IV AD symptom covariance was described using two multivariate genetic factor models. FINDINGS Common SNPs explained 30% (standard error=0.136, P=0.012) of the variance in AD diagnosis. Additive genetic effects varied across AD symptoms. The common pathway model approach suggested that symptoms could be described by a single latent variable that had a SNP heritability of 31% (0.130, P=0.008). Similarly, the exploratory genetic factor model approach suggested that the genetic variance/covariance across symptoms could be represented by a single genetic factor that accounted for at least 60% of the genetic variance in any one symptom. CONCLUSION Additive genetic effects on DSM-IV alcohol dependence criteria overlap. The assumption of common genetic effects across alcohol dependence symptoms appears to be a valid assumption.
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Affiliation(s)
- Rohan H. C. Palmer
- Division of Behavioral Genetics, Department of Psychiatry, Rhode Island Hospital, Providence RI,Department of Psychiatry and Human Behavior, Brown University, Providence, RI, 02903
| | - John E. McGeary
- Division of Behavioral Genetics, Department of Psychiatry, Rhode Island Hospital, Providence RI,Department of Psychiatry and Human Behavior, Brown University, Providence, RI, 02903,Providence Veterans Affairs Medical Center, Providence, RI, 02908
| | - Andrew C. Heath
- Midwest Alcoholism Research Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew C. Keller
- Department of Psychology and Neuroscience and Institute for Behavioral Genetics at the University of Colorado at Boulder, Boulder, CO
| | - Leslie A. Brick
- Division of Behavioral Genetics, Department of Psychiatry, Rhode Island Hospital, Providence RI
| | - Valerie S. Knopik
- Division of Behavioral Genetics, Department of Psychiatry, Rhode Island Hospital, Providence RI,Department of Psychiatry and Human Behavior, Brown University, Providence, RI, 02903
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Mackey S, Kan KJ, Chaarani B, Alia-Klein N, Batalla A, Brooks S, Cousijn J, Dagher A, de Ruiter M, Desrivieres S, Feldstein Ewing SW, Goldstein RZ, Goudriaan AE, Heitzeg MM, Hutchison K, Li CSR, London ED, Lorenzetti V, Luijten M, Martin-Santos R, Morales AM, Paulus MP, Paus T, Pearlson G, Schluter R, Momenan R, Schmaal L, Schumann G, Sinha R, Sjoerds Z, Stein DJ, Stein EA, Solowij N, Tapert S, Uhlmann A, Veltman D, van Holst R, Walter H, Wright MJ, Yucel M, Yurgelun-Todd D, Hibar DP, Jahanshad N, Thompson PM, Glahn DC, Garavan H, Conrod P. Genetic imaging consortium for addiction medicine: From neuroimaging to genes. PROGRESS IN BRAIN RESEARCH 2015; 224:203-23. [PMID: 26822360 PMCID: PMC4820288 DOI: 10.1016/bs.pbr.2015.07.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the sample size of a typical neuroimaging study lacks sufficient statistical power to explore unknown genomic associations with brain phenotypes, several international genetic imaging consortia have been organized in recent years to pool data across sites. The challenges and achievements of these consortia are considered here with the goal of leveraging these resources to study addiction. The authors of this review have joined together to form an Addiction working group within the framework of the ENIGMA project, a meta-analytic approach to multisite genetic imaging data. Collectively, the Addiction working group possesses neuroimaging and genomic data obtained from over 10,000 subjects. The deadline for contributing data to the first round of analyses occurred at the beginning of May 2015. The studies performed on this data should significantly impact our understanding of the genetic and neurobiological basis of addiction.
