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Icick R, Forget B, Cloëz-Tayarani I, Pons S, Maskos U, Besson M. Genetic susceptibility to nicotine addiction: Advances and shortcomings in our understanding of the CHRNA5/A3/B4 gene cluster contribution. Neuropharmacology 2020; 177:108234. [PMID: 32738310 DOI: 10.1016/j.neuropharm.2020.108234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/28/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
Over the last decade, robust human genetic findings have been instrumental in elucidating the heritable basis of nicotine addiction (NA). They highlight coding and synonymous polymorphisms in a cluster on chromosome 15, encompassing the CHRNA5, CHRNA3 and CHRNB4 genes, coding for three subunits of the nicotinic acetylcholine receptor (nAChR). They have inspired an important number of preclinical studies, and will hopefully lead to the definition of novel drug targets for treating NA. Here, we review these candidate gene and genome-wide association studies (GWAS) and their direct implication in human brain function and NA-related phenotypes. We continue with a description of preclinical work in transgenic rodents that has led to a mechanistic understanding of several of the genetic hits. We also highlight important issues with regards to CHRNA3 and CHRNB4 where we are still lacking a dissection of their role in NA, including even in preclinical models. We further emphasize the use of human induced pluripotent stem cell-derived models for the analysis of synonymous and intronic variants on a human genomic background. Finally, we indicate potential avenues to further our understanding of the role of this human genetic variation. This article is part of the special issue on 'Contemporary Advances in Nicotine Neuropharmacology'.
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Affiliation(s)
- Romain Icick
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; Département de Psychiatrie et de Médecine Addictologique, Groupe Hospitalier Saint-Louis, Lariboisière, Fernand Widal, Assistance-Publique Hôpitaux de Paris, Paris, F-75010, France; INSERM UMR-S1144, Paris, F-75006, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Benoît Forget
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; Génétique Humaine et Fonctions Cognitives, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Isabelle Cloëz-Tayarani
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Stéphanie Pons
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Uwe Maskos
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Morgane Besson
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France.
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2
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Yang X, Guo X, Huang Z, Da Y, Xing W, Li F, Li M, Sun K, Jia H, Zhu Y. CHRNA5/CHRNA3 gene cluster is a risk factor for lumbar disc herniation: a case-control study. J Orthop Surg Res 2019; 14:243. [PMID: 31362771 PMCID: PMC6668080 DOI: 10.1186/s13018-019-1254-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/02/2019] [Indexed: 12/13/2022] Open
Abstract
Background Lumbar disc herniation, a type of chronic low back pain syndrome, is caused by the lumbar intervertebral disk degeneration. Genetic variation in the CHRNA5/CHRNA3 has shown strong associations with smoking-related diseases. This study’s aim is to test whether single-nucleotide polymorphisms in the CHRNA5/CHRNA3 gene are associated with lumbar disc herniation risk. Methods The genotype frequency distributions of the polymorphisms were detected by polymerase chain reaction-restriction fragment length polymorphism in 380 lumbar disc herniation patients (case group) and 400 healthy individuals (control group). Allelic, genotypic, and haplotype analyses were performed. Results We found that the individuals with rs8040868 CT genotype had a 0.46-fold higher risk of lumbar disc herniation than those with rs8040868 TT genotype, in men group (OR = 0.46, 95% CI 0.25–0.84, p = 0.012). Also among women, rs8040868 CT + CC genotype still reduced the risk of lumbar disc herniation under the dominant model (OR = 0.50, 95% CI 0.28–0.89, p = 0.019). Haplotype analysis showed that compared with the CHRNA5 “TACAACCG” wild-type, the “TACACCCG” haplotype was found to be associated with a decreased risk of lumbar disc herniation (LDH) (OR = 0.79, 95% CI 0.63–1.00, p = 0.047), while, in the less than 50-year-old group, CHRNA5 “TACACCCG” increased the risk of LDH (OR = 1.46, 95% CI 1.01–2.13, p = 0.047). Conclusions Our data suggest that gene variance in the CHRNA5/CHRNA3 is associated with risk of lumbar disc herniation in the case-control study.
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Affiliation(s)
- Xuejun Yang
- Spine (Thoracic and Vertebra) Department, the Second Affiliated Hospital of Inner Mongolia University, #1 Yingfang Road, Hohhot, 010050, Inner Mongolia, China
| | - Xiaodong Guo
- Inner Mongolia People's Hospital, Hohhot, Inner Mongolia, China
| | - Zhi Huang
- Spine (Thoracic and Vertebra) Department, the Second Affiliated Hospital of Inner Mongolia University, #1 Yingfang Road, Hohhot, 010050, Inner Mongolia, China
| | - Yifeng Da
- Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Wenhua Xing
- Spine (Thoracic and Vertebra) Department, the Second Affiliated Hospital of Inner Mongolia University, #1 Yingfang Road, Hohhot, 010050, Inner Mongolia, China
| | - Feng Li
- Spine (Thoracic and Vertebra) Department, the Second Affiliated Hospital of Inner Mongolia University, #1 Yingfang Road, Hohhot, 010050, Inner Mongolia, China
| | - Manglai Li
- Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Ke Sun
- Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Haiyu Jia
- The Affiliated Hospital of Inner Mongolia Medical College, #1 North Tongdao Road, Hohhot, 010020, Inner Mongolia, China.
| | - Yong Zhu
- Spine (Thoracic and Vertebra) Department, the Second Affiliated Hospital of Inner Mongolia University, #1 Yingfang Road, Hohhot, 010050, Inner Mongolia, China.
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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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Smalheiser NR. The search for endogenous siRNAs in the mammalian brain. Exp Neurol 2011; 235:455-63. [PMID: 22062046 DOI: 10.1016/j.expneurol.2011.10.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 09/28/2011] [Accepted: 10/17/2011] [Indexed: 02/08/2023]
Abstract
A decade ago, RNA interference was proposed to serve as a physiologic means of regulating long-term gene expression in the mammalian brain. However, during the intervening years, this hypothesis appeared to be contradicted by both experimental data and theoretical considerations. More recently, the advent of deep sequencing technology has permitted a re-assessment of this issue. As reviewed here, a large population of small RNAs having features characteristic of endogenous siRNAs are detected within adult mouse hippocampus, which derive from genes involved in synaptic structure and signaling, and which show a significant, though modest (16-22%) up-regulation during olfactory discrimination training. Small RNAs derived from abundant cellular noncoding RNAs are also detected; in particular, a subpopulation of RNAs 25-30 nt. in length shows very large (>100 fold) up-regulation during olfactory discrimination training. Preliminary data suggest that the 25-30 nt. RNAs may associate with MIWI rather than Argonaute 1-4 homologues. I conclude that, despite their apparent low abundance, endogenous siRNAs and noncoding RNA-derived small RNAs are likely to play an important role in regulating synaptic plasticity.
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Affiliation(s)
- Neil R Smalheiser
- University of Illinois at Chicago, Psychiatric Institute MC912, Chicago, IL 60612, USA.
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Greenbaum L, Kanyas KS, Rigbi A, Alkelai A, Kohn Y, Lerer B. Why do young women smoke? VII COMT as a risk modifying gene for Nicotine dependence - role of gene-gene interaction, personality, and environmental factors. Hum Psychopharmacol 2010; 25:536-42. [PMID: 21312287 DOI: 10.1002/hup.1149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 08/11/2010] [Indexed: 01/25/2023]
Abstract
OBJECTIVES Catechol-O-methyltransferase (COMT) may be a risk modifying gene for Nicotine dependence (ND) rather than a direct susceptibility gene for this phenotype. Brain nicotinic cholinergic receptors modulate dopaminergic transmission, and several variants within the neighboring CHRNA5-CHRNA3 genes have been associated with ND. Therefore, it is biologically reasonable to study the interactive contribution of COMT and the CHRNA5 and CHRNA3 genes to ND. METHODS Using a case-control sample of 90 young, Israeli, Jewish female smokers (FTND ≥ 4) and 108 controls (FTND = 0 during heaviest period of smoking), we studied association with ND of 8 COMT tagging SNPs, their interaction with tagging CHRNA5-A3 SNPs and the role of background, personality, and environmental factors. RESULTS None of the COMT SNPs were associated directly with ND. In pairwise interaction analysis of SNPs from the two loci (COMT SNP-CHRNA5-CHRNA3 SNP), the interaction of intronic COMT SNP, rs9332377, with CHRNA3 3'UTR SNP rs660652 was significantly associated with ND (p = 0.0005), withstanding correction for multiple testing. CONCLUSION Addition of the genetic interaction variable into a model of non-genetic ND predictors [parental smoking, novelty seeking (NS), and lifetime history of trauma], substantially increases the percentage of ND variance explained by the model, as well as the percentage of cases correctly identified by it.
