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Cinciripini PM, Wetter DW, Wang J, Yu R, Kypriotakis G, Kumar T, Robinson JD, Cui Y, Green CE, Bergen AW, Kosten TR, Scherer SE, Shete S. Deep sequencing of candidate genes identified 14 variants associated with smoking abstinence in an ethnically diverse sample. Sci Rep 2024; 14:6385. [PMID: 38493193 PMCID: PMC10944542 DOI: 10.1038/s41598-024-56750-7] [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: 07/18/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Despite the large public health toll of smoking, genetic studies of smoking cessation have been limited with few discoveries of risk or protective loci. We investigated common and rare variant associations with success in quitting smoking using a cohort from 8 randomized controlled trials involving 2231 participants and a total of 10,020 common and 24,147 rare variants. We identified 14 novel markers including 6 mapping to genes previously related to psychiatric and substance use disorders, 4 of which were protective (CYP2B6 (rs1175607105), HTR3B (rs1413172952; rs1204720503), rs80210037 on chr15), and 2 of which were associated with reduced cessation (PARP15 (rs2173763), SCL18A2 (rs363222)). The others mapped to areas associated with cancer including FOXP1 (rs1288980) and ZEB1 (rs7349). Network analysis identified significant canonical pathways for the serotonin receptor signaling pathway, nicotine and bupropion metabolism, and several related to tumor suppression. Two novel markers (rs6749438; rs6718083) on chr2 are flanked by genes associated with regulation of bodyweight. The identification of novel loci in this study can provide new targets of pharmacotherapy and inform efforts to develop personalized treatments based on genetic profiles.
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Affiliation(s)
- Paul M Cinciripini
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - David W Wetter
- Department of Department of Population Health Sciences, University of Utah and Huntsman Cancer Institute, Salt Lake City, Utah, 84112, USA
| | - Jian Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Robert Yu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - George Kypriotakis
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Tapsi Kumar
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jason D Robinson
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yong Cui
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Charles E Green
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, 77030, USA
| | | | - Thomas R Kosten
- Department of Psychiatry, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Steven E Scherer
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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2
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Rybnicek J, Chen Y, Milic M, Tio ES, McLaurin J, Hohman TJ, De Jager PL, Schneider JA, Wang Y, Bennett DA, Tripathy S, Felsky D, Lambe EK. CHRNA5 links chandelier cells to severity of amyloid pathology in aging and Alzheimer's disease. Transl Psychiatry 2024; 14:83. [PMID: 38331937 PMCID: PMC10853183 DOI: 10.1038/s41398-024-02785-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
Changes in high-affinity nicotinic acetylcholine receptors are intricately connected to neuropathology in Alzheimer's Disease (AD). Protective and cognitive-enhancing roles for the nicotinic α5 subunit have been identified, but this gene has not been closely examined in the context of human aging and dementia. Therefore, we investigate the nicotinic α5 gene CHRNA5 and the impact of relevant single nucleotide polymorphisms (SNPs) in prefrontal cortex from 922 individuals with matched genotypic and post-mortem RNA sequencing in the Religious Orders Study and Memory and Aging Project (ROS/MAP). We find that a genotype robustly linked to increased expression of CHRNA5 (rs1979905A2) predicts significantly reduced cortical β-amyloid load. Intriguingly, co-expression analysis suggests CHRNA5 has a distinct cellular expression profile compared to other nicotinic receptor genes. Consistent with this prediction, single nucleus RNA sequencing from 22 individuals reveals CHRNA5 expression is disproportionately elevated in chandelier neurons, a distinct subtype of inhibitory neuron known for its role in excitatory/inhibitory (E/I) balance. We show that chandelier neurons are enriched in amyloid-binding proteins compared to basket cells, the other major subtype of PVALB-positive interneurons. Consistent with the hypothesis that nicotinic receptors in chandelier cells normally protect against β-amyloid, cell-type proportion analysis from 549 individuals reveals these neurons show amyloid-associated vulnerability only in individuals with impaired function/trafficking of nicotinic α5-containing receptors due to homozygosity of the missense CHRNA5 SNP (rs16969968A2). Taken together, these findings suggest that CHRNA5 and its nicotinic α5 subunit exert a neuroprotective role in aging and Alzheimer's disease centered on chandelier interneurons.
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Affiliation(s)
- Jonas Rybnicek
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Yuxiao Chen
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Milos Milic
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Earvin S Tio
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - JoAnne McLaurin
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Timothy J Hohman
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Julie A Schneider
- Department of Pathology, Rush University, Chicago, IL, USA
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - Yanling Wang
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - David A Bennett
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - Shreejoy Tripathy
- Department of Physiology, University of Toronto, Toronto, ON, Canada.
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
| | - Evelyn K Lambe
- Department of Physiology, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
- Department of OBGYN, University of Toronto, Toronto, ON, Canada.
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3
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Lor CS, Haugg A, Zhang M, Schneider L, Herdener M, Quednow BB, Golestani N, Scharnowski F. Thalamic volume and functional connectivity are associated with nicotine dependence severity and craving. Addict Biol 2023; 28:e13261. [PMID: 36577730 PMCID: PMC10078543 DOI: 10.1111/adb.13261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022]
Abstract
Tobacco smoking is associated with deleterious health outcomes. Most smokers want to quit smoking, yet relapse rates are high. Understanding neural differences associated with tobacco use may help generate novel treatment options. Several animal studies have recently highlighted the central role of the thalamus in substance use disorders, but this research focus has been understudied in human smokers. Here, we investigated associations between structural and functional magnetic resonance imaging measures of the thalamus and its subnuclei to distinct smoking characteristics. We acquired anatomical scans of 32 smokers as well as functional resting-state scans before and after a cue-reactivity task. Thalamic functional connectivity was associated with craving and dependence severity, whereas the volume of the thalamus was associated with dependence severity only. Craving, which fluctuates rapidly, was best characterized by differences in brain function, whereas the rather persistent syndrome of dependence severity was associated with both brain structural differences and function. Our study supports the notion that functional versus structural measures tend to be associated with behavioural measures that evolve at faster versus slower temporal scales, respectively. It confirms the importance of the thalamus to understand mechanisms of addiction and highlights it as a potential target for brain-based interventions to support smoking cessation, such as brain stimulation and neurofeedback.
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Affiliation(s)
- Cindy Sumaly Lor
- Department of Cognition, Emotion, and Methods in Psychology, University of Vienna, Vienna, Austria.,Department of Psychiatry, Psychotherapy and Psychosomatics
- Psychiatric University Hospital Zurich, University of Zurich, Zürich, Switzerland
| | - Amelie Haugg
- Department of Child and Adolescent Psychiatry and Psychotherapy
- Psychiatric University Hospital Zurich, University of Zurich, Zürich, Switzerland
| | - Mengfan Zhang
- Department of Cognition, Emotion, and Methods in Psychology, University of Vienna, Vienna, Austria.,Department of Psychiatry, Psychotherapy and Psychosomatics
- Psychiatric University Hospital Zurich, University of Zurich, Zürich, Switzerland
| | - Letitia Schneider
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
| | - Marcus Herdener
- Department of Psychiatry, Psychotherapy and Psychosomatics
- Psychiatric University Hospital Zurich, University of Zurich, Zürich, Switzerland
| | - Boris B Quednow
- Department of Psychiatry, Psychotherapy and Psychosomatics
- Psychiatric University Hospital Zurich, University of Zurich, Zürich, Switzerland
| | - Narly Golestani
- Brain and Language Lab
- Cognitive Science Hub, University of Vienna, Vienna, Austria.,Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria.,Department of Psychology
- Faculty of Psychology and Educational Sciences, University of Geneva, Geneva, Switzerland
| | - Frank Scharnowski
- Department of Cognition, Emotion, and Methods in Psychology, University of Vienna, Vienna, Austria.,Department of Psychiatry, Psychotherapy and Psychosomatics
- Psychiatric University Hospital Zurich, University of Zurich, Zürich, Switzerland
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Fan R, Cui W, Chen J, Ma Y, Yang Z, Payne TJ, Ma JZ, Li MD. Gene-based association analysis reveals involvement of LAMA5 and cell adhesion pathways in nicotine dependence in African- and European-American samples. Addict Biol 2021; 26:e12898. [PMID: 32281736 DOI: 10.1111/adb.12898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 03/07/2020] [Accepted: 03/09/2020] [Indexed: 01/01/2023]
Abstract
Nicotine dependence (ND) is a chronic brain disorder that causes heavy social and economic burdens. Although many susceptibility genetic loci have been reported, they can explain only approximately 5%-10% of the genetic variance for the disease. To further explore the genetic etiology of ND, we genotyped 242 764 SNPs using an exome chip from both European-American (N = 1572) and African-American (N = 3371) samples. Gene-based association analysis revealed 29 genes associated significantly with ND. Of the genes in the AA sample, six (i.e., PKD1L2, LAMA5, MUC16, MROH5, ATP8B1, and FREM1) were replicated in the EA sample with p values ranging from 0.0031 to 0.0346. Subsequently, gene enrichment analysis revealed that cell adhesion-related pathways were significantly associated with ND in both the AA and EA samples. Considering that LAMA5 is the most significant gene in cell adhesion-related pathways, we did in vitro functional analysis of this gene, which showed that nicotine significantly suppressed its mRNA expression in HEK293T cells (p < 0.001). Further, our cell migration experiment showed that the migration rate was significantly different in wild-type and LAMA5-knockout (LAMA5-KO)-HEK293T cells. Importantly, nicotine-induced cell migration was abolished in LAMA5-KO cells. Taken together, these findings indicate that LAMA5, as well as cell adhesion-related pathways, play an important role in the etiology of smoking addiction, which warrants further investigation.
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Affiliation(s)
- Rongli Fan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Wenyan Cui
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Jiali Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Yunlong Ma
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Zhongli Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Thomas J. Payne
- ACT Center for Tobacco Treatment, Education and Research, Department of Otolaryngology and Communicative Sciences University of Mississippi Medical Center Jackson Mississippi USA
| | - Jennie Z. Ma
- Department of Public Health Sciences University of Virginia Charlottesville Virginia USA
| | - Ming D. Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
- Research Center for Air Pollution and Health Zhejiang University Hangzhou China
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5
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Deak JD, Gizer IR, Otto JM, Bizon C, Wilhelmsen KC. Effects of Common and Rare Chromosome 4 GABAergic Gene Variation on Alcohol Use and Antisocial Behavior. J Stud Alcohol Drugs 2019; 80:585-593. [PMID: 31790348 PMCID: PMC6900988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE Epidemiological estimates suggest that nearly half of individuals diagnosed with alcohol use disorder will be diagnosed with another mental health disorder, with strong associations involving other externalizing disorders. Molecular genetic studies investigating the relation between alcohol use disorder and externalizing behaviors (e.g., antisocial behavior) have focused on a cluster of chromosome 4 γ-aminobutyric acid (GABA) receptor genes (GABRG1-A2-A4-B1) but have generated varying results. METHOD The current study examined associations between common and rare variation in this region with alcohol use disorder and antisocial behavior using genetic sequencing data. Specifically, the University of California at San Francisco Family Alcoholism Sample (n = 1,610; 62% female) was used to conduct common and rare variant association tests in the GABRG1-A2-A4-B1 cluster with DSM-5 alcohol use disorder symptom counts, antisocial behavior, and a product term representing their interaction. RESULTS Gene-based analyses of rare variation resulted in a significant association between rare GABRA2 variation and the interaction term. Single-variant analysis yielded only nominally significant associations. The strongest association for alcohol use disorder (rs3756007) was located in GABRA2, the strongest association for antisocial behavior (rs11941860) was located in GABRG1, and the interaction term yielded top associations in GABRA2 (rs2119183) and the intergenic region between GABRA2 and GABRG1 (rs536599). Common and rare variant associations for the interaction remained similar when covarying for the effects of the other type of variation, suggesting that the significant rare variant signal is independent of common variant contributions. CONCLUSIONS The present study suggests that both rare and common variant associations in GABRA2 confer risk for alcohol use disorder and antisocial behaviors, indicating a potential liability toward externalizing behavior more broadly.