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Affiliation(s)
- Scott Mackey
- Departments of Psychiatry and Psychology, University of Vermont, Burlington, VT, USA.
| | - Kees-Jan Kan
- Departments of Psychiatry and Psychology, University of Vermont, Burlington, VT, USA
| | - Bader Chaarani
- Departments of Psychiatry and Psychology, University of Vermont, Burlington, VT, USA
| | - Nelly Alia-Klein
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Albert Batalla
- Department of Psychiatry and Psychology, Hospital Clínic, IDIBAPS, CIBERSAM, University of Barcelona, Barcelona, Spain; Department of Psychiatry, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Samantha Brooks
- Department of Psychiatry and MRC Unit on Anxiety & Stress Disorders, University of Cape Town, Cape Town, South Africa
| | - Janna Cousijn
- Department of Psychiatry and MRC Unit on Anxiety & Stress Disorders, University of Cape Town, Cape Town, South Africa
| | - Alain Dagher
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Michiel de Ruiter
- Department of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Rita Z Goldstein
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anna E Goudriaan
- Department of Psychiatry and MRC Unit on Anxiety & Stress Disorders, University of Cape Town, Cape Town, South Africa; Department of Psychiatry, University of Amsterdam, Amsterdam, The Netherlands
| | - Mary M Heitzeg
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Kent Hutchison
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Chiang-Shan R Li
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Edythe D London
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Valentina Lorenzetti
- School of Psychological Sciences, Monash Institute of Cognitive and Clinical Neurosciences and Monash Biomedical Imaging, Monash University, Melbourne, Australia
| | - Maartje Luijten
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Rocio Martin-Santos
- Department of Psychiatry and Psychology, Hospital Clínic, IDIBAPS, CIBERSAM, University of Barcelona, Barcelona, Spain
| | - Angelica M Morales
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Martin P Paulus
- VA San Diego Healthcare System and Department of Psychiatry, University of California San Diego, La Jolla, CA, USA; Laureate Institute for Brain Research, Tulsa, OK, USA
| | - Tomas Paus
- Rotman Research Institute, University of Toronto, Toronto, ON, Canada
| | - Godfrey Pearlson
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Renée Schluter
- Department of Psychiatry, University of Amsterdam, Amsterdam, The Netherlands
| | - Reza Momenan
- Section on Brain Electrophysiology and Imaging, Institute on Alcohol Abuse and Alcoholism, Bethesda, USA
| | - Lianne Schmaal
- Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Rajita Sinha
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Zsuzsika Sjoerds
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Dan J Stein
- Department of Psychiatry and MRC Unit on Anxiety & Stress Disorders, University of Cape Town, Cape Town, South Africa
| | - Elliot A Stein
- Intramural Research Program-Neuroimaging Research Branch, National Institute on Drug Abuse, Baltimore, MD, USA
| | - Nadia Solowij
- School of Psychology, University of Wollongong, Wollongong, NSW, Australia
| | - Susan Tapert
- Laureate Institute for Brain Research, Tulsa, OK, USA
| | - Anne Uhlmann
- Department of Psychiatry and MRC Unit on Anxiety & Stress Disorders, University of Cape Town, Cape Town, South Africa
| | - Dick Veltman
- Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
| | - Ruth van Holst
- Department of Psychiatry, University of Amsterdam, Amsterdam, The Netherlands
| | - Henrik Walter
- Department of Psychiatry and Psychotherapy, Charité Universitatsmedizin, Berlin, Germany
| | | | - Murat Yucel
- School of Psychological Sciences, Monash Institute of Cognitive and Clinical Neurosciences and Monash Biomedical Imaging, Monash University, Melbourne, Australia
| | - Deborah Yurgelun-Todd
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Derrek P Hibar
- Department of Neurology, Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - Neda Jahanshad
- Department of Neurology, Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - Paul M Thompson
- Department of Neurology, Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - David C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Hugh Garavan
- Departments of Psychiatry and Psychology, University of Vermont, Burlington, VT, USA
| | - Patricia Conrod
- Department of Psychiatry, Université de Montreal, CHU Ste Justine Hospital, Montreal, QC, Canada
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11
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Wei SC, Tan YY, Weng MT, Lai LC, Hsiao JH, Chuang EY, Shun CT, Wu DC, Kao AW, Chuang CS, Ni YH, Shieh MJ, Tung CC, Chen Y, Wang CY, Xavier RJ, Podolsky DK, Wong JM. SLCO3A1, A novel crohn's disease-associated gene, regulates nf-κB activity and associates with intestinal perforation. PLoS One 2014; 9:e100515. [PMID: 24945726 PMCID: PMC4063938 DOI: 10.1371/journal.pone.0100515] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/28/2014] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND & AIMS To date, only one gene (TNFSF15) has been identified and validated as a Crohn's disease (CD)-associated gene in non-Caucasian populations. This study was designed to identify novel CD-associated single nucleotide polymorphisms (SNPs)/genes and to validate candidate genes using a functional assay. METHODS SNPs from 16 CD patients and 16 age- and sex-matched control patients were analyzed using Illumina platform analysis. Subsequently, we expanded the study and followed 53 CD patients and 41 control patients by Sequenom MassArray analysis. Quantitative PCR and immunohistochemical staining were performed to assess mRNA and protein expression of the candidate gene on tissue isolated from CD patients. Genotype was correlated with CD phenotypes. Finally, the candidate gene was cloned and its effect on NF-κB activity assessed using a reporter luciferase assay. RESULTS SLCO3A1 (rs207959) reached statistical significance in the first-stage analysis (P = 2.3E-02) and was further validated in the second-stage analysis (P = 1.0E-03). Genotype and phenotype analysis showed that the rs207959 (T) allele is a risk allele that alters SLCO3A1 mRNA expression and is associated with intestinal perforation in CD patients. Higher levels of mRNA and protein expression of SLCO3A1 were seen in CD patients compared with the control group. Overexpression of SLCO3A1 induced increased NF-κB activity and increased phosphorylation of P65, ERK, and JNK. Nicotine augmented the activation of NF-κB in the presence of SLCO3A1. CONCLUSIONS SLCO3A1, a novel CD-associated gene, mediates inflammatory processes in intestinal epithelial cells through NF-κB transcription activation, resulting in a higher incidence of bowel perforation in CD patients.
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Affiliation(s)
- Shu-Chen Wei
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yan-Yin Tan
- Graduate Institute of Medical Engineering, National Taiwan University, Taipei, Taiwan
| | - Meng-Tzu Weng
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Departments of Internal Medicine, Far Eastern Memorial Hospital, New Taipei, Taiwan
| | - Liang-Chuan Lai
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
| | - Jen-Hao Hsiao
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
| | - Eric Y. Chuang
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Chia-Tung Shun
- Department of Pathology and Forensic Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Deng-Cheng Wu
- Department of Internal Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ai-Wen Kao
- Department of Internal Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chiao-Shung Chuang
- Department of Internal Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Hsuan Ni
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Jium Shieh
- Graduate Institute of Medical Engineering, National Taiwan University, Taipei, Taiwan
- Deparment of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Chih Tung
- Department of Integrated Diagnostics and Therapeutics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yun Chen
- Pediatric Surgery, Far Eastern Memorial Hospital, New Taipei, Taiwan
| | - Cheng-Yi Wang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ramnik J. Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | | | - Jau-Min Wong
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Engineering, National Taiwan University, Taipei, Taiwan
- * E-mail:
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12
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Argos M, Tong L, Pierce BL, Rakibuz-Zaman M, Ahmed A, Islam T, Rahman M, Paul-Brutus R, Rahaman R, Roy S, Jasmine F, Kibriya MG, Ahsan H. Genome-wide association study of smoking behaviours among Bangladeshi adults. J Med Genet 2014; 51:327-33. [PMID: 24665060 DOI: 10.1136/jmedgenet-2013-102151] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND The high prevalence of tobacco use in some developing nations, including Bangladesh, poses several public health challenges for these populations. Smoking behaviour is determined by genetic and environmental factors; however, the genetic determinants of smoking behaviour have not been previously examined in a Bangladeshi or South Asian population. We performed a genome-wide association study (GWAS) of tobacco smoking behaviour among a population-based sample of 5354 (2035 ever smokers and 3319 never smokers) men and women in Bangladesh. METHODS Genome-wide association analyses were conducted for smoking initiation (ever vs never smokers), smoking quantity (cigarettes per day), age of smoking initiation, and smoking cessation (former vs current smokers). Sex-stratified associations were performed for smoking initiation. RESULTS We observed associations for smoking initiation in the SLC39A11 region at 17q21.31 (rs2567519, p=1.33×10⁻⁷) among men and in the SLCO3A1 region at 15q26 (rs12912184, p=9.32×10⁻⁸) among women. CONCLUSIONS These findings suggest possible underlying mechanisms related to solute carrier transporter genes, which transport neurotransmitters, nutrients, heavy metals and other substrates into cells, for smoking initiation in a South Asian population in a sex-specific pattern. Genetic markers could have potential translational implications for the prevention or treatment of tobacco use and addiction in South Asian populations and warrant further exploration.
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Affiliation(s)
- Maria Argos
- Department of Health Studies, The University of Chicago, Chicago, Illinois, USA
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13
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von Renesse A, Petkova MV, Lützkendorf S, Heinemeyer J, Gill E, Hübner C, von Moers A, Stenzel W, Schuelke M. POMK mutation in a family with congenital muscular dystrophy with merosin deficiency, hypomyelination, mild hearing deficit and intellectual disability. J Med Genet 2014; 51:275-82. [PMID: 24556084 DOI: 10.1136/jmedgenet-2013-102236] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Congenital muscular dystrophies (CMD) with hypoglycosylation of α-dystroglycan are clinically and genetically heterogeneous disorders that are often associated with brain malformations and eye defects. Presently, 16 proteins are known whose dysfunction impedes glycosylation of α-dystroglycan and leads to secondary dystroglycanopathy. OBJECTIVE To identify the cause of CMD with secondary merosin deficiency, hypomyelination and intellectual disability in two siblings from a consanguineous family. METHODS Autozygosity mapping followed by whole exome sequencing and immunochemistry were used to discover and verify a new genetic defect in two siblings with CMD. RESULTS We identified a homozygous missense mutation (c.325C>T, p.Q109*) in protein O-mannosyl kinase (POMK) that encodes a glycosylation-specific kinase (SGK196) required for function of the dystroglycan complex. The protein was absent from skeletal muscle and skin fibroblasts of the patients. In patient muscle, β-dystroglycan was normally expressed at the sarcolemma, while α-dystroglycan failed to do so. Further, we detected co-localisation of POMK with desmin at the costameres in healthy muscle, and a substantial loss of desmin from the patient muscle. CONCLUSIONS Homozygous truncating mutations in POMK lead to CMD with secondary merosin deficiency, hypomyelination and intellectual disability. Loss of desmin suggests that failure of proper α-dystroglycan glycosylation impedes the binding to extracellular matrix proteins and also affects the cytoskeleton.
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Affiliation(s)
- Anja von Renesse
- Department of Neuropediatrics, Charité-Universitätsmedizin Berlin, Berlin, Germany
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14
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Jiang Y, Li N, Zhang H. Identifying Genetic Variants for Addiction via Propensity Score Adjusted Generalized Kendall's Tau. J Am Stat Assoc 2014; 109:905-930. [PMID: 25382885 PMCID: PMC4219655 DOI: 10.1080/01621459.2014.901223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 12/01/2013] [Indexed: 12/18/2022]
Abstract
Identifying replicable genetic variants for addiction has been extremely challenging. Besides the common difficulties with genome-wide association studies (GWAS), environmental factors are known to be critical to addiction, and comorbidity is widely observed. Despite the importance of environmental factors and comorbidity for addiction study, few GWAS analyses adequately considered them due to the limitations of the existing statistical methods. Although parametric methods have been developed to adjust for covariates in association analysis, difficulties arise when the traits are multivariate because there is no ready-to-use model for them. Recent nonparametric development includes U-statistics to measure the phenotype-genotype association weighted by a similarity score of covariates. However, it is not clear how to optimize the similarity score. Therefore, we propose a semiparametric method to measure the association adjusted by covariates. In our approach, the nonparametric U-statistic is adjusted by parametric estimates of propensity scores using the idea of inverse probability weighting. The new measurement is shown to be asymptotically unbiased under our null hypothesis while the previous non-weighted and weighted ones are not. Simulation results show that our test improves power as opposed to the non-weighted and two other weighted U-statistic methods, and it is particularly powerful for detecting gene-environment interactions. Finally, we apply our proposed test to the Study of Addiction: Genetics and Environment (SAGE) to identify genetic variants for addiction. Novel genetic variants are found from our analysis, which warrant further investigation in the future.
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Affiliation(s)
- Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon 97331-4606
| | - Ni Li
- School of Mathematics and Statistics, Hainan Normal University, Haikou 571158, China
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