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Affiliation(s)
- Lior Greenbaum
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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6
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Lipovich L, Johnson R, Lin CY. MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:597-615. [PMID: 20951849 DOI: 10.1016/j.bbagrm.2010.10.001] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 08/13/2010] [Accepted: 10/06/2010] [Indexed: 12/19/2022]
Abstract
The central dogma of molecular biology relegates RNAs to the role of "messengers" of genetic information, with proteins as the end products that perform key roles as regulators and effectors of biological processes. Notable exceptions include non-protein-coding RNAs, which function as adaptors (tRNAs) and ribosomal components (rRNAs) during translation, as well as in splicing (snRNAs) and RNA maturation including editing (snoRNAs). Genome and transcriptome projects have revealed, however, a significant number, rivaling the protein-coding transcripts, of non-protein-coding RNAs not related to these previously characterized transcript classes. Non-protein-coding RNA research has primarily focused on microRNAs, a small subclass of non-protein-coding RNAs, and their regulatory roles in gene expression, and these findings have been reviewed extensively. Here, we turn our attention to the larger, in number and size, long non-coding RNAs (lncRNAs), and review their evolutionary complexity and the growing evidence for their diverse mechanisms of action and functional roles in basic molecular and cellular biology and in human disease. In contrast to the focus on in-silico and expression studies in existing lncRNA literature, we emphasize direct evidence for lncRNA function, presenting experimental approaches and strategies for systematic characterization of lncRNA activities, with applications to known gene regulatory networks and diseases.
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Affiliation(s)
- Leonard Lipovich
- Department of Neurology, Wayne State University, Detroit, MI, USA.
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Differential contribution of genetic variation in multiple brain nicotinic cholinergic receptors to nicotine dependence: recent progress and emerging open questions. Mol Psychiatry 2009; 14:912-45. [PMID: 19564872 DOI: 10.1038/mp.2009.59] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nicotine dependence (ND), a major public health challenge, is a complex, multifactorial behavior, in which both genetic and environmental factors have a role. Brain nicotinic acetylcholine receptor (nAChR)-encoding genes are among the most prominent candidate genes studied in the context of ND, because of their biological relevance as binding sites for nicotine. Until recently, most research on the role of nAChRs in ND has focused on two of these genes (encoding the alpha4- and beta2-subunits) and not much attention has been paid to the possible contribution of the other nine brain nAChR subunit genes (alpha2-alpha3, alpha5-alpha7, alpha9-alpha10, beta3-beta4) to the pathophysiology and genetics of ND. This situation has changed dramatically in the last 2 years during which intensive research had addressed the issue, mainly from the genetics perspective, and has shown the importance of the CHRNA5-CHRNA3-CHRNB4 and CHRNA6-CHRNB3 loci in ND-related phenotypes. In this review, we highlight recent findings regarding the contribution of non-alpha4/beta2-subunit containing nAChRs to ND, based on several lines of evidence: (1) human genetics studies (including linkage analysis, candidate-gene association studies and whole-genome association studies) of several ND-related phenotypes; (2) differential pharmacological and biochemical properties of receptors containing these subunits; (3) evidence from genetically manipulated mice; and (4) the contribution of nAChR genes to ND-related personality traits and neurocognitive profiles. Combining neurobiological genetic and behavioral perspectives, we suggest that genetic susceptibility to ND is not linked to one or two specific nAChR subtype genes but to several. In particular, the alpha3, alpha5-6 and beta3-4 nAChR subunit-encoding genes may play a much more pivotal role in the neurobiology and genetics of ND than was appreciated earlier. At the functional level, variants in these subunit genes (most likely regulatory) may have independent as well as interactive contributions to the ND phenotype spectrum. We address methodological challenges in the field, highlight open questions and suggest possible pathways for future research.
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8
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Non-coding RNA transcripts: sensors of neuronal stress, modulators of synaptic plasticity, and agents of change in the onset of Alzheimer's disease. Neurosci Lett 2009; 466:81-8. [PMID: 19699259 DOI: 10.1016/j.neulet.2009.08.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 08/04/2009] [Accepted: 08/06/2009] [Indexed: 12/20/2022]
Abstract
Non-protein-coding RNAs (ncRNAs) play critical roles on many levels of cellular information processing and pervasive expression of ncRNAs in the nervous system could help explain brain complexity. NcRNAs are enriched in the central nervous system and are associated with specific neuroanatomical regions. Additionally, several recent publications have revealed an important role for deregulation of ncRNAs in various human neuropathologies, such as Alzheimer's disease, Parkinson's disease and Fragile X mental retardation. Herein, we summarize reports on functional ncRNA molecules involved in cellular stress response, particularly related to Alzheimer's disease. We conclude that ncRNAs have a prominent role in maintaining precise physiological levels of gene products directly implicated in Alzheimer's disease pathology.
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9
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Lee TL, Pang ALY, Rennert OM, Chan WY. Genomic landscape of developing male germ cells. BIRTH DEFECTS RESEARCH. PART C, EMBRYO TODAY : REVIEWS 2009; 87:43-63. [PMID: 19306351 PMCID: PMC2939912 DOI: 10.1002/bdrc.20147] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Spermatogenesis is a highly orchestrated developmental process by which spermatogonia develop into mature spermatozoa. This process involves many testis- or male germ cell-specific gene products whose expressions are strictly regulated. In the past decade the advent of high-throughput gene expression analytical techniques has made functional genomic studies of this process, particularly in model animals such as mice and rats, feasible and practical. These studies have just begun to reveal the complexity of the genomic landscape of the developing male germ cells. Over 50% of the mouse and rat genome are expressed during testicular development. Among transcripts present in germ cells, 40% - 60% are uncharacterized. A number of genes, and consequently their associated biological pathways, are differentially expressed at different stages of spermatogenesis. Developing male germ cells present a rich repertoire of genetic processes. Tissue-specific as well as spermatogenesis stage-specific alternative splicing of genes exemplifies the complexity of genome expression. In addition to this layer of control, discoveries of abundant presence of antisense transcripts, expressed psuedogenes, non-coding RNAs (ncRNA) including long ncRNAs, microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and retrogenes all point to the presence of multiple layers of expression and functional regulation in male germ cells. It is anticipated that application of systems biology approaches will further our understanding of the regulatory mechanism of spermatogenesis.
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Affiliation(s)
- Tin-Lap Lee
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Alan Lap-Yin Pang
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Owen M. Rennert
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Wai-Yee Chan
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Department of Pediatrics, Georgetown University College of Medicine, Washington, DC
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10
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Volkow N, Rutter J, Pollock JD, Shurtleff D, Baler R. One SNP linked to two diseases-addiction and cancer: a double whammy? Nicotine addiction and lung cancer susceptibility. Mol Psychiatry 2008; 13:990-2. [PMID: 18936755 PMCID: PMC4827504 DOI: 10.1038/mp.2008.71] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- N Volkow
- Office of the Director, National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA,
| | - J Rutter
- Division of Basic Neuroscience and Behavioral Research, National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA
| | - JD Pollock
- Division of Basic Neuroscience and Behavioral Research, National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA
| | - D Shurtleff
- Division of Basic Neuroscience and Behavioral Research, National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA
| | - R Baler
- Office of Science Policy and Communications, National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA
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11
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Schlaepfer IR, Hoft NR, Collins AC, Corley RP, Hewitt JK, Hopfer CJ, Lessem J, McQueen MB, Rhee SH, Ehringer MA. The CHRNA5/A3/B4 gene cluster variability as an important determinant of early alcohol and tobacco initiation in young adults. Biol Psychiatry 2008; 63:1039-46. [PMID: 18163978 PMCID: PMC2526976 DOI: 10.1016/j.biopsych.2007.10.024] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2007] [Revised: 10/22/2007] [Accepted: 10/31/2007] [Indexed: 11/26/2022]
Abstract
BACKGROUND One potential site of convergence of the nicotine and alcohol actions is the family of the neuronal nicotinic acetylcholine receptors. Our study examines the genetic association between variations in the genomic region containing the CHRNA5, A3, and B4 gene cluster (A5A3B4) and several phenotypes of alcohol and tobacco use in an ethnically diverse young adult sample. Significant results were then replicated in a separate adult population-representative sample. METHODS In a selected sample, nine single nucleotide polymorphisms (SNPs) were tested for association with various nicotine and alcohol phenotypes, including age of initiation and measures of frequency, quantity, and subjective responses to the substances. Analysis was conducted with the statistical genetics program WHAP in the full sample (1075 subjects) including ethnicities as covariates and within each ethnic group sub-sample. Replication of the significant results in a separate population-based sample was carried out with the PBAT statistical genetics program. RESULTS Two linked SNPs (rs8023462 and rs1948) located in a conserved region of the A5A3B4 gene cluster significantly predicted early age of initiation for tobacco with a hazard ratio (HR) of 1.35 (95% confidence interval [CI]1.08-1.70) for the CC genotype of rs8023462 and a HR of 1.29 (95% CI 1.01-1.63) for the TT genotype of rs1948 [corrected]. These findings were then replicated in a separate population-representative sample, showing rs1948 and rs8023462 to be associated with age of initiation for both tobacco and alcohol use (p < .01 and p < .001). CONCLUSIONS Variations in A5A3B4 genes might influence behaviors that promote early age of experimentation with drugs.
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Affiliation(s)
- Isabel R. Schlaepfer
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, Department of Integrative Physiology, University of Colorado, Boulder, CO,*Correspondence to: Isabel R. Schlaepfer, University of Colorado, Institute for Behavioral Genetics 447 UCB, Boulder, CO 80309. E-mail:
| | - Nicole R. Hoft
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO
| | - Allan C. Collins
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO
| | - Robin P. Corley
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO
| | - John K. Hewitt
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, Department of Psychology, University of Colorado, Boulder, CO
| | - Christian J. Hopfer
- Division of Substance Dependence, Department of Psychiatry, University of Colorado School of Medicine, Denver, CO
| | - Jeffrey Lessem
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO
| | - Matthew B. McQueen
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, Department of Psychology, University of Colorado, Boulder, CO
| | - Soo Hyun Rhee
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, Department of Psychology, University of Colorado, Boulder, CO
| | - Marissa A. Ehringer
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, Department of Integrative Physiology, University of Colorado, Boulder, CO
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Berrettini W, Yuan X, Tozzi F, Song K, Francks C, Chilcoat H, Waterworth D, Muglia P, Mooser V. Alpha-5/alpha-3 nicotinic receptor subunit alleles increase risk for heavy smoking. Mol Psychiatry 2008; 13:368-73. [PMID: 18227835 PMCID: PMC2507863 DOI: 10.1038/sj.mp.4002154] [Citation(s) in RCA: 375] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Twin studies indicate that additive genetic effects explain most of the variance in nicotine dependence (ND), a construct emphasizing habitual heavy smoking despite adverse consequences, tolerance and withdrawal. To detect ND alleles, we assessed cigarettes per day (CPD) regularly smoked, in two European populations via whole genome association techniques. In these approximately 7500 persons, a common haplotype in the CHRNA3-CHRNA5 nicotinic receptor subunit gene cluster was associated with CPD (nominal P=6.9 x 10(-5)). In a third set of European populations (n= approximately 7500) which had been genotyped for approximately 6000 SNPs in approximately 2000 genes, an allele in the same haplotype was associated with CPD (nominal P=2.6 x 10(-6)). These results (in three independent populations of European origin, totaling approximately 15 000 individuals) suggest that a common haplotype in the CHRNA5/CHRNA3 gene cluster on chromosome 15 contains alleles, which predispose to ND.
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Affiliation(s)
- W Berrettini
- Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
| | - X Yuan
- Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Upper Merion, PA, USA,Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Verona, Italy
| | - F Tozzi
- Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Upper Merion, PA, USA,Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Verona, Italy
| | - K Song
- Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Upper Merion, PA, USA,Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Verona, Italy
| | - C Francks
- Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Upper Merion, PA, USA,Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Verona, Italy
| | - H Chilcoat
- Worldwide Epidemiology, GlaxoSmithKline, Research Triangle Park, NC, USA
| | - D Waterworth
- Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Upper Merion, PA, USA,Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Verona, Italy
| | - P Muglia
- Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Upper Merion, PA, USA,Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Verona, Italy,University of Toronto, Toronto, ON, Canada
| | - V Mooser
- Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Upper Merion, PA, USA,Clinical Pharmacology and Discovery Medicine, GlaxoSmithKline, Verona, Italy
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13
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Hertveldt V, De Mees C, Scohy S, Van Vooren P, Szpirer J, Szpirer C. The Sp6 locus uses several promoters and generates sense and antisense transcripts. Biochimie 2007; 89:1381-7. [PMID: 17624655 DOI: 10.1016/j.biochi.2007.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Accepted: 05/29/2007] [Indexed: 11/22/2022]
Abstract
The SP/KLF transcription factor family contains over 25 members sharing a DNA-binding domain composed of three zinc fingers of the C(2)H(2) type. We previously identified the sixth member of the SP subfamily (Sp6). The 5' end of the Sp6 transcript was not cloned and was predicted bioinformatically. A mouse molar tooth cDNA was then isolated differing from the Sp6 sequence by its 5' end, and was named epiprofin. Sp6 and epiprofin are currently used as synonyms. Here, we show that the Sp6 transcript possesses a first exon distinct from the epiprofin one: the Sp6 gene thus uses two promoters, generating two transcript variants which differ in their first exon. Furthermore, we identified an Sp6 opposite strand transcript (Sp6os) and examined, by quantitative RT-PCR experiments, the presence and the abundance of these two transcripts in mouse tissues. We also mapped the mouse locus by FISH to chromosome 11D.
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Affiliation(s)
- V Hertveldt
- Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, Rue Profs Jeener & Brachet, 12, B-6041, Gosselies (Charleroi), Belgium
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14
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Numata K, Okada Y, Saito R, Kiyosawa H, Kanai A, Tomita M. Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene 2006; 392:134-41. [PMID: 17250976 DOI: 10.1016/j.gene.2006.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 11/17/2006] [Accepted: 12/06/2006] [Indexed: 10/23/2022]
Abstract
Recent large-scale transcriptomic analyses have identified numerous endogenously encoded cis-antisense RNAs that are thought to play important roles in diverse cellular processes although comprehensive comparative studies among multiple species have yet to be performed. To investigate conserved genomic features across various species that may be related to sense-antisense regulation, we performed comparative analysis of approximately 1000-2000 cis-encoded antisense RNA pairs from five model eukaryotes (Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, and Oryza sativa). Analysis of overlapping patterns relative to the exon-intron structure revealed that the number of pairs sharing the 3' part of the transcripts was larger than that of the 5'-sharing pairs except in rice. Moreover, most of the well-conserved sense-antisense pairs between human and mouse exhibited 3'-overlaps, suggesting that regulatory mechanisms involving these regions may be important in sense-antisense transcription. Functional classification using Gene Ontology revealed that genes related to catalytic activity, nucleotide binding, DNA metabolism, and mitochondria were preferentially distributed within the set of exon-overlapping sense-antisense genes compared to the non-exon-overlapping group in animals. Despite the numerous sense-antisense pairs identified in human and mouse individually, the number of conserved pairs was extremely small (6.6% of the entire set). Whereas both genes of most of the conserved sense-antisense pairs had protein-coding potential, nearly half of the non-conserved pairs included a non-coding RNA, suggesting that non-coding sense-antisense RNAs may function in species-specific regulatory pathways.
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Affiliation(s)
- Koji Numata
- Graduate School of Media and Governance, Bioinformatics Program, Keio University, Fujisawa, 252-8520, Japan
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15
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Yin GL, Chen Q, Yang WJ. Naturally occurring antisense RNA of allatostatin gene in the prawn, Macrobrachium rosenbergii. Comp Biochem Physiol B Biochem Mol Biol 2006; 146:20-5. [PMID: 17055761 DOI: 10.1016/j.cbpb.2006.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 08/06/2006] [Accepted: 08/21/2006] [Indexed: 11/15/2022]
Abstract
Allatostatins are important regulatory neuropeptides which are widely distributed in invertebrates and execute their functions through either neural or humoral routes. However, the regulatory mechanism of the gene expression is unclear. In this paper, we report a naturally occurring antisense transcript, named as asMacro-AST A, of the crustacean FGLamide allatostatin gene (Macro-AST A) from the prawn, Macrobrachium rosenbergii. The asMacro-AST A contains an 843-bp sequence fully complementary to the 3' end of the Macro-AST A. To our knowledge, this is the first report of a natural antisense transcript in crustacean and the first endogenous antisense transcript of all identified allatostatin genes. Northern blotting analysis demonstrated that the gene was expressed in the thoracic ganglia where the sense gene was also expressed. Furthermore, we have detected a RNA-RNA duplex between the sense-antisense complementary region by using RNase protection analysis and RT-PCR. These results suggest that the antisense gene may play a role in the regulation of Macro-AST A gene expression.
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Affiliation(s)
- Guo-Li Yin
- Institute of Cell Biology and Genetics, College of Life Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang, 310058 P. R. China
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16
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Zhang Y, Liu XS, Liu QR, Wei L. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res 2006; 34:3465-75. [PMID: 16849434 PMCID: PMC1524920 DOI: 10.1093/nar/gkl473] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We developed a fast, integrative pipeline to identify cis natural antisense transcripts (cis-NATs) at genome scale. The pipeline mapped mRNAs and ESTs in UniGene to genome sequences in GoldenPath to find overlapping transcripts and combining information from coding sequence, poly(A) signal, poly(A) tail and splicing sites to deduce transcription orientation. We identified cis-NATs in 10 eukaryotic species, including 7830 candidate sense–antisense (SA) genes in 3915 SA pairs in human. The abundance of SA genes is remarkably low in worm and does not seem to be caused by the prevalence of operons. Hundreds of SA pairs are conserved across different species, even maintaining the same overlapping patterns. The convergent SA class is prevalent in fly, worm and sea squirt, but not in human or mouse as reported previously. The percentage of SA genes among imprinted genes in human and mouse is 24–47%, a range between the two previous reports. There is significant shortage of SA genes on Chromosome X in human and mouse but not in fly or worm, supporting X-inactivation in mammals as a possible cause. SA genes are over-represented in the catalytic activities and basic metabolism functions. All candidate cis-NATs can be downloaded from .
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Affiliation(s)
| | - X. Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health44 Binney Street, M1B22, Boston, MA 02115, USA
| | - Qing-Rong Liu
- Molecular Neurobiology Branch, National Institute on Drug Abuse-Intramural Research Program (NIDA-IRP), NIH, Department of Health and Human Services (DHHS)Box 5180, Baltimore, MD 21224, USA
| | - Liping Wei
- To whom correspondence should be addressed. Tel: +86 10 6276 4970; Fax: +86 10 6275 2438;
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17
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Chan WY, Wu SM, Ruszczyk L, Law E, Lee TL, Baxendale V, Lap-Yin Pang A, Rennert OM. The complexity of antisense transcription revealed by the study of developing male germ cells. Genomics 2006; 87:681-92. [PMID: 16458478 DOI: 10.1016/j.ygeno.2005.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2005] [Revised: 11/24/2005] [Accepted: 12/13/2005] [Indexed: 11/29/2022]
Abstract
Computational analyses have identified the widespread occurrence of antisense transcripts in the human and the mouse genome. However, the structure and the origin of the majority of the antisense transcripts are unknown. The presence of antisense transcripts for 19 of 64 differentially expressed genes during mouse spermatogenesis was demonstrated with orientation-specific RT-PCR. These antisense transcripts were derived from a wide variety of origins, including processed sense transcripts, intronic and exonic sequences of a single gene or multiple genes, intergenic sequences, and pseudogenes. They underwent normal and alternative splicing, 5' capping, and 3' polyadenylation, similar to the sense transcripts. There were also antisense transcripts that were not capped and/or polyadenylated. The testicular levels of the sense transcripts were higher than those of the antisense transcripts in all cases, while the relative expression in nontesticular tissues was variable. Thus antisense transcripts have complex origins and structures and the sense and antisense transcripts can be regulated independently.
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Affiliation(s)
- Wai-Yee Chan
- Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Building 49, Room 2A08, 49 Convent Drive, MSC 4429, Bethesda, MD 20892-4429, USA.
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