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Affiliation(s)
- Joseph D. Deak
- Department of Psychological Sciences, University of Missouri, Columbia, Missouri,Correspondence may be sent to Joseph D. Deak at the Department of Psychological Sciences, University of Missouri, Columbia, MO 65211, or via email at:
| | - Ian R. Gizer
- Department of Psychological Sciences, University of Missouri, Columbia, Missouri
| | - Jacqueline M. Otto
- Department of Psychological Sciences, University of Missouri, Columbia, Missouri
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kirk C. Wilhelmsen
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina,Department of Genetics and Neurology, University of North Carolina, Chapel Hill, North Carolina
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6
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Brazel DM, Jiang Y, Hughey JM, Turcot V, Zhan X, Gong J, Batini C, Weissenkampen JD, Liu M, Barnes DR, Bertelsen S, Chou YL, Erzurumluoglu AM, Faul JD, Haessler J, Hammerschlag AR, Hsu C, Kapoor M, Lai D, Le N, de Leeuw CA, Loukola A, Mangino M, Melbourne CA, Pistis G, Qaiser B, Rohde R, Shao Y, Stringham H, Wetherill L, Zhao W, Agrawal A, Bierut L, Chen C, Eaton CB, Goate A, Haiman C, Heath A, Iacono WG, Martin NG, Polderman TJ, Reiner A, Rice J, Schlessinger D, Scholte HS, Smith JA, Tardif JC, Tindle HA, van der Leij AR, Boehnke M, Chang-Claude J, Cucca F, David SP, Foroud T, Howson JMM, Kardia SLR, Kooperberg C, Laakso M, Lettre G, Madden P, McGue M, North K, Posthuma D, Spector T, Stram D, Tobin MD, Weir DR, Kaprio J, Abecasis GR, Liu DJ, Vrieze S. Exome Chip Meta-analysis Fine Maps Causal Variants and Elucidates the Genetic Architecture of Rare Coding Variants in Smoking and Alcohol Use. Biol Psychiatry 2019; 85:946-955. [PMID: 30679032 PMCID: PMC6534468 DOI: 10.1016/j.biopsych.2018.11.024] [Citation(s) in RCA: 55] [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: 09/15/2017] [Revised: 11/05/2018] [Accepted: 11/29/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Smoking and alcohol use have been associated with common genetic variants in multiple loci. Rare variants within these loci hold promise in the identification of biological mechanisms in substance use. Exome arrays and genotype imputation can now efficiently genotype rare nonsynonymous and loss of function variants. Such variants are expected to have deleterious functional consequences and to contribute to disease risk. METHODS We analyzed ∼250,000 rare variants from 16 independent studies genotyped with exome arrays and augmented this dataset with imputed data from the UK Biobank. Associations were tested for five phenotypes: cigarettes per day, pack-years, smoking initiation, age of smoking initiation, and alcoholic drinks per week. We conducted stratified heritability analyses, single-variant tests, and gene-based burden tests of nonsynonymous/loss-of-function coding variants. We performed a novel fine-mapping analysis to winnow the number of putative causal variants within associated loci. RESULTS Meta-analytic sample sizes ranged from 152,348 to 433,216, depending on the phenotype. Rare coding variation explained 1.1% to 2.2% of phenotypic variance, reflecting 11% to 18% of the total single nucleotide polymorphism heritability of these phenotypes. We identified 171 genome-wide associated loci across all phenotypes. Fine mapping identified putative causal variants with double base-pair resolution at 24 of these loci, and between three and 10 variants for 65 loci. Twenty loci contained rare coding variants in the 95% credible intervals. CONCLUSIONS Rare coding variation significantly contributes to the heritability of smoking and alcohol use. Fine-mapping genome-wide association study loci identifies specific variants contributing to the biological etiology of substance use behavior.
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Affiliation(s)
- David M Brazel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado; Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado
| | - Yu Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Jordan M Hughey
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Valérie Turcot
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada; Montreal Heart Institute, Montreal, Quebec, Canada
| | - Xiaowei Zhan
- Department of Clinical Science, Center for Genetics of Host Defense, University of Texas Southwestern, Dallas, Texas
| | - Jian Gong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - J Dylan Weissenkampen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - MengZhen Liu
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | - Daniel R Barnes
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Bertelsen
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yi-Ling Chou
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | | | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan
| | - Jeff Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Anke R Hammerschlag
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Chris Hsu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Nhung Le
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois
| | - Christiaan A de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Anu Loukola
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom; National Institute for Health Research Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, United Kingdom
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Giorgio Pistis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Beenish Qaiser
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Rebecca Rohde
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yaming Shao
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Heather Stringham
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Laura Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Chu Chen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, Head and Neck Surgery Center, University of Washington, Seattle, Washington; Department of Otolaryngology, Head and Neck Surgery Center, University of Washington, Seattle, Washington
| | - Charles B Eaton
- Department of Family Medicine, Brown University, Providence, Rhode Island
| | - Alison Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Andrew Heath
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - William G Iacono
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | | | - Tinca J Polderman
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Alex Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, Head and Neck Surgery Center, University of Washington, Seattle, Washington
| | - John Rice
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri; Department of Mathematics, Washington University in St. Louis, St. Louis, Missouri
| | - David Schlessinger
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - H Steven Scholte
- Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, the Netherlands
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | - Jean-Claude Tardif
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada; Montreal Heart Institute, Montreal, Quebec, Canada
| | - Hilary A Tindle
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Andries R van der Leij
- Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, the Netherlands
| | - Michael Boehnke
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Sean P David
- Department of Medicine, Stanford University, Stanford, California
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Joanna M M Howson
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Markku Laakso
- Department of Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Guillaume Lettre
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada; Montreal Heart Institute, Montreal, Quebec, Canada
| | - Pamela Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | - Kari North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, University of Amsterdam, Amsterdam, the Netherlands; Department of Clinical Genetics, VU University Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Timothy Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Daniel Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Gonçalo R Abecasis
- Regeneron Pharmaceuticals, Tarrytown, New York; Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Dajiang J Liu
- Institute of Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania.
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota.
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7
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Sharp BM, Chen H. Neurogenetic determinants and mechanisms of addiction to nicotine and smoked tobacco. Eur J Neurosci 2018; 50:2164-2179. [DOI: 10.1111/ejn.14171] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/31/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Burt M. Sharp
- Department of Genetics, Genomics and Informatics College of Medicine University of Tennessee Health Science Center 19 S. Manassas, CRB #220 Memphis TN 38103 USA
| | - Hao Chen
- Department of Pharmacology University of Tennessee Health Science Center Memphis TN USA
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8
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Liu W, Li MD. Insights Into Nicotinic Receptor Signaling in Nicotine Addiction: Implications for Prevention and Treatment. Curr Neuropharmacol 2018; 16:350-370. [PMID: 28762314 PMCID: PMC6018190 DOI: 10.2174/1570159x15666170801103009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/18/2017] [Accepted: 07/28/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Nicotinic acetylcholine receptors (nAChRs) belong to the Cys-loop ligandgated ion-channel (LGIC) superfamily, which also includes the GABA, glycine, and serotonin receptors. Many nAChR subunits have been identified and shown to be involved in signal transduction on binding to them of either the neurotransmitter acetylcholine or exogenous ligands such as nicotine. The nAChRs are pentameric assemblies of homologous subunits surrounding a central pore that gates cation flux, and they are expressed at neuromuscular junctions throughout the nervous system. METHODS AND RESULTS Because different nAChR subunits assemble into a variety of pharmacologically distinct receptor subtypes, and different nAChRs are implicated in various physiological functions and pathophysiological conditions, nAChRs represent potential molecular targets for drug addiction and medical therapeutic research. This review intends to provide insights into recent advances in nAChR signaling, considering the subtypes and subunits of nAChRs and their roles in nicotinic cholinergic systems, including structure, diversity, functional allosteric modulation, targeted knockout mutations, and rare variations of specific subunits, and the potency and functional effects of mutations by focusing on their effects on nicotine addiction (NA) and smoking cessation (SC). Furthermore, we review the possible mechanisms of action of nAChRs in NA and SC based on our current knowledge. CONCLUSION Understanding these cellular and molecular mechanisms will lead to better translational and therapeutic operations and outcomes for the prevention and treatment of NA and other drug addictions, as well as chronic diseases, such as Alzheimer's and Parkinson's. Finally, we put forward some suggestions and recommendations for therapy and treatment of NA and other chronic diseases.
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Affiliation(s)
- Wuyi Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China.,School of Biological Sciences and Food Engineering, Fuyang Normal University, Fuyang, Anuhi 236041, China
| | - Ming D Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China.,Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China.,Institute of NeuroImmune Pharmacology, Seton Hall University, South Orange, NJ, United States
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9
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Saccone NL, Baurley JW, Bergen AW, David SP, Elliott HR, Foreman MG, Kaprio J, Piasecki TM, Relton CL, Zawertailo L, Bierut LJ, Tyndale RF, Chen LS. The Value of Biosamples in Smoking Cessation Trials: A Review of Genetic, Metabolomic, and Epigenetic Findings. Nicotine Tob Res 2018; 20:403-413. [PMID: 28472521 PMCID: PMC5896536 DOI: 10.1093/ntr/ntx096] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/01/2017] [Indexed: 02/03/2023]
Abstract
Introduction Human genetic research has succeeded in definitively identifying multiple genetic variants associated with risk for nicotine dependence and heavy smoking. To build on these advances, and to aid in reducing the prevalence of smoking and its consequent health harms, the next frontier is to identify genetic predictors of successful smoking cessation and also of the efficacy of smoking cessation treatments ("pharmacogenomics"). More broadly, additional biomarkers that can be quantified from biosamples also promise to aid "Precision Medicine" and the personalization of treatment, both pharmacological and behavioral. Aims and Methods To motivate ongoing and future efforts, here we review several compelling genetic and biomarker findings related to smoking cessation and treatment. Results These Key results involve genetic variants in the nicotinic receptor subunit gene CHRNA5, variants in the nicotine metabolism gene CYP2A6, and the nicotine metabolite ratio. We also summarize reports of epigenetic changes related to smoking behavior. Conclusions The results to date demonstrate the value and utility of data generated from biosamples in clinical treatment trial settings. This article cross-references a companion paper in this issue that provides practical guidance on how to incorporate biosample collection into a planned clinical trial and discusses avenues for harmonizing data and fostering consortium-based, collaborative research on the pharmacogenomics of smoking cessation. Implications Evidence is emerging that certain genotypes and biomarkers are associated with smoking cessation success and efficacy of smoking cessation treatments. We review key findings that open potential avenues for personalizing smoking cessation treatment according to an individual's genetic or metabolic profile. These results provide important incentive for smoking cessation researchers to collect biosamples and perform genotyping in research studies and clinical trials.
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Affiliation(s)
- Nancy L Saccone
- Department of Genetics and Division of Biostatistics, Washington University School of Medicine, St. Louis, MO
| | | | | | - Sean P David
- Department of Medicine, Stanford University, Stanford, CA
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Marilyn G Foreman
- Pulmonary and Critical Care Medicine, Morehouse School of Medicine, Atlanta, GA
| | - Jaakko Kaprio
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Thomas M Piasecki
- Department of Psychological Sciences, University of Missouri, Columbia, MO
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Laurie Zawertailo
- Nicotine Dependence Service, Centre for Addiction and Mental Health, and Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Laura J Bierut
- Siteman Cancer Center, Institute of Public Health, and Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, and Departments of Pharmacology & Toxicology and Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Li-Shiun Chen
- Siteman Cancer Center, Institute of Public Health, and Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
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10
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Abstract
PURPOSE OF REVIEW With the advent of the genome-wide association study (GWAS), our understanding of the genetics of addiction has made significant strides forward. Here, we summarize genetic loci containing variants identified at genome-wide statistical significance (P < 5 × 10-8) and independently replicated, review evidence of functional or regulatory effects for GWAS-identified variants, and outline multi-omics approaches to enhance discovery and characterize addiction loci. RECENT FINDINGS Replicable GWAS findings span 11 genetic loci for smoking, eight loci for alcohol, and two loci for illicit drugs combined and include missense functional variants and noncoding variants with regulatory effects in human brain tissues traditionally viewed as addiction-relevant (e.g., prefrontal cortex [PFC]) and, more recently, tissues often overlooked (e.g., cerebellum). GWAS analyses have discovered several novel, replicable variants contributing to addiction. Using larger sample sizes from harmonized datasets and new approaches to integrate GWAS with multiple 'omics data across human brain tissues holds great promise to significantly advance our understanding of the biology underlying addiction.
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Affiliation(s)
- Dana B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, 3040 East Cornwallis Road, P. O. Box 12194, Research Triangle Park, NC, 27709, USA.
| | - Christina A Markunas
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, 3040 East Cornwallis Road, P. O. Box 12194, Research Triangle Park, NC, 27709, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Eric O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
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11
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Pharmacogenetic study of seven polymorphisms in three nicotinic acetylcholine receptor subunits in smoking-cessation therapies. Sci Rep 2017; 7:16730. [PMID: 29196725 PMCID: PMC5711795 DOI: 10.1038/s41598-017-16946-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/19/2017] [Indexed: 11/23/2022] Open
Abstract
Smoking-cessation therapy reduces the risk of smoking-related diseases, but is successful only in a fraction of smokers. There is growing evidence that genetic variations in nicotinic acetylcholine receptor (nAChR) subunits influence the risk of nicotine dependence and the ability to quit smoking. To investigate the role of polymorphisms in nAChR genes on smoking quantity and the outcome of smoking-cessation therapies, we carried out an association study on 337 smokers who underwent pharmacotherapy with varenicline, bupropion, nicotine replacement therapy (NRT) alone, or NRT plus bupropion. Smoking habit and abstention were assessed from the number of cigarettes smoked per day (CPD) and the exhaled CO (eCO), at baseline and up to 12 months. We genotyped seven polymorphisms in genes encoding the nAChR subunits CHRNA4, CHRNA5, and CHRNB2. At baseline, both CPD and eCO were associated with polymorphisms in the CHRNA5 locus (rs503464, rs55853698, rs55781567 and rs16969968; P < 0.01). rs503464, a variant in the 5′-UTR of CHRNA5, was also associated with short-, mid- and long-term responses to therapy (P = 0.011, P = 0.0043, P = 0.020, respectively), although after correction for multiple testing only the association at the mid-term assessment remained significant (FDR = 0.03). These data support the role of individual genetic makeup in the ability to quit smoking.
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12
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Melroy-Greif WE, Simonson MA, Corley RP, Lutz SM, Hokanson JE, Ehringer MA. Examination of the Involvement of Cholinergic-Associated Genes in Nicotine Behaviors in European and African Americans. Nicotine Tob Res 2017; 19:417-425. [PMID: 27613895 DOI: 10.1093/ntr/ntw200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/20/2016] [Indexed: 12/18/2022]
Abstract
Introduction Cigarette smoking is a physiologically harmful habit. Nicotinic acetylcholine receptors (nAChRs) are bound by nicotine and upregulated in response to chronic exposure to nicotine. It is known that upregulation of these receptors is not due to a change in mRNA of these genes, however, more precise details on the process are still uncertain, with several plausible hypotheses describing how nAChRs are upregulated. We have manually curated a set of genes believed to play a role in nicotine-induced nAChR upregulation. Here, we test the hypothesis that these genes are associated with and contribute risk for nicotine dependence (ND) and the number of cigarettes smoked per day (CPD). Methods Studies with genotypic data on European and African Americans (EAs and AAs, respectively) were collected and a gene-based test was run to test for an association between each gene and ND and CPD. Results Although several novel genes were associated with CPD and ND at P < 0.05 in EAs and AAs, these associations did not survive correction for multiple testing. Previous associations between CHRNA3, CHRNA5, CHRNB4 and CPD in EAs were replicated. Conclusions Our hypothesis-driven approach avoided many of the limitations inherent in pathway analyses and provided nominal evidence for association between cholinergic-related genes and nicotine behaviors. Implications We evaluated the evidence for association between a manually curated set of genes and nicotine behaviors in European and African Americans. Although no genes were associated after multiple testing correction, this study has several strengths: by manually curating a set of genes we circumvented the limitations inherent in many pathway analyses and tested several genes that had not yet been examined in a human genetic study; gene-based tests are a useful way to test for association with a set of genes; and these genes were collected based on literature review and conversations with experts, highlighting the importance of scientific collaboration.
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Affiliation(s)
- Whitney E Melroy-Greif
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA
| | | | - Robin P Corley
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO
| | - Sharon M Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO.,Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
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13
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Converging findings from linkage and association analyses on susceptibility genes for smoking and other addictions. Mol Psychiatry 2016; 21:992-1008. [PMID: 27166759 PMCID: PMC4956568 DOI: 10.1038/mp.2016.67] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/05/2016] [Accepted: 03/09/2016] [Indexed: 12/18/2022]
Abstract
Experimental approaches to genetic studies of complex traits evolve with technological advances. How do discoveries using different approaches advance our knowledge of the genetic architecture underlying complex diseases/traits? Do most of the findings of newer techniques, such as genome-wide association study (GWAS), provide more information than older ones, for example, genome-wide linkage study? In this review, we address these issues by developing a nicotine dependence (ND) genetic susceptibility map based on the results obtained by the approaches commonly used in recent years, namely, genome-wide linkage, candidate gene association, GWAS and targeted sequencing. Converging and diverging results from these empirical approaches have elucidated a preliminary genetic architecture of this intractable psychiatric disorder and yielded new hypotheses on ND etiology. The insights we obtained by putting together results from diverse approaches can be applied to other complex diseases/traits. In sum, developing a genetic susceptibility map and keeping it updated are effective ways to keep track of what we know about a disease/trait and what the next steps may be with new approaches.
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14
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Olfson E, Saccone NL, Johnson EO, Chen LS, Culverhouse R, Doheny K, Foltz SM, Fox L, Gogarten SM, Hartz S, Hetrick K, Laurie CC, Marosy B, Amin N, Arnett D, Barr RG, Bartz TM, Bertelsen S, Borecki IB, Brown MR, Chasman DI, van Duijn CM, Feitosa MF, Fox ER, Franceschini N, Franco OH, Grove ML, Guo X, Hofman A, Kardia SLR, Morrison AC, Musani SK, Psaty BM, Rao DC, Reiner AP, Rice K, Ridker PM, Rose LM, Schick UM, Schwander K, Uitterlinden AG, Vojinovic D, Wang JC, Ware EB, Wilson G, Yao J, Zhao W, Breslau N, Hatsukami D, Stitzel JA, Rice J, Goate A, Bierut LJ. Rare, low frequency and common coding variants in CHRNA5 and their contribution to nicotine dependence in European and African Americans. Mol Psychiatry 2016; 21:601-7. [PMID: 26239294 PMCID: PMC4740321 DOI: 10.1038/mp.2015.105] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/29/2015] [Accepted: 06/22/2015] [Indexed: 02/04/2023]
Abstract
The common nonsynonymous variant rs16969968 in the α5 nicotinic receptor subunit gene (CHRNA5) is the strongest genetic risk factor for nicotine dependence in European Americans and contributes to risk in African Americans. To comprehensively examine whether other CHRNA5 coding variation influences nicotine dependence risk, we performed targeted sequencing on 1582 nicotine-dependent cases (Fagerström Test for Nicotine Dependence score⩾4) and 1238 non-dependent controls, with independent replication of common and low frequency variants using 12 studies with exome chip data. Nicotine dependence was examined using logistic regression with individual common variants (minor allele frequency (MAF)⩾0.05), aggregate low frequency variants (0.05>MAF⩾0.005) and aggregate rare variants (MAF<0.005). Meta-analysis of primary results was performed with replication studies containing 12 174 heavy and 11 290 light smokers. Next-generation sequencing with 180 × coverage identified 24 nonsynonymous variants and 2 frameshift deletions in CHRNA5, including 9 novel variants in the 2820 subjects. Meta-analysis confirmed the risk effect of the only common variant (rs16969968, European ancestry: odds ratio (OR)=1.3, P=3.5 × 10(-11); African ancestry: OR=1.3, P=0.01) and demonstrated that three low frequency variants contributed an independent risk (aggregate term, European ancestry: OR=1.3, P=0.005; African ancestry: OR=1.4, P=0.0006). The remaining 22 rare coding variants were associated with increased risk of nicotine dependence in the European American primary sample (OR=12.9, P=0.01) and in the same risk direction in African Americans (OR=1.5, P=0.37). Our results indicate that common, low frequency and rare CHRNA5 coding variants are independently associated with nicotine dependence risk. These newly identified variants likely influence the risk for smoking-related diseases such as lung cancer.
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Affiliation(s)
- E Olfson
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - N L Saccone
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - E O Johnson
- Behavioral Health Epidemiology program, RTI International, Research Triangle Park, NC, USA
| | - L-S Chen
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - R Culverhouse
- Department of Medicine and Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
| | - K Doheny
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, MD, USA
| | - S M Foltz
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - L Fox
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - S M Gogarten
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - S Hartz
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - K Hetrick
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, MD, USA
| | - C C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - B Marosy
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, MD, USA
| | - N Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - D Arnett
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - R G Barr
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY, USA
| | - T M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - S Bertelsen
- Department of Neurosciences, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - I B Borecki
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - M R Brown
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - D I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - C M van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - E R Fox
- University of Mississippi Medical Center, Jackson, MS, USA
| | - N Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - O H Franco
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M L Grove
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - X Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - A Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - S L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - A C Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - S K Musani
- University of Mississippi Medical Center, Jackson, MS, USA
| | - B M Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, USA
- Group Health Research Institute, Group Health, Seattle, WA, USA
| | - D C Rao
- Division of Biostatistics, Washington University School of Medicine in St. Louis, St Louis, MO, USA
| | - A P Reiner
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - K Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - P M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - L M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - U M Schick
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, USA
| | - K Schwander
- Division of Biostatistics, Washington University School of Medicine in St. Louis, St Louis, MO, USA
| | - A G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - D Vojinovic
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - J-C Wang
- Department of Neurosciences, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - E B Ware
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - G Wilson
- Jackson State University, School of Public Service, Jackson, MS, USA
| | - J Yao
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - N Breslau
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - D Hatsukami
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - J A Stitzel
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - J Rice
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - A Goate
- Department of Neurosciences, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - L J Bierut
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
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15
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Kamens HM, Corley RP, Richmond PA, Darlington TM, Dowell R, Hopfer CJ, Stallings MC, Hewitt JK, Brown SA, Ehringer MA. Evidence for Association Between Low Frequency Variants in CHRNA6/CHRNB3 and Antisocial Drug Dependence. Behav Genet 2016; 46:693-704. [PMID: 27085880 DOI: 10.1007/s10519-016-9792-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 04/05/2016] [Indexed: 11/24/2022]
Abstract
Common SNPs in nicotinic acetylcholine receptor genes (CHRN genes) have been associated with drug behaviors and personality traits, but the influence of rare genetic variants is not well characterized. The goal of this project was to identify novel rare variants in CHRN genes in the Center for Antisocial Drug Dependence (CADD) and Genetics of Antisocial Drug Dependence (GADD) samples and to determine if low frequency variants are associated with antisocial drug dependence. Two samples of 114 and 200 individuals were selected using a case/control design including the tails of the phenotypic distribution of antisocial drug dependence. The capture, sequencing, and analysis of all variants in 16 CHRN genes (CHRNA1-7, 9, 10, CHRNB1-4, CHRND, CHRNG, CHRNE) were performed independently for each subject in each sample. Sequencing reads were aligned to the human reference sequence using BWA prior to variant calling with the Genome Analysis ToolKit (GATK). Low frequency variants (minor allele frequency < 0.05) were analyzed using SKAT-O and C-alpha to examine the distribution of rare variants among cases and controls. In our larger sample, the region containing the CHRNA6/CHRNB3 gene cluster was significantly associated with disease status using both SKAT-O and C-alpha (unadjusted p values <0.05). More low frequency variants in the CHRNA6/CHRNB3 gene region were observed in cases compared to controls. These data support a role for genetic variants in CHRN genes and antisocial drug behaviors.
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Affiliation(s)
- Helen M Kamens
- Department of Biobehavioral Health, Pennsylvania State University, University Park, PA, USA
| | - Robin P Corley
- Institute for Behavioral Genetics, University of Colorado, 447 UCB, Boulder, CO, 80309, USA
| | | | - Todd M Darlington
- Institute for Behavioral Genetics, University of Colorado, 447 UCB, Boulder, CO, 80309, USA
| | - Robin Dowell
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA.,Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Christian J Hopfer
- Department of Psychiatry, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael C Stallings
- Institute for Behavioral Genetics, University of Colorado, 447 UCB, Boulder, CO, 80309, USA.,Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
| | - John K Hewitt
- Institute for Behavioral Genetics, University of Colorado, 447 UCB, Boulder, CO, 80309, USA.,Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
| | - Sandra A Brown
- Department of Psychology and Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado, 447 UCB, Boulder, CO, 80309, USA. .,Department of Integrative Physiology, University of Colorado, Boulder, CO, USA.
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16
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Shmulewitz D, Meyers JL, Wall MM, Aharonovich E, Frisch A, Spivak B, Weizman A, Edenberg HJ, Gelernter J, Hasin DS. CHRNA5/A3/B4 Variant rs3743078 and Nicotine-Related Phenotypes: Indirect Effects Through Nicotine Craving. J Stud Alcohol Drugs 2016; 77:227-37. [PMID: 26997181 DOI: 10.15288/jsad.2016.77.227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE Nicotine craving is considered an important element in the persistence of cigarette smoking, but little is known about the role of craving in the widely recognized association between variants mapped to the neuronal nicotinic acetylcholine receptor (CHRN) genes on chromosome 15 and nicotine phenotypes. METHOD The associations between CHRNA5-CHRNA3-CHRNB4 variants and cigarettes per day (CPD), the Fagerström Test for Nicotine Dependence (FTND), and craving were analyzed in data from 662 lifetime smokers from an Israeli adult Jewish household sample. Indirect effects of genotype on nicotine phenotypes through craving were formally tested using regression and bootstrapping procedures. RESULTS At CHRNA3, allele G of rs3743078 was associated with increased craving, CPD, and FTND scores: Participants with one or two copies of the G allele had, on average, higher scores on the craving scale (p = .0025), more cigarettes smoked (p = .0057), and higher scores on the FTND (p =.0024). With craving in the model, variant rs3743078 showed a significant indirect effect through craving on CPD (p = .0026) and on FTND score (p = .0024). A sizeable proportion of the total rs3743078 effect on CPD (56.4%) and FTND (65.2%) was indirect through craving. CONCLUSIONS These results suggest that nicotine craving may play a central role in nicotine use disorders and may have utility as a therapeutic target.
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Affiliation(s)
- Dvora Shmulewitz
- Department of Psychiatry, Columbia University, NewYork, NewYork.,NewYork State Psychiatric Institute, NewYork, NewYork
| | - Jacquelyn L Meyers
- Department of Epidemiology, Mailman School of Public Health, Columbia University, NewYork, NewYork
| | - Melanie M Wall
- Department of Psychiatry, Columbia University, NewYork, NewYork.,NewYork State Psychiatric Institute, NewYork, NewYork.,Department of Biostatistics, Mailman School of Public Health, Columbia University, NewYork, NewYork
| | - Efrat Aharonovich
- Department of Psychiatry, Columbia University, NewYork, NewYork.,NewYork State Psychiatric Institute, NewYork, NewYork
| | - Amos Frisch
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Baruch Spivak
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abraham Weizman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel.,Research Unit, Geha Mental Health Center, Petach Tikva, Israel
| | - Howard J Edenberg
- Departments of Biochemistry and Molecular Biology and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Joel Gelernter
- Departments of Psychiatry and Genetics and Neurobiology, Yale University School of Medicine, New Haven, Connecticut
| | - Deborah S Hasin
- Department of Psychiatry, Columbia University, NewYork, NewYork.,NewYork State Psychiatric Institute, NewYork, NewYork.,Department of Epidemiology, Mailman School of Public Health, Columbia University, NewYork, NewYork
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17
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Melroy-Greif WE, Stitzel JA, Ehringer MA. Nicotinic acetylcholine receptors: upregulation, age-related effects and associations with drug use. GENES, BRAIN, AND BEHAVIOR 2016; 15:89-107. [PMID: 26351737 PMCID: PMC4780670 DOI: 10.1111/gbb.12251] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/16/2022]
Abstract
Nicotinic acetylcholine receptors are ligand-gated ion channels that exogenously bind nicotine. Nicotine produces rewarding effects by interacting with these receptors in the brain's reward system. Unlike other receptors, chronic stimulation by an agonist induces an upregulation of receptor number that is not due to increased gene expression in adults; while upregulation also occurs during development and adolescence there have been some opposing findings regarding a change in corresponding gene expression. These receptors have also been well studied with regard to human genetic associations and, based on evidence suggesting shared genetic liabilities between substance use disorders, numerous studies have pointed to a role for this system in comorbid drug use. This review will focus on upregulation of these receptors in adulthood, adolescence and development, as well as the findings from human genetic association studies which point to different roles for these receptors in risk for initiation and continuation of drug use.
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Affiliation(s)
- Whitney E. Melroy-Greif
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - Jerry A. Stitzel
- Institute for Behavioral Genetics, University of Colorado Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado Boulder, CO, USA
| | - Marissa A. Ehringer
- Institute for Behavioral Genetics, University of Colorado Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado Boulder, CO, USA
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18
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Yang J, Wang S, Yang Z, Hodgkinson CA, Iarikova P, Ma JZ, Payne TJ, Goldman D, Li MD. The contribution of rare and common variants in 30 genes to risk nicotine dependence. Mol Psychiatry 2015; 20:1467-78. [PMID: 25450229 PMCID: PMC4452458 DOI: 10.1038/mp.2014.156] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 09/28/2014] [Accepted: 10/08/2014] [Indexed: 01/17/2023]
Abstract
Genetic and functional studies have revealed that both common and rare variants of several nicotinic acetylcholine receptor subunits are associated with nicotine dependence (ND). In this study, we identified variants in 30 candidate genes including nicotinic receptors in 200 sib pairs selected from the Mid-South Tobacco Family population with equal numbers of African Americans (AAs) and European Americans (EAs). We selected 135 of the rare and common variants and genotyped them in the Mid-South Tobacco Case-Control (MSTCC) population, which consists of 3088 AAs and 1430 EAs. None of the genotyped common variants showed significant association with smoking status (smokers vs non-smokers), Fagerström Test for ND scores or indexed cigarettes per day after Bonferroni correction. Rare variants in NRXN1, CHRNA9, CHRNA2, NTRK2, GABBR2, GRIN3A, DNM1, NRXN2, NRXN3 and ARRB2 were significantly associated with smoking status in the MSTCC AA sample, with weighted sum statistic (WSS) P-values ranging from 2.42 × 10(-3) to 1.31 × 10(-4) after 10(6) phenotype rearrangements. We also observed a significant excess of rare nonsynonymous variants exclusive to EA smokers in NRXN1, CHRNA9, TAS2R38, GRIN3A, DBH, ANKK1/DRD2, NRXN3 and CDH13 with WSS P-values between 3.5 × 10(-5) and 1 × 10(-6). Variants rs142807401 (A432T) and rs139982841 (A452V) in CHRNA9 and variants V132L, V389L, rs34755188 (R480H) and rs75981117 (N549S) in GRIN3A are of particular interest because they are found in both the AA and EA samples. A significant aggregate contribution of rare and common coding variants in CHRNA9 to the risk for ND (SKAT-C: P=0.0012) was detected by applying the combined sum test in MSTCC EAs. Together, our results indicate that rare variants alone or combined with common variants in a subset of 30 biological candidate genes contribute substantially to the risk of ND.
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Affiliation(s)
- Jiekun Yang
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA 22903
| | - Shaolin Wang
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA 22903
| | - Zhongli Yang
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA 22903
| | | | | | - Jennie Z. Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville
| | - Thomas J. Payne
- ACT Center for Tobacco Treatment, Education and Research, Department of Otolaryngology and Communicative Sciences, University of Mississippi Medical Center, Jackson, MS 39213
| | - David Goldman
- Laboratory of Neurogenetics, NIAAA, NIH; Bethesda, MD 20852
| | - Ming D. Li
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA 22903
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19
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Bühler KM, Giné E, Echeverry-Alzate V, Calleja-Conde J, de Fonseca FR, López-Moreno JA. Common single nucleotide variants underlying drug addiction: more than a decade of research. Addict Biol 2015; 20:845-71. [PMID: 25603899 DOI: 10.1111/adb.12204] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug-related phenotypes are common complex and highly heritable traits. In the last few years, candidate gene (CGAS) and genome-wide association studies (GWAS) have identified a huge number of single nucleotide polymorphisms (SNPs) associated with drug use, abuse or dependence, mainly related to alcohol or nicotine. Nevertheless, few of these associations have been replicated in independent studies. The aim of this study was to provide a review of the SNPs that have been most significantly associated with alcohol-, nicotine-, cannabis- and cocaine-related phenotypes in humans between the years of 2000 and 2012. To this end, we selected CGAS, GWAS, family-based association and case-only studies published in peer-reviewed international scientific journals (using the PubMed/MEDLINE and Addiction GWAS Resource databases) in which a significant association was reported. A total of 371 studies fit the search criteria. We then filtered SNPs with at least one replication study and performed meta-analysis of the significance of the associations. SNPs in the alcohol metabolizing genes, in the cholinergic gene cluster CHRNA5-CHRNA3-CHRNB4, and in the DRD2 and ANNK1 genes, are, to date, the most replicated and significant gene variants associated with alcohol- and nicotine-related phenotypes. In the case of cannabis and cocaine, a far fewer number of studies and replications have been reported, indicating either a need for further investigation or that the genetics of cannabis/cocaine addiction are more elusive. This review brings a global state-of-the-art vision of the behavioral genetics of addiction and collaborates on formulation of new hypothesis to guide future work.
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Affiliation(s)
- Kora-Mareen Bühler
- Department of Psychobiology; School of Psychology; Complutense University of Madrid; Málaga Spain
| | - Elena Giné
- Department of Cellular Biology; School of Medicine; Complutense University of Madrid; Málaga Spain
| | - Victor Echeverry-Alzate
- Department of Psychobiology; School of Psychology; Complutense University of Madrid; Málaga Spain
| | - Javier Calleja-Conde
- Department of Psychobiology; School of Psychology; Complutense University of Madrid; Málaga Spain
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20
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Featherstone RE, Siegel SJ. The Role of Nicotine in Schizophrenia. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 124:23-78. [PMID: 26472525 DOI: 10.1016/bs.irn.2015.07.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Schizophrenia is associated with by severe disruptions in thought, cognition, emotion, and behavior. Patients show a marked increase in rates of smoking and nicotine dependence relative to nonaffected individuals, a finding commonly ascribed to the potential ameliorative effects of nicotine on symptom severity and cognitive impairment. Indeed, many studies have demonstrated improvement in patients following the administration of nicotine. Such findings have led to an increased emphasis on the development of therapeutic agents to target the nicotinic system as well as increasing the impetus to understand the genetic basis for nicotinic dysfunction in schizophrenia. The goal of this review article is to provide a critical summary of evidence for the role of the nicotinic system in schizophrenia. The first part will review the role of nicotine in normalization of primary dysfunctions and endophenotypical changes found in schizophrenia. The second part will provide a summary of genetic evidence linking polymorphisms in nicotinic receptor genes to smoking and schizophrenia. The third part will summarize attempts to treat schizophrenia using agents specifically targeting nicotinic and nicotinic receptor subtypes. Although currently available antipsychotic treatments are generally able to manage some aspects of schizophrenia (e.g., positive symptoms) they fail to address several other critically effected aspects of the disease. As such, the search for novel mechanisms to treat this disease is necessary.
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Affiliation(s)
- Robert E Featherstone
- Translational Neuroscience Program, Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Steven J Siegel
- Translational Neuroscience Program, Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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21
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Clark SL, McClay JL, Adkins DE, Aberg KA, Kumar G, Nerella S, Xie L, Collins AL, Crowley JJ, Quakenbush CR, Hillard CE, Gao G, Shabalin AA, Peterson RE, Copeland WE, Silberg JL, Maes H, Sullivan PF, Costello EJ, van den Oord EJ. Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses. Nicotine Tob Res 2015; 18:626-31. [PMID: 26283763 DOI: 10.1093/ntr/ntv166] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 07/17/2015] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Genome-wide association study meta-analyses have robustly implicated three loci that affect susceptibility for smoking: CHRNA5\CHRNA3\CHRNB4, CHRNB3\CHRNA6 and EGLN2\CYP2A6. Functional follow-up studies of these loci are needed to provide insight into biological mechanisms. However, these efforts have been hampered by a lack of knowledge about the specific causal variant(s) involved. In this study, we prioritized variants in terms of the likelihood they account for the reported associations. METHODS We employed targeted capture of the CHRNA5\CHRNA3\CHRNB4, CHRNB3\CHRNA6, and EGLN2\CYP2A6 loci and flanking regions followed by next-generation deep sequencing (mean coverage 78×) to capture genomic variation in 363 individuals. We performed single locus tests to determine if any single variant accounts for the association, and examined if sets of (rare) variants that overlapped with biologically meaningful annotations account for the associations. RESULTS In total, we investigated 963 variants, of which 71.1% were rare (minor allele frequency < 0.01), 6.02% were insertion/deletions, and 51.7% were catalogued in dbSNP141. The single variant results showed that no variant fully accounts for the association in any region. In the variant set results, CHRNB4 accounts for most of the signal with significant sets consisting of directly damaging variants. CHRNA6 explains most of the signal in the CHRNB3\CHRNA6 locus with significant sets indicating a regulatory role for CHRNA6. Significant sets in CYP2A6 involved directly damaging variants while the significant variant sets suggested a regulatory role for EGLN2. CONCLUSIONS We found that multiple variants implicating multiple processes explain the signal. Some variants can be prioritized for functional follow-up.
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Affiliation(s)
- Shaunna L Clark
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA;
| | - Joseph L McClay
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Daniel E Adkins
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Gaurav Kumar
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Sri Nerella
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Linying Xie
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Ann L Collins
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - James J Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Corey R Quakenbush
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Christopher E Hillard
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Guimin Gao
- Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, VA
| | - Andrey A Shabalin
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Roseann E Peterson
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - William E Copeland
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC
| | - Judy L Silberg
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Hermine Maes
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Elizabeth J Costello
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC
| | - Edwin J van den Oord
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
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22
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Androsova G, Krause R, Winterer G, Schneider R. Biomarkers of postoperative delirium and cognitive dysfunction. Front Aging Neurosci 2015; 7:112. [PMID: 26106326 PMCID: PMC4460425 DOI: 10.3389/fnagi.2015.00112] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/28/2015] [Indexed: 01/19/2023] Open
Abstract
Elderly surgical patients frequently experience postoperative delirium (POD) and the subsequent development of postoperative cognitive dysfunction (POCD). Clinical features include deterioration in cognition, disturbance in attention and reduced awareness of the environment and result in higher morbidity, mortality and greater utilization of social financial assistance. The aging Western societies can expect an increase in the incidence of POD and POCD. The underlying pathophysiological mechanisms have been studied on the molecular level albeit with unsatisfying small research efforts given their societal burden. Here, we review the known physiological and immunological changes and genetic risk factors, identify candidates for further studies and integrate the information into a draft network for exploration on a systems level. The pathogenesis of these postoperative cognitive impairments is multifactorial; application of integrated systems biology has the potential to reconstruct the underlying network of molecular mechanisms and help in the identification of prognostic and diagnostic biomarkers.
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Affiliation(s)
- Ganna Androsova
- Bioinformatics core, Luxembourg Centre for Systems Biomedicine (LCSB), University of LuxembourgBelvaux, Luxembourg
| | - Roland Krause
- Bioinformatics core, Luxembourg Centre for Systems Biomedicine (LCSB), University of LuxembourgBelvaux, Luxembourg
| | - Georg Winterer
- Experimental and Clinical Research Center (ECRC), Department of Anesthesiology and Operative Intensive Care Medicine, Charité University Medicine BerlinBerlin, Germany
| | - Reinhard Schneider
- Bioinformatics core, Luxembourg Centre for Systems Biomedicine (LCSB), University of LuxembourgBelvaux, Luxembourg
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23
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Csala I, Egervari L, Dome P, Faludi G, Dome B, Lazary J. The possible role of maternal bonding style and CHRNB2 gene polymorphisms in nicotine dependence and related depressive phenotype. Prog Neuropsychopharmacol Biol Psychiatry 2015; 59:84-90. [PMID: 25640319 DOI: 10.1016/j.pnpbp.2015.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 01/21/2015] [Accepted: 01/21/2015] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Neuronal nicotinic acetylcholinergic receptors (nAChR) and especially α4β2 nAChRs are the major targets for cessation medications and also for some promising antidepressant agents. Furthermore, depressive symptoms pose multifacet difficulties during cessation therapy. However, gene encoding for the β2 subunit of nAChRs has been poorly investigated in association with depression. Since both nicotine dependence (ND) and depressive phenotype are complex disorders, we investigated the effects of a significant early life experience, maternal bonding style (MB) and CHRNB2 gene SNPs on smoking-related depression. METHODS We recruited two hundred and thirty-two treatment-seeking smokers in our study. Phenotypic variants were evaluated using the Fagerstrom Test for Nicotine Dependence (FTND), the Zung Self-Rating Depression Scale (ZSDS) and the Parental Bonding Instrument (PBI). Besides the total score (TS) of ZSDS, impulsivity (ZSDS-I) and suicidal ideation (ZSDS-S) were distinguished as phenotypic variable. DNAs were extracted from buccal mucosa samples and one SNP in promoter and two SNPs in 3' UTR of CHRNB2 gene were genotyped. GLM and ANOVA tests were performed for genotype associations and interaction analyses. RESULTS Maternal bonding had a significant impact on depressive phenotypes. Low care, high protection and affectionless control (ALC) were associated with ZSDS-TS and all subphenotypes of ZSDS. One SNP, the rs2072660 in 3' UTR, had a significant effect on the FTND score (p=0.010). Direct association of CHRNB2 variants and depressive phenotypes were not significant. However, in interaction with ALC, rs2072660 was significantly associated with ZSDS-S (p=0.005). MB had no significant effect on smoking-related phenotype. CONCLUSIONS Our results highlight the important role of 3' UTR in the CHRNB2 gene in the shared molecular background of ND and depressive phenotype. Parental bonding style can be suggested as a significant environmental factor in further GxE studies of depression. The presented significant GxE interaction on smoking-related suicidal subphenotype may help establish further investigations on development of more effective and safer smoking cessation and antidepressant agents.
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Affiliation(s)
- Iren Csala
- Department of Clinical and Theoretical Mental Health, Semmelweis University, Budapest, Hungary; Institute of Behavioral Sciences, Semmelweis University, Budapest, Hungary
| | - Luca Egervari
- Department of Clinical and Theoretical Mental Health, Semmelweis University, Budapest, Hungary
| | - Peter Dome
- Department of Clinical and Theoretical Mental Health, Semmelweis University, Budapest, Hungary; National Institute of Psychiatry and Addiction, Budapest, Hungary
| | - Gabor Faludi
- Department of Clinical and Theoretical Mental Health, Semmelweis University, Budapest, Hungary
| | - Balazs Dome
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary; Department of Thoracic Surgery, Medical University of Vienna, Austria; Department of Thoracic Surgery, National Institute of Oncology and Semmelweis University, Budapest, Hungary; Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Medical University of Vienna, Austria
| | - Judit Lazary
- Department of Clinical and Theoretical Mental Health, Semmelweis University, Budapest, Hungary.
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24
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Kao CF, Liu JR, Hung H, Kuo PH. A robust GWSS method to simultaneously detect rare and common variants for complex disease. PLoS One 2015; 10:e0120873. [PMID: 25880329 PMCID: PMC4399906 DOI: 10.1371/journal.pone.0120873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/26/2015] [Indexed: 11/19/2022] Open
Abstract
The rapid advances in sequencing technologies and the resulting next-generation sequencing data provide the opportunity to detect disease-associated variants with a better solution, in particular for low-frequency variants. Although both common and rare variants might exert their independent effects on the risk for the trait of interest, previous methods to detect the association effects rarely consider them simultaneously. We proposed a class of test statistics, the generalized weighted-sum statistic (GWSS), to detect disease associations in the presence of common and rare variants with a case-control study design. Information of rare variants was aggregated using a weighted sum method, while signal directions and strength of the variants were considered at the same time. Permutations were performed to obtain the empirical p-values of the test statistics. Our simulation showed that, compared to the existing methods, the GWSS method had better performance in most of the scenarios. The GWSS (in particular VDWSS-t) method is particularly robust for opposite association directions, association strength, and varying distributions of minor-allele frequencies. It is therefore promising for detecting disease-associated loci. For empirical data application, we also applied our GWSS method to the Genetic Analysis Workshop 17 data, and the results were consistent with the simulation, suggesting good performance of our method. As re-sequencing studies become more popular to identify putative disease loci, we recommend the use of this newly developed GWSS to detect associations with both common and rare variants.
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Affiliation(s)
- Chung-Feng Kao
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Jia-Rou Liu
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
- Department of Public Health, Chang Gung University, Taoyuan,Taiwan
| | - Hung Hung
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
- Research Center for Genes, Environment and Human Health, National Taiwan University, Taipei, Taiwan
- * E-mail: (PHK); (HH)
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
- Research Center for Genes, Environment and Human Health, National Taiwan University, Taipei, Taiwan
- * E-mail: (PHK); (HH)
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25
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Eicher JD, Stein CM, Deng F, Ciesla AA, Powers NR, Boada R, Smith SD, Pennington BF, Iyengar SK, Lewis BA, Gruen JR. The DYX2 locus and neurochemical signaling genes contribute to speech sound disorder and related neurocognitive domains. GENES BRAIN AND BEHAVIOR 2015; 14:377-85. [PMID: 25778907 PMCID: PMC4492462 DOI: 10.1111/gbb.12214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 03/05/2015] [Accepted: 03/12/2015] [Indexed: 12/17/2022]
Abstract
A major milestone of child development is the acquisition and use of speech and language. Communication disorders, including speech sound disorder (SSD), can impair a child's academic, social and behavioral development. Speech sound disorder is a complex, polygenic trait with a substantial genetic component. However, specific genes that contribute to SSD remain largely unknown. To identify associated genes, we assessed the association of the DYX2 dyslexia risk locus and markers in neurochemical signaling genes (e.g., nicotinic and dopaminergic) with SSD and related endophenotypes. We first performed separate primary associations in two independent samples - Cleveland SSD (210 affected and 257 unaffected individuals in 127 families) and Denver SSD (113 affected individuals and 106 unaffected individuals in 85 families) - and then combined results by meta-analysis. DYX2 markers, specifically those in the 3' untranslated region of DCDC2 (P = 1.43 × 10(-4) ), showed the strongest associations with phonological awareness. We also observed suggestive associations of dopaminergic-related genes ANKK1 (P = 1.02 × 10(-2) ) and DRD2 (P = 9.22 × 10(-3) ) and nicotinic-related genes CHRNA3 (P = 2.51 × 10(-3) ) and BDNF (P = 8.14 × 10(-3) ) with case-control status and articulation. Our results further implicate variation in putative regulatory regions in the DYX2 locus, particularly in DCDC2, influencing language and cognitive traits. The results also support previous studies implicating variation in dopaminergic and nicotinic neural signaling influencing human communication and cognitive development. Our findings expand the literature showing genetic factors (e.g., DYX2) contributing to multiple related, yet distinct neurocognitive domains (e.g., dyslexia, language impairment, and SSD). How these factors interactively yield different neurocognitive and language-related outcomes remains to be elucidated.
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Affiliation(s)
- J D Eicher
- Department of Genetics, Yale University School of Medicine, New Haven, CT
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26
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Rocha Santos J, Tomaz PRX, Issa JS, Abe TO, Krieger JE, Pereira AC, Santos PCJL. CHRNA4 rs1044396 is associated with smoking cessation in varenicline therapy. Front Genet 2015; 6:46. [PMID: 25774163 PMCID: PMC4343187 DOI: 10.3389/fgene.2015.00046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/30/2015] [Indexed: 11/13/2022] Open
Abstract
Background: The large individual variability in response to drugs for smoking cessation suggests that specific treatments can be more effective in particular subgroups of smokers. In the context of personalized medicine, the main aim of the present study was to evaluate whether the CHRNA4 and CHRNB2 polymorphisms are associated with response to smoking cessation therapies in patients from a smoker assistance program. Methods: This cohort study enrolled 483 smoking patients who received behavioral counseling and drug treatment (varenicline, bupropion, and/or nicotine replacement therapy). Smoking cessation success was considered for patients who completed 6 months of continuous abstinence. Fagerström test for nicotine dependence (FTND) and Issa situational smoking scores were analyzed for nicotine dependence. The CHRNA4 (rs1044396 and rs2236196) and CHRNB2 (rs2072660 and rs2072661) polymorphisms were genotyped by high resolution melting analysis. Results: Patients with rs1044396 CC genotype had lower success rate in treatment with varenicline (29.5%) compared with carriers of CT or TT genotypes (50.9%; p = 0.007, n = 167). The CT or TT genotypes were associated with higher odds ratio for success (OR = 1.67, 95% CI = 1.10–2.53, p = 0.02), in a multivariate model. We did not observe significant differences in the FTND and Issa scores according to the studied polymorphisms. Conclusion: The CHRNA4 rs1044396 is associated with smoking cessation in individuals on varenicline therapy. We suggest that this polymorphism influences the varenicline response, but replications of this finding are needed.
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Affiliation(s)
- Juliana Rocha Santos
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School São Paulo, Brazil
| | - Paulo R X Tomaz
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School São Paulo, Brazil
| | - Jaqueline S Issa
- Smoking Cessation Program Department, Heart Institute, University of Sao Paulo Medical School São Paulo, Brazil
| | - Tânia O Abe
- Smoking Cessation Program Department, Heart Institute, University of Sao Paulo Medical School São Paulo, Brazil
| | - José E Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School São Paulo, Brazil
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School São Paulo, Brazil
| | - Paulo C J L Santos
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School São Paulo, Brazil
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Brunzell DH, Stafford AM, Dixon CI. Nicotinic receptor contributions to smoking: insights from human studies and animal models. CURRENT ADDICTION REPORTS 2015; 2:33-46. [PMID: 26301171 DOI: 10.1007/s40429-015-0042-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
It is becoming increasingly evident that a variety of factors contribute to smoking behavior. Nicotine is a constituent of tobacco smoke that exerts its psychoactive effects via binding to nicotinic acetylcholine receptors (nAChRs) in brain. Human genetic studies have identified polymorphisms in nAChR genes, which predict vulnerability to risk for tobacco dependence. In vitro studies and animal models have identified the functional relevance of specific polymorphisms. Together with animal behavioral models, which parse behaviors believed to contribute to tobacco use in humans, these studies demonstrate that nicotine action at a diversity of nAChRs is important for expression of independent behavioral phenotypes, which support smoking behavior.
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Affiliation(s)
- Darlene H Brunzell
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA
| | - Alexandra M Stafford
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA
| | - Claire I Dixon
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA
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Association between genetic variants on chromosome 15q25 locus and several nicotine dependence traits in Polish population: a case-control study. BIOMED RESEARCH INTERNATIONAL 2015; 2015:350348. [PMID: 25632390 PMCID: PMC4303006 DOI: 10.1155/2015/350348] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/19/2014] [Indexed: 11/28/2022]
Abstract
Tobacco smoking continues to be a leading cause of disease and mortality. Recent research has confirmed the important role of nicotinic acetylcholine receptor (nAChR) gene cluster on chromosome 15q 24-25 in nicotine dependence and smoking. In this study we tested the association of smoking initiation, age at onset of daily smoking, and heaviness of smoking with five single nucleotide polymorphisms (SNPs) within the CHRNA5-CHRNA3-CHRNB4 cluster. The group of 389 adult subjects of European ancestry from the north of Poland, including 212 ever (140 current and 72 former) and 177 never smokers with mean age 49.26, was genotyped for rs16969868, rs1051730, rs588765, rs6495308, and rs578776 polymorphisms. Distributions of genotypes for rs16969868 and rs1051730 were identical so they were analyzed together. Further analysis revealed the association between rs16969868-1051730 (OR = 2.66; 95% CI: 1.30–5.42) and number of cigarettes smoked per day (CPD) with heaviness of nicotine addiction measured by the Fagerström Test for Nicotine Dependence (FTND) (OR = 2.60; 95% CI: 1.24–5.43). No association between these polymorphisms and other phenotypes was found. Similarly, the association between rs588765, rs6495308, rs578776, and analyzed phenotypes was not confirmed. This study provides strong evidence for the role of the CHRNA5-CHRNA3-CHRNB4 cluster in heaviness of nicotine addiction.
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Abstract
BACKGROUND The common CHRNA5 mis-sense coding single-nucleotide polymorphism (SNP) rs16969968:G>A (D398N) has repeatedly been shown to confer risk for heavy smoking in individuals who carry the 'A' allele (encoding the 398N amino acid). The mis-sense SNP has a minor allele frequency of ∼40% in European-Americans, but only ∼7% in African-Americans (http://www.ncbi.nlm.nih.gov/projects/SNP/). We reasoned that there might be other mis-sense variants among African-Americans that could confer the heavy smoking phenotype (defined here as ≥20 cigarettes per day), perhaps in a manner similar to that of the D398N polymorphism in Europeans. MATERIALS AND METHODS As such, we resequenced 250 African-American heavy smokers, most of whom were homozygous 'G' at rs16969968:G>A (minor allele frequency of 9.6% within the population). RESULTS Although many novel coding SNPs were not observed, we report an interesting, although rare (perhaps personal), variant in CHRNA5 that could result in nonsense-mediated decay of the aberrant transcript. CONCLUSION We conclude that, in African-Americans, variants (common or rare) in genes other than CHRNA5 most likely contribute toward the nicotine-dependent phenotype, either independently or in combination with variants in CHRNA5. The functional significance, on CHRNA5 expression or protein function, of the variants found here should be determined in future studies.
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Contribution of Variants in CHRNA5/A3/B4 Gene Cluster on Chromosome 15 to Tobacco Smoking: From Genetic Association to Mechanism. Mol Neurobiol 2014; 53:472-484. [PMID: 25471942 DOI: 10.1007/s12035-014-8997-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/11/2014] [Indexed: 10/24/2022]
Abstract
Cigarette smoking is the major cause of preventable death and morbidity throughout the world. Many compounds are present in tobacco, but nicotine is the primary addictive one. Nicotine exerts its physiological and pharmacological roles in the brain through neuronal nicotinic acetylcholine receptors (nAChRs), which are ligand-gated ion channels consisting of five membrane-spanning subunits that can modulate the release of neurotransmitters, such as dopamine, glutamate, and GABA and mediate fast signal transmission at synapses. Considering that there are 12 nAChR subunits, it is highly likely that subunits other than α4 and β2, which have been intensively investigated, also are involved in nicotine addiction. Consistent with this hypothesis, a number of genome-wide association studies (GWAS) and subsequent candidate gene-based associated studies investigating the genetic variants associated with nicotine dependence (ND) and smoking-related phenotypes have shed light on the CHRNA5/A3/B4 gene cluster on chromosome 15, which encodes the α5, α3, and β4 nAChR subunits, respectively. These studies demonstrate two groups of risk variants in this region. The first one is marked by single nucleotide polymorphism (SNP) rs16969968 in exon 5 of CHRNA5, which changes an aspartic acid residue into asparagine at position 398 (D398N) of the α5 subunit protein sequence, and it is tightly linked SNP rs1051730 in CHRNA3. The second one is SNP rs578776 in the 3'-untranslated region (UTR) of CHRNA3, which has a low correlation with rs16969968. Although the detailed molecular mechanisms underlying these associations remain to be further elucidated, recent findings have shown that α5* (where "*" indicates the presence of additional subunits) nAChRs located in the medial habenulo-interpeduncular nucleus (mHb-IPN) are involved in the control of nicotine self-administration in rodents. Disruption of α5* nAChR signaling diminishes the aversive effects of nicotine on the mHb-IPN pathway and thereby permits more nicotine consumption. To gain a better understanding of the function of the highly significant genetic variants identified in this region in controlling smoking-related behaviors, in this communication, we provide an up-to-date review of the progress of studies focusing on the CHRNA5/A3/B4 gene cluster and its role in ND.
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Dash B, Lukas RJ, Li MD. A signal peptide missense mutation associated with nicotine dependence alters α2*-nicotinic acetylcholine receptor function. Neuropharmacology 2014; 79:715-25. [PMID: 24467848 DOI: 10.1016/j.neuropharm.2014.01.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
A cytosine to thymidine (C → T) missense mutation in the signal peptide (SP) sequence (rs2472553) of the nicotinic acetylcholine receptor (nAChR) α2 subunit produces a threonine-to-isoleucine substitution (T22I) often associated with nicotine dependence (ND). We assessed effects on function of α2*-nAChR ('*'indicates presence of additional subunits) of this mutation, which could alter SP cleavage, RNA/protein secondary structure, and/or efficiency of transcription, translation, subunit assembly, receptor trafficking or cell surface expression. Two-electrode voltage clamp analyses indicate peak current responses to ACh or nicotine are decreased 2.8-5.8-fold for putative low sensitivity (LS; 10:1 ratio of α:β subunit cRNAs injected) α2β2- or α2β4-nAChR and increased for putative high sensitivity (HS; 1:10 α:β subunit ratio) α2β2- (5.7-15-fold) or α2β4- (1.9-2.2-fold) nAChR as a result of the mutation. Agonist potencies are decreased 1.6-4-fold for putative LS or HS α2(T22I)β2-nAChR or for either α2*-nAChR subtype formed in the presence of equal amounts of subunit cRNA, slightly decreased for LS α2(T22I)β4-nAChR, but increased 1.4-2.4-fold for HS α2(T22I)β4-nAChR relative to receptors containing wild-type α2 subunits. These effects suggest that the α2 subunit SP mutation generally favors formation of LS receptor isoforms. We hypothesize that lower sensitivity of human α2*-nAChR to nicotine could contribute to increased susceptibility to ND. To our knowledge this is the first report of a SP mutation having a functional effect in a member of cys-loop family of ligand-gated ion channels.
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Affiliation(s)
- Bhagirathi Dash
- Department of Psychiatry and Neurobehavioral Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22911, USA
| | - Ronald J Lukas
- Division of Neurobiology, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Ming D Li
- Department of Psychiatry and Neurobehavioral Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22911, USA.
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Haller G, Kapoor M, Budde J, Xuei X, Edenberg H, Nurnberger J, Kramer J, Brooks A, Tischfield J, Almasy L, Agrawal A, Bucholz K, Rice J, Saccone N, Bierut L, Goate A. Rare missense variants in CHRNB3 and CHRNA3 are associated with risk of alcohol and cocaine dependence. Hum Mol Genet 2013; 23:810-9. [PMID: 24057674 DOI: 10.1093/hmg/ddt463] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Previous findings have demonstrated that variants in nicotinic receptor genes are associated with nicotine, alcohol and cocaine dependence. Because of the substantial comorbidity, it has often been unclear whether a variant is associated with multiple substances or whether the association is actually with a single substance. To investigate the possible contribution of rare variants to the development of substance dependencies other than nicotine dependence, specifically alcohol and cocaine dependence, we undertook pooled sequencing of the coding regions and flanking sequence of CHRNA5, CHRNA3, CHRNB4, CHRNA6 and CHRNB3 in 287 African American and 1028 European American individuals from the Collaborative Study of the Genetics of Alcoholism (COGA). All members of families for whom any individual was sequenced (2504 African Americans and 7318 European Americans) were then genotyped for all variants identified by sequencing. For each gene, we then tested for association using FamSKAT. For European Americans, we find increased DSM-IV cocaine dependence symptoms (FamSKAT P = 2 × 10(-4)) and increased DSM-IV alcohol dependence symptoms (FamSKAT P = 5 × 10(-4)) among carriers of missense variants in CHRNB3. Additionally, one variant (rs149775276; H329Y) shows association with both cocaine dependence symptoms (P = 7.4 × 10(-5), β = 2.04) and alcohol dependence symptoms (P = 2.6 × 10(-4), β = 2.04). For African Americans, we find decreased cocaine dependence symptoms among carriers of missense variants in CHRNA3 (FamSKAT P = 0.005). Replication in an independent sample supports the role of rare variants in CHRNB3 and alcohol dependence (P = 0.006). These are the first results to implicate rare variants in CHRNB3 or CHRNA3 in risk for alcohol dependence or cocaine dependence.
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Bierut LJ, Johnson EO, Saccone NL. A glimpse into the future - Personalized medicine for smoking cessation. Neuropharmacology 2013; 76 Pt B:592-9. [PMID: 24055496 DOI: 10.1016/j.neuropharm.2013.09.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 10/26/2022]
Abstract
The devastating consequences of tobacco smoking for individuals and societies motivate studies to identify and understand the biological pathways that drive smoking behaviors, so that more effective preventions and treatments can be developed. Cigarette smokers respond to nicotine in different ways, with a small number of smokers remaining lifelong low-level smokers who never exhibit any symptoms of dependence, and a larger group becoming nicotine dependent. Whether or not a smoker transitions to nicotine dependence has clear genetic contributions, and variants in the genes encoding the α5-α3-β4 nicotinic receptor subunits most strongly contribute to differences in the risk for developing nicotine dependence among smokers. More recent work reveals a differential response to pharmacologic treatment for smoking cessation based on these same genetic variants in the α5-α3-β4 nicotinic receptor gene cluster. We anticipate a continuing acceleration of the translation of genetic discoveries into more successful treatment for smoking cessation. Given that over 400,000 people in the United States and over 5 million people world-wide die each year from smoking related illnesses, an improved understanding of the mechanisms underlying smoking behavior and smoking cessation must be a high public health priority so we can best intervene at both the public health level and the individual level. This article is part of a Special Issue entitled 'NIDA 40th Anniversary Issue'.
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Affiliation(s)
- Laura Jean Bierut
- Department of Psychiatry, Washington University School of Medicine, Box 8134, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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Wang S, Yang Z, Ma JZ, Payne TJ, Li MD. Introduction to deep sequencing and its application to drug addiction research with a focus on rare variants. Mol Neurobiol 2013; 49:601-14. [PMID: 23990377 DOI: 10.1007/s12035-013-8541-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 08/16/2013] [Indexed: 11/30/2022]
Abstract
Through linkage analysis, candidate gene approach, and genome-wide association studies (GWAS), many genetic susceptibility factors for substance dependence have been discovered such as the alcohol dehydrogenase gene (ALDH2) for alcohol dependence (AD) and nicotinic acetylcholine receptor (nAChR) subunit variants on chromosomes 8 and 15 for nicotine dependence (ND). However, these confirmed genetic factors contribute only a small portion of the heritability responsible for each addiction. Among many potential factors, rare variants in those identified and unidentified susceptibility genes are supposed to contribute greatly to the missing heritability. Several studies focusing on rare variants have been conducted by taking advantage of next-generation sequencing technologies, which revealed that some rare variants of nAChR subunits are associated with ND in both genetic and functional studies. However, these studies investigated variants for only a small number of genes and need to be expanded to broad regions/genes in a larger population. This review presents an update on recently developed methods for rare-variant identification and association analysis and on studies focused on rare-variant discovery and function related to addictions.
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Affiliation(s)
- Shaolin Wang
- Department of Psychiatry & Neurobiology Science, University of Virginia, 1670 Discovery Drive, Suite 110, Charlottesville, VA, 22911, USA
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35
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Nicotinic acetylcholine receptor variation and response to smoking cessation therapies. Pharmacogenet Genomics 2013; 23:94-103. [PMID: 23249876 DOI: 10.1097/fpc.0b013e32835cdabd] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To evaluate the association of nicotinic acetylcholine receptor (nAChR) single nucleotide polymorphism (SNP) with 7-day point prevalence abstinence (abstinence) in randomized clinical trials of smoking cessation therapies in individuals grouped by pharmacotherapy randomization to inform the development of personalized smoking cessation therapy. MATERIALS AND METHODS We quantified association of four SNPs at three nAChRs with abstinence in eight randomized clinical trials. Participants were 2633 outpatient treatment-seeking, self-identified European ancestry individuals smoking at least 10 cigarettes/day, recruited through advertisement, prescribed pharmacotherapy, and provided with behavioral therapy. Interventions included nicotine replacement therapy (NRT), bupropion, varenicline, placebo (PLA), or combined NRT and bupropion, and five modes of group and individual behavioral therapy. Outcome measures tested in multivariate logistic regression were end of treatment and 6 month (6MO) abstinence, with demographic, behavioral, and genetic covariates. RESULTS 'Risk' alleles previously associated with smoking heaviness were significantly (P<0.05) associated with reduced abstinence in the PLA pharmacotherapy group (PG) at 6MO [for rs588765, odds ratio (95% confidence interval) 0.41 (0.17-0.99)], and at end of treatment and at 6MO [for rs1051730, 0.42 (0.19-0.93) and 0.31 (0.12-0.80)], and with increased abstinence in the NRT PG at 6MO [for rs588765, 2.07 (1.11-3.87) and for rs1051730, 2.54 (1.29-4.99)]. We observed significant heterogeneity in rs1051730 effects (F=2.48, P=0.021) between PGs. CONCLUSION chr15q25.1 nAChR SNP risk alleles for smoking heaviness significantly increase relapse with PLA treatment and significantly increase abstinence with NRT. These SNP-PG associations require replication in independent samples for validation, and testing in larger sample sizes to evaluate whether similar effects occur in other PGs.
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Clarke TK, Crist RC, Kampman KM, Dackis CA, Pettinati HM, O'Brien CP, Oslin DW, Ferraro TN, Lohoff FW, Berrettini WH. Low frequency genetic variants in the μ-opioid receptor (OPRM1) affect risk for addiction to heroin and cocaine. Neurosci Lett 2013; 542:71-5. [PMID: 23454283 PMCID: PMC3640707 DOI: 10.1016/j.neulet.2013.02.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 01/31/2013] [Accepted: 02/11/2013] [Indexed: 11/29/2022]
Abstract
The μ-opioid receptor (MOR) binds exogenous and endogenous opioids and is known to mediate the rewarding effects of drugs of abuse. Numerous genetic studies have sought to identify common genetic variation in the gene encoding MOR (OPRM1) that affects risk for drug addiction. The purpose of this study was to examine the contribution of rare coding variants in OPRM1 to the risk for addiction. Rare and low frequency variants were selected using the National Heart Lung and Blood Institute - Exome Sequencing Project (NHLBI-ESP) database, which has screened the exomes of over 6500 individuals. Two SNPs (rs62638690 and rs17174794) were selected for genotyping in 1377 European American individuals addicted to heroin and/or cocaine. Two different SNPs (rs1799971 and rs17174801) were genotyped in 1238 African American individuals addicted to heroin and/or cocaine. Using the minor allele frequencies from the NHLBI-ESP dataset as a comparison group, case-control association analyses were performed. Results revealed an association between rs62638690 and cocaine and heroin addiction in European Americans (p=0.02; 95% C.I. 0.47 [0.24-0.92]). This study suggests a potential role for rare OPRM1 variants in addiction disorders and highlights an area worthy of future study.
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Affiliation(s)
- Toni-Kim Clarke
- Center for Neurobiology and Behavior, Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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Kishi T, Fukuo Y, Okochi T, Kawashima K, Moriwaki M, Furukawa O, Musso GM, Fujita K, Correll CU, Iwata N. Relationship between nicotine dependence and the endophenotype-related trait of cognitive function but not acoustic startle reponses in Japanese patients with schizophrenia. Hum Psychopharmacol 2013; 28:220-9. [PMID: 23553665 DOI: 10.1002/hup.2310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 02/26/2013] [Indexed: 01/10/2023]
Abstract
OBJECTIVES We investigated whether nicotine dependence affects these endophenotypes in Japanese schizophrenia patients and whether alpha4 and beta2 subunits of neuronal nicotinic acetylcholine receptor genes (alpha4 subunit of the nAChR gene (CHRNA4)/beta2 subunit of the nAChR gene (CHRNB2)) were associated with nicotine dependence in patients (n = 100) and healthy controls (n = 107). METHODS First, in patients, we evaluated cognitive function, using the Brief Assessment of Cognition in Schizophrenia, and acoustic startle responses. Second, we evaluated the severity of nicotine dependence, using the Tobacco Dependence Screener, the Fagerström Test for Nicotine Dependence, and the Brinkman index in current smokers in both groups. Third, we evaluated the relationship between acoustic startle responses, cognitive function, and severity of nicotine dependence. Finally, using 12 tagging single-nucleotide polymorphisms in each the CHRNA4/CHRNB2, we used multiple linear regression analysis to examine the association between nicotine dependence measures and each selected single-nucleotide polymorphism. RESULTS The presence and severity of nicotine dependence were associated with verbal memory and executive function in schizophrenia patients. However, nicotine dependence was not correlated with any acoustic startle response. In addition, rs755203 and rs1044397 in CHRNA4 were associated with nicotine dependence in healthy controls. CONCLUSIONS Nicotine dependence might influence the level of verbal memory and executive function in schizophrenia patients. In addition, rs755203 and rs1044397 in CHRNA4 might play a role in the pathophysiology of nicotine dependence in healthy controls in the Japanese population.
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Affiliation(s)
- Taro Kishi
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA.
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Choquet H, Joslyn G, Lee A, Kasberger J, Robertson M, Brush G, Schuckit MA, White R, Jorgenson E. Examination of rare missense variants in the CHRNA5-A3-B4 gene cluster to level of response to alcohol in the San Diego Sibling Pair study. Alcohol Clin Exp Res 2013; 37:1311-6. [PMID: 23458267 DOI: 10.1111/acer.12099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/22/2012] [Indexed: 11/28/2022]
Abstract
BACKGROUND Common variants in the CHRNA5-A3-B4 gene cluster have been shown to be associated with nicotine dependence and alcohol use disorders (AUDs) and related traits, including the level of response (LR) to alcohol. Recently, rare variants (MAF < 0.05) in CHRNB4 have been reported to be associated with a decreased risk of developing nicotine dependence. However, the role of rare variants in the CHRNA5-A3-B4 gene cluster to the LR to alcohol has not yet been established. METHODS To determine whether rare variants in the CHRNA5-A3-B4 gene cluster contribute to the LR to alcohol, the coding regions of these 3 genes were sequenced in 538 subjects from the San Diego Sibling Pair study. RESULTS The analyses identified 16 rare missense variants, 9 of which were predicted to be damaging using in silico analysis tools. Carriers of these variants were compared to noncarriers using a family-based design for each gene and for the gene cluster as a whole. In these analyses, a CHRNA5 carrier status was significantly associated with the phenotype related to the feeling of intoxication experienced during the alcohol challenge (p = 0.039). CONCLUSIONS These results indicate that rare genetic variation in the CHRNA5-A3-B4 gene cluster contributes modestly to the LR to alcohol in the San Diego Sibling Pair study and may protect against AUDs. However, replication studies are needed to confirm our findings.
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Affiliation(s)
- Hélène Choquet
- Department of Anesthesia and Perioperative Care, Center for Cerebrovascular Research, University of California, San Francisco, San Francisco, CA 94110, USA.
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Turner JR, Gold A, Schnoll R, Blendy JA. Translational research in nicotine dependence. Cold Spring Harb Perspect Med 2013; 3:a012153. [PMID: 23335115 PMCID: PMC3579204 DOI: 10.1101/cshperspect.a012153] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Nicotine addiction accounts for 4.9 million deaths each year. Furthermore, although smoking represents a significant health burden in the United States, at present there are only three FDA-approved pharmacotherapies currently on the market: (1) nicotine replacement therapy, (2) bupropion, and (3) varenicline. Despite this obvious gap in the market, the complexity of nicotine addiction in addition to the increasing cost of drug development makes targeted drug development prohibitive. Furthermore, using combinations of mouse and human studies, additional treatments could be developed from off-the-shelf, currently approved medication lists. This article reviews translational studies targeting manipulations of the cholinergic system as a viable therapeutic target for nicotine addiction.
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Affiliation(s)
- Jill R Turner
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
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40
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Kamens HM, Corley RP, McQueen MB, Stallings MC, Hopfer CJ, Crowley TJ, Brown SA, Hewitt JK, Ehringer MA. Nominal association with CHRNA4 variants and nicotine dependence. GENES BRAIN AND BEHAVIOR 2013; 12:297-304. [PMID: 23350800 DOI: 10.1111/gbb.12021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/06/2012] [Accepted: 01/10/2013] [Indexed: 01/05/2023]
Abstract
Nicotine binds to nicotinic acetylcholine receptors and studies in animal models have shown that α4β2 receptors mediate many behavioral effects of nicotine. Human genetics studies have provided support that variation in the gene that codes for the α4 subunit influences nicotine dependence (ND), but the evidence for the involvement of the β2 subunit gene is less convincing. In this study, we examined the genetic association between variation in the genes that code for the α4 (CHRNA4) and β2 (CHRNB2) subunits of the nicotinic acetylcholine receptor and a quantitative measure of lifetime DSM-IV ND symptom counts. We performed this analysis in two longitudinal family-based studies focused on adolescent antisocial drug abuse: the Center on Antisocial Drug Dependence (CADD, N = 313 families) and Genetics of Antisocial Drug Dependence (GADD, N = 111 families). Family-based association tests were used to examine associations between 14 single nucleotide polymorphisms (SNPs) in CHRNA4 and CHRNB2 and ND symptoms. Symptom counts were corrected for age, sex and clinical status prior to the association analysis. Results, when the samples were combined, provided modest evidence that SNPs in CHRNA4 are associated with ND. The minor allele at both rs1044394 (A; Z = 1.988, P = 0.047, unadjusted P-value) and rs1044396 (G; Z = 2.398, P = 0.017, unadjusted P-value) was associated with increased risk of ND symptoms. These data provide suggestive evidence that variation in the α4 subunit of the nicotinic acetylcholine receptor may influence ND liability.
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Affiliation(s)
- H M Kamens
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
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Mao X, Li Y, Liu Y, Lange L, Li M. Testing genetic association with rare variants in admixed populations. Genet Epidemiol 2013; 37:38-47. [PMID: 23032398 PMCID: PMC3524352 DOI: 10.1002/gepi.21687] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/23/2012] [Accepted: 09/07/2012] [Indexed: 11/07/2022]
Abstract
Recent studies suggest that rare variants play an important role in the etiology of many traits. Although a number of methods have been developed for genetic association analysis of rare variants, they all assume a relatively homogeneous population under study. Such an assumption may not be valid for samples collected from admixed populations such as African Americans and Hispanic Americans as there is a great extent of local variation in ancestry in these populations. To ensure valid and more powerful rare variant association tests performed in admixed populations, we have developed a local ancestry-based weighted dosage test, which is able to take into account local ancestry of rare alleles, uncertainties in rare variant imputation when imputed data are included, and the direction of effect that rare variants exert on phenotypic outcome. We used simulated sequence data to show that our proposed test has controlled type I error rates, whereas naïve application of existing rare variants tests and tests that adjust for global ancestry lead to inflated type I error rates. We showed that our test has higher power than tests without proper adjustment of ancestry. We also applied the proposed method to a candidate gene study on low-density lipoprotein cholesterol. Our results suggest that it is important to appropriately control for potential population stratification induced by local ancestry difference in the analysis of rare variants in admixed populations.
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Affiliation(s)
- Xianyun Mao
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina
| | - Yichuan Liu
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Leslie Lange
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
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Abstract
The Twin Research Registry (TRR) at SRI International is a community-based registry of twins established in 1995 by advertising in local media, mainly on radio stations and in newspapers. As of August 2012, there are 3,120 same- and opposite-sex twins enrolled; 86% are 18 years of age or older (mean age 44.9 years, SD 16.9 years) and 14% less than 18 years of age (mean age 8.9 years, SD 4.5); 67% are female, and 62% are self-reported monozygotic (MZ). More than 1,375 twins have participated in studies over the last 15 years in collaboration with the University of California Medical Center in San Francisco, the University of Texas MD Anderson Cancer Center, and the Stanford University School of Medicine. Each twin completes a registration form with basic demographic information either online at the TRR Web site or during a telephone interview. Contact is maintained with members by means of annual newsletters and birthday cards. The managers of the TRR protect the confidentiality of twin data with established policies; no information is given to other researchers without prior permission from the twins; and all methods and procedures are reviewed by an Institutional Review Board. Phenotypes studied thus far include those related to nicotine metabolism, mutagen sensitivity, pain response before and after administration of an opioid, and a variety of immunological responses to environmental exposures, including second-hand smoke and vaccination for seasonal influenza virus and Varicella zoster virus. Twins in the TRR have participated in studies of complex, clinically relevant phenotypes that would not be feasible to measure in larger samples.
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Abstract
A large segment of the population suffers from addiction to alcohol, smoking, or illicit drugs. Not only do substance abuse and addiction pose a threat to health, but the consequences of addiction also impose a social and economic burden on families, communities, and nations. Genome-wide linkage and association studies have been used for addiction research with varying degrees of success. The most well-established genetic factors associated with alcohol dependence are in the genes encoding alcohol dehydrogenase (ADH), which oxidizes alcohol to acetaldehyde, and aldehyde dehydrogenase (ALDH2), which oxidizes acetaldehyde to acetate. Recently emerging genetic studies have linked variants in the genes encoding the α3, α5, and β4 nicotinic acetylcholine receptor subunits to smoking risk. However, the influence of these well-established genetic variants accounts for only a small portion of the heritability of alcohol and nicotine addiction, and it is likely that there are both common and rare risk variants yet to be identified. Newly developed DNA sequencing technologies could potentially advance the detection of rare variants with a larger impact on addiction risk.
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Affiliation(s)
- Jen-Chyong Wang
- Department of Psychiatry, School of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA.
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Rose EJ, Ross TJ, Salmeron BJ, Lee M, Shakleya DM, Huestis M, Stein EA. Chronic exposure to nicotine is associated with reduced reward-related activity in the striatum but not the midbrain. Biol Psychiatry 2012; 71:206-13. [PMID: 22032832 PMCID: PMC3253900 DOI: 10.1016/j.biopsych.2011.09.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 09/05/2011] [Accepted: 09/06/2011] [Indexed: 11/24/2022]
Abstract
BACKGROUND The reinforcing effects of nicotine are mediated by brain regions that also support temporal difference error (TDE) processing; yet, the impact of nicotine on TDE is undetermined. METHODS Dependent smokers (n = 21) and matched control subjects (n = 21) were trained to associate a juice reward with a visual cue in a classical conditioning paradigm. Subjects subsequently underwent functional magnetic resonance imaging sessions in which they were exposed to trials where they either received juice as temporally predicted or where the juice was withheld (negative TDE) and later received unexpectedly (positive TDE). Subjects were scanned in two sessions that were identical, except that smokers had a transdermal nicotine (21 mg) or placebo patch placed before scanning. Analysis focused on regions along the trajectory of mesocorticolimbic and nigrostriatal dopaminergic pathways. RESULTS There was a reduction in TDE-related function in smokers in the striatum, which did not differ as a function of patch manipulation but was predicted by the duration (years) of smoking. Activation in midbrain regions was not impacted by group or drug condition. CONCLUSIONS These data suggest a differential effect of smoking status on the neural substrates of reward in distinct dopaminergic pathway regions, which may be partially attributable to chronic nicotine exposure. The failure of transdermal nicotine to alter reward-related functional processes, either within smokers or between smokers and control subjects, implies that acute nicotine patch administration is insufficient to modify reward processing, which has been linked to abstinence-induced anhedonia in smokers and may play a critical role in smoking relapse.
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Affiliation(s)
- Emma Jane Rose
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Thomas J. Ross
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Betty Jo Salmeron
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Mary Lee
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Diaa M. Shakleya
- Chemistry and Drug Metabolism Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Marilyn Huestis
- Chemistry and Drug Metabolism Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Elliot A. Stein
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
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New associations of the genetic polymorphisms in nicotinic receptor genes with the risk of lung cancer. Life Sci 2012; 91:1103-8. [PMID: 22280835 DOI: 10.1016/j.lfs.2011.12.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 12/23/2011] [Accepted: 12/30/2011] [Indexed: 11/23/2022]
Abstract
AIMS Previous studies revealed association of lung cancer risk with single nucleotide polymorphisms (SNPs) in chromosome 15q25 region containing CHRNA5-CHRNA3-CHRNB4 nicotinic acetylcholine receptor (nAChR) subunit gene cluster. The genetic variations in other lung nAChRs remained unknown. In this study, we perform case-control analysis of CHRNA9 and CHRNA3 genes using 340 non-small cell lung cancer cases and 435 controls. MAIN METHODS All exons, 3'UTR, intron 1 and parts of other introns surrounding exons 2-5 of CHRNA9 gene as well as exons 2, 3 of CHRNA3 gene and parts of surrounding intronic regions were sequenced. The study was controlled for gender, age and ethnicity related differences. Each SNP in analyzed groups was assessed by allele frequency, genotype distribution and haplotype analysis. KEY FINDINGS The case-control analysis revealed that an increased risk is associated with two SNPs in CHRNA9, rs56159866 and rs6819385, and one in CHRNA3, rs8040868. The risk was reduced for three SNPs in CHRNA9, rs55998310, rs56291234, and newly discovered rs182073550, and also in carriers of the haplotype NP_060051.2 containing ancestral N442 variant of α9. SIGNIFICANCE The nonsynonymous substitutions can produce receptors exhibiting unique ligand-binding and downstream signaling characteristics, synonymous as well all intronic SNPs may affect protein production at the transcriptional and/or translational levels, or just manifest association with cancer by genetic linkage to other alleles. Elucidation of the mechanisms by which individual genetic variations in α9 affect predisposition to lung cancer may lead to development of personalized approaches to cancer prevention and treatment as well as protection against tobacco consumption.
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Broms U, Wedenoja J, Largeau MR, Korhonen T, Pitkäniemi J, Keskitalo-Vuokko K, Häppölä A, Heikkilä KH, Heikkilä K, Ripatti S, Sarin AP, Salminen O, Paunio T, Pergadia ML, Madden PAF, Kaprio J, Loukola A. Analysis of detailed phenotype profiles reveals CHRNA5-CHRNA3-CHRNB4 gene cluster association with several nicotine dependence traits. Nicotine Tob Res 2012; 14:720-33. [PMID: 22241830 DOI: 10.1093/ntr/ntr283] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
INTRODUCTION The role of the nicotinic acetylcholine receptor gene cluster on chromosome 15q24-25 in the etiology of nicotine dependence (ND) is still being defined. In this study, we included all 15 tagging single nucleotide polymorphisms (SNPs) within the CHRNA5-CHRNA3-CHRNB4 cluster and tested associations with 30 smoking-related phenotypes. METHODS The study sample was ascertained from the Finnish Twin Cohort study. Twin pairs born 1938-1957 and concordant for a history of cigarette smoking were recruited along with their family members (mainly siblings), as part of the Nicotine Addiction Genetics consortium. The study sample consisted of 1,428 individuals (59% males) from 735 families, with mean age 55.6 years. RESULTS We detected multiple novel associations for ND. DSM-IV ND symptoms associated significantly with the proxy SNP Locus 1 (rs2036527, p = .000009) and Locus 2 (rs578776, p = .0001) and tolerance factor of the Nicotine Dependence Syndrome Scale (NDSS) showed suggestive association to rs11636753 (p = .0059), rs11634351 (p = .0069), and rs1948 (p = .0071) in CHRNB4. Furthermore, we report significant association with DSM-IV ND diagnosis (rs2036527, p = .0003) for the first time in a Caucasian population. Several SNPs indicated suggestive association for traits related to ages at smoking initiation. Also, rs11636753 in CHRNB4 showed suggestive association with regular drinking (p = .0029) and the comorbidity of depression and ND (p = .0034). CONCLUSIONS We demonstrate novel associations of DSM-IV ND symptoms and the NDSS tolerance subscale. Our results confirm and extend association findings for other ND measures. We show pleiotropic effects of this gene cluster on multiple measures of ND and also regular drinking and the comorbidity of ND and depression.
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Affiliation(s)
- Ulla Broms
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
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Haller G, Druley T, Vallania FL, Mitra RD, Li P, Akk G, Steinbach JH, Breslau N, Johnson E, Hatsukami D, Stitzel J, Bierut LJ, Goate AM. Rare missense variants in CHRNB4 are associated with reduced risk of nicotine dependence. Hum Mol Genet 2011; 21:647-55. [PMID: 22042774 DOI: 10.1093/hmg/ddr498] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genome-wide association studies have identified common variation in the CHRNA5-CHRNA3-CHRNB4 and CHRNA6-CHRNB3 gene clusters that contribute to nicotine dependence. However, the role of rare variation in risk for nicotine dependence in these nicotinic receptor genes has not been studied. We undertook pooled sequencing of the coding regions and flanking sequence of the CHRNA5, CHRNA3, CHRNB4, CHRNA6 and CHRNB3 genes in African American and European American nicotine-dependent smokers and smokers without symptoms of dependence. Carrier status of individuals harboring rare missense variants at conserved sites in each of these genes was then compared in cases and controls to test for an association with nicotine dependence. Missense variants at conserved residues in CHRNB4 are associated with lower risk for nicotine dependence in African Americans and European Americans (AA P = 0.0025, odds-ratio (OR) = 0.31, 95% confidence-interval (CI) = 0.31-0.72; EA P = 0.023, OR = 0.69, 95% CI = 0.50-0.95). Furthermore, these individuals were found to smoke fewer cigarettes per day than non-carriers (AA P = 6.6 × 10(-5), EA P = 0.021). Given the possibility of stochastic differences in rare allele frequencies between groups replication of this association is necessary to confirm these findings. The functional effects of the two CHRNB4 variants contributing most to this association (T375I and T91I) and a missense variant in CHRNA3 (R37H) in strong linkage disequilibrium with T91I were examined in vitro. The minor allele of each polymorphism increased cellular response to nicotine (T375I P = 0.01, T91I P = 0.02, R37H P = 0.003), but the largest effect on in vitro receptor activity was seen in the presence of both CHRNB4 T91I and CHRNA3 R37H (P = 2 × 10(-6)).
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Affiliation(s)
- Gabe Haller
- Department of Psychiatry, Washington University, St Louis, MO 63110, USA
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Xie P, Kranzler HR, Krauthammer M, Cosgrove KP, Oslin D, Anton RF, Farrer LA, Picciotto MR, Krystal JH, Zhao H, Gelernter J. Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence. Biol Psychiatry 2011; 70:528-36. [PMID: 21683344 PMCID: PMC3199609 DOI: 10.1016/j.biopsych.2011.04.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/04/2011] [Accepted: 04/19/2011] [Indexed: 12/01/2022]
Abstract
BACKGROUND Several studies report association of alpha-4 nicotinic acetylcholine receptors (encoded by CHRNA4) with nicotine dependence (ND). A meta-analysis of genomewide linkage studies for ND implicated a single chromosomal region, which includes CHRNA4, as genome-wide significant. METHODS After establishing that common variants are unlikely to completely account for this linkage, we investigated the distribution of CHRNA4 rare variants by sequencing the coding exons and flanking intronic regions of CHRNA4 in 209 European American (EA) ND cases and 183 EA control subjects. Because most of the rare variants that we detected (and all nonsynonymous changes) were in Exon 5, we sequenced Exon 5 in an additional 1000 ND cases and 1000 non-ND comparison subjects, both of which included equal numbers of EAs and African Americans. RESULTS Comparison subjects had a higher frequency of rare nonsynonymous variants in the Exon 5 region (encoding the large intercellular loop of the α4 subunit; Fisher's Exact Test p = .009; association test p = .009, odds ratio = .43; weighted-sum method p = .014), indicating a protective effect against ND. Considering data from the two stages combined and only nonsynonymous variants predicted to alter protein function, the association was stronger (Fisher's Exact Test p = .005; association test p = .008, odds ratio = .29; weighted-sum method p = .005). Single-photon emission computed tomography imaging results were consistent with functionality. CONCLUSIONS CHRNA4 functional rare variants may reduce ND risk. This is the first demonstration that rare functional variants at a candidate locus protect against substance dependence to our knowledge, suggesting a novel mechanism of substance dependence heritability that is potentially of general importance.
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Affiliation(s)
- Pingxing Xie
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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Maes HH, Neale MC, Chen X, Chen J, Prescott CA, Kendler KS. A twin association study of nicotine dependence with markers in the CHRNA3 and CHRNA5 genes. Behav Genet 2011; 41:680-90. [PMID: 21748402 DOI: 10.1007/s10519-011-9476-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 05/19/2011] [Indexed: 11/29/2022]
Abstract
Twin and family studies have provided overwhelming evidence for the genetic basis of individual differences in tobacco initiation (TI), regular smoking (RS) and nicotine dependence (ND). However, only a few genes have been reliably associated with ND. We used a finite mixture distribution model to examine the significance and effect size of the association of previously identified and replicated specific variants in the CHRNA5 and CHRNA3 receptor genes with ND, against the background of genetic and environmental risk factors for ND. We hypothesize that additional phenotypic information in relatives who have not been genotyped can be used to increase the power of detecting the genetic variant. The nicotine measures were assessed by personal interview in female, male and opposite sex twin pairs (N = 4,153) from the population-based Virginia Twin Registry. Three SNPs in the CHRNA5 and CHRNA3 receptor genes, previously shown to be significantly associated with ND in this sample, were replicated in the augmented analyses; they accounted for less than one percent of the genetic variance in liability to ND, which is estimated to be over 50% of the phenotypic variance. The significance of these effects was increased by adding twins with phenotype but without genotype data, but gains are limited and variable. The SNPs associated with ND did not show a significant association with either TI or RS and appear to be specific to the addictive stage of ND, characterized by current smoking and smoking a large amount of cigarettes per day. Furthermore, these SNPs did not appear to be associated with the remaining items comprising the FTND scale. This study confirmed a significant contribution of the CHRNA receptor on different forms of tobacco dependence. However, the genetic variant only accounted for little of the total genetic variance for liability to ND. Including phenotypic data on ungenotyped relatives can improve the statistical power to detect the effects of genetic variants when they contribute to individual differences in the phenotype.
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Affiliation(s)
- Hermine H Maes
- Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, P.O. Box 980003, Richmond, VA 23298-0003, USA.
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Varenicline for smoking cessation: nausea severity and variation in nicotinic receptor genes. THE PHARMACOGENOMICS JOURNAL 2011; 12:349-58. [PMID: 21606948 PMCID: PMC3405554 DOI: 10.1038/tpj.2011.19] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This study evaluated association between common and rare sequence variants in 10 nicotinic acetylcholine receptor subunit genes and the severity of nausea 21 days after initiating the standard, FDA-approved varenicline regimen for smoking cessation. Included in the analysis were 397 participants from a randomized clinical effectiveness trial with complete clinical and DNA resequencing data (mean age = 49.2 years; 68.0% female). Evidence for significant association between common sequence variants in CHRNB2 and nausea severity was obtained after adjusting for age, gender, and correlated tests (all PACT<.05). Individuals with the minor allele of CHRNB2 variants experienced less nausea than did those without the minor allele, consistent with previously reported findings for CHRNB2 and the occurrence of nausea and dizziness as a consequence of first smoking attempt in adolescents, and with the known neurophysiology of nausea. As nausea is the most common reason for discontinuance of varenicline, further pharmacogenetic investigations are warranted.
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