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Seo J, Gaddis NC, Patchen BK, Xu J, Barr RG, O'Connor G, Manichaikul AW, Gharib SA, Dupuis J, North KE, Cassano PA, Hancock DB. Exploiting meta-analysis of genome-wide interaction with serum 25-hydroxyvitamin D to identify novel genetic loci associated with pulmonary function. Am J Clin Nutr 2024; 119:1227-1237. [PMID: 38484975 DOI: 10.1016/j.ajcnut.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/12/2024] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Higher 25-hydroxyvitamin D (25(OH)D) concentrations in serum has a positive association with pulmonary function. Investigating genome-wide interactions with 25(OH)D may reveal new biological insights into pulmonary function. OBJECTIVES We aimed to identify novel genetic variants associated with pulmonary function by accounting for 25(OH)D interactions. METHODS We included 211,264 participants from the observational United Kingdom Biobank study with pulmonary function tests (PFTs), genome-wide genotypes, and 25(OH)D concentrations from 4 ancestral backgrounds-European, African, East Asian, and South Asian. Among PFTs, we focused on forced expiratory volume in the first second (FEV1) and forced vital capacity (FVC) because both were previously associated with 25(OH)D. We performed genome-wide association study (GWAS) analyses that accounted for variant×25(OH)D interaction using the joint 2 degree-of-freedom (2df) method, stratified by participants' smoking history and ancestry, and meta-analyzed results. We evaluated interaction effects to determine how variant-PFT associations were modified by 25(OH)D concentrations and conducted pathway enrichment analysis to examine the biological relevance of our findings. RESULTS Our GWAS meta-analyses, accounting for interaction with 25(OH)D, revealed 30 genetic variants significantly associated with FEV1 or FVC (P2df <5.00×10-8) that were not previously reported for PFT-related traits. These novel variant signals were enriched in lung function-relevant pathways, including the p38 MAPK pathway. Among variants with genome-wide-significant 2df results, smoking-stratified meta-analyses identified 5 variants with 25(OH)D interactions that influenced FEV1 in both smoking groups (never smokers P1df interaction<2.65×10-4; ever smokers P1df interaction<1.71×10-5); rs3130553, rs2894186, rs79277477, and rs3130929 associations were only evident in never smokers, and the rs4678408 association was only found in ever smokers. CONCLUSION Genetic variant associations with lung function can be modified by 25(OH)D, and smoking history can further modify variant×25(OH)D interactions. These results expand the known genetic architecture of pulmonary function and add evidence that gene-environment interactions, including with 25(OH)D and smoking, influence lung function.
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Affiliation(s)
- Jungkyun Seo
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Nathan C Gaddis
- RTI International, Research Triangle Park, NC, United States
| | - Bonnie K Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States
| | - Jiayi Xu
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
| | - R Graham Barr
- Divisions of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York, NY, United States
| | - George O'Connor
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States; Division of Pulmonary, Critical Care and Sleep Medicine, Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, WA, United States
| | - Josée Dupuis
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States; Division of Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, NY, United States
| | - Dana B Hancock
- RTI International, Research Triangle Park, NC, United States.
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Toikumo S, Jennings MV, Pham BK, Lee H, Mallard TT, Bianchi SB, Meredith JJ, Vilar-Ribó L, Xu H, Hatoum AS, Johnson EC, Pazdernik VK, Jinwala Z, Pakala SR, Leger BS, Niarchou M, Ehinmowo M, Jenkins GD, Batzler A, Pendegraft R, Palmer AA, Zhou H, Biernacka JM, Coombes BJ, Gelernter J, Xu K, Hancock DB, Cox NJ, Smoller JW, Davis LK, Justice AC, Kranzler HR, Kember RL, Sanchez-Roige S. Multi-ancestry meta-analysis of tobacco use disorder identifies 461 potential risk genes and reveals associations with multiple health outcomes. Nat Hum Behav 2024:10.1038/s41562-024-01851-6. [PMID: 38632388 DOI: 10.1038/s41562-024-01851-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024]
Abstract
Tobacco use disorder (TUD) is the most prevalent substance use disorder in the world. Genetic factors influence smoking behaviours and although strides have been made using genome-wide association studies to identify risk variants, most variants identified have been for nicotine consumption, rather than TUD. Here we leveraged four US biobanks to perform a multi-ancestral meta-analysis of TUD (derived via electronic health records) in 653,790 individuals (495,005 European, 114,420 African American and 44,365 Latin American) and data from UK Biobank (ncombined = 898,680). We identified 88 independent risk loci; integration with functional genomic tools uncovered 461 potential risk genes, primarily expressed in the brain. TUD was genetically correlated with smoking and psychiatric traits from traditionally ascertained cohorts, externalizing behaviours in children and hundreds of medical outcomes, including HIV infection, heart disease and pain. This work furthers our biological understanding of TUD and establishes electronic health records as a source of phenotypic information for studying the genetics of TUD.
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Affiliation(s)
- Sylvanus Toikumo
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mariela V Jennings
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Benjamin K Pham
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Hyunjoon Lee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Sevim B Bianchi
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - John J Meredith
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Laura Vilar-Ribó
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Heng Xu
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Alexander S Hatoum
- Psychological & Brain Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Emma C Johnson
- Psychological & Brain Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Zeal Jinwala
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shreya R Pakala
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Brittany S Leger
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Program in Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Maria Niarchou
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA
| | | | - Greg D Jenkins
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Anthony Batzler
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Richard Pendegraft
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hang Zhou
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Joanna M Biernacka
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Brandon J Coombes
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Ke Xu
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | | | - Nancy J Cox
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Lea K Davis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amy C Justice
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
- Yale University School of Public Health, New Haven, CT, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - Henry R Kranzler
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rachel L Kember
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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3
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White JD, Minto MS, Willis C, Quach BC, Han S, Tao R, Deep-Soboslay A, Zillich L, Clark SL, van den Oord EJCG, Hyde TM, Mayfield RD, Webb BT, Johnson EO, Kleinman JE, Bierut LJ, Hancock DB. Alcohol Use Disorder-Associated DNA Methylation in the Nucleus Accumbens and Dorsolateral Prefrontal Cortex. medRxiv 2024:2024.01.17.23300238. [PMID: 38293028 PMCID: PMC10827272 DOI: 10.1101/2024.01.17.23300238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Alcohol use disorder (AUD) has a profound public health impact. However, understanding of the molecular mechanisms underlying the development and progression of AUD remain limited. Here, we interrogate AUD-associated DNA methylation (DNAm) changes within and across addiction-relevant brain regions: the nucleus accumbens (NAc) and dorsolateral prefrontal cortex (DLPFC). Methods Illumina HumanMethylation EPIC array data from 119 decedents of European ancestry (61 cases, 58 controls) were analyzed using robust linear regression, with adjustment for technical and biological variables. Associations were characterized using integrative analyses of public gene regulatory data and published genetic and epigenetic studies. We additionally tested for brain region-shared and -specific associations using mixed effects modeling and assessed implications of these results using public gene expression data. Results At a false discovery rate ≤ 0.05, we identified 53 CpGs significantly associated with AUD status for NAc and 31 CpGs for DLPFC. In a meta-analysis across the regions, we identified an additional 21 CpGs associated with AUD, for a total of 105 unique AUD-associated CpGs (120 genes). AUD-associated CpGs were enriched in histone marks that tag active promoters and our strongest signals were specific to a single brain region. Of the 120 genes, 23 overlapped with previous genetic associations for substance use behaviors; all others represent novel associations. Conclusions Our findings identify AUD-associated methylation signals, the majority of which are specific within NAc or DLPFC. Some signals may constitute predisposing genetic and epigenetic variation, though more work is needed to further disentangle the neurobiological gene regulatory differences associated with AUD.
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Affiliation(s)
- Julie D. White
- GenOmics and Translational Research Center, RTI International
| | | | - Caryn Willis
- GenOmics and Translational Research Center, RTI International
| | - Bryan C. Quach
- GenOmics and Translational Research Center, RTI International
| | | | - Ran Tao
- Lieber Institute for Brain Development (LIBD)
| | | | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Shaunna L. Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University
| | | | | | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin
| | - Bradley T. Webb
- GenOmics and Translational Research Center, RTI International
| | - Eric O. Johnson
- GenOmics and Translational Research Center, RTI International
- Fellow Program, RTI International
| | | | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine
| | - Dana B. Hancock
- GenOmics and Translational Research Center, RTI International
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4
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Carter JK, Quach BC, Willis C, Minto MS, Hancock DB, Montalvo-Ortiz J, Corradin O, Logan RW, Walss-Bass C, Maher BS, Johnson EO. Identifying novel gene dysregulation associated with opioid overdose death: A meta-analysis of differential gene expression in human prefrontal cortex. medRxiv 2024:2024.01.12.24301153. [PMID: 38260365 PMCID: PMC10802752 DOI: 10.1101/2024.01.12.24301153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Only recently have human postmortem brain studies of differential gene expression (DGE) associated with opioid overdose death (OOD) been published; sample sizes from these studies have been modest (N = 40-153). To increase statistical power to identify OOD-associated genes, we leveraged human prefrontal cortex RNAseq data from four independent OOD studies and conducted a transcriptome-wide DGE meta-analysis (N = 285). Using a unified gene expression data processing and analysis framework across studies, we meta-analyzed 20 098 genes and found 335 significant differentially expressed genes (DEGs) by OOD status (false discovery rate < 0.05). Of these, 66 DEGs were among the list of 303 genes reported as OOD-associated in prior prefrontal cortex molecular studies, including genes/gene families (e.g., OPRK1, NPAS4, DUSP, EGR). The remaining 269 DEGs were not previously reported (e.g., NR4A2, SYT1, HCRTR2, BDNF). There was little evidence of genetic drivers for the observed differences in gene expression between opioid addiction cases and controls. Enrichment analyses for the DEGs across molecular pathway and biological process databases highlight an interconnected set of genes and pathways from orexin and tyrosine kinase receptors through MEK/ERK/MAPK signaling to affect neuronal plasticity.
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Affiliation(s)
- Javan K. Carter
- Omics, Epidemiology, and Analytics Program, RTI International, Research Triangle Park, North Carolina, USA
| | - Bryan C. Quach
- Omics, Epidemiology, and Analytics Program, RTI International, Research Triangle Park, North Carolina, USA
| | - Caryn Willis
- Omics, Epidemiology, and Analytics Program, RTI International, Research Triangle Park, North Carolina, USA
| | - Melyssa S. Minto
- Omics, Epidemiology, and Analytics Program, RTI International, Research Triangle Park, North Carolina, USA
| | | | - Dana B. Hancock
- Omics, Epidemiology, and Analytics Program, RTI International, Research Triangle Park, North Carolina, USA
| | - Janitza Montalvo-Ortiz
- Department of Psychiatry, Division of Human Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Clinical Neurosciences Division, National Center of PTSD, VA CT Healthcare System, West Haven, Connecticut, USA
| | - Olivia Corradin
- Whitehead Institute Biomedical Research, Cambridge, Massachusetts, USA
| | - Ryan W. Logan
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Consuelo Walss-Bass
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
- MD Anderson Cancer Center University of Texas Health Science Center at Houston Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Brion S. Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Eric Otto Johnson
- Omics, Epidemiology, and Analytics Program, RTI International, Research Triangle Park, North Carolina, USA
- Fellow Program, RTI International, Research Triangle Park, North Carolina, USA
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5
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Chang Y, Thornton V, Chaloemtoem A, Anokhin AP, Bijsterbosch J, Bogdan R, Hancock DB, Johnson EO, Bierut LJ. Investigating the Relationship Between Smoking Behavior and Global Brain Volume. Biol Psychiatry Glob Open Sci 2024; 4:74-82. [PMID: 38130847 PMCID: PMC10733671 DOI: 10.1016/j.bpsgos.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 12/23/2023] Open
Abstract
Background Previous studies have shown that brain volume is negatively associated with cigarette smoking, but there is an ongoing debate about whether smoking causes lowered brain volume or a lower brain volume is a risk factor for smoking. We address this debate through multiple methods that evaluate directionality: Bradford Hill's criteria, which are commonly used to understand a causal relationship in epidemiological studies, and mediation analysis. Methods In 32,094 participants of European descent from the UK Biobank dataset, we examined the relationship between a history of daily smoking and brain volumes, as well as an association of genetic risk score to ever smoking with brain volume. Results A history of daily smoking was strongly associated with decreased brain volume, and a history of heavier smoking was associated with a greater decrease in brain volume. The strongest association was between total gray matter volume and a history of daily smoking (effect size = -2964 mm3, p = 2.04 × 10-16), and there was a dose-response relationship with more pack years smoked associated with a greater decrease in brain volume. A polygenic risk score for smoking initiation was strongly associated with a history of daily smoking (effect size = 0.05, p = 4.20 × 10-84), but only modestly associated with total gray matter volume (effect size = -424 mm3, p = .01). Mediation analysis indicated that a history of daily smoking mediated the relationship between the smoking initiation polygenic risk score and total gray matter volume. Conclusions A history of daily smoking is strongly associated with a decreased total brain volume.
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Affiliation(s)
- Yoonhoo Chang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Vera Thornton
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Ariya Chaloemtoem
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Andrey P. Anokhin
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Janine Bijsterbosch
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Ryan Bogdan
- Department of Psychological and Brain Sciences, Washington University in St. Louis, St. Louis, Missouri
| | - Dana B. Hancock
- Social, Statistical and Environmental Sciences, Research Triangle Institute International, Research Triangle Park, North Carolina
| | - Eric Otto Johnson
- Fellow Program, Research Triangle Institute International, Research Triangle Park, North Carolina
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
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6
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Moore A, Marks JA, Quach BC, Guo Y, Bierut LJ, Gaddis NC, Hancock DB, Page GP, Johnson EO. Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value. Commun Biol 2023; 6:1199. [PMID: 38001305 PMCID: PMC10673847 DOI: 10.1038/s42003-023-05413-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/03/2023] [Indexed: 11/26/2023] Open
Abstract
Where sufficiently large genome-wide association study (GWAS) samples are not currently available or feasible, methods that leverage increasing knowledge of the biological function of variants may illuminate discoveries without increasing sample size. We comprehensively evaluated 17 functional weighting methods for identifying novel associations. We assessed the performance of these methods using published results from multiple GWAS waves across each of five complex traits. Although no method achieved both high sensitivity and positive predictive value (PPV) for any trait, a subset of methods utilizing pleiotropy and expression quantitative trait loci nominated variants with high PPV (>75%) for multiple traits. Application of functionally weighting methods to enhance GWAS power for locus discovery is unlikely to circumvent the need for larger sample sizes in truly underpowered GWAS, but these results suggest that applying functional weighting to GWAS can accurately nominate additional novel loci from available samples for follow-up studies.
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Affiliation(s)
- Amy Moore
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA.
| | - Jesse A Marks
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA
| | - Bryan C Quach
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA
| | - Yuelong Guo
- GeneCentric Therapeutics, Inc., Cary, NC, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Nathan C Gaddis
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA
| | - Dana B Hancock
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA
| | - Grier P Page
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA
- Fellow Program, RTI International, Research Triangle Park, NC, 27709, USA
| | - Eric O Johnson
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, 27709, USA.
- Fellow Program, RTI International, Research Triangle Park, NC, 27709, USA.
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7
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Fang F, Quach B, Lawrence KG, van Dongen J, Marks JA, Lundgren S, Lin M, Odintsova VV, Costeira R, Xu Z, Zhou L, Mandal M, Xia Y, Vink JM, Bierut LJ, Ollikainen M, Taylor JA, Bell JT, Kaprio J, Boomsma DI, Xu K, Sandler DP, Hancock DB, Johnson EO. Trans-ancestry epigenome-wide association meta-analysis of DNA methylation with lifetime cannabis use. Mol Psychiatry 2023:10.1038/s41380-023-02310-w. [PMID: 37935791 DOI: 10.1038/s41380-023-02310-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
Cannabis is widely used worldwide, yet its links to health outcomes are not fully understood. DNA methylation can serve as a mediator to link environmental exposures to health outcomes. We conducted an epigenome-wide association study (EWAS) of peripheral blood-based DNA methylation and lifetime cannabis use (ever vs. never) in a meta-analysis including 9436 participants (7795 European and 1641 African ancestry) from seven cohorts. Accounting for effects of cigarette smoking, our trans-ancestry EWAS meta-analysis revealed four CpG sites significantly associated with lifetime cannabis use at a false discovery rate of 0.05 [Formula: see text]: cg22572071 near gene ADGRF1, cg15280358 in ADAM12, cg00813162 in ACTN1, and cg01101459 near LINC01132. Additionally, our EWAS analysis in participants who never smoked cigarettes identified another epigenome-wide significant CpG site, cg14237301 annotated to APOBR. We used a leave-one-out approach to evaluate methylation scores constructed as a weighted sum of the significant CpGs. The best model can explain 3.79% of the variance in lifetime cannabis use. These findings unravel the DNA methylation changes associated with lifetime cannabis use that are independent of cigarette smoking and may serve as a starting point for further research on the mechanisms through which cannabis exposure impacts health outcomes.
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Affiliation(s)
- Fang Fang
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA.
| | - Bryan Quach
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Kaitlyn G Lawrence
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jesse A Marks
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Sara Lundgren
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Mingkuan Lin
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
| | - Veronika V Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ricardo Costeira
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Linran Zhou
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Meisha Mandal
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Yujing Xia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jacqueline M Vink
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Laura J Bierut
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO, USA
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Dana B Hancock
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
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8
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Patchen BK, Balte P, Bartz TM, Barr RG, Fornage M, Graff M, Jacobs DR, Kalhan R, Lemaitre RN, O'Connor G, Psaty B, Seo J, Tsai MY, Wood AC, Xu H, Zhang J, Gharib SA, Manichaikul A, North K, Steffen LM, Dupuis J, Oelsner E, Hancock DB, Cassano PA. Investigating Associations of Omega-3 Fatty Acids, Lung Function Decline, and Airway Obstruction. Am J Respir Crit Care Med 2023; 208:846-857. [PMID: 37470492 DOI: 10.1164/rccm.202301-0074oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/26/2023] [Indexed: 07/21/2023] Open
Abstract
Rationale: Inflammation contributes to lung function decline and the development of chronic obstructive pulmonary disease. Omega-3 fatty acids have antiinflammatory properties and may benefit lung health. Objectives: To investigate associations of omega-3 fatty acids with lung function decline and incident airway obstruction in a diverse sample of adults from general-population cohorts. Methods: Complementary study designs: 1) longitudinal study of plasma phospholipid omega-3 fatty acids and repeated FEV1 and FVC measures in the NHLBI Pooled Cohorts Study and 2) two-sample Mendelian randomization (MR) study of genetically predicted omega-3 fatty acids and lung function parameters. Measurements and Main Results: The longitudinal study found that higher omega-3 fatty acid levels were associated with attenuated lung function decline in 15,063 participants, with the largest effect sizes for the most metabolically downstream omega-3 fatty acid, docosahexaenoic acid (DHA). An increase in DHA of 1% of total fatty acids was associated with attenuations of 1.4 ml/yr for FEV1 (95% confidence interval [CI], 1.1-1.8) and 2.0 ml/yr for FVC (95% CI, 1.6-2.4) and a 7% lower incidence of spirometry-defined airway obstruction (95% CI, 0.89-0.97). DHA associations persisted across sexes and smoking histories and in Black, White, and Hispanic participants, with associations of the largest magnitude in former smokers and Hispanic participants. The MR study showed similar trends toward positive associations of genetically predicted downstream omega-3 fatty acids with FEV1 and FVC. Conclusions: The longitudinal and MR studies provide evidence supporting beneficial effects of higher levels of downstream omega-3 fatty acids, especially DHA, on lung health.
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Affiliation(s)
- Bonnie K Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
| | - Pallavi Balte
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health
| | - R Graham Barr
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - David R Jacobs
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, Minnesota
| | - Ravi Kalhan
- Departments of Medicine and Preventative Medicine, Northwestern Medicine, Chicago, Illinois
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health
| | - George O'Connor
- Pulmonary, Allergy, Sleep and Critical Care Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health
| | - Jungkyun Seo
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Alexis C Wood
- U.S. Department of Agriculture/Agricultural Research Service Children Nutrition Research Center, Houston, Texas
| | - Hanfei Xu
- Departments of Biostatistics and Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Jingwen Zhang
- Departments of Biostatistics and Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Sina A Gharib
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, Washington
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Kari North
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Lyn M Steffen
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Josée Dupuis
- U.S. Department of Agriculture/Agricultural Research Service Children Nutrition Research Center, Houston, Texas
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montréal, Québec, Canada
| | - Elizabeth Oelsner
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Dana B Hancock
- RTI International, Research Triangle Park, North Carolina; and
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York
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9
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Cheng Y, Justice A, Wang Z, Li B, Hancock DB, Johnson EO, Xu K. Cis-meQTL for cocaine use-associated DNA methylation in an HIV-positive cohort show pleiotropic effects on multiple traits. BMC Genomics 2023; 24:556. [PMID: 37730558 PMCID: PMC10510240 DOI: 10.1186/s12864-023-09661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Cocaine use (CU) is associated with psychiatric and medical diseases. Little is known about the mechanisms of CU-related comorbidities. Findings from preclinical and clinical studies have suggested that CU is associated with aberrant DNA methylation (DNAm) that may be influenced by genetic variants [i.e., methylation quantitative trait loci (meQTLs)]. In this study, we mapped cis-meQTLs for CU-associated DNAm sites (CpGs) in an HIV-positive cohort (Ntotal = 811) and extended the meQTLs to multiple traits. RESULTS We conducted cis-meQTL analysis for 224 candidate CpGs selected for their association with CU in blood. We identified 7,101 significant meQTLs [false discovery rate (FDR) < 0.05], which mostly mapped to genes involved in immunological functions and were enriched in immune pathways. We followed up the meQTLs using phenome-wide association study and trait enrichment analyses, which revealed 9 significant traits. We tested for causal effects of CU on these 9 traits using Mendelian Randomization and found evidence that CU plays a causal role in increasing hypertension (p-value = 2.35E-08) and decreasing heel bone mineral density (p-value = 1.92E-19). CONCLUSIONS These findings suggest that genetic variants for CU-associated DNAm have pleiotropic effects on other relevant traits and provide new insights into the causal relationships between cocaine use and these complex traits.
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Affiliation(s)
- Youshu Cheng
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Amy Justice
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA.
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA.
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10
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Toikumo S, Jennings MV, Pham BK, Lee H, Mallard TT, Bianchi SB, Meredith JJ, Vilar-Ribó L, Xu H, Hatoum AS, Johnson EC, Pazdernik V, Jinwala Z, Pakala SR, Leger BS, Niarchou M, Ehinmowo M, Jenkins GD, Batzler A, Pendegraft R, Palmer AA, Zhou H, Biernacka JM, Coombes BJ, Gelernter J, Xu K, Hancock DB, Cox NJ, Smoller JW, Davis LK, Justice AC, Kranzler HR, Kember RL, Sanchez-Roige S. Multi-ancestry meta-analysis of tobacco use disorder prioritizes novel candidate risk genes and reveals associations with numerous health outcomes. medRxiv 2023:2023.03.27.23287713. [PMID: 37034728 PMCID: PMC10081388 DOI: 10.1101/2023.03.27.23287713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Tobacco use disorder (TUD) is the most prevalent substance use disorder in the world. Genetic factors influence smoking behaviors, and although strides have been made using genome-wide association studies (GWAS) to identify risk variants, the majority of variants identified have been for nicotine consumption, rather than TUD. We leveraged five biobanks to perform a multi-ancestral meta-analysis of TUD (derived via electronic health records, EHR) in 898,680 individuals (739,895 European, 114,420 African American, 44,365 Latin American). We identified 88 independent risk loci; integration with functional genomic tools uncovered 461 potential risk genes, primarily expressed in the brain. TUD was genetically correlated with smoking and psychiatric traits from traditionally ascertained cohorts, externalizing behaviors in children, and hundreds of medical outcomes, including HIV infection, heart disease, and pain. This work furthers our biological understanding of TUD and establishes EHR as a source of phenotypic information for studying the genetics of TUD.
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Affiliation(s)
- Sylvanus Toikumo
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mariela V Jennings
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Benjamin K Pham
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Hyunjoon Lee
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Sevim B Bianchi
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - John J Meredith
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Laura Vilar-Ribó
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Heng Xu
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Alexander S Hatoum
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Vanessa Pazdernik
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Zeal Jinwala
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shreya R Pakala
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Brittany S Leger
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
- Program in Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Maria Niarchou
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Greg D Jenkins
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Anthony Batzler
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Richard Pendegraft
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hang Zhou
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Joanna M Biernacka
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Brandon J Coombes
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Ke Xu
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Dana B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
| | - Nancy J Cox
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Lea K Davis
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amy C Justice
- Yale University School of Public Health, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - Henry R Kranzler
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rachel L Kember
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA
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11
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Carnes MU, Quach BC, Zhou L, Han S, Tao R, Mandal M, Deep-Soboslay A, Marks JA, Page GP, Maher BS, Jaffe AE, Won H, Bierut LJ, Hyde TM, Kleinman JE, Johnson EO, Hancock DB. Smoking-informed methylation and expression QTLs in human brain and colocalization with smoking-associated genetic loci. medRxiv 2023:2023.09.18.23295431. [PMID: 37790540 PMCID: PMC10543041 DOI: 10.1101/2023.09.18.23295431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Smoking is a leading cause of preventable morbidity and mortality. Smoking is heritable, and genome-wide association studies (GWAS) of smoking behaviors have identified hundreds of significant loci. Most GWAS-identified variants are noncoding with unknown neurobiological effects. We used genome-wide genotype, DNA methylation, and RNA sequencing data in postmortem human nucleus accumbens (NAc) to identify cis-methylation/expression quantitative trait loci (meQTLs/eQTLs), investigate variant-by-cigarette smoking interactions across the genome, and overlay QTL evidence at smoking GWAS-identified loci to evaluate their regulatory potential. Active smokers (N=52) and nonsmokers (N=171) were defined based on cotinine biomarker levels and next-of-kin reporting. We simultaneously tested variant and variant-by-smoking interaction effects on methylation and expression, separately, adjusting for biological and technical covariates and using a two-stage multiple testing approach with eigenMT and Bonferroni corrections. We found >2 million significant meQTL variants (padj<0.05) corresponding to 41,695 unique CpGs. Results were largely driven by main effects; five meQTLs, mapping to NUDT12, FAM53B, RNF39, and ADRA1B, showed a significant interaction with smoking. We found 57,683 significant eQTLs for 958 unique eGenes (padj<0.05) and no smoking interactions. Colocalization analyses identified loci with smoking-associated GWAS variants that overlapped meQTLs/eQTLs, suggesting that these heritable factors may influence smoking behaviors through functional effects on methylation/expression. One locus containing MUSTIN1 and ITIH4 colocalized across all data types (GWAS + meQTL + eQTL). In this first genome-wide meQTL map in the human NAc, the enriched overlap with smoking GWAS-identified genetic loci provides evidence that gene regulation in the brain helps explain the neurobiology of smoking behaviors.
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Affiliation(s)
- Megan Ulmer Carnes
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Bryan C. Quach
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Linran Zhou
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Shizhong Han
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Ran Tao
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Meisha Mandal
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | | | - Jesse A. Marks
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Grier P. Page
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
- Fellow Program, RTI International, Research Triangle Park, North Carolina
| | - Brion S. Maher
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, Maryland
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Laura J. Bierut
- Department of Psychiatry, Washington University in St. Louis, Missouri
| | - Thomas M. Hyde
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
| | - Joel E. Kleinman
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Eric O. Johnson
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
- Fellow Program, RTI International, Research Triangle Park, North Carolina
| | - Dana B. Hancock
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
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12
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Bravo MA, Fang F, Hancock DB, Johnson EO, Harris KM. Long-term air pollution exposure and markers of cardiometabolic health in the National Longitudinal Study of Adolescent to Adult Health (Add Health). Environ Int 2023; 177:107987. [PMID: 37267730 PMCID: PMC10664021 DOI: 10.1016/j.envint.2023.107987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND Air pollution exposure is associated with cardiovascular morbidity and mortality. Although exposure to air pollution early in life may represent a critical window for development of cardiovascular disease risk factors, few studies have examined associations of long-term air pollution exposure with markers of cardiovascular and metabolic health in young adults. OBJECTIVES By combining health data from the National Longitudinal Study of Adolescent to Adult Health (Add Health) with air pollution data from the Fused Air Quality Surface using Downscaling (FAQSD) archive, we: (1) calculated multi-year estimates of exposure to ozone (O3) and particulate matter with an aerodynamic diameter ≤ 2.5 µm (PM2.5) for Add Health participants; and (2) estimated associations between air pollution exposures and multiple markers of cardiometabolic health. METHODS Add Health is a nationally representative longitudinal cohort study of over 20,000 adolescents aged 12-19 in the United States (US) in 1994-95 (Wave I). Participants have been followed through adolescence and into adulthood with five in-home interviews. Estimated daily concentrations of O3 and PM2.5 at census tracts were obtained from the FAQSD archive and used to generate tract-level annual averages of O3 and PM2.5 concentrations. We estimated associations between average O3 and PM2.5 exposures from 2002 to 2007 and markers of cardiometabolic health measured at Wave IV (2008-09), including hypertension, hyperlipidemia, body mass index (BMI), diabetes, C-reactive protein, and metabolic syndrome. RESULTS The final sample size was 11,259 individual participants. The average age of participants at Wave IV was 28.4 years (range: 24-34 years). In models adjusting for age, race/ethnicity, and sex, long-term O3 exposure (2002-07) was associated with elevated odds of hypertension, with an odds ratio (OR) of 1.015 (95% confidence interval [CI]: 1.011, 1.029); obesity (1.022 [1.004, 1.040]); diabetes (1.032 [1.009,1.054]); and metabolic syndrome (1.028 [1.014, 1.041]); PM2.5 exposure (2002-07) was associated with elevated odds of hypertension (1.022 [1.001, 1.045]). CONCLUSION Findings suggest that long-term ambient air pollution exposure, particularly O3 exposure, is associated with cardiometabolic health in early adulthood.
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Affiliation(s)
- Mercedes A Bravo
- Global Health Institute, School of Medicine, Duke University, Durham, NC, USA.
| | - Fang Fang
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Dana B Hancock
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA; Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Kathleen Mullan Harris
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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13
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Abstract
Cigarette smoking has been associated with epigenetic alterations that may be reversible upon cessation. As the most-studied epigenetic modification, DNA methylation is strongly associated with smoking exposure, providing a potential mechanism that links smoking to adverse health outcomes. Here, we reviewed the reversibility of DNA methylation in accessible peripheral tissues, mainly blood, in relation to cigarette smoking cessation and the utility of DNA methylation as a biomarker signature to differentiate current, former, and never smokers and to quantify time since cessation. We summarized thousands of differentially methylated Cytosine-Guanine (CpG) dinucleotides and regions associated with smoking cessation from candidate gene and epigenome-wide association studies, as well as the prediction accuracy of the multi-CpG predictors for smoking status. Overall, there is robust evidence for DNA methylation signature of cigarette smoking cessation. However, there are still gaps to fill, including (1) cell-type heterogeneity in measuring blood DNA methylation; (2) underrepresentation of non-European ancestry populations; (3) limited longitudinal data to quantitatively measure DNA methylation after smoking cessation over time; and (4) limited data to study the impact of smoking cessation on other epigenetic features, noncoding RNAs, and histone modifications. Epigenetic machinery provides promising biomarkers that can improve success in smoking cessation in the clinical setting. To achieve this goal, larger and more-diverse samples with longitudinal measures of a broader spectrum of epigenetic marks will be essential to developing a robust DNA methylation biomarker assay, followed by meeting validation requirements for the assay before being implemented as a clinically useful tool.
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Affiliation(s)
- Fang Fang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA
| | - Allan M. Andersen
- Department of Psychiatry, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
- Behavioral Diagnostics LLC, 2500 Crosspark Rd, Coralville, IA 52241, USA
- Department of Biomedical Engineering, 5601 Seamans Center for the Engineering Arts and Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Dana B. Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA
- Corresponding author. (D.B. Hancock)
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14
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Chen F, Wang X, Jang SK, Quach BC, Weissenkampen JD, Khunsriraksakul C, Yang L, Sauteraud R, Albert CM, Allred NDD, Arnett DK, Ashley-Koch AE, Barnes KC, Barr RG, Becker DM, Bielak LF, Bis JC, Blangero J, Boorgula MP, Chasman DI, Chavan S, Chen YDI, Chuang LM, Correa A, Curran JE, David SP, Fuentes LDL, Deka R, Duggirala R, Faul JD, Garrett ME, Gharib SA, Guo X, Hall ME, Hawley NL, He J, Hobbs BD, Hokanson JE, Hsiung CA, Hwang SJ, Hyde TM, Irvin MR, Jaffe AE, Johnson EO, Kaplan R, Kardia SLR, Kaufman JD, Kelly TN, Kleinman JE, Kooperberg C, Lee IT, Levy D, Lutz SM, Manichaikul AW, Martin LW, Marx O, McGarvey ST, Minster RL, Moll M, Moussa KA, Naseri T, North KE, Oelsner EC, Peralta JM, Peyser PA, Psaty BM, Rafaels N, Raffield LM, Reupena MS, Rich SS, Rotter JI, Schwartz DA, Shadyab AH, Sheu WHH, Sims M, Smith JA, Sun X, Taylor KD, Telen MJ, Watson H, Weeks DE, Weir DR, Yanek LR, Young KA, Young KL, Zhao W, Hancock DB, Jiang B, Vrieze S, Liu DJ. Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing. Nat Genet 2023; 55:291-300. [PMID: 36702996 PMCID: PMC9925385 DOI: 10.1038/s41588-022-01282-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/08/2022] [Indexed: 01/27/2023]
Abstract
Most transcriptome-wide association studies (TWASs) so far focus on European ancestry and lack diversity. To overcome this limitation, we aggregated genome-wide association study (GWAS) summary statistics, whole-genome sequences and expression quantitative trait locus (eQTL) data from diverse ancestries. We developed a new approach, TESLA (multi-ancestry integrative study using an optimal linear combination of association statistics), to integrate an eQTL dataset with a multi-ancestry GWAS. By exploiting shared phenotypic effects between ancestries and accommodating potential effect heterogeneities, TESLA improves power over other TWAS methods. When applied to tobacco use phenotypes, TESLA identified 273 new genes, up to 55% more compared with alternative TWAS methods. These hits and subsequent fine mapping using TESLA point to target genes with biological relevance. In silico drug-repurposing analyses highlight several drugs with known efficacy, including dextromethorphan and galantamine, and new drugs such as muscle relaxants that may be repurposed for treating nicotine addiction.
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Affiliation(s)
- Fang Chen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Xingyan Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Seon-Kyeong Jang
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | | | - J Dylan Weissenkampen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychology, Penn State College of Medicine, Hershey, PA, USA
| | | | - Lina Yang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Renan Sauteraud
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Christine M Albert
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
| | - Kathleen C Barnes
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Diane M Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C Bis
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Meher Preethi Boorgula
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sameer Chavan
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Yii-Der I Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lee-Ming Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Joanne E Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Sean P David
- University of Chicago, Chicago, IL, USA
- NorthShore University Health System, Evanston, IL, USA
| | - Lisa de Las Fuentes
- Department of Medicine, Division of Biostatistics and Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Ranjan Deka
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Jessica D Faul
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Sina A Gharib
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Computational Medicine Core at Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael E Hall
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Nicola L Hawley
- Department of Epidemiology (Chronic Disease), School of Public Health, Yale University, New Haven, CT, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Brian D Hobbs
- Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Chao A Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Shih-Jen Hwang
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Mental Health and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Human Genetics and Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, The Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joel D Kaufman
- Departments of Environmental & Occupational Health Sciences, Medicine, and Epidemiology, University of Washington Seattle, Seattle, WA, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - I-Te Lee
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Daniel Levy
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon M Lutz
- Department of Population Medicine, Harvard Pilgrim Health Care, Boston, MA, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Lisa W Martin
- Division of Cardiology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Olivia Marx
- Department of Biomedical Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Stephen T McGarvey
- Department of Epidemiology, International Health Institute, Brown University School of Public Health, Providence, RI, USA
| | - Ryan L Minster
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew Moll
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Karine A Moussa
- Penn State Huck Institutes of Life Sciences, Penn State College of Medicine, University Park, PA, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth C Oelsner
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Juan M Peralta
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M Psaty
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Mario Sims
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J Telen
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Harold Watson
- Faculty of Medical Sciences, University of the West Indies, Cave Hill Campus, Barbados
| | - Daniel E Weeks
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - David R Weir
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA.
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
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15
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Patchen BK, Balte P, Bartz TM, Barr RG, Fornage M, Graff M, Jacobs DR, Kalhan R, Lemaitre RN, O'Connor G, Psaty B, Seo J, Tsai MY, Wood AC, Xu H, Zhang J, Gharib SA, Manichaikul A, North K, Steffen LM, Dupuis J, Oelsner E, Hancock DB, Cassano PA. Investigating associations of omega-3 fatty acids, lung function decline, and airway obstruction. medRxiv 2023:2023.01.18.23284671. [PMID: 36711663 PMCID: PMC9882557 DOI: 10.1101/2023.01.18.23284671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Rationale Inflammation contributes to lung function decline and the development of chronic obstructive pulmonary disease. Omega-3 fatty acids have anti-inflammatory properties and may benefit lung health. Objectives Investigate associations of omega-3 fatty acids with lung function decline and incident airway obstruction in adults of diverse races/ethnicities from general population cohorts. Methods Complementary study designs: (1) longitudinal study of plasma phospholipid omega-3 fatty acids and repeated FEV 1 and FVC measures in the National Heart, Lung, and Blood Institute Pooled Cohorts Study, and (2) two-sample Mendelian Randomization (MR) study of genetically predicted omega-3 fatty acids and lung function parameters. Measurements and Main Results The longitudinal study found that higher omega-3 fatty acid concentrations were associated with attenuated lung function decline in 15,063 participants, with the largest effect sizes for docosahexaenoic acid (DHA). One standard deviation higher DHA was associated with an attenuation of 1.8 mL/year for FEV 1 (95% confidence interval [CI] 1.3-2.2) and 2.4 mL/year for FVC (95% CI 1.9-3.0). One standard deviation higher DHA was also associated with a 9% lower incidence of spirometry-defined airway obstruction (95% CI 0.86-0.97). DHA associations persisted across sexes, smoking histories, and Black, white and Hispanic participants, with the largest magnitude associations in former smokers and Hispanics. The MR study showed positive associations of genetically predicted omega-3 fatty acids with FEV 1 and FVC, with statistically significant findings across multiple MR methods. Conclusions The longitudinal and MR studies provide evidence supporting beneficial effects of higher circulating omega-3 fatty acids, especially DHA, on lung health.
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Affiliation(s)
- Bonnie K Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Palavi Balte
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, Health Systems and Population Health, University of Washington, Seattle, WA
| | - R Graham Barr
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, TX
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - David R Jacobs
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, Health Systems and Population Health, University of Washington, Seattle, WA
| | | | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, Health Systems and Population Health, University of Washington, Seattle, WA
| | - Jungkyun Seo
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Alexis C Wood
- USDA/ARS Children's Nutrition Research Center, Houston, TX
| | - Hanfei Xu
- Boston University School of Public Health, Boston, MA
| | - Jingwen Zhang
- Boston University School of Public Health, Boston, MA
| | - Sina A Gharib
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Kari North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - Lyn M Steffen
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN
| | - Josée Dupuis
- Boston University School of Public Health, Boston, MA
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montréal, Québec
| | - Elizabeth Oelsner
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | | | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY
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16
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Saunders GRB, Wang X, Chen F, Jang SK, Liu M, Wang C, Gao S, Jiang Y, Khunsriraksakul C, Otto JM, Addison C, Akiyama M, Albert CM, Aliev F, Alonso A, Arnett DK, Ashley-Koch AE, Ashrani AA, Barnes KC, Barr RG, Bartz TM, Becker DM, Bielak LF, Benjamin EJ, Bis JC, Bjornsdottir G, Blangero J, Bleecker ER, Boardman JD, Boerwinkle E, Boomsma DI, Boorgula MP, Bowden DW, Brody JA, Cade BE, Chasman DI, Chavan S, Chen YDI, Chen Z, Cheng I, Cho MH, Choquet H, Cole JW, Cornelis MC, Cucca F, Curran JE, de Andrade M, Dick DM, Docherty AR, Duggirala R, Eaton CB, Ehringer MA, Esko T, Faul JD, Fernandes Silva L, Fiorillo E, Fornage M, Freedman BI, Gabrielsen ME, Garrett ME, Gharib SA, Gieger C, Gillespie N, Glahn DC, Gordon SD, Gu CC, Gu D, Gudbjartsson DF, Guo X, Haessler J, Hall ME, Haller T, Harris KM, He J, Herd P, Hewitt JK, Hickie I, Hidalgo B, Hokanson JE, Hopfer C, Hottenga J, Hou L, Huang H, Hung YJ, Hunter DJ, Hveem K, Hwang SJ, Hwu CM, Iacono W, Irvin MR, Jee YH, Johnson EO, Joo YY, Jorgenson E, Justice AE, Kamatani Y, Kaplan RC, Kaprio J, Kardia SLR, Keller MC, Kelly TN, Kooperberg C, Korhonen T, Kraft P, Krauter K, Kuusisto J, Laakso M, Lasky-Su J, Lee WJ, Lee JJ, Levy D, Li L, Li K, Li Y, Lin K, Lind PA, Liu C, Lloyd-Jones DM, Lutz SM, Ma J, Mägi R, Manichaikul A, Martin NG, Mathur R, Matoba N, McArdle PF, McGue M, McQueen MB, Medland SE, Metspalu A, Meyers DA, Millwood IY, Mitchell BD, Mohlke KL, Moll M, Montasser ME, Morrison AC, Mulas A, Nielsen JB, North KE, Oelsner EC, Okada Y, Orrù V, Palmer ND, Palviainen T, Pandit A, Park SL, Peters U, Peters A, Peyser PA, Polderman TJC, Rafaels N, Redline S, Reed RM, Reiner AP, Rice JP, Rich SS, Richmond NE, Roan C, Rotter JI, Rueschman MN, Runarsdottir V, Saccone NL, Schwartz DA, Shadyab AH, Shi J, Shringarpure SS, Sicinski K, Skogholt AH, Smith JA, Smith NL, Sotoodehnia N, Stallings MC, Stefansson H, Stefansson K, Stitzel JA, Sun X, Syed M, Tal-Singer R, Taylor AE, Taylor KD, Telen MJ, Thai KK, Tiwari H, Turman C, Tyrfingsson T, Wall TL, Walters RG, Weir DR, Weiss ST, White WB, Whitfield JB, Wiggins KL, Willemsen G, Willer CJ, Winsvold BS, Xu H, Yanek LR, Yin J, Young KL, Young KA, Yu B, Zhao W, Zhou W, Zöllner S, Zuccolo L, Batini C, Bergen AW, Bierut LJ, David SP, Gagliano Taliun SA, Hancock DB, Jiang B, Munafò MR, Thorgeirsson TE, Liu DJ, Vrieze S. Genetic diversity fuels gene discovery for tobacco and alcohol use. Nature 2022; 612:720-724. [PMID: 36477530 PMCID: PMC9771818 DOI: 10.1038/s41586-022-05477-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 10/25/2022] [Indexed: 12/12/2022]
Abstract
Tobacco and alcohol use are heritable behaviours associated with 15% and 5.3% of worldwide deaths, respectively, due largely to broad increased risk for disease and injury1-4. These substances are used across the globe, yet genome-wide association studies have focused largely on individuals of European ancestries5. Here we leveraged global genetic diversity across 3.4 million individuals from four major clines of global ancestry (approximately 21% non-European) to power the discovery and fine-mapping of genomic loci associated with tobacco and alcohol use, to inform function of these loci via ancestry-aware transcriptome-wide association studies, and to evaluate the genetic architecture and predictive power of polygenic risk within and across populations. We found that increases in sample size and genetic diversity improved locus identification and fine-mapping resolution, and that a large majority of the 3,823 associated variants (from 2,143 loci) showed consistent effect sizes across ancestry dimensions. However, polygenic risk scores developed in one ancestry performed poorly in others, highlighting the continued need to increase sample sizes of diverse ancestries to realize any potential benefit of polygenic prediction.
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Affiliation(s)
| | - Xingyan Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Fang Chen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Seon-Kyeong Jang
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Chen Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Shuang Gao
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Yu Jiang
- Department of Epidemiology & Population Health at Stanford University, Stanford, CA, USA
| | | | - Jacqueline M Otto
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Clifton Addison
- Jackson Heart Study (JHS) Graduate Training and Education Center (GTEC), Department of Epidemiology and Biostatistics, School of Public Health, Jackson State University, Jackson, MS, USA
| | - Masato Akiyama
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Ocular Pathology and Imaging Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Christine M Albert
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Fazil Aliev
- Department of Psychiatry, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Donna K Arnett
- Dean's Office and Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Allison E Ashley-Koch
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Aneel A Ashrani
- Division of Hematology, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Tempus, Chicago, IL, USA
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Diane M Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Emelia J Benjamin
- Department of Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | | | - Jason D Boardman
- Institute of Behavioral Science, University of Colorado Boulder, Boulder, CO, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dorret I Boomsma
- Netherlands Twin Register, Dept Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sameer Chavan
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Iona Cheng
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Hélène Choquet
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
| | - John W Cole
- Department of Neurology, Baltimore Veterans Affairs Medical Center, Baltimore, MD, USA
- Division of Vascular Neurology, Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marilyn C Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Mariza de Andrade
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Danielle M Dick
- Department of Psychiatry, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Anna R Docherty
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Virginia, USA
- Huntsman Mental Health Institute, Salt Lake City, UT, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Charles B Eaton
- Department of Family Medicine, Brown University, Providence, RI, USA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Lilian Fernandes Silva
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Barry I Freedman
- Department of Internal Medicine-Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Melanie E Garrett
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Center for Lung Biology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nathan Gillespie
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Virginia, USA
| | - David C Glahn
- Department of Psychiatry & Behavioral Sciences, Boston Children's Hospital & Harvard Medical School, Boston, MA, USA
| | - Scott D Gordon
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Charles C Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Dongfeng Gu
- Department of Epidemiology and Key Laboratory of Cardiovascular Epidemiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeffrey Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael E Hall
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Toomas Haller
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kathleen Mullan Harris
- Department of Sociology and the Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jiang He
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
- Translational Sciences Institute, Tulane University, New Orleans, LA, USA
| | - Pamela Herd
- McCourt School of Public Policy, Georgetown University, Washington, DC, USA
| | - John K Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department Of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Ian Hickie
- Youth Mental Health & Technology Team, Brain and Mind Centre, University of Sydney, Sydney, Australia
| | - Bertha Hidalgo
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Christian Hopfer
- Department of Psychiatry, University of Colorado Anschutz Medical Center, Denver, CO, USA
| | - JoukeJan Hottenga
- Netherlands Twin Register, Dept Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hongyan Huang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - David J Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Center, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Research, Innovation and Education, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Shih-Jen Hwang
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - William Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yon Ho Jee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Yoonjung Y Joo
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Institute of Data Science, Korea University, Seoul, South Korea
| | | | - Anne E Justice
- Department of Population Health Sciences, Geisinger, Danville, PA, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Robert C Kaplan
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland - FIMM, University of Helsinki, Helsinki, Finland
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Matthew C Keller
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department Of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
- Translational Sciences Institute, Tulane University, New Orleans, LA, USA
| | - Charles Kooperberg
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tellervo Korhonen
- Institute for Molecular Medicine Finland - FIMM, University of Helsinki, Helsinki, Finland
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kenneth Krauter
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
- Center for Medicine and Clinical Research, Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Jessica Lasky-Su
- Brigham and Women's Hospital, Department of Medicine, Channing Division of Network Medicine, Boston, MA, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung City, Taiwan
| | - James J Lee
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Kevin Li
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Yuqing Li
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
| | - Kuang Lin
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Penelope A Lind
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Donald M Lloyd-Jones
- Departments of Preventive Medicine, Medicine, and Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sharon M Lutz
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Department of Biostatics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jiantao Ma
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Nutrition Epidemiology and Data Science, Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Reedik Mägi
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Ravi Mathur
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Nana Matoba
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genetics, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick F McArdle
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Sarah E Medland
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | | | - Iona Y Millwood
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew Moll
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Jonas B Nielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth C Oelsner
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Yukinori Okada
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland - FIMM, University of Helsinki, Helsinki, Finland
| | - Anita Pandit
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - S Lani Park
- Population Sciences of the Pacific Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig Maximilians University Munich, Munich, Germany
- German Centre for Cardiovascular Research, DZHK, Partner Site Munich, Munich, Germany
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tinca J C Polderman
- Department of Clinical Developmental Psychology, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Amsterdam UMC, Amsterdam, The Netherlands
| | - Nicholas Rafaels
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert M Reed
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - John P Rice
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Nicole E Richmond
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Carol Roan
- Center for Demography of Health and Aging, University of Wisconsin-Madison, Madison, WI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael N Rueschman
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Nancy L Saccone
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - David A Schwartz
- Division of Pulmonary Sciences and Critical Care Medicine; Department of Medicine and Immunology, University of Colorado, Aurora, CO, USA
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Kamil Sicinski
- Center for Demography of Health and Aging, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne Heidi Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael C Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department Of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jerry A Stitzel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Xiao Sun
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - Moin Syed
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | | | - Amy E Taylor
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
- National Institute for Health Research Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J Telen
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University School of Medicine, Durham, NC, USA
| | - Khanh K Thai
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
| | - Hemant Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Tamara L Wall
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Scott T Weiss
- Brigham and Women's Hospital, Department of Medicine, Channing Division of Network Medicine, Boston, MA, USA
| | - Wendy B White
- Jackson Heart Study Undergraduate Training and Education Center, Tougaloo College, Tougaloo, MS, USA
| | - John B Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kerri L Wiggins
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Gonneke Willemsen
- Netherlands Twin Register, Dept Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Bendik S Winsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Huichun Xu
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jie Yin
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bing Yu
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Luisa Zuccolo
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Health Data Science Centre, Fondazione Human Technopole, Milan, Italy
| | - Chiara Batini
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Andrew W Bergen
- Oregon Research Institute, Springfield, OR, USA
- BioRealm, LLC, Walnut, CA, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean P David
- Outcomes Research Network & Department of Family Medicine, NorthShore University HealthSystem, Evanston, IL, USA
- Department of Family Medicine, University of Chicago, Chicago, IL, USA
| | - Sarah A Gagliano Taliun
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- Department of Neurosciences, Université de Montréal, Montréal, Québec, Canada
- Research Centre, Montréal Heart Institute, Montréal, Québec, Canada
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
- National Institute for Health Research Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
- School of Psychological Science, University of Bristol, Bristol, UK
| | | | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA.
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Barr PB, Driver MN, Kuo SIC, Stephenson M, Aliev F, Linnér RK, Marks J, Anokhin AP, Bucholz K, Chan G, Edenberg HJ, Edwards AC, Francis MW, Hancock DB, Harden KP, Kamarajan C, Kaprio J, Kinreich S, Kramer JR, Kuperman S, Latvala A, Meyers JL, Palmer AA, Plawecki MH, Porjesz B, Rose RJ, Schuckit MA, Salvatore JE, Dick DM. Clinical, environmental, and genetic risk factors for substance use disorders: characterizing combined effects across multiple cohorts. Mol Psychiatry 2022; 27:4633-4641. [PMID: 36195638 PMCID: PMC9938102 DOI: 10.1038/s41380-022-01801-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Substance use disorders (SUDs) incur serious social and personal costs. The risk for SUDs is complex, with risk factors ranging from social conditions to individual genetic variation. We examined whether models that include a clinical/environmental risk index (CERI) and polygenic scores (PGS) are able to identify individuals at increased risk of SUD in young adulthood across four longitudinal cohorts for a combined sample of N = 15,134. Our analyses included participants of European (NEUR = 12,659) and African (NAFR = 2475) ancestries. SUD outcomes included: (1) alcohol dependence, (2) nicotine dependence; (3) drug dependence, and (4) any substance dependence. In the models containing the PGS and CERI, the CERI was associated with all three outcomes (ORs = 01.37-1.67). PGS for problematic alcohol use, externalizing, and smoking quantity were associated with alcohol dependence, drug dependence, and nicotine dependence, respectively (OR = 1.11-1.33). PGS for problematic alcohol use and externalizing were also associated with any substance dependence (ORs = 1.09-1.18). The full model explained 6-13% of the variance in SUDs. Those in the top 10% of CERI and PGS had relative risk ratios of 3.86-8.04 for each SUD relative to the bottom 90%. Overall, the combined measures of clinical, environmental, and genetic risk demonstrated modest ability to distinguish between affected and unaffected individuals in young adulthood. PGS were significant but added little in addition to the clinical/environmental risk index. Results from our analysis demonstrate there is still considerable work to be done before tools such as these are ready for clinical applications.
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Affiliation(s)
- Peter B Barr
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA.
- VA New York Harbor Healthcare System, Brooklyn, NY, USA.
| | - Morgan N Driver
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Sally I-Chun Kuo
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Mallory Stephenson
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Fazil Aliev
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
- Rutgers Addiction Research Center, Rutgers University, Piscataway, NJ, USA
| | | | - Jesse Marks
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Durham, NC, USA
| | - Andrey P Anokhin
- Department of Psychiatry, School of Medicine, Washington University in St. Louis, St Louis, MO, USA
| | - Kathleen Bucholz
- Department of Psychiatry, School of Medicine, Washington University in St. Louis, St Louis, MO, USA
| | - Grace Chan
- Department of Psychiatry, School of Medicine, University of Connecticut, Farmington, CT, USA
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Alexis C Edwards
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Meredith W Francis
- Department of Psychiatry, School of Medicine, Washington University in St. Louis, St Louis, MO, USA
| | - Dana B Hancock
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Durham, NC, USA
| | - K Paige Harden
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
- Population Research Center, University of Texas at Austin, Austin, TX, USA
| | - Chella Kamarajan
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Sivan Kinreich
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - John R Kramer
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Samuel Kuperman
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Antti Latvala
- Institute of Criminology and Legal Policy, University of Helsinki, Helsinki, Finland
| | - Jacquelyn L Meyers
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
- VA New York Harbor Healthcare System, Brooklyn, NY, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Martin H Plawecki
- Department of Psychiatry, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Richard J Rose
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Marc A Schuckit
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jessica E Salvatore
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Danielle M Dick
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
- Rutgers Addiction Research Center, Rutgers University, Piscataway, NJ, USA
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Gaddis N, Mathur R, Marks J, Zhou L, Quach B, Waldrop A, Levran O, Agrawal A, Randesi M, Adelson M, Jeffries PW, Martin NG, Degenhardt L, Montgomery GW, Wetherill L, Lai D, Bucholz K, Foroud T, Porjesz B, Runarsdottir V, Tyrfingsson T, Einarsson G, Gudbjartsson DF, Webb BT, Crist RC, Kranzler HR, Sherva R, Zhou H, Hulse G, Wildenauer D, Kelty E, Attia J, Holliday EG, McEvoy M, Scott RJ, Schwab SG, Maher BS, Gruza R, Kreek MJ, Nelson EC, Thorgeirsson T, Stefansson K, Berrettini WH, Gelernter J, Edenberg HJ, Bierut L, Hancock DB, Johnson EO. Multi-trait genome-wide association study of opioid addiction: OPRM1 and beyond. Sci Rep 2022; 12:16873. [PMID: 36207451 PMCID: PMC9546890 DOI: 10.1038/s41598-022-21003-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/21/2022] [Indexed: 12/02/2022] Open
Abstract
Opioid addiction (OA) is moderately heritable, yet only rs1799971, the A118G variant in OPRM1, has been identified as a genome-wide significant association with OA and independently replicated. We applied genomic structural equation modeling to conduct a GWAS of the new Genetics of Opioid Addiction Consortium (GENOA) data together with published studies (Psychiatric Genomics Consortium, Million Veteran Program, and Partners Health), comprising 23,367 cases and effective sample size of 88,114 individuals of European ancestry. Genetic correlations among the various OA phenotypes were uniformly high (rg > 0.9). We observed the strongest evidence to date for OPRM1: lead SNP rs9478500 (p = 2.56 × 10-9). Gene-based analyses identified novel genome-wide significant associations with PPP6C and FURIN. Variants within these loci appear to be pleiotropic for addiction and related traits.
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Affiliation(s)
- Nathan Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Ravi Mathur
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Jesse Marks
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Linran Zhou
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Bryan Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Alex Waldrop
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Orna Levran
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew Randesi
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY, USA
| | - Miriam Adelson
- Dr. Miriam and Sheldon G. Adelson Clinic for Drug Abuse, Treatment and Research, Las Vegas, NV, USA
| | - Paul W Jeffries
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre, University of New South Wales, Randwick, NSW, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Leah Wetherill
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dongbing Lai
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathleen Bucholz
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Tatiana Foroud
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bernice Porjesz
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | | | | | | | | | - Bradley Todd Webb
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Richard C Crist
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard Sherva
- Genome Science Institute, Boston University, Boston, MA, USA
| | - Hang Zhou
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA
| | - Gary Hulse
- School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, WA, Australia
| | - Dieter Wildenauer
- School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, WA, Australia
| | - Erin Kelty
- School of Population and Global Health, Population and Public Health, The University of Western Australia, Perth, WA, Australia
| | - John Attia
- Hunter Medical Research Institute, Newcastle, Australia
| | - Elizabeth G Holliday
- Hunter Medical Research Institute, Newcastle, Australia
- School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | - Mark McEvoy
- Hunter Medical Research Institute, Newcastle, Australia
- School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy College of Health, Medicine and Wellbeing, The University of Newcastle, New Lambton Heights, NSW, Australia
| | - Sibylle G Schwab
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Brion S Maher
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Richard Gruza
- Department of Family and Community Medicine, Saint Louis University, Saint Louis, MO, USA
| | - Mary Jeanne Kreek
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY, USA
| | - Elliot C Nelson
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reyjavik, Iceland
| | - Wade H Berrettini
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Joel Gelernter
- Department of Psychiatry, Genetics, & Neuroscience, Yale University School of Medicine, West Haven, CT, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Laura Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric Otto Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.
- Fellow Program, RTI International, Research Triangle Park, NC, USA.
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Sey NYA, Hu B, Iskhakova M, Lee S, Sun H, Shokrian N, Ben Hutta G, Marks JA, Quach BC, Johnson EO, Hancock DB, Akbarian S, Won H. Correction: Chromatin architecture in addiction circuitry identifies risk genes and potential biological mechanisms underlying cigarette smoking and alcohol use traits. Mol Psychiatry 2022; 27:4368. [PMID: 35794187 DOI: 10.1038/s41380-022-01678-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nancy Y A Sey
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Benxia Hu
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Marina Iskhakova
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sool Lee
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Huaigu Sun
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Neda Shokrian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriella Ben Hutta
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jesse A Marks
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Bryan C Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
- Fellow Program, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Hyejung Won
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
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Mathur R, Fang F, Gaddis N, Hancock DB, Cho MH, Hokanson JE, Bierut LJ, Lutz SM, Young K, Smith AV, Silverman EK, Page GP, Johnson EO. GAWMerge expands GWAS sample size and diversity by combining array-based genotyping and whole-genome sequencing. Commun Biol 2022; 5:806. [PMID: 35953715 PMCID: PMC9372058 DOI: 10.1038/s42003-022-03738-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Genome-wide association studies (GWAS) have made impactful discoveries for complex diseases, often by amassing very large sample sizes. Yet, GWAS of many diseases remain underpowered, especially for non-European ancestries. One cost-effective approach to increase sample size is to combine existing cohorts, which may have limited sample size or be case-only, with public controls, but this approach is limited by the need for a large overlap in variants across genotyping arrays and the scarcity of non-European controls. We developed and validated a protocol, Genotyping Array-WGS Merge (GAWMerge), for combining genotypes from arrays and whole-genome sequencing, ensuring complete variant overlap, and allowing for diverse samples like Trans-Omics for Precision Medicine to be used. Our protocol involves phasing, imputation, and filtering. We illustrated its ability to control technology driven artifacts and type-I error, as well as recover known disease-associated signals across technologies, independent datasets, and ancestries in smoking-related cohorts. GAWMerge enables genetic studies to leverage existing cohorts to validly increase sample size and enhance discovery for understudied traits and ancestries.
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Affiliation(s)
- Ravi Mathur
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Fang Fang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Nathan Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA, USA
| | - Kendra Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Albert V Smith
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Grier P Page
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA.
- Fellow Program, RTI International, Research Triangle Park, NC, USA.
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21
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Sey NYA, Hu B, Iskhakova M, Lee S, Sun H, Shokrian N, Ben Hutta G, Marks JA, Quach BC, Johnson EO, Hancock DB, Akbarian S, Won H. Chromatin architecture in addiction circuitry identifies risk genes and potential biological mechanisms underlying cigarette smoking and alcohol use traits. Mol Psychiatry 2022; 27:3085-3094. [PMID: 35422469 PMCID: PMC9853312 DOI: 10.1038/s41380-022-01558-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 03/21/2022] [Accepted: 03/30/2022] [Indexed: 01/25/2023]
Abstract
Cigarette smoking and alcohol use are among the most prevalent substances used worldwide and account for a substantial proportion of preventable morbidity and mortality, underscoring the public health significance of understanding their etiology. Genome-wide association studies (GWAS) have successfully identified genetic variants associated with cigarette smoking and alcohol use traits. However, the vast majority of risk variants reside in non-coding regions of the genome, and their target genes and neurobiological mechanisms are unknown. Chromosomal conformation mappings can address this knowledge gap by charting the interaction profiles of risk-associated regulatory variants with target genes. To investigate the functional impact of common variants associated with cigarette smoking and alcohol use traits, we applied Hi-C coupled MAGMA (H-MAGMA) built upon cortical and newly generated midbrain dopaminergic neuronal Hi-C datasets to GWAS summary statistics of nicotine dependence, cigarettes per day, problematic alcohol use, and drinks per week. The identified risk genes mapped to key pathways associated with cigarette smoking and alcohol use traits, including drug metabolic processes and neuronal apoptosis. Risk genes were highly expressed in cortical glutamatergic, midbrain dopaminergic, GABAergic, and serotonergic neurons, suggesting them as relevant cell types in understanding the mechanisms by which genetic risk factors influence cigarette smoking and alcohol use. Lastly, we identified pleiotropic genes between cigarette smoking and alcohol use traits under the assumption that they may reveal substance-agnostic, shared neurobiological mechanisms of addiction. The number of pleiotropic genes was ~26-fold higher in dopaminergic neurons than in cortical neurons, emphasizing the critical role of ascending dopaminergic pathways in mediating general addiction phenotypes. Collectively, brain region- and neuronal subtype-specific 3D genome architecture helps refine neurobiological hypotheses for smoking, alcohol, and general addiction phenotypes by linking genetic risk factors to their target genes.
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Affiliation(s)
- Nancy Y A Sey
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Benxia Hu
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Marina Iskhakova
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sool Lee
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Huaigu Sun
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Neda Shokrian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriella Ben Hutta
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jesse A Marks
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Bryan C Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
- Fellow Program, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Hyejung Won
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
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Xu J, Guertin KA, Gaddis NC, Agler AH, Parker RS, Feldman JM, Kristal AR, Arnold KB, Goodman PJ, Tangen CM, Hancock DB, Cassano PA. Change in plasma α-tocopherol associations with attenuated pulmonary function decline and with CYP4F2 missense variation. Am J Clin Nutr 2022; 115:1205-1216. [PMID: 35040869 PMCID: PMC8970985 DOI: 10.1093/ajcn/nqac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/14/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Vitamin E (vitE) is hypothesized to attenuate age-related decline in pulmonary function. OBJECTIVES We investigated the association between change in plasma vitE (∆vitE) and pulmonary function decline [forced expiratory volume in the first second (FEV1)] and examined genetic and nongenetic factors associated with ∆vitE. METHODS We studied 1144 men randomly assigned to vitE in SELECT (Selenium and Vitamin E Cancer Prevention Trial). ∆vitE was the difference between baseline and year 3 vitE concentrations measured with GC-MS. FEV1 was measured longitudinally by spirometry. We genotyped 555 men (vitE-only arm) using the Illumina Expanded Multi-Ethnic Genotyping Array (MEGAex). We used mixed-effects linear regression modeling to examine the ∆vitE-FEV1 association. RESULTS Higher ∆vitE was associated with lower baseline α-tocopherol (α-TOH), higher baseline γ-tocopherol, higher baseline free cholesterol, European ancestry (as opposed to African) (all P < 0.05), and the minor allele of a missense variant in cytochrome P450 family 4 subfamily F member 2 (CYP4F2) (rs2108622-T; 2.4 µmol/L higher ∆vitE, SE: 0.8 µmol/L; P = 0.0032). Higher ∆vitE was associated with attenuated FEV1 decline, with stronger effects in adherent participants (≥80% of supplements consumed): a statistically significant ∆vitE × time interaction (P = 0.014) indicated that a 1-unit increase in ∆vitE was associated with a 2.2-mL/y attenuation in FEV1 decline (SE: 0.9 mL/y). The effect size for 1 SD higher ∆vitE (+4 µmol/mmol free-cholesterol-adjusted α-TOH) was roughly one-quarter of the effect of 1 y of aging, but in the opposite direction. The ∆vitE-FEV1 association was similar in never smokers (2.4-mL/y attenuated FEV1 decline, SE: 1.0 mL/y; P = 0.017, n = 364), and current smokers (2.8-mL/y, SE: 1.6 mL/y; P = 0.079, n = 214), but there was little to no effect in former smokers (-0.64-mL/y, SE: 0.9 mL/y; P = 0.45, n = 564). CONCLUSIONS Greater response to vitE supplementation was associated with attenuated FEV1 decline. The response to supplementation differed by rs2108622 such that individuals with the C allele, compared with the T allele, may need a higher dietary intake to reach the same plasma vitE concentration.
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Affiliation(s)
- Jiayi Xu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristin A Guertin
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Department of Public Health Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Nathan C Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Anne H Agler
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Abbott, Columbus, OH, USA
| | - Robert S Parker
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Jared M Feldman
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Alan R Kristal
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | | | | | | | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Division of Epidemiology, Department of Population Health Sciences, Weill Cornell Medical College, New York, NY, USA
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Affiliation(s)
- Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, North Carolina
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Bray MJ, Chen LS, Fox L, Ma Y, Grucza RA, Hartz SM, Culverhouse RC, Saccone NL, Hancock DB, Johnson EO, McKay JD, Baker TB, Bierut LJ. Studying the Utility of Using Genetics to Predict Smoking-Related Outcomes in a Population-Based Study and a Selected Cohort. Nicotine Tob Res 2021; 23:2110-2116. [PMID: 33991188 PMCID: PMC8570670 DOI: 10.1093/ntr/ntab100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/10/2021] [Indexed: 01/20/2023]
Abstract
INTRODUCTION The purpose of this study is to examine the predictive utility of polygenic risk scores (PRSs) for smoking behaviors. AIMS AND METHODS Using summary statistics from the Sequencing Consortium of Alcohol and Nicotine use consortium, we generated PRSs of ever smoking, age of smoking initiation, cigarettes smoked per day, and smoking cessation for participants in the population-based Atherosclerosis Risk in Communities (ARIC) study (N = 8638), and the Collaborative Genetic Study of Nicotine Dependence (COGEND) (N = 1935). The outcomes were ever smoking, age of smoking initiation, heaviness of smoking, and smoking cessation. RESULTS In the European ancestry cohorts, each PRS was significantly associated with the corresponding smoking behavior outcome. In the ARIC cohort, the PRS z-score for ever smoking predicted smoking (odds ratio [OR]: 1.37; 95% confidence interval [CI]: 1.31, 1.43); the PRS z-score for age of smoking initiation was associated with age of smoking initiation (OR: 0.87; 95% CI: 0.82, 0.92); the PRS z-score for cigarettes per day was associated with heavier smoking (OR: 1.17; 95% CI: 1.11, 1.25); and the PRS z-score for smoking cessation predicted successful cessation (OR: 1.24; 95% CI: 1.17, 1.32). In the African ancestry cohort, the PRSs did not predict smoking behaviors. CONCLUSIONS Smoking-related PRSs were associated with smoking-related behaviors in European ancestry populations. This improvement in prediction is greatest in the lowest and highest genetic risk categories. The lack of prediction in African ancestry populations highlights the urgent need to increase diversity in research so that scientific advances can be applied to populations other than those of European ancestry. IMPLICATIONS This study shows that including both genetic ancestry and PRSs in a single model increases the ability to predict smoking behaviors compared with the model including only demographic characteristics. This finding is observed for every smoking-related outcome. Even though adding genetics is more predictive, the demographics alone confer substantial and meaningful predictive power. However, with increasing work in PRSs, the predictive ability will continue to improve.
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Affiliation(s)
- Michael J Bray
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- The Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Louis Fox
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Yinjiao Ma
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard A Grucza
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Sarah M Hartz
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert C Culverhouse
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Nancy L Saccone
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - James D McKay
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Timothy B Baker
- Department of Medicine, Center for Tobacco Research and Intervention, University of Wisconsin, School of Medicine and Public Health, Madison, WI, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- The Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
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Evans LM, Jang S, Hancock DB, Ehringer MA, Otto JM, Vrieze SI, Keller MC. Genetic architecture of four smoking behaviors using partitioned SNP heritability. Addiction 2021; 116:2498-2508. [PMID: 33620764 PMCID: PMC8759147 DOI: 10.1111/add.15450] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/08/2020] [Accepted: 02/02/2021] [Indexed: 01/23/2023]
Abstract
BACKGROUND AND AIMS Although genome-wide association studies have identified many loci that influence smoking behaviors, much of the genetic variance remains unexplained. We characterized the genetic architecture of four smoking behaviors using single nucleotide polymorphism (SNP) heritability (h2SNP ). This is an estimate of narrow-sense heritability specifically estimating the proportion of phenotypic variation due to causal variants (CVs) tagged by SNPs. DESIGN Partitioned h2SNP analysis of smoking behavior traits. SETTING UK Biobank. PARTICIPANTS UK Biobank participants of European ancestry. The number of participants varied depending on the trait, from 54 792 to 323 068. MEASUREMENTS Smoking initiation, age of initiation, cigarettes per day (CPD; count, log-transformed, binned and dichotomized into heavy versus light) and smoking cessation with imputed genome-wide SNPs. FINDINGS We estimated that, in aggregate, approximately 18% of the phenotypic variance in smoking initiation was captured by imputed SNPs [h2SNP = 0.18, standard error (SE) = 0.01] and 12% [SE = 0.02] for smoking cessation, both of which were more than twice the previously reported estimates. Estimated age of initiation (h2SNP = 0.05, SE = 0.01) and binned CPD (h2SNP = 0.1, SE = 0.01) were substantially below published twin-based h2 of 50%. CPD encoding influenced estimates, with dichotomized CPD h2SNP = 0.28. There was no evidence of dominance genetic variance for any trait. CONCLUSION A biobank study of smoking behavior traits suggested that the phenotypic variance explained by SNPs of smoking initiation, age of initiation, cigarettes per day and smoking cessation is modest overall.
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Affiliation(s)
- Luke M. Evans
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Seonkyeong Jang
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Dana B. Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Marissa A. Ehringer
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA,Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | | | - Scott I. Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Matthew C. Keller
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA,Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
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Patchen BK, Clark AG, Gaddis N, Hancock DB, Cassano PA. Genetically predicted serum vitamin D and COVID-19: a Mendelian randomisation study. BMJ Nutr Prev Health 2021; 4:213-225. [PMID: 34308129 PMCID: PMC8098235 DOI: 10.1136/bmjnph-2021-000255] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES To investigate causality of the association of serum vitamin D with the risk and severity of COVID-19 infection. DESIGN Two-sample Mendelian randomisation study. SETTING Summary data from genome-wide analyses in the population-based UK Biobank and SUNLIGHT Consortium, applied to meta-analysed results of genome-wide analyses in the COVID-19 Host Genetics Initiative. PARTICIPANTS 17 965 COVID-19 cases including 11 085 laboratory or physician-confirmed cases, 7885 hospitalised cases and 4336 severe respiratory cases, and 1 370 547 controls, primarily of European ancestry. EXPOSURES Genetically predicted variation in serum vitamin D status, instrumented by genome-wide significant single nucleotide polymorphisms (SNPs) associated with serum vitamin D or risk of vitamin D deficiency/insufficiency. MAIN OUTCOME MEASURES Susceptibility to and severity of COVID-19 infection, including severe respiratory infection and hospitalisation. RESULTS Mendelian randomisation analysis, sufficiently powered to detect effects comparable to those seen in observational studies, provided little to no evidence for an effect of genetically predicted serum vitamin D on susceptibility to or severity of COVID-19 infection. Using SNPs in loci related to vitamin D metabolism as genetic instruments for serum vitamin D concentrations, the OR per SD higher serum vitamin D was 1.04 (95% CI 0.92 to 1.18) for any COVID-19 infection versus population controls, 1.05 (0.84 to 1.31) for hospitalised COVID-19 versus population controls, 0.96 (0.64 to 1.43) for severe respiratory COVID-19 versus population controls, 1.15 (0.99 to 1.35) for COVID-19 positive versus COVID-19 negative and 1.44 (0.75 to 2.78) for hospitalised COVID-19 versus non-hospitalised COVID-19. Results were similar in analyses using SNPs with genome-wide significant associations with serum vitamin D (ie, including SNPs in loci with no known relationship to vitamin D metabolism) and in analyses using SNPs with genome-wide significant associations with risk of vitamin D deficiency or insufficiency. CONCLUSIONS These findings suggest that genetically predicted differences in long-term vitamin D nutritional status do not causally affect susceptibility to and severity of COVID-19 infection, and that associations observed in previous studies may have been driven by confounding. These results do not exclude the possibility of low-magnitude causal effects or causal effects of acute responses to therapeutic doses of vitamin D.
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Affiliation(s)
- Bonnie K Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Nathan Gaddis
- GenOmics, Bioinformatics and Translational Research Center, Research Triangle Institute, Research Triangle Park, North Carolina, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics and Translational Research Center, Research Triangle Institute, Research Triangle Park, North Carolina, USA
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Population Health Sciences, Weill Cornell Medical College, New York, New York, USA
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Palmer RHC, Johnson EC, Won H, Polimanti R, Kapoor M, Chitre A, Bogue MA, Benca‐Bachman CE, Parker CC, Verma A, Reynolds T, Ernst J, Bray M, Kwon SB, Lai D, Quach BC, Gaddis NC, Saba L, Chen H, Hawrylycz M, Zhang S, Zhou Y, Mahaffey S, Fischer C, Sanchez‐Roige S, Bandrowski A, Lu Q, Shen L, Philip V, Gelernter J, Bierut LJ, Hancock DB, Edenberg HJ, Johnson EO, Nestler EJ, Barr PB, Prins P, Smith DJ, Akbarian S, Thorgeirsson T, Walton D, Baker E, Jacobson D, Palmer AA, Miles M, Chesler EJ, Emerson J, Agrawal A, Martone M, Williams RW. Integration of evidence across human and model organism studies: A meeting report. Genes Brain Behav 2021; 20:e12738. [PMID: 33893716 PMCID: PMC8365690 DOI: 10.1111/gbb.12738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/11/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022]
Abstract
The National Institute on Drug Abuse and Joint Institute for Biological Sciences at the Oak Ridge National Laboratory hosted a meeting attended by a diverse group of scientists with expertise in substance use disorders (SUDs), computational biology, and FAIR (Findability, Accessibility, Interoperability, and Reusability) data sharing. The meeting's objective was to discuss and evaluate better strategies to integrate genetic, epigenetic, and 'omics data across human and model organisms to achieve deeper mechanistic insight into SUDs. Specific topics were to (a) evaluate the current state of substance use genetics and genomics research and fundamental gaps, (b) identify opportunities and challenges of integration and sharing across species and data types, (c) identify current tools and resources for integration of genetic, epigenetic, and phenotypic data, (d) discuss steps and impediment related to data integration, and (e) outline future steps to support more effective collaboration-particularly between animal model research communities and human genetics and clinical research teams. This review summarizes key facets of this catalytic discussion with a focus on new opportunities and gaps in resources and knowledge on SUDs.
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Affiliation(s)
- Rohan H. C. Palmer
- Behavioral Genetics of Addiction Laboratory, Department of PsychologyEmory UniversityAtlantaGeorgiaUSA
| | - Emma C. Johnson
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Hyejung Won
- Department of Genetics and Neuroscience CenterUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Renato Polimanti
- Department of PsychiatryYale University School of MedicineWest HavenConnecticutUSA
| | - Manav Kapoor
- Nash Family Department of Neuroscience and Friedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Apurva Chitre
- Department of PsychiatryUniversity of California, San DiegoLa JollaCaliforniaUSA
| | | | - Chelsie E. Benca‐Bachman
- Behavioral Genetics of Addiction Laboratory, Department of PsychologyEmory UniversityAtlantaGeorgiaUSA
| | - Clarissa C. Parker
- Department of Psychology and Program in NeuroscienceMiddlebury CollegeMiddleburyVermontUSA
| | - Anurag Verma
- Biomedical and Translational Informatics LaboratoryUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | | | - Jason Ernst
- Department of Biological ChemistryUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Michael Bray
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Soo Bin Kwon
- Department of Biological ChemistryUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Dongbing Lai
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Bryan C. Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology DivisionRTI InternationalResearch Triangle ParkNorth CarolinaUSA
| | - Nathan C. Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology DivisionRTI InternationalResearch Triangle ParkNorth CarolinaUSA
| | - Laura Saba
- Department of Pharmaceutical SciencesUniversity of Colorado, Anschutz Medical CampusAuroraColoradoUSA
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and ToxicologyUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | | | - Shan Zhang
- Department of Statistics and ProbabilityMichigan State UniversityEast LansingMichiganUSA
| | - Yuan Zhou
- Department of Department of BiostatisticsUniversity of FloridaGainesvilleFloridaUSA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, School of PharmacyUniversity of Colorado DenverAuroraColoradoUSA
| | - Christian Fischer
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Sandra Sanchez‐Roige
- Department of PsychiatryUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Anita Bandrowski
- Department of NeuroscienceUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Qing Lu
- Department of Department of BiostatisticsUniversity of FloridaGainesvilleFloridaUSA
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | | | - Joel Gelernter
- Department of PsychiatryYale University School of MedicineWest HavenConnecticutUSA
| | - Laura J. Bierut
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Dana B. Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology DivisionRTI InternationalResearch Triangle ParkNorth CarolinaUSA
| | - Howard J. Edenberg
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Eric O. Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology DivisionRTI InternationalResearch Triangle ParkNorth CarolinaUSA
| | - Eric J. Nestler
- Nash Family Department of Neuroscience and Friedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Peter B. Barr
- Department of PsychologyVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Pjotr Prins
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Desmond J. Smith
- Department of Molecular and Medical PharmacologyDavid Geffen School of Medicine, UCLALos AngelesCaliforniaUSA
| | - Schahram Akbarian
- Friedman Brain Institute and Departments of Psychiatry and NeuroscienceIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | | | | | - Erich Baker
- Department of Computer ScienceBaylor UniversityWacoTexasUSA
| | - Daniel Jacobson
- Computational and Predictive Biology, BiosciencesOak Ridge National LaboratoryOak RidgeTennesseeUSA
- Department of PsychologyUniversity of Tennessee KnoxvilleKnoxvilleTennesseeUSA
| | - Abraham A. Palmer
- Department of PsychiatryUniversity of California, San DiegoLa JollaCaliforniaUSA
- Institute for Genomic Medicine, University of California San DiegoLa JollaCaliforniaUSA
| | - Michael Miles
- Department of Pharmacology and ToxicologyVirginia Commonwealth UniversityRichmondVirginiaUSA
| | | | | | - Arpana Agrawal
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Maryann Martone
- Department of NeuroscienceUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Robert W. Williams
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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Markunas CA, Hancock DB, Xu Z, Quach BC, Fang F, Sandler DP, Johnson EO, Taylor JA. Epigenome-wide analysis uncovers a blood-based DNA methylation biomarker of lifetime cannabis use. Am J Med Genet B Neuropsychiatr Genet 2021; 186:173-182. [PMID: 32803843 PMCID: PMC8296847 DOI: 10.1002/ajmg.b.32813] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/30/2020] [Accepted: 06/15/2020] [Indexed: 12/14/2022]
Abstract
Cannabis use is highly prevalent and is associated with adverse and beneficial effects. To better understand the full spectrum of health consequences, biomarkers that accurately classify cannabis use are needed. DNA methylation (DNAm) is an excellent candidate, yet no blood-based epigenome-wide association studies (EWAS) in humans exist. We conducted an EWAS of lifetime cannabis use (ever vs. never) using blood-based DNAm data from a case-cohort study within Sister Study, a prospective cohort of women at risk of developing breast cancer (Discovery N = 1,730 [855 ever users]; Replication N = 853 [392 ever users]). We identified and replicated an association with lifetime cannabis use at cg15973234 (CEMIP): combined p = 3.3 × 10-8 . We found no overlap between published blood-based cis-meQTLs of cg15973234 and reported lifetime cannabis use-associated single nucleotide polymorphism (SNPs; p < .05), suggesting that the observed DNAm difference was driven by cannabis exposure. We also developed a multi-CpG classifier of lifetime cannabis use using penalized regression of top EWAS CpGs. The resulting 50-CpG classifier produced an area under the curve (AUC) = 0.74 (95% CI [0.72, 0.76], p = 2.00 × 10-5 ) in the discovery sample and AUC = 0.54 ([0.51, 0.57], p = 2.87 × 10-2 ) in the replication sample. Our EWAS findings provide evidence that blood-based DNAm is associated with lifetime cannabis use.
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Affiliation(s)
- Christina A. Markunas
- Center for Omics Discovery and Epidemiology, RTI International, Research Triangle Park, NC, USA
| | - Dana B. Hancock
- Center for Omics Discovery and Epidemiology, RTI International, Research Triangle Park, NC, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Bryan C. Quach
- Center for Omics Discovery and Epidemiology, RTI International, Research Triangle Park, NC, USA
| | - Fang Fang
- Center for Genomics in Public Health and Medicine, RTI International, Research Triangle Park, NC, USA
| | - Dale P. Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Eric O. Johnson
- Center for Omics Discovery and Epidemiology, RTI International, Research Triangle Park, NC, USA,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA,Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA,Corresponding author: Jack A. Taylor, PhD, A303 Rall Building, 111 T W Alexander Dr, Research Triangle Park, NC 27709, , Telephone: 1- 984-287-3684
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29
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Sanchez-Roige S, Cox NJ, Johnson EO, Hancock DB, Davis LK. Alcohol and cigarette smoking consumption as genetic proxies for alcohol misuse and nicotine dependence. Drug Alcohol Depend 2021; 221:108612. [PMID: 33631543 PMCID: PMC8026738 DOI: 10.1016/j.drugalcdep.2021.108612] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/24/2020] [Accepted: 01/21/2021] [Indexed: 11/28/2022]
Abstract
PURPOSE To investigate the role of consumption phenotypes as genetic proxies for alcohol misuse and nicotine dependence. METHODS We leveraged GWAS data from well-powered studies of consumption, alcohol misuse, and nicotine dependence phenotypes measured in individuals of European ancestry from the UK Biobank (UKB) and other population-based cohorts (largest total N = 263,954), and performed genetic correlations within a medical-center cohort, BioVU (N = 66,915). For alcohol, we used quantitative measures of consumption and misuse via AUDIT from UKB. For smoking, we used cigarettes per day from UKB and non-UKB cohorts comprising the GSCAN consortium, and nicotine dependence via ICD codes from UKB and Fagerström Test for Nicotine Dependence from non-UKB cohorts. RESULTS In a large phenome-wide association study, we show that smoking consumption and dependence phenotypes show similar strongly negatively associations with a plethora of diseases, whereas alcohol consumption shows patterns of genetic association that diverge from those of alcohol misuse. CONCLUSIONS Our study suggests that cigarette smoking consumption, which can be easily measured in the general population, may be good a genetic proxy for nicotine dependence, whereas alcohol consumption is not a direct genetic proxy of alcohol misuse.
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Affiliation(s)
- Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - Nancy J Cox
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA; Fellow Program, RTI International, Research Triangle Park, NC 27709, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Lea K Davis
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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30
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Munn‐Chernoff MA, Johnson EC, Chou Y, Coleman JR, Thornton LM, Walters RK, Yilmaz Z, Baker JH, Hübel C, Gordon S, Medland SE, Watson HJ, Gaspar HA, Bryois J, Hinney A, Leppä VM, Mattheisen M, Ripke S, Yao S, Giusti‐Rodríguez P, Hanscombe KB, Adan RA, Alfredsson L, Ando T, Andreassen OA, Berrettini WH, Boehm I, Boni C, Boraska Perica V, Buehren K, Burghardt R, Cassina M, Cichon S, Clementi M, Cone RD, Courtet P, Crow S, Crowley JJ, Danner UN, Davis OS, Zwaan M, Dedoussis G, Degortes D, DeSocio JE, Dick DM, Dikeos D, Dina C, Dmitrzak‐Weglarz M, Docampo E, Duncan LE, Egberts K, Ehrlich S, Escaramís G, Esko T, Estivill X, Farmer A, Favaro A, Fernández‐Aranda F, Fichter MM, Fischer K, Föcker M, Foretova L, Forstner AJ, Forzan M, Franklin CS, Gallinger S, Giegling I, Giuranna J, Gonidakis F, Gorwood P, Gratacos Mayora M, Guillaume S, Guo Y, Hakonarson H, Hatzikotoulas K, Hauser J, Hebebrand J, Helder SG, Herms S, Herpertz‐Dahlmann B, Herzog W, Huckins LM, Hudson JI, Imgart H, Inoko H, Janout V, Jiménez‐Murcia S, Julià A, Kalsi G, Kaminská D, Karhunen L, Karwautz A, Kas MJ, Kennedy JL, Keski‐Rahkonen A, Kiezebrink K, Kim Y, Klump KL, Knudsen GPS, La Via MC, Le Hellard S, Levitan RD, Li D, Lilenfeld L, Lin BD, Lissowska J, Luykx J, Magistretti PJ, Maj M, Mannik K, Marsal S, Marshall CR, Mattingsdal M, McDevitt S, McGuffin P, Metspalu A, Meulenbelt I, Micali N, Mitchell K, Monteleone AM, Monteleone P, Nacmias B, Navratilova M, Ntalla I, O'Toole JK, Ophoff RA, Padyukov L, Palotie A, Pantel J, Papezova H, Pinto D, Rabionet R, Raevuori A, Ramoz N, Reichborn‐Kjennerud T, Ricca V, Ripatti S, Ritschel F, Roberts M, Rotondo A, Rujescu D, Rybakowski F, Santonastaso P, Scherag A, Scherer SW, Schmidt U, Schork NJ, Schosser A, Seitz J, Slachtova L, Slagboom PE, Slof‐Op't Landt MC, Slopien A, Sorbi S, Świątkowska B, Szatkiewicz JP, Tachmazidou I, Tenconi E, Tortorella A, Tozzi F, Treasure J, Tsitsika A, Tyszkiewicz‐Nwafor M, Tziouvas K, Elburg AA, Furth EF, Wagner G, Walton E, Widen E, Zeggini E, Zerwas S, Zipfel S, Bergen AW, Boden JM, Brandt H, Crawford S, Halmi KA, Horwood LJ, Johnson C, Kaplan AS, Kaye WH, Mitchell J, Olsen CM, Pearson JF, Pedersen NL, Strober M, Werge T, Whiteman DC, Woodside DB, Grove J, Henders AK, Larsen JT, Parker R, Petersen LV, Jordan J, Kennedy MA, Birgegård A, Lichtenstein P, Norring C, Landén M, Mortensen PB, Polimanti R, McClintick JN, Adkins AE, Aliev F, Bacanu S, Batzler A, Bertelsen S, Biernacka JM, Bigdeli TB, Chen L, Clarke T, Degenhardt F, Docherty AR, Edwards AC, Foo JC, Fox L, Frank J, Hack LM, Hartmann AM, Hartz SM, Heilmann‐Heimbach S, Hodgkinson C, Hoffmann P, Hottenga J, Konte B, Lahti J, Lahti‐Pulkkinen M, Lai D, Ligthart L, Loukola A, Maher BS, Mbarek H, McIntosh AM, McQueen MB, Meyers JL, Milaneschi Y, Palviainen T, Peterson RE, Ryu E, Saccone NL, Salvatore JE, Sanchez‐Roige S, Schwandt M, Sherva R, Streit F, Strohmaier J, Thomas N, Wang J, Webb BT, Wedow R, Wetherill L, Wills AG, Zhou H, Boardman JD, Chen D, Choi D, Copeland WE, Culverhouse RC, Dahmen N, Degenhardt L, Domingue BW, Frye MA, Gäebel W, Hayward C, Ising M, Keyes M, Kiefer F, Koller G, Kramer J, Kuperman S, Lucae S, Lynskey MT, Maier W, Mann K, Männistö S, Müller‐Myhsok B, Murray AD, Nurnberger JI, Preuss U, Räikkönen K, Reynolds MD, Ridinger M, Scherbaum N, Schuckit MA, Soyka M, Treutlein J, Witt SH, Wodarz N, Zill P, Adkins DE, Boomsma DI, Bierut LJ, Brown SA, Bucholz KK, Costello EJ, Wit H, Diazgranados N, Eriksson JG, Farrer LA, Foroud TM, Gillespie NA, Goate AM, Goldman D, Grucza RA, Hancock DB, Harris KM, Hesselbrock V, Hewitt JK, Hopfer CJ, Iacono WG, Johnson EO, Karpyak VM, Kendler KS, Kranzler HR, Krauter K, Lind PA, McGue M, MacKillop J, Madden PA, Maes HH, Magnusson PK, Nelson EC, Nöthen MM, Palmer AA, Penninx BW, Porjesz B, Rice JP, Rietschel M, Riley BP, Rose RJ, Shen P, Silberg J, Stallings MC, Tarter RE, Vanyukov MM, Vrieze S, Wall TL, Whitfield JB, Zhao H, Neale BM, Wade TD, Heath AC, Montgomery GW, Martin NG, Sullivan PF, Kaprio J, Breen G, Gelernter J, Edenberg HJ, Bulik CM, Agrawal A. Shared genetic risk between eating disorder‐ and substance‐use‐related phenotypes: Evidence from genome‐wide association studies. Addict Biol 2021; 26:e12880. [DOI: 10.1111/adb.12880] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/09/2019] [Accepted: 01/13/2020] [Indexed: 02/01/2023]
Affiliation(s)
- Melissa A. Munn‐Chernoff
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Emma C. Johnson
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Yi‐Ling Chou
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Jonathan R.I. Coleman
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
- National Institute for Health Research Biomedical Research Centre King's College London and South London and Maudsley National Health Service Trust London UK
| | - Laura M. Thornton
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Raymond K. Walters
- Analytic and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston Massachusetts USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts USA
| | - Zeynep Yilmaz
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Department of Genetics University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Jessica H. Baker
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Christopher Hübel
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
- National Institute for Health Research Biomedical Research Centre King's College London and South London and Maudsley National Health Service Trust London UK
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Scott Gordon
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - Sarah E. Medland
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - Hunna J. Watson
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- School of Psychology Curtin University Perth Western Australia Australia
- School of Paediatrics and Child Health University of Western Australia Perth Western Australia Australia
| | - Héléna A. Gaspar
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
- National Institute for Health Research Biomedical Research Centre King's College London and South London and Maudsley National Health Service Trust London UK
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry University Hospital Essen, University of Duisburg‐Essen Essen Germany
| | - Virpi M. Leppä
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Manuel Mattheisen
- Department of Biomedicine Aarhus University Aarhus Denmark
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
- Center for Psychiatry Research, Stockholm Health Care Services Stockholm County Council Stockholm Sweden
- Department of Psychiatry, Psychosomatics and Psychotherapy University of Würzburg Germany
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston Massachusetts USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts USA
- Department of Psychiatry and Psychotherapy Charité ‐ Universitätsmedizin Berlin Germany
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Paola Giusti‐Rodríguez
- Department of Genetics University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Ken B. Hanscombe
- Department of Medical and Molecular Genetics King's College London, Guy's Hospital London UK
| | - Roger A.H. Adan
- Department of Translational Neuroscience, Brain Center Rudolf Magnus University Medical Center Utrecht Utrecht The Netherlands
- Center for Eating Disorders Rintveld Altrecht Mental Health Institute Zeist The Netherlands
- Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - Tetsuya Ando
- Department of Behavioral Medicine, National Institute of Mental Health National Center of Neurology and Psychiatry Kodaira Tokyo Japan
| | - Ole A. Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, NORMENT Centre University of Oslo, Oslo University Hospital Oslo Norway
| | - Wade H. Berrettini
- Department of Psychiatry, Center for Neurobiology and Behavior University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
| | - Ilka Boehm
- Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine Technische Universität Dresden Dresden Germany
| | - Claudette Boni
- Centre of Psychiatry and Neuroscience INSERM U894 Paris France
| | - Vesna Boraska Perica
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton Cambridge UK
- Department of Medical Biology, School of Medicine University of Split Split Croatia
| | - Katharina Buehren
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy RWTH Aachen University Aachen Germany
| | | | - Matteo Cassina
- Clinical Genetics Unit, Department of Woman and Child Health University of Padova Italy
| | - Sven Cichon
- Institute of Medical Genetics and Pathology University Hospital Basel Basel Switzerland
- Department of Biomedicine University of Basel Basel Switzerland
- Institute of Neuroscience and Medicine (INM‐1) Research Center Juelich Germany
| | - Maurizio Clementi
- Clinical Genetics Unit, Department of Woman and Child Health University of Padova Italy
| | - Roger D. Cone
- Department of Molecular and Integrative Physiology, Life Sciences Institute University of Michigan Ann Arbor Michigan USA
| | - Philippe Courtet
- Department of Emergency Psychiatry and Post‐Acute Care, CHRU Montpellier University of Montpellier Montpellier France
| | - Scott Crow
- Department of Psychiatry University of Minnesota Minneapolis Minnesota USA
| | - James J. Crowley
- Department of Genetics University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
| | - Unna N. Danner
- Altrecht Eating Disorders Rintveld Altrecht Mental Health Institute Zeist The Netherlands
| | - Oliver S.P. Davis
- MRC Integrative Epidemiology Unit University of Bristol Bristol UK
- School of Social and Community Medicine University of Bristol Bristol UK
| | - Martina Zwaan
- Department of Psychosomatic Medicine and Psychotherapy Hannover Medical School Hannover Germany
| | - George Dedoussis
- Department of Nutrition and Dietetics Harokopio University Athens Greece
| | | | | | - Danielle M. Dick
- Department of Psychology Virginia Commonwealth University Richmond Virginia USA
- College Behavioral and Emotional Health Institute Virginia Commonwealth University Richmond Virginia USA
- Department of Human & Molecular Genetics Virginia Commonwealth University Richmond Virginia USA
| | - Dimitris Dikeos
- Department of Psychiatry, Athens University Medical School Athens University Athens Greece
| | - Christian Dina
- l'institut du thorax INSERM, CNRS, Univ Nantes Nantes France
| | | | - Elisa Docampo
- Barcelona Institute of Science and Technology Barcelona Spain
- Universitat Pompeu Fabra Barcelona Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
| | - Laramie E. Duncan
- Department of Psychiatry and Behavioral Sciences Stanford University Stanford California USA
| | - Karin Egberts
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Centre for Mental Health University Hospital of Würzburg Würzburg Germany
| | - Stefan Ehrlich
- Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine Technische Universität Dresden Dresden Germany
| | - Geòrgia Escaramís
- Barcelona Institute of Science and Technology Barcelona Spain
- Universitat Pompeu Fabra Barcelona Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
| | - Tõnu Esko
- Estonian Genome Center University of Tartu Tartu Estonia
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge Massachusetts USA
| | - Xavier Estivill
- Barcelona Institute of Science and Technology Barcelona Spain
- Universitat Pompeu Fabra Barcelona Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Genomics and Disease, Bioinformatics and Genomics Programme Centre for Genomic Regulation Barcelona Spain
| | - Anne Farmer
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | - Angela Favaro
- Department of Neurosciences University of Padova Padova Italy
| | - Fernando Fernández‐Aranda
- Department of Psychiatry University Hospital of Bellvitge –IDIBELL and CIBERobn Barcelona Spain
- Department of Clinical Sciences, School of Medicine University of Barcelona Barcelona Spain
| | - Manfred M. Fichter
- Department of Psychiatry and Psychotherapy Ludwig‐Maximilians‐University Munich Germany
- Schön Klinik Roseneck affiliated with the Medical Faculty of the University of Munich Munich Germany
| | - Krista Fischer
- Estonian Genome Center University of Tartu Tartu Estonia
| | - Manuel Föcker
- Department of Child and Adolescent Psychiatry University of Münster Münster Germany
| | - Lenka Foretova
- Department of Cancer, Epidemiology and Genetics Masaryk Memorial Cancer Institute Brno Czech Republic
| | - Andreas J. Forstner
- Department of Biomedicine University of Basel Basel Switzerland
- Centre for Human Genetics University of Marburg Marburg Germany
- Institute of Human Genetics School of Medicine & University Hospital Bonn, University of Bonn Bonn Germany
- Department of Psychiatry (UPK) University of Basel Basel Switzerland
| | - Monica Forzan
- Clinical Genetics Unit, Department of Woman and Child Health University of Padova Italy
| | | | - Steven Gallinger
- Department of Surgery, Faculty of Medicine University of Toronto Toronto Ontario Canada
| | - Ina Giegling
- Department of Psychiatry, Psychotherapy and Psychosomatics Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Johanna Giuranna
- Department of Child and Adolescent Psychiatry University Hospital Essen, University of Duisburg‐Essen Essen Germany
| | - Fragiskos Gonidakis
- 1st Psychiatric Department National and Kapodistrian University of Athens, Medical School, Eginition Hospital Athens Greece
| | - Philip Gorwood
- Institute of Psychiatry and Neuroscience of Paris INSERM U1266 Paris France
- CMME (GHU Paris Psychiatrie et Neurosciences), Paris Descartes University Paris France
| | - Monica Gratacos Mayora
- Barcelona Institute of Science and Technology Barcelona Spain
- Universitat Pompeu Fabra Barcelona Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
| | - Sébastien Guillaume
- Department of Emergency Psychiatry and Post‐Acute Care, CHRU Montpellier University of Montpellier Montpellier France
| | - Yiran Guo
- Center for Applied Genomics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Hakon Hakonarson
- Center for Applied Genomics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Department of Pediatrics University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
| | - Konstantinos Hatzikotoulas
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton Cambridge UK
- Institute of Translational Genomics, Helmholtz Zentrum München ‐ German Research Centre for Environmental Health Neuherberg Germany
| | - Joanna Hauser
- Department of Adult Psychiatry Poznan University of Medical Sciences Poznan Poland
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry University Hospital Essen, University of Duisburg‐Essen Essen Germany
| | - Sietske G. Helder
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
- Zorg op Orde Delft The Netherlands
| | - Stefan Herms
- Institute of Medical Genetics and Pathology University Hospital Basel Basel Switzerland
- Department of Biomedicine University of Basel Basel Switzerland
| | - Beate Herpertz‐Dahlmann
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy RWTH Aachen University Aachen Germany
| | - Wolfgang Herzog
- Department of General Internal Medicine and Psychosomatics Heidelberg University Hospital, Heidelberg University Heidelberg Germany
| | - Laura M. Huckins
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton Cambridge UK
- Department of Psychiatry, and Genetics and Genomics Sciences, Division of Psychiatric Genomics Icahn School of Medicine at Mount Sinai New York New York USA
| | - James I. Hudson
- Biological Psychiatry Laboratory McLean Hospital/Harvard Medical School Boston Massachusetts USA
| | - Hartmut Imgart
- Eating Disorders Unit Parklandklinik Bad Wildungen Germany
| | - Hidetoshi Inoko
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine Tokai University Isehara Japan
| | - Vladimir Janout
- Faculty of Health Sciences Palacky University Olomouc Czech Republic
| | - Susana Jiménez‐Murcia
- Department of Psychiatry University Hospital of Bellvitge –IDIBELL and CIBERobn Barcelona Spain
- Department of Clinical Sciences, School of Medicine University of Barcelona Barcelona Spain
| | - Antonio Julià
- Rheumatology Research Group Vall d'Hebron Research Institute Barcelona Spain
| | - Gursharan Kalsi
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | - Deborah Kaminská
- Department of Psychiatry, First Faculty of Medicine Charles University Prague Czech Republic
| | - Leila Karhunen
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition University of Eastern Finland Kuopio Finland
| | - Andreas Karwautz
- Eating Disorders Unit, Department of Child and Adolescent Psychiatry Medical University of Vienna Vienna Austria
| | - Martien J.H. Kas
- Department of Translational Neuroscience, Brain Center Rudolf Magnus University Medical Center Utrecht Utrecht The Netherlands
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - James L. Kennedy
- Centre for Addiction and Mental Health Toronto Ontario Canada
- Institute of Medical Science University of Toronto Toronto Ontario Canada
- Department of Psychiatry University of Toronto Toronto Ontario Canada
| | | | - Kirsty Kiezebrink
- Institute of Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition University of Aberdeen Aberdeen UK
| | - Youl‐Ri Kim
- Department of Psychiatry Seoul Paik Hospital, Inje University Seoul Korea
| | - Kelly L. Klump
- Department of Psychology Michigan State University East Lansing Michigan USA
| | | | - Maria C. La Via
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Stephanie Le Hellard
- Department of Clinical Science, Norwegian Centre for Mental Disorders Research (NORMENT) University of Bergen Bergen Norway
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine Haukeland University Hospital Bergen Norway
- Department of Clinical Medicine, Laboratory Building Haukeland University Hospital Bergen Norway
| | - Robert D. Levitan
- Centre for Addiction and Mental Health Toronto Ontario Canada
- Institute of Medical Science University of Toronto Toronto Ontario Canada
- Department of Psychiatry University of Toronto Toronto Ontario Canada
| | - Dong Li
- Center for Applied Genomics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Lisa Lilenfeld
- The Chicago School of Professional Psychology, Washington DC Campus Washington District of Columbia USA
| | - Bochao Danae Lin
- Department of Translational Neuroscience, Brain Center Rudolf Magnus University Medical Center Utrecht Utrecht The Netherlands
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention M Skłodowska‐Curie Cancer Center ‐ Oncology Center Warsaw Poland
| | - Jurjen Luykx
- Department of Translational Neuroscience, Brain Center Rudolf Magnus University Medical Center Utrecht Utrecht The Netherlands
| | - Pierre J. Magistretti
- BESE Division King Abdullah University of Science and Technology Thuwal Saudi Arabia
- Department of Psychiatry University of Lausanne‐University Hospital of Lausanne (UNIL‐CHUV) Lausanne Switzerland
| | - Mario Maj
- Department of Psychiatry University of Campania "Luigi Vanvitelli" Naples Italy
| | - Katrin Mannik
- Estonian Genome Center University of Tartu Tartu Estonia
- Center for Integrative Genomics University of Lausanne Lausanne Switzerland
| | - Sara Marsal
- Rheumatology Research Group Vall d'Hebron Research Institute Barcelona Spain
| | - Christian R. Marshall
- Department of Paediatric Laboratory Medicine, Division of Genome Diagnostics The Hospital for Sick Children Toronto Ontario Canada
| | - Morten Mattingsdal
- NORMENT KG Jebsen Centre, Division of Mental Health and Addiction University of Oslo, Oslo University Hospital Oslo Norway
| | - Sara McDevitt
- Department of Psychiatry University College Cork Cork Ireland
- Eist Linn Adolescent Unit, Bessborough Health Service Executive South Cork Ireland
| | - Peter McGuffin
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | - Andres Metspalu
- Estonian Genome Center University of Tartu Tartu Estonia
- Institute of Molecular and Cell Biology University of Tartu Tartu Estonia
| | - Ingrid Meulenbelt
- Molecular Epidemiology Section (Department of Biomedical Datasciences) Leiden University Medical Centre Leiden The Netherlands
| | - Nadia Micali
- Department of Psychiatry, Faculty of Medicine University of Geneva Geneva Switzerland
- Division of Child and Adolescent Psychiatry Geneva University Hospital Geneva Switzerland
| | - Karen Mitchell
- National Center for PTSD VA Boston Healthcare System Boston Massachusetts USA
- Department of Psychiatry Boston University School of Medicine Boston Massachusetts USA
| | | | - Palmiero Monteleone
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana" University of Salerno Salerno Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA) University of Florence Florence Italy
| | - Marie Navratilova
- Department of Cancer, Epidemiology and Genetics Masaryk Memorial Cancer Institute Brno Czech Republic
| | - Ioanna Ntalla
- Department of Nutrition and Dietetics Harokopio University Athens Greece
| | | | - Roel A. Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior University of California Los Angeles Los Angeles California USA
- Department of Psychiatry, Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Leonid Padyukov
- Department of Medicine, Center for Molecular Medicine, Division of Rheumatology Karolinska Institutet and Karolinska University Hospital Stockholm Sweden
| | - Aarno Palotie
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge Massachusetts USA
- Institute for Molecular Medicine FIMM, HiLIFE University of Helsinki Helsinki Finland
- Center for Human Genome Research Massachusetts General Hospital Boston Massachusetts USA
| | - Jacques Pantel
- Centre of Psychiatry and Neuroscience INSERM U894 Paris France
| | - Hana Papezova
- Department of Psychiatry, First Faculty of Medicine Charles University Prague Czech Republic
| | - Dalila Pinto
- Department of Psychiatry, and Genetics and Genomics Sciences, Division of Psychiatric Genomics Icahn School of Medicine at Mount Sinai New York New York USA
| | - Raquel Rabionet
- Saint Joan de Déu Research Institute Saint Joan de Déu Barcelona Children's Hospital Barcelona Spain
- Institute of Biomedicine (IBUB) University of Barcelona Barcelona Spain
- Department of Genetics, Microbiology and Statistics University of Barcelona Barcelona Spain
| | - Anu Raevuori
- Department of Public Health University of Helsinki Helsinki Finland
| | - Nicolas Ramoz
- Institute of Psychiatry and Neuroscience of Paris INSERM U1266 Paris France
| | - Ted Reichborn‐Kjennerud
- Department of Mental Disorders Norwegian Institute of Public Health Oslo Norway
- Institute of Clinical Medicine University of Oslo Oslo Norway
| | - Valdo Ricca
- Department of Health Science University of Florence Florence Italy
| | - Samuli Ripatti
- Department of Biometry University of Helsinki Helsinki Finland
| | - Franziska Ritschel
- Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine Technische Universität Dresden Dresden Germany
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Eating Disorders Research and Treatment Center Technische Universität Dresden Dresden Germany
| | - Marion Roberts
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | - Alessandro Rotondo
- Department of Psychiatry, Neurobiology, Pharmacology, and Biotechnologies University of Pisa Pisa Italy
| | - Dan Rujescu
- Department of Psychiatry, Psychotherapy and Psychosomatics Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Filip Rybakowski
- Department of Psychiatry Poznan University of Medical Sciences Poznan Poland
| | - Paolo Santonastaso
- Department of Neurosciences, Padua Neuroscience Center University of Padova Padova Italy
| | - André Scherag
- Institute of Medical Statistics, Computer and Data Sciences Jena University Hospital Jena Germany
| | - Stephen W. Scherer
- Department of Genetics and Genomic Biology The Hospital for Sick Children Toronto Ontario Canada
- McLaughlin Centre University of Toronto Toronto Ontario Canada
| | - Ulrike Schmidt
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | | | - Alexandra Schosser
- Department of Psychiatry and Psychotherapy Medical University of Vienna Vienna Austria
| | - Jochen Seitz
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy RWTH Aachen University Aachen Germany
| | - Lenka Slachtova
- Department of Pediatrics and Center of Applied Genomics, First Faculty of Medicine Charles University Prague Czech Republic
| | - P. Eline Slagboom
- Molecular Epidemiology Section (Department of Medical Statistics) Leiden University Medical Centre Leiden The Netherlands
| | - Margarita C.T. Slof‐Op't Landt
- Center for Eating Disorders Ursula Rivierduinen Leiden The Netherlands
- Department of Psychiatry Leiden University Medical Centre Leiden The Netherlands
| | - Agnieszka Slopien
- Department of Child and Adolescent Psychiatry Poznan University of Medical Sciences Poznan Poland
| | - Sandro Sorbi
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA) University of Florence Florence Italy
- IRCCS Fondazione Don Carlo Gnocchi Florence Italy
| | - Beata Świątkowska
- Department of Environmental Epidemiology Nofer Institute of Occupational Medicine Lodz Poland
| | - Jin P. Szatkiewicz
- Department of Genetics University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | | | - Elena Tenconi
- Department of Neurosciences University of Padova Padova Italy
| | - Alfonso Tortorella
- Department of Psychiatry University of Naples SUN Naples Italy
- Department of Psychiatry University of Perugia Perugia Italy
| | - Federica Tozzi
- Brain Sciences Department Stremble Ventures Limassol Cyprus
| | - Janet Treasure
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
| | - Artemis Tsitsika
- Adolescent Health Unit, Second Department of Pediatrics "P. & A. Kyriakou" Children's Hospital, University of Athens Athens Greece
| | - Marta Tyszkiewicz‐Nwafor
- Department of Child and Adolescent Psychiatry Poznan University of Medical Sciences Poznan Poland
| | - Konstantinos Tziouvas
- Pediatric Intensive Care Unit "P. & A. Kyriakou" Children's Hospital, University of Athens Athens Greece
| | - Annemarie A. Elburg
- Center for Eating Disorders Rintveld Altrecht Mental Health Institute Zeist The Netherlands
- Faculty of Social and Behavioral Sciences Utrecht University Utrecht The Netherlands
| | - Eric F. Furth
- Center for Eating Disorders Ursula Rivierduinen Leiden The Netherlands
- Department of Psychiatry Leiden University Medical Centre Leiden The Netherlands
| | - Gudrun Wagner
- Eating Disorders Unit, Department of Child and Adolescent Psychiatry Medical University of Vienna Vienna Austria
| | - Esther Walton
- Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine Technische Universität Dresden Dresden Germany
| | - Elisabeth Widen
- Institute for Molecular Medicine FIMM, HiLIFE University of Helsinki Helsinki Finland
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton Cambridge UK
- Institute of Translational Genomics, Helmholtz Zentrum München ‐ German Research Centre for Environmental Health Neuherberg Germany
| | - Stephanie Zerwas
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Stephan Zipfel
- Department of Internal Medicine VI, Psychosomatic Medicine and Psychotherapy University Medical Hospital Tuebingen Tuebingen Germany
| | - Andrew W. Bergen
- BioRealm, LLC Walnut California USA
- Oregon Research Institute Eugene Oregon USA
| | - Joseph M. Boden
- Christchurch Health and Development Study University of Otago Christchurch New Zealand
| | - Harry Brandt
- The Center for Eating Disorders at Sheppard Pratt Baltimore Maryland USA
| | - Steven Crawford
- The Center for Eating Disorders at Sheppard Pratt Baltimore Maryland USA
| | - Katherine A. Halmi
- Department of Psychiatry Weill Cornell Medical College New York New York USA
| | - L. John Horwood
- Christchurch Health and Development Study University of Otago Christchurch New Zealand
| | | | - Allan S. Kaplan
- Centre for Addiction and Mental Health Toronto Ontario Canada
- Institute of Medical Science University of Toronto Toronto Ontario Canada
- Department of Psychiatry University of Toronto Toronto Ontario Canada
| | - Walter H. Kaye
- Department of Psychiatry University of California San Diego La Jolla California USA
| | - James Mitchell
- Department of Psychiatry and Behavioral Science University of North Dakota School of Medicine and Health Sciences Fargo North Dakota USA
| | - Catherine M. Olsen
- Population Health Department QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - John F. Pearson
- Biostatistics and Computational Biology Unit University of Otago Christchurch New Zealand
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Michael Strober
- Department of Psychiatry and Biobehavioral Science, Semel Institute for Neuroscience and Human Behavior University of California Los Angeles Los Angeles California USA
- David Geffen School of Medicine University of California Los Angeles Los Angeles California USA
| | - Thomas Werge
- Department of Clinical Medicine University of Copenhagen Copenhagen Denmark
| | - David C. Whiteman
- Population Health Department QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - D. Blake Woodside
- Institute of Medical Science University of Toronto Toronto Ontario Canada
- Department of Psychiatry University of Toronto Toronto Ontario Canada
- Centre for Mental Health University Health Network Toronto Ontario Canada
- Program for Eating Disorders University Health Network Toronto Ontario Canada
| | - Jakob Grove
- Department of Biomedicine Aarhus University Aarhus Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) Aarhus Denmark
- Centre for Integrative Sequencing, iSEQ Aarhus University Aarhus Denmark
- Bioinformatics Research Centre Aarhus University Aarhus Denmark
| | - Anjali K. Henders
- Institute for Molecular Bioscience University of Queensland Brisbane Queensland Australia
| | - Janne T. Larsen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) Aarhus Denmark
- National Centre for Register‐Based Research, Aarhus BSS Aarhus University Aarhus Denmark
- Centre for Integrated Register‐based Research (CIRRAU) Aarhus University Aarhus Denmark
| | - Richard Parker
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - Liselotte V. Petersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) Aarhus Denmark
- National Centre for Register‐Based Research, Aarhus BSS Aarhus University Aarhus Denmark
- Centre for Integrated Register‐based Research (CIRRAU) Aarhus University Aarhus Denmark
| | - Jennifer Jordan
- Department of Psychological Medicine University of Otago Christchurch New Zealand
- Canterbury District Health Board Christchurch New Zealand
| | - Martin A. Kennedy
- Department of Pathology and Biomedical Science University of Otago Christchurch New Zealand
| | - Andreas Birgegård
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
- Center for Psychiatry Research, Stockholm Health Care Services Stockholm County Council Stockholm Sweden
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Claes Norring
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
- Center for Psychiatry Research, Stockholm Health Care Services Stockholm County Council Stockholm Sweden
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology The Sahlgrenska Academy at the University of Gothenburg Gothenburg Sweden
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) Aarhus Denmark
- National Centre for Register‐Based Research, Aarhus BSS Aarhus University Aarhus Denmark
- Centre for Integrated Register‐based Research (CIRRAU) Aarhus University Aarhus Denmark
| | - Renato Polimanti
- Department of Psychiatry, Division of Human Genetics Yale School of Medicine New Haven Connecticut USA
- Veterans Affairs Connecticut Healthcare System West Haven Connecticut USA
| | - Jeanette N. McClintick
- Department of Biochemistry and Molecular Biology Indiana University School of Medicine Indianapolis Indiana USA
| | - Amy E. Adkins
- Department of Psychology Virginia Commonwealth University Richmond Virginia USA
- College Behavioral and Emotional Health Institute Virginia Commonwealth University Richmond Virginia USA
| | - Fazil Aliev
- Department of Psychology Virginia Commonwealth University Richmond Virginia USA
- Faculty of Business Karabuk University Karabuk Turkey
| | - Silviu‐Alin Bacanu
- Virginia Commonwealth University Alcohol Research Center Virginia Commonwealth University Richmond Virginia USA
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Anthony Batzler
- Psychiatric Genomics and Pharmacogenomics Program Mayo Clinic Rochester Minnesota USA
| | - Sarah Bertelsen
- Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York USA
| | - Joanna M. Biernacka
- Department of Health Sciences Research Mayo Clinic Rochester Minnesota USA
- Department of Psychiatry and Psychology Mayo Clinic Rochester Minnesota USA
| | - Tim B. Bigdeli
- Department of Psychiatry and Behavioral Sciences State University of New York Downstate Medical Center Brooklyn New York USA
| | - Li‐Shiun Chen
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | | | - Franziska Degenhardt
- Institute of Human Genetics University of Bonn School of Medicine & University Hospital Bonn Bonn Germany
| | - Anna R. Docherty
- Department of Psychiatry University of Utah Salt Lake City Utah USA
| | - Alexis C. Edwards
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Jerome C. Foo
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Louis Fox
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Laura M. Hack
- Department of Psychiatry and Behavioral Sciences Stanford University Stanford California USA
| | - Annette M. Hartmann
- Department of Psychiatry, Psychotherapy and Psychosomatics Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Sarah M. Hartz
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Stefanie Heilmann‐Heimbach
- Institute of Human Genetics University of Bonn School of Medicine & University Hospital Bonn Bonn Germany
| | | | - Per Hoffmann
- Institute of Medical Genetics and Pathology University Hospital Basel Basel Switzerland
- Institute of Human Genetics School of Medicine & University Hospital Bonn, University of Bonn Bonn Germany
- Human Genomics Research Group, Department of Biomedicine University of Basel Basel Switzerland
| | - Jouke‐Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Bettina Konte
- Department of Psychiatry, Psychotherapy and Psychosomatics Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Jari Lahti
- Turku Institute for Advanced Studies University of Turku Turku Finland
| | | | - Dongbing Lai
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana USA
| | - Lannie Ligthart
- Department of Biological Psychology, Amsterdam Public Health Research Institute Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Anu Loukola
- Institute for Molecular Medicine FIMM, HiLIFE University of Helsinki Helsinki Finland
| | - Brion S. Maher
- Johns Hopkins Bloomberg School of Public Health Baltimore Maryland USA
| | - Hamdi Mbarek
- Department of Biological Psychology, Amsterdam Public Health Research Institute Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Andrew M. McIntosh
- Division of Psychiatry, Centre for Cognitive Ageing and Cognitive Epidemiology University of Edinburgh Edinburgh UK
| | - Matthew B. McQueen
- Department of Integrative Physiology University of Colorado Boulder Boulder Colorado USA
| | - Jacquelyn L. Meyers
- Department of Psychiatry and Behavioral Sciences, Henri Begleiter Neurodynamics Laboratory SUNY Downstate Medical Center Brooklyn New York USA
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health Research Institute VU University Medical Center/GGz inGeest Amsterdam The Netherlands
| | - Teemu Palviainen
- Institute for Molecular Medicine FIMM, HiLIFE University of Helsinki Helsinki Finland
| | - Roseann E. Peterson
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Euijung Ryu
- Department of Health Sciences Research Mayo Clinic Rochester Minnesota USA
| | - Nancy L. Saccone
- Department of Genetics Washington University School of Medicine Saint Louis Missouri USA
| | - Jessica E. Salvatore
- Department of Psychology Virginia Commonwealth University Richmond Virginia USA
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Sandra Sanchez‐Roige
- Department of Psychiatry University of California San Diego La Jolla California USA
| | | | - Richard Sherva
- Department of Medicine (Biomedical Genetics) Boston University School of Medicine Boston Massachusetts USA
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Nathaniel Thomas
- Department of Psychology Virginia Commonwealth University Richmond Virginia USA
- College Behavioral and Emotional Health Institute Virginia Commonwealth University Richmond Virginia USA
| | - Jen‐Chyong Wang
- Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York USA
| | - Bradley T. Webb
- Virginia Commonwealth University Alcohol Research Center Virginia Commonwealth University Richmond Virginia USA
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Robbee Wedow
- Analytic and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston Massachusetts USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health Harvard University Cambridge Massachusetts USA
- Department of Sociology Harvard University Cambridge Massachusetts USA
| | - Leah Wetherill
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana USA
| | - Amanda G. Wills
- Department of Pharmacology University of Colorado School of Medicine Aurora Colorado USA
| | - Hang Zhou
- Department of Psychiatry, Division of Human Genetics Yale School of Medicine New Haven Connecticut USA
- Veterans Affairs Connecticut Healthcare System West Haven Connecticut USA
| | - Jason D. Boardman
- Institute of Behavioral Science University of Colorado Boulder Colorado USA
- Department of Sociology University of Colorado Boulder Colorado USA
| | - Danfeng Chen
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts USA
| | - Doo‐Sup Choi
- Department of Molecular Pharmacology and Experimental Therapeutics Mayo Clinic Rochester Minnesota USA
| | - William E. Copeland
- Department of Psychiatry University of Vermont Medical Center Burlington Vermont USA
| | - Robert C. Culverhouse
- Department of Medicine, Division of Biostatistics Washington University School of Medicine Saint Louis Missouri USA
| | - Norbert Dahmen
- Department of Psychiatry University of Mainz Mainz Germany
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre University of New South Wales Sydney New South Wales Australia
| | - Benjamin W. Domingue
- Stanford University Graduate School of Education Stanford University Stanford California USA
| | - Mark A. Frye
- Department of Psychiatry and Psychology Mayo Clinic Rochester Minnesota USA
| | - Wolfgang Gäebel
- Department of Psychiatry and Psychotherapy University of Düsseldorf Duesseldorf Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine University of Edinburgh Edinburgh UK
| | - Marcus Ising
- Max‐Planck‐Institute of Psychiatry Munich Germany
| | - Margaret Keyes
- Department of Psychology University of Minnesota Minneapolis Minnesota USA
| | - Falk Kiefer
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Gabriele Koller
- Department of Psychiatry and Psychotherapy University Hospital, LMU Munich Munich Germany
| | - John Kramer
- Department of Psychiatry University of Iowa Roy J and Lucille A Carver College of Medicine Iowa City Iowa USA
| | - Samuel Kuperman
- Department of Psychiatry University of Iowa Roy J and Lucille A Carver College of Medicine Iowa City Iowa USA
| | | | - Michael T. Lynskey
- Addictions Department, Institute of Psychiatry, Psychology & Neuroscience King's College London London UK
| | - Wolfgang Maier
- Department of Psychiatry University of Bonn Bonn Germany
| | - Karl Mann
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Satu Männistö
- Department of Public Health Solutions National Institute for Health and Welfare Helsinki Finland
| | - Bertram Müller‐Myhsok
- Department of Statistical Genetics Max‐Planck‐Institute of Psychiatry München Germany
| | - Alison D. Murray
- Aberdeen Biomedical Imaging Centre, School of Medicine, Medical Sciences & Nutrition University of Aberdeen Foresterhill Aberdeen UK
| | - John I. Nurnberger
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana USA
- Department of Psychiatry Indiana University School of Medicine Indianapolis Indiana USA
| | - Ulrich Preuss
- Department of Psychiatry, Psychotherapy and Psychosomatics Martin‐Luther‐University Halle‐Wittenberg Herborn Germany
- Department of Psychiatry and Psychotherapy Vitos Hospital Herborn Herborn Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics University of Helsinki Helsinki Finland
| | | | - Monika Ridinger
- Department of Psychiatry and Psychotherapy University of Regensburg Psychiatric Health Care Aargau Regensburg Germany
| | - Norbert Scherbaum
- Department of Psychiatry and Psychotherapy and Department of Addictive Behaviour and Addiction Medicine, Medical Faculty LVR‐Hospital Essen, University of Duisburg‐Essen Essen Germany
| | - Marc A. Schuckit
- Department of Psychiatry University of California San Diego La Jolla California USA
| | - Michael Soyka
- Medical Park Chiemseeblick in Bernau‐Felden Ludwig‐Maximilians‐University Bernau am Chiemsee Germany
- Psychiatric Hospital, Ludwig‐Maximilians‐University Bernau am Chiemsee Germany
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Stephanie H. Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Norbert Wodarz
- Department of Psychiatry and Psychotherapy University of Regensburg Regensburg Germany
| | - Peter Zill
- Department of Psychiatry Psychiatric Hospital, Ludwig‐Maximilians‐University Munich Germany
| | - Daniel E. Adkins
- Department of Psychiatry University of Utah Salt Lake City Utah USA
- Department of Sociology University of Utah Salt Lake City Utah USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Laura J. Bierut
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Sandra A. Brown
- Department of Psychiatry University of California San Diego La Jolla California USA
- Department of Psychology University of California San Diego La Jolla California USA
| | - Kathleen K. Bucholz
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - E. Jane Costello
- Department of Psychiatry and Behavioral Sciences Duke University Medical Center Durham North Carolina USA
| | - Harriet Wit
- Department of Psychiatry and Behavioral Neuroscience University of Chicago Chicago Illinois USA
| | | | - Johan G. Eriksson
- Department of General Practice and Primary Health Care University of Helsinki Helsinki Finland
- National Institute for Health and Welfare Helsinki Finland
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics) Boston University School of Medicine Boston Massachusetts USA
- Department of Neurology Boston University School of Medicine Boston Massachusetts USA
- Department of Ophthalmology Boston University School of Medicine Boston Massachusetts USA
- Department of Epidemiology, School of Public Health Boston University Boston Massachusetts USA
- Department of Biostatistics, School of Public Health Boston University Boston Massachusetts USA
| | - Tatiana M. Foroud
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana USA
| | - Nathan A. Gillespie
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
| | - Alison M. Goate
- Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York USA
| | - David Goldman
- Laboratory of Neurogenetics NIH/NIAAA Bethesda Maryland USA
- Office of the Clinical Director NIH/NIAAA Besthesda Maryland USA
| | - Richard A. Grucza
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Dana B. Hancock
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division RTI International Research Triangle Park North Carolina USA
| | - Kathleen Mullan Harris
- Department of Sociology University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Carolina Population Center University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Victor Hesselbrock
- Department of Psychiatry University of Connecticut School of Medicine Farmington Connecticut USA
| | - John K. Hewitt
- Institute for Behavioral Genetics University of Colorado Boulder Boulder Colorado USA
| | | | - William G. Iacono
- Department of Psychology University of Minnesota Minneapolis Minnesota USA
| | - Eric O. Johnson
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division RTI International Research Triangle Park North Carolina USA
- Fellow Program RTI International Research Triangle Park North Carolina USA
| | - Victor M. Karpyak
- Department of Psychiatry and Psychology Mayo Clinic Rochester Minnesota USA
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Henry R. Kranzler
- Center for Studies of Addiction University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
- VISN 4 MIRECC Crescenz VAMC Philadelphia Pennsylvania USA
| | - Kenneth Krauter
- Department of Molecular, Cellular, and Developmental Biology University of Colorado Boulder Boulder Colorado USA
| | - Penelope A. Lind
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - Matt McGue
- Department of Psychology University of Minnesota Minneapolis Minnesota USA
| | - James MacKillop
- Peter Boris Centre for Addictions Research McMaster University/St. Joseph's Healthcare Hamilton Hamilton Ontario Canada
- Michael G. DeGroote Centre for Medicinal Cannabis Research McMaster University/St. Joseph's Healthcare Hamilton Hamilton Ontario Canada
| | - Pamela A.F. Madden
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Hermine H. Maes
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
| | - Patