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Li MD, Liu Q, Shi X, Wang Y, Zhu Z, Guan Y, He J, Han H, Mao Y, Ma Y, Yuan W, Yao J, Yang Z. Integrative analysis of genetics, epigenetics and RNA expression data reveal three susceptibility loci for smoking behavior in Chinese Han population. Mol Psychiatry 2024:10.1038/s41380-024-02599-1. [PMID: 38789676 DOI: 10.1038/s41380-024-02599-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/18/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Despite numerous studies demonstrate that genetics and epigenetics factors play important roles on smoking behavior, our understanding of their functional relevance and coordinated regulation remains largely unknown. Here we present a multiomics study on smoking behavior for Chinese smoker population with the goal of not only identifying smoking-associated functional variants but also deciphering the pathogenesis and mechanism underlying smoking behavior in this under-studied ethnic population. After whole-genome sequencing analysis of 1329 Chinese Han male samples in discovery phase and OpenArray analysis of 3744 samples in replication phase, we discovered that three novel variants located near FOXP1 (rs7635815), and between DGCR6 and PRODH (rs796774020), and in ARVCF (rs148582811) were significantly associated with smoking behavior. Subsequently cis-mQTL and cis-eQTL analysis indicated that these variants correlated significantly with the differential methylation regions (DMRs) or differential expressed genes (DEGs) located in the regions where these variants present. Finally, our in silico multiomics analysis revealed several hub genes, like DRD2, PTPRD, FOXP1, COMT, CTNNAP2, to be synergistic regulated each other in the etiology of smoking.
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Affiliation(s)
- Ming D Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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.
| | - Qiang Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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
| | - Xiaoqiang Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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
| | - Yan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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
| | - Zhouhai Zhu
- Joint Institute of Tobacco and Health, Kunming, Yunnan, China
| | - Ying Guan
- Joint Institute of Tobacco and Health, Kunming, Yunnan, China
| | - Jingmin He
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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
- College of Biological Sciences, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Haijun Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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
| | - Ying Mao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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, National Medical 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
| | - Wenji Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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
| | - Jianhua Yao
- Joint Institute of Tobacco and Health, Kunming, Yunnan, China
| | - Zhongli Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical 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.
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Muenstermann C, Clemens KJ. Epigenetic mechanisms of nicotine dependence. Neurosci Biobehav Rev 2024; 156:105505. [PMID: 38070842 DOI: 10.1016/j.neubiorev.2023.105505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/09/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023]
Abstract
Smoking continues to be a leading cause of preventable disease and death worldwide. Nicotine dependence generates a lifelong propensity towards cravings and relapse, presenting an ongoing challenge for the development of treatments. Accumulating evidence supports a role for epigenetics in the development and maintenance of addiction to many drugs of abuse, however, the involvement of epigenetics in nicotine dependence is less clear. Here we review evidence that nicotine interacts with epigenetic mechanisms to enable the maintenance of nicotine-seeking across time. Research across species suggests that nicotine increases permissive histone acetylation, decreases repressive histone methylation, and modulates levels of DNA methylation and noncoding RNA expression throughout the brain. These changes are linked to the promoter regions of genes critical for learning and memory, reward processing and addiction. Pharmacological manipulation of enzymes that catalyze core epigenetic modifications regulate nicotine reward and associative learning, demonstrating a functional role of epigenetic modifications in nicotine dependence. These findings are consistent with nicotine promoting an overall permissive chromatin state at genes important for learning, memory and reward. By exploring these links through next-generation sequencing technologies, epigenetics provides a promising avenue for future interventions to treat nicotine dependence.
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Affiliation(s)
| | - Kelly J Clemens
- School of Psychology, University of New South Wales, Sydney, Australia.
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Ortega LA, Aragon-Carvajal DM, Cortes-Corso KT, Forero-Castillo F. Early developmental risks for tobacco addiction: A probabilistic epigenesis framework. Neurosci Biobehav Rev 2024; 156:105499. [PMID: 38056543 DOI: 10.1016/j.neubiorev.2023.105499] [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: 07/03/2023] [Revised: 11/23/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Considerable progress has been made in elucidating the relationships between early life psychobiological and environmental risk factors and the development of tobacco addiction. However, a comprehensive understanding of the heterogeneity in tobacco addiction phenotypes requires integrating research findings. The probabilistic epigenesis meta-theory offers a valuable framework for this integration, considering systemic, multilevel, developmental, and evolutionary perspectives. In this paper, we critically review relevant research on early developmental risks associated with tobacco addiction and highlight the integrative heuristic value of the probabilistic epigenesis framework for this research. For this, we propose a four-level systems approach as an initial step towards integration, analyzing complex interactions among different levels of influence. Additionally, we explore a coaction approach to examine key interactions between early risk factors. Moreover, we introduce developmental pathways to understand interindividual differences in tobacco addiction risk during development. This integrative approach holds promise for advancing our understanding of tobacco addiction etiology and informing potentially effective intervention strategies.
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Affiliation(s)
- Leonardo A Ortega
- Facultad de Psicologia, Fundacion Universitaria Konrad Lorenz, Colombia.
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Yang Z, Chen J, Han H, Wang Y, Shi X, Zhang B, Mao Y, Li AN, Yuan W, Yao J, Li MD. Single nucleotide polymorphisms rs148582811 regulates its host gene ARVCF expression to affect nicotine-associated hippocampus-dependent memory. iScience 2023; 26:108335. [PMID: 38025780 PMCID: PMC10679859 DOI: 10.1016/j.isci.2023.108335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/24/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Although numerous susceptibility loci are nominated for nicotine dependence (ND), no report showed any association of ARVCF with ND. Through genome-wide sequencing analysis, we first identified genetic variants associated nominally with ND and then replicated them in an independent sample. Of the six replicated variants, rs148582811 in ARVCF located in the enhancer-associated marker peak is attractive. The effective-median-based Mendelian randomization analysis indicated that ARVCF is a causal gene for ND. RNA-seq analysis detected decreased ARVCF expression in smokers compared to nonsmokers. Luciferase reporter assays indicated that rs148582811 and its located DNA fragment allele-specifically regulated ARVCF expression. Immunoprecipitation analysis revealed that transcription factor X-ray repair cross-complementing protein 5 (XRCC5) bound to the DNA fragment containing rs148582811 and allele-specifically regulated ARVCF expression at the mRNA and protein levels. With the Arvcf knockout mouse model, we showed that Arvcf deletion not only impairs hippocampus-dependent learning and memory, but also alleviated nicotine-induced memory deficits.
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Affiliation(s)
- Zhongli Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Joint Institute of Smoking and Health, Kunming, Yunnan 650024, China
| | - Jiali Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Haijun Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Xiaoqiang Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Bin Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Ying Mao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Andria N. Li
- Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Wenji Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Jianhua Yao
- Joint Institute of Smoking and Health, Kunming, Yunnan 650024, China
| | - Ming D. Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou 310058, China
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Qi FY, Zhu ZH, Li M, Guan Y, Peng QY, Lu SM, Liu ZH, Wang MF, Miao MM, Chen ZY, Li XM, Bai J, Yao JH, Yao J. Genetic variations in the bitter taste receptor gene TAS2R38 are related to cigarette smoking behavior in Han Chinese smokers. Genes Genomics 2022; 44:1363-1374. [PMID: 36125655 DOI: 10.1007/s13258-022-01311-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Smoking behavior is influenced by multiple genes, including the bitter taste gene TAS2R38. It has been reported that the correlation between TAS2R38 and smoking behavior has ethnicity-based differences. However, the TAS2R38 status in Chinese smokers is still unclear. OBJECTIVE This study aims to investigate the possible relationship between genetic variations in TAS2R38 (A49P, V262A and I296V) and smoking behaviors in the Han Chinese population. METHODS The haplotype analyses were performed and smoking behavior questionnaire was completed by 1271 individuals. Genetic association analyses for smoking behavior were analyzed using chi-square test. Further, for investigating the molecular mechanism of TAS2R38 variants effect on smoking behavior, we conducted TAS2R38-PAV and TAS2R38-AVI expression plasmids and tested the cellular calcium assay by cigarette smoke compounds stimulus in HEK293. RESULTS Significant associations of genetic variants within TAS2R38 were identified with smoking behavior. We found a higher PAV/PAV frequency than AVI/AVI in moderate and high nicotine dependence (FTND ≥ 4; X2 = 4.611, 1 df, p = 0.032) and strong cigarette smoke flavor intensity preference (X2 = 4.5383, 1 df, p = 0.033) in participants. Furthermore, in the in vitro cellular calcium assay, total particle matter (TPM), N-formylnornicotine and cotinine, existing in cigarette smoke, activated TAS2R38-PAV but not TAS2R38-AVI-transfected cells. CONCLUSION Our data highlights that genetic variations in TAS2R38 are related to smoking behavior, especially nicotine dependence and cigarette smoke flavor intensity preference. Our findings may encourage further consideration of the taste process to identify individuals susceptible to nicotine dependence, particularly Han Chinese smokers.
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Affiliation(s)
- Fei-Yan Qi
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Zhou-Hai Zhu
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Meng Li
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Ying Guan
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Qi-Yuan Peng
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - She-Ming Lu
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Zhi-Hua Liu
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Ming-Feng Wang
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Ming-Ming Miao
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Zhang-Yu Chen
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Xue-Mei Li
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Jie Bai
- Medical Faculty, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jian-Hua Yao
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China.
| | - Jianhua Yao
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
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6
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Zhang R, Dang W, Zhang J, He R, Li G, Zhang L, Wang Z, Zong H, Liu N, Jia W. Methylation quantitative locus rs3758653 in the DRD4 gene is associated with duration from first heroin exposure to addiction. Brain Res 2022; 1775:147746. [PMID: 34864042 DOI: 10.1016/j.brainres.2021.147746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/14/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022]
Abstract
Opioid addiction is a chronic brain disease with a high heritability. However, the genetic underpinnings remain uncertain. DNA methylation is involved in the adaptive changes in neuroplasticity after prolonged drug use. The dopamine receptor D4 (DRD4) has an essential role in the reward processes associated with addictive drugs. To further elucidate the potential role and mechanism of the DRD4 gene variants in heroin addiction, we detected the methylation level of 46 CpG sites in the promoter region and the genotypes of three SNPs in the DRD4 gene. Correlations between the SNPs and methylation levels of the CpG sites, i.e., the analysis of methylation quantitative trait loci (mQTLs) was conducted. Following the identification of mQTLs that are unique in the heroin addiction group, we performed an association study between the mQTLs and traits of heroin addiction. Our results revealed that there were several correlations of SNPs rs3758653 and rs11246226 with the methylation levels of some CpG sites in the DRD4 gene. Among these SNP-CpG pairs, rs3758653-DRD4_04, rs3758653-DRD4_05, rs3758653-DRD4_13 and rs3758653-DRD4_03 were unique in the heroin addiction group. Moreover, we found that mQTL rs3758653 was associated with duration from first heroin exposure to addiction, and the expression level of the DRD4 gene in human brain regions of the frontal cortex and hippocampus. Our findings suggested that some mQTLs in the genome may be associated with traits of opioid addiction through implicating the processes of DNA methylation and gene expression.
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Affiliation(s)
- Rui Zhang
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Wei Dang
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China.
| | - Jianbo Zhang
- Key Laboratory of National Health Commission for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ruifeng He
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Guibin Li
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Luying Zhang
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Zhikang Wang
- Psychiatry Department, Xi'an Daxing Hospital, Xi'an, Shaanxi, China
| | - Hua Zong
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Ning Liu
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Wei Jia
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
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Wills L, Ables JL, Braunscheidel KM, Caligiuri SPB, Elayouby KS, Fillinger C, Ishikawa M, Moen JK, Kenny PJ. Neurobiological Mechanisms of Nicotine Reward and Aversion. Pharmacol Rev 2022; 74:271-310. [PMID: 35017179 PMCID: PMC11060337 DOI: 10.1124/pharmrev.121.000299] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/24/2021] [Indexed: 12/27/2022] Open
Abstract
Neuronal nicotinic acetylcholine receptors (nAChRs) regulate the rewarding actions of nicotine contained in tobacco that establish and maintain the smoking habit. nAChRs also regulate the aversive properties of nicotine, sensitivity to which decreases tobacco use and protects against tobacco use disorder. These opposing behavioral actions of nicotine reflect nAChR expression in brain reward and aversion circuits. nAChRs containing α4 and β2 subunits are responsible for the high-affinity nicotine binding sites in the brain and are densely expressed by reward-relevant neurons, most notably dopaminergic, GABAergic, and glutamatergic neurons in the ventral tegmental area. High-affinity nAChRs can incorporate additional subunits, including β3, α6, or α5 subunits, with the resulting nAChR subtypes playing discrete and dissociable roles in the stimulatory actions of nicotine on brain dopamine transmission. nAChRs in brain dopamine circuits also participate in aversive reactions to nicotine and the negative affective state experienced during nicotine withdrawal. nAChRs containing α3 and β4 subunits are responsible for the low-affinity nicotine binding sites in the brain and are enriched in brain sites involved in aversion, including the medial habenula, interpeduncular nucleus, and nucleus of the solitary tract, brain sites in which α5 nAChR subunits are also expressed. These aversion-related brain sites regulate nicotine avoidance behaviors, and genetic variation that modifies the function of nAChRs in these sites increases vulnerability to tobacco dependence and smoking-related diseases. Here, we review the molecular, cellular, and circuit-level mechanisms through which nicotine elicits reward and aversion and the adaptations in these processes that drive the development of nicotine dependence. SIGNIFICANCE STATEMENT: Tobacco use disorder in the form of habitual cigarette smoking or regular use of other tobacco-related products is a major cause of death and disease worldwide. This article reviews the actions of nicotine in the brain that contribute to tobacco use disorder.
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Affiliation(s)
- Lauren Wills
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Jessica L Ables
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Kevin M Braunscheidel
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Stephanie P B Caligiuri
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Karim S Elayouby
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Clementine Fillinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Masago Ishikawa
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Janna K Moen
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
| | - Paul J Kenny
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York
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Mao Y, Huang P, Wang Y, Wang M, Li MD, Yang Z. Genome-wide methylation and expression analyses reveal the epigenetic landscape of immune-related diseases for tobacco smoking. Clin Epigenetics 2021; 13:215. [PMID: 34886889 PMCID: PMC8662854 DOI: 10.1186/s13148-021-01208-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Smoking is a major causal risk factor for lung cancer, chronic obstructive pulmonary disease (COPD), cardiovascular disease (CVD), and is the main preventable cause of deaths in the world. The components of cigarette smoke are involved in immune and inflammatory processes, which may increase the prevalence of cigarette smoke-related diseases. However, the underlying molecular mechanisms linking smoking and diseases have not been well explored. This study was aimed to depict a global map of DNA methylation and gene expression changes induced by tobacco smoking and to explore the molecular mechanisms between smoking and human diseases through whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). RESULTS We performed WGBS on 72 samples (36 smokers and 36 nonsmokers) and RNA-seq on 75 samples (38 smokers and 37 nonsmokers), and cytokine immunoassay on plasma from 22 males (9 smokers and 13 nonsmokers) who were recruited from the city of Jincheng in China. By comparing the data of the two groups, we discovered a genome-wide methylation landscape of differentially methylated regions (DMRs) associated with smoking. Functional enrichment analyses revealed that both smoking-related hyper-DMR genes (DMGs) and hypo-DMGs were related to synapse-related pathways, whereas the hypo-DMGs were specifically related to cancer and addiction. The differentially expressed genes (DEGs) revealed by RNA-seq analysis were significantly enriched in the "immunosuppression" pathway. Correlation analysis of DMRs with their corresponding gene expression showed that genes affected by tobacco smoking were mostly related to immune system diseases. Finally, by comparing cytokine concentrations between smokers and nonsmokers, we found that vascular endothelial growth factor (VEGF) was significantly upregulated in smokers. CONCLUSIONS In sum, we found that smoking-induced DMRs have different distribution patterns in hypermethylated and hypomethylated areas between smokers and nonsmokers. We further identified and verified smoking-related DMGs and DEGs through multi-omics integration analysis of DNA methylome and transcriptome data. These findings provide us a comprehensive genomic map of the molecular changes induced by smoking which would enhance our understanding of the harms of smoking and its relationship with diseases.
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Affiliation(s)
- Ying Mao
- 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
| | - Peng Huang
- 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
| | - Yan Wang
- 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
| | - Maiqiu Wang
- 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
| | - 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.
| | - 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.
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9
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Zhang J, Fan Y, Zhou J, Ma T, Gao K, Xu M, Xiao Y, Zhu Y. Methylation quantitative trait locus rs5326 is associated with susceptibility and effective dosage of methadone maintenance treatment for heroin use disorder. Psychopharmacology (Berl) 2021; 238:3511-3518. [PMID: 34476566 DOI: 10.1007/s00213-021-05968-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/18/2021] [Indexed: 01/01/2023]
Abstract
RATIONALE Opioid use disorder is a complicated brain disease with high heritability. The underlying mechanisms of the genetic underpinnings in the susceptibility and treatment response of opioid use disorder remain elusive. OBJECTIVES To reveal the potential associations of genotypes and gene methylations of dopaminergic system genes, as well as roles of them in opioid use disorder. In the present study, we detected the DNA methylation in the promoter regions of five representative dopaminergic system genes (DRD1, DRD2, SLC6A3, TH, and COMT) between 120 patients with heroin use disorder in methadone maintenance treatment (MMT) program and 111 healthy controls. The associations of 25 SNPs in the above genes and methylation of 237 CpG sites, known as methylation quantitative trait loci (mQTLs), were determined. Then, the correlations of the above mQTLs and traits of heroin use disorder were analyzed in a sample set of 801 patients with heroin use disorder and 930 healthy controls. RESULTS Our results demonstrated that several mQTLs in the DRD1 and DRD2 genes were identified both in the heroin use disorder and healthy control groups. Interestingly, rs4867798-CpG_174872884 and rs5326-CpG_174872884 in the DRD1 gene were the unique SNP-CpG pairs in the patients with heroin use disorder. Furthermore, mQTL rs5326 was associated with the susceptibility and effective dosage of MMT for heroin use disorder, and demonstrated allele-specific correlation with the expression of the DRD1 gene in the human caudate. CONCLUSIONS Our findings suggest that some mQTLs may be associated with traits of opioid use disorder by implicating the DNA methylation and gene expression.
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Affiliation(s)
- Jianbo Zhang
- Key Laboratory of National Health Commission for Forensic Science, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.,Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, 712000, Shaanxi, China
| | - Yajuan Fan
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Jinting Zhou
- Key Laboratory of National Health Commission for Forensic Science, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.,Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, 712000, Shaanxi, China
| | - Tengfei Ma
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Keqiang Gao
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Min Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Yifan Xiao
- Key Laboratory of National Health Commission for Forensic Science, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.,Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, 712000, Shaanxi, China
| | - Yongsheng Zhu
- Key Laboratory of National Health Commission for Forensic Science, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China. .,Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, 712000, Shaanxi, China.
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10
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A Constrained Generalized Functional Linear Model for Multi-Loci Genetic Mapping. STATS 2021. [DOI: 10.3390/stats4030033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In genome-wide association studies (GWAS), efficient incorporation of linkage disequilibria (LD) among densely typed genetic variants into association analysis is a critical yet challenging problem. Functional linear models (FLM), which impose a smoothing structure on the coefficients of correlated covariates, are advantageous in genetic mapping of multiple variants with high LD. Here we propose a novel constrained generalized FLM (cGFLM) framework to perform simultaneous association tests on a block of linked SNPs with various trait types, including continuous, binary and zero-inflated count phenotypes. The new cGFLM applies a set of inequality constraints on the FLM to ensure model identifiability under different genetic codings. The method is implemented via B-splines, and an augmented Lagrangian algorithm is employed for parameter estimation. For hypotheses testing, a test statistic that accounts for the model constraints was derived, following a mixture of chi-square distributions. Simulation results show that cGFLM is effective in identifying causal loci and gene clusters compared to several competing methods based on single markers and SKAT-C. We applied the proposed method to analyze a candidate gene-based COGEND study and a large-scale GWAS data on dental caries risk.
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11
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Al-Omoush TK, Alzoubi KH, Khabour OF, Alsheyab FM, Abu-Siniyeh A, Al-Sawalha NA, Mayyas FA, Cobb CO, Eissenberg T. The CHRNA5 Polymorphism (rs16969968) and its Association with Waterpipe Smoking Addiction among Jordanians. ARAB JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 27:450-455. [PMID: 33511332 DOI: 10.1080/25765299.2020.1849491] [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] [Indexed: 01/19/2023] Open
Abstract
Waterpipe smoking is a form of tobacco use that causes nicotine/tobacco dependence and has become a global health problem. In the current study, the association of rs16969968 SNP in the CHRNA5 gene with waterpipe dependence was investigated. A total of 386 men and women who used a waterpipe to smoke tobacco were recruited and divided into less dependent and more dependent smokers based on their score on the Lebanon Waterpipe Dependence Scale (LWDS). Results showed a significant difference in the distribution of GG, GA, and AA genotypes by waterpipe dependence status (P<0.001). The more dependent group showed a higher frequency of the AA genotype than the less dependent smokers' group (38% versus 23% respectively). In addition, the more dependent smokers exhibited more A allele than less dependent smokers (53% versus 37% respectively, P<0.001). In conclusion, there is an association between the rs16969968 SNP and waterpipe dependence as assessed by the LWDS.
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Affiliation(s)
- Thaka'a K Al-Omoush
- Department of Applied Biology, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Karem H Alzoubi
- Department of Clinical Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Omar F Khabour
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Fawzi M Alsheyab
- Department of Applied Biology, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Ahmed Abu-Siniyeh
- Department of Medical Laboratories, Faculty of Health Sciences, American University of Madaba, Madaba, Jordan
| | - Nour A Al-Sawalha
- Department of Clinical Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Fadia A Mayyas
- Department of Clinical Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Caroline O Cobb
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA.,Center for the Study of Tobacco Products, Virginia Commonwealth University, Richmond, VA, USA
| | - Thomas Eissenberg
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA.,Center for the Study of Tobacco Products, Virginia Commonwealth University, Richmond, VA, USA
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12
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Liu Q, Xu Y, Mao Y, Ma Y, Wang M, Han H, Cui W, Yuan W, Payne TJ, Xu Y, Li MD, Yang Z. Genetic and Epigenetic Analysis Revealing Variants in the NCAM1-TTC12-ANKK1-DRD2 Cluster Associated Significantly With Nicotine Dependence in Chinese Han Smokers. Nicotine Tob Res 2020; 22:1301-1309. [PMID: 31867628 DOI: 10.1093/ntr/ntz240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 12/17/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUNDS Although studies have demonstrated that the NCAM1-TTC12-ANKK1-DRD2 gene cluster plays essential roles in addictions in subjects of European and African origin, study of Chinese Han subjects is limited. Further, the underlying biological mechanisms of detected associations are largely unknown. METHODS Sixty-four single-nucleotide polymorphisms (SNPs) in this cluster were analyzed for association with Fagerstrőm Test for Nicotine Dependence score (FTND) and cigarettes per day (CPD) in male Chinese Han smokers (N = 2616). Next-generation bisulfite sequencing was used to discover smoking-associated differentially methylated regions (DMRs). Both cis-eQTL and cis-mQTL analyses were applied to assess the cis-regulatory effects of these risk SNPs. RESULTS Association analysis revealed that rs4648317 was significantly associated with FTND and CPD (p = .00018; p = .00072). Moreover, 14 additional SNPs were marginally significantly associated with FTND or CPD (p = .05-.01). Haplotype-based association analysis showed that one haplotype in DRD2, C-T-A-G, formed by rs4245148, rs4581480, rs4648317, and rs11214613, was significantly associated with CPD (p = .0005) and marginally associated with FTND (p = .003). Further, we identified four significant smoking-associated DMRs, three of which are located in the DRD2/ANKK1 region (p = .0012-.00005). Finally, we found five significant CpG-SNP pairs (p = 7.9 × 10-9-6.6 × 10-6) formed by risk SNPs rs4648317, rs11604671, and rs2734849 and three methylation loci. CONCLUSIONS We found two missense variants (rs11604671; rs2734849) and an intronic variant (rs4648317) with significant effects on ND and further explored their mechanisms of action through expression and methylation analysis. We found the majority of smoking-related DMRs are located in the ANKK1/DRD2 region, indicating a likely causative relation between non-synonymous SNPs and DMRs. IMPLICATIONS This study shows that there exist significant association of variants and haplotypes in ANKK1/DRD2 region with ND in Chinese male smokers. Further, this study also shows that DNA methylation plays an important role in mediating such associations.
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Affiliation(s)
- Qiang Liu
- 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
| | - Yi Xu
- 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
| | - Ying Mao
- 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
| | - Maiqiu Wang
- 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
| | - Haijun Han
- 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
| | - Wenji Yuan
- 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, MS
| | - Yizhou Xu
- The Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - 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
| | - 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
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13
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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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14
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Shi XY, Wang G, Li T, Li Z, Leo P, Liu Z, Wu G, Zhu H, Zhang Y, Li D, Gao L, Yang L, Wang W, Liao J, Wang J, Zhou S, Wang H, Li X, Gao J, Zhang L, Shu X, Li D, Li Y, Chen C, Zhang X, Partida GC, Lundberg M, Reutens D, Bartlett P, Brown MA, Zou LP, Xu H. Identification of susceptibility variants to benign childhood epilepsy with centro-temporal spikes (BECTS) in Chinese Han population. EBioMedicine 2020; 57:102840. [PMID: 32580138 PMCID: PMC7317238 DOI: 10.1016/j.ebiom.2020.102840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/11/2020] [Accepted: 06/02/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Benign Childhood Epilepsy with Centro-temporal Spikes (BECTS) is the most common form of idiopathic epilepsy in children, accounting for up to 23% of pediatric epilepsy. The pathogenesis of BECTS is unknown, but it is thought that genetic factors play a role in susceptibility to the disease. METHODS To investigate the role of common genetic variants in BECTS pathogenesis, a 2-stage genome-wide association study (GWAS) was performed in 1,800 Chinese Han BECTS patients, and 7,090 healthy controls. Genetic findings were used in a Mendelian Randomization study in the UK Biobank dataset to investigate the potential role of smoking in BECTS. FINDINGS Definitive evidence of a role for common-variant heritability was demonstrated, with heritability of BECTS of >10% observed even with conservative disease prevalence assumptions. Although no individual locus achieved genome-wide significance, twelve loci achieved suggestive evidence of association (5 × 10-8<P<10-5). Using combined genetic and brain tissue gene expression data analyzed by Summary-data-based Mendelian Randomization (SMR), causative association of BECTS was demonstrated with SNP rs1948 and the CHRNA5 t3603436 transcript (Peqtl = 2·10 × 10-12, Psmr = 7·9 × 10-5). This finding indicates rs1948 is significantly associated with BECTS through effects on expression of CHRNA5 in brain tissue. The identification of novel loci suggests involvements of KALRN and the CHRNA5-A3-B4 cluster in BECTS. Using a generalized SMR approach we demonstrate that maternal smoking around birth is significantly associated with increased risk of BECTS (odds ratio = 3·90, P = 0·0099). INTERPRETATION This study shows that BECTS risk is at least partially heritable and due to common genetic variants. Additionally, we demonstrate that BECTS risk is substantially increased by maternal smoking around birth.
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Affiliation(s)
- Xiu-Yu Shi
- Department of Pediatrics, Chinese PLA General Hospital, 28 Fuxing Road, Haidian district, Beijing, China
| | - Geng Wang
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China; University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Ting Li
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhixiu Li
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, Australia
| | - Paul Leo
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, Australia
| | - Zhisheng Liu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology Wuhan, Hubei, China
| | - Gefei Wu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology Wuhan, Hubei, China
| | - Hongmin Zhu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology Wuhan, Hubei, China
| | - Yuqin Zhang
- Department of Neurology, Tian Jin Children's hospital, 238 Longyan road, Beichen district, Tianjin, China
| | - Dong Li
- Department of Neurology, Tian Jin Children's hospital, 238 Longyan road, Beichen district, Tianjin, China
| | - Li Gao
- Department of Pediatrics, Henan Provincial People's Hospital, 7 Weiwu Road, Jinshui District, Zhengzhou, Henan Province, China
| | - Liu Yang
- Department of Pediatrics, Henan Provincial People's Hospital, 7 Weiwu Road, Jinshui District, Zhengzhou, Henan Province, China
| | - Wei Wang
- Department of Neurology, Harbin Children's Hospital, 57 YouYi Road, DaoLi District, Harbin, Heilongjiang Province, China
| | - Jianxiang Liao
- Department of Neurology, Shenzhen Children's Hospital, 7019 Yitian Road Futian, Shenzhen, Guangdong Province, China
| | - Jiwen Wang
- Department of Neurology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, 1678 Dongfang Road, New Pudong district, Shanghai, China
| | - Shuizhen Zhou
- Department of Neurology, Children's Hospital of Fudan University, 399 Wanyuan Road, Minhang District, Shanghai, China
| | - Hua Wang
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, Liaoning Province, China
| | - Xiaojing Li
- Department of Neurology, Guangzhou Women and Children's Medical Center, 9 Jinsui Road, Tianhe district, Guangzhou, Guangdong Province, China
| | - Jingyun Gao
- Department of Pediatric Neurology, Hebei Tangshan City maternal and child health care hospital,14 South Jianhe Road, Tangshan, Hebei Province, China
| | - Li Zhang
- Department of Pediatrics, Linyi People's Hospital, 130 Yizhou Road, Lanshan, Linyi, Shandong Province, China
| | - Xiaomei Shu
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, 149 Dalian Road, Zunyi, Guizhou Province, China
| | - Dan Li
- Department of Pediatrics, the Second affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi Province, China
| | - Yan Li
- Department of Neurology, Children's Hospital Affiliated to Soochow University, 92 Zhongnan Street, Suzhou, Jiangsu Province, China
| | - Chunhong Chen
- Department of Neurology, Beijing Children's Hospital, 56 South Lishi Road, Xicheng District, Beijing, China
| | - Xiuju Zhang
- Department of Pediatrics, Xingtai People's Hospital,16 Hongxing Street, Xingtai, Hebei Province, China
| | - Gabriel Cuellar Partida
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Mischa Lundberg
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - David Reutens
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Perry Bartlett
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Matthew A Brown
- Guy's & St Thomas' NHS Foundation Trust and King's College London, NIHR Biomedical Research Centre, London, England United Kingdom.
| | - Li-Ping Zou
- Department of Pediatrics, Chinese PLA General Hospital, 28 Fuxing Road, Haidian district, Beijing, China; Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing, China.
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China; Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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15
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Ma Y, Li J, Xu Y, Wang Y, Yao Y, Liu Q, Wang M, Zhao X, Fan R, Chen J, Zhang B, Cai Z, Han H, Yang Z, Yuan W, Zhong Y, Chen X, Ma JZ, Payne TJ, Xu Y, Ning Y, Cui W, Li MD. Identification of 34 genes conferring genetic and pharmacological risk for the comorbidity of schizophrenia and smoking behaviors. Aging (Albany NY) 2020; 12:2169-2225. [PMID: 32012119 PMCID: PMC7041787 DOI: 10.18632/aging.102735] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/02/2020] [Indexed: 12/13/2022]
Abstract
The prevalence of smoking is significantly higher in persons with schizophrenia (SCZ) than in the general population. However, the biological mechanisms of the comorbidity of smoking and SCZ are largely unknown. This study aimed to reveal shared biological pathways for the two diseases by analyzing data from two genome-wide association studies with a total sample size of 153,898. With pathway-based analysis, we first discovered 18 significantly enriched pathways shared by SCZ and smoking, which were classified into five groups: postsynaptic density, cadherin binding, dendritic spine, long-term depression, and axon guidance. Then, by using an integrative analysis of genetic, epigenetic, and expression data, we found not only 34 critical genes (e.g., PRKCZ, ARHGEF3, and CDKN1A) but also various risk-associated SNPs in these genes, which convey susceptibility to the comorbidity of the two disorders. Finally, using both in vivo and in vitro data, we demonstrated that the expression profiles of the 34 genes were significantly altered by multiple psychotropic drugs. Together, this multi-omics study not only reveals target genes for new drugs to treat SCZ but also reveals new insights into the shared genetic vulnerabilities of SCZ and smoking behaviors.
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Affiliation(s)
- 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
| | - Jingjing 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
| | - Yi Xu
- 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
| | - Yan Wang
- 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
| | - Yinghao Yao
- 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
| | - Qiang Liu
- 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
| | - Maiqiu Wang
- 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
| | - Xinyi Zhao
- 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
| | - 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
| | - 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
| | - Bin Zhang
- 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
| | - Zhen Cai
- 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
| | - Haijun Han
- 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
| | - Wenji Yuan
- 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
| | - Yigang Zhong
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangning Chen
- Institute of Personalized Medicine, University of Nevada at Las Vegas, Las Vegas, NV 89154, USA
| | - Jennie Z Ma
- , Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22904, USA
| | - Thomas J Payne
- Department of Otolaryngology and Communicative Sciences, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Yizhou Xu
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuping Ning
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, 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
| | - 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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16
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Chen J, Liu Q, Fan R, Han H, Yang Z, Cui W, Song G, Li MD. Demonstration of critical role of GRIN3A in nicotine dependence through both genetic association and molecular functional studies. Addict Biol 2020; 25:e12718. [PMID: 30741440 DOI: 10.1111/adb.12718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/19/2018] [Accepted: 01/08/2019] [Indexed: 11/27/2022]
Abstract
Nicotine dependence (ND) is a chronic disease with catastrophic effects on individual and public health. The glutamate receptor subunit gene, ionotropic N-methyl-d-aspartate 3A (GRIN3A), encodes a crucial subunit of N-methyl-d-aspartate receptors (NMDARs), which play an essential role in synaptic plasticity in the brain. Although various variants of GRIN3A have been associated with ND in European-American and African-American samples, no study has been reported for the association between GRIN3A and ND in Chinese Han population. We performed an association study of 16 single nucleotide polymorphisms (SNPs) in GRIN3A with ND in 2616 Chinese individuals. SNP-based association analysis indicated that SNP rs1323423 was significantly associated with the Fagerström Test for Nicotine Dependence (FTND) score after correction for multiple testing (P = 0.0026). Haplotype-based association analysis revealed that Block 3, formed by rs1323423-rs10989591, was significantly associated with the FTND score after correction for multiple testing (global P = 0.0183). Furthermore, luciferase reporter assay demonstrated that the DNA region containing rs1323423 was an enhancer element, the activity of which was significantly impacted by rs1323423 genotype. Considering that rs1323423 is located in a potential enhancer region, we performed GRIN3A editing in HEK293T cells with CRISPR/Cas9 and found that the DNA region around rs1323423 has a regulatory function and the expression of GRIN3A affects the expression of other NMDA subunits. Moreover, we demonstrated that nicotine at a concentration of 100 μM decreased expression of GRIN3A in SH-SY5Y and HEK293T cells at the RNA and protein level, respectively. This study provides novel evidence for the involvement of GRIN3A in ND.
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Affiliation(s)
- Jiali Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesZhejiang University School of Medicine China
| | - Qiang Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesZhejiang University School of Medicine China
| | - Rongli Fan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesZhejiang University School of Medicine China
| | - Haijun Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesZhejiang University School of Medicine China
| | - Zhongli Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesZhejiang University School of Medicine China
| | - Wenyan Cui
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesZhejiang University School of Medicine China
| | - Guohua Song
- Animal Research CenterShanxi Medical University 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 DiseasesZhejiang University School of Medicine China
- Research Center for Air Pollution and HealthZhejiang University China
- Institute of NeuroImmune PharmacologySeton Hall University South Orange New Jersey USA
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17
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Li M, Chen Y, Yao J, Lu S, Guan Y, Xu Y, Liu Q, Sun S, Mi Q, Mei J, Li X, Miao M, Zhao S, Zhu Z. Genome-Wide Association Study of Smoking Behavior Traits in a Chinese Han Population. Front Psychiatry 2020; 11:564239. [PMID: 33033484 PMCID: PMC7509597 DOI: 10.3389/fpsyt.2020.564239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/17/2020] [Indexed: 01/12/2023] Open
Abstract
Tobacco use is one of the leading causes of preventable disease worldwide. Genetic studies have elucidated numerous smoking-associated risk loci in American and European populations. However, genetic determinants for cigarette smoking in Chinese populations are under investigated. In this study, a whole-genome sequencing (WGS)-based genome-wide association study (GWAS) was performed in a Chinese Han population comprising 620 smokers and 564 nonsmokers. Thirteen single-nucleotide polymorphisms (SNPs) of the raftlin lipid linker 1 (RFTN1) gene achieved genome-wide significance levels (P < 5 x 10-8) for smoking initiation. The rs139753473 from RFTN1 and six other suggestively significant loci from CUB and sushi multiple domains 1 (CSMD1) gene were also associated with cigarettes per day (CPD) in an independent Chinese sample consisting of 1,329 subjects (805 smokers and 524 nonsmokers). When treating males separately, associations between smoking initiation and PCAT5/ANKRD30A, two genes involved in cancer development, were identified and replicated. Within RFTN1, two haplotypes (i.e., C-A-C-G and A-G-T-C) formed by rs796812630-rs796584733-rs796349027-rs879511366 and three haplotypes (i.e., T-T-C-C-C, T-T-A-T-T, and C-A-A-T-T) formed by rs879401109-rs879453873-rs75180423-rs541378415-rs796757175 were strongly associated with smoking initiation. In addition, we also revealed two haplotypes (i.e., C-A-G-G and T-C-T-T derived from rs4875371-rs4875372-rs17070935-rs11991366) in the CSMD1 gene showing a significant association with smoking initiation. Further bioinformatics functional assessment suggested that RFTN1 may participate in smoking behavior through modulating immune responses or interactions with the glucocorticoid receptor alpha and the androgen receptor. Together, our results may help understand the mechanisms underlying smoking behavior in the Chinese Han population.
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Affiliation(s)
- Meng Li
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Ying Chen
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Jianhua Yao
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Sheming Lu
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Ying Guan
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Yuqiong Xu
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Qiang Liu
- Hangzhou Global Biotechnology and Bioinformatics Co. Ltd, Hangzhou, China
| | - Silong Sun
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Qili Mi
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Junpu Mei
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Xuemei Li
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Mingming Miao
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Shancen Zhao
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
| | - Zhouhai Zhu
- Joint Institute of Tobacco and Health, Yunnan Academy of Tobacco Science, Kunming, China
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18
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Han H, Liu Q, Yang Z, Wang M, Ma Y, Cao L, Cui W, Yuan W, Payne TJ, Li L, Li MD. Association and cis-mQTL analysis of variants in serotonergic genes associated with nicotine dependence in Chinese Han smokers. Transl Psychiatry 2018; 8:243. [PMID: 30405098 PMCID: PMC6221882 DOI: 10.1038/s41398-018-0290-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/11/2022] Open
Abstract
Variants in serotonergic genes are implicated in nicotine dependence (ND) in subjects of European and African origin, but their involvement with smoking in Asians is largely unknown. Moreover, mechanisms underlying the ND risk-associated single-nucleotide polymorphisms (SNPs) in these genes are rarely investigated. The Fagerström Test for Nicotine Dependence (FTND) score was used to assess ND in 2616 male Chinese Han smokers. Both association and interaction analysis were used to examine the association of variants in the serotonergic genes with FTND. Further, expression and methylation quantitative trait loci (cis-mQTL) analysis was employed to determine the association of individual SNPs with the extent of methylation of each CpG locus. Individual SNP-based association analysis revealed that rs1176744 in HTR3B was marginally associated with FTND (p = 0.042). Haplotype-based association analysis found that one major haplotype, T-T-A-G, formed by SNPs rs3758987-rs4938056-rs1176744-rs2276305, located in the 5' region of HTR3B, showed a significant association with FTND (p = 0.00025). Further, a significant genetic interactive effect affecting ND was detected among SNPs rs10160548 in HTR3A, and rs3758987, rs2276305, and rs1672717 in HTR3B (p = 0.0074). Finally, we found four CpG sites (CpG_4543549, CpG_4543464, CpG_4543682, and CpG_4546888) to be significantly associated with three cis-mQTL SNPs (i.e., rs3758987, rs4938056, and rs1176744) located in our detected haplotype within HTR3B. In sum, we showed SNP rs1176744 (Tyr129Ser) to be associated with ND. Together with the SNPs rs3758987 and rs4938056 in HTR3B, they formed a major haplotype, which had significant association with ND. We further showed these SNPs contribute to ND through four methylated sites in HTR3B. All these findings suggest that variants in the serotonergic system play an important role in ND in the Chinese Han population. More importantly, these findings demonstrated that the involvement of this system in ND is through gene-by-gene interaction and methylation.
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Affiliation(s)
- Haijun Han
- 0000 0004 1759 700Xgrid.13402.34State 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
| | - Qiang Liu
- 0000 0004 1759 700Xgrid.13402.34State 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
| | - Zhongli Yang
- 0000 0004 1759 700Xgrid.13402.34State 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
| | - Mu Wang
- 0000 0004 1759 700Xgrid.13402.34State 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
| | - Yunlong Ma
- 0000 0004 1759 700Xgrid.13402.34State 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
| | - Liyu Cao
- 0000 0004 1759 700Xgrid.13402.34State 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
| | - Wenyan Cui
- 0000 0004 1759 700Xgrid.13402.34State 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
| | - Wenji Yuan
- 0000 0004 1759 700Xgrid.13402.34State 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
| | - Thomas J. Payne
- 0000 0004 1937 0407grid.410721.1ACT Center for Tobacco Treatment, Education and Research, Department of Otolaryngology and Communicative Sciences, University of Mississippi Medical Center, Jackson, MS USA
| | - Lanjuan 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.
| | - Ming D. Li
- 0000 0004 1759 700Xgrid.13402.34State 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 ,0000 0004 1759 700Xgrid.13402.34Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China ,0000 0001 2172 0072grid.263379.aInstitute of Neuroimmune Pharmacology, Seton Hall University, South Orange, NJ USA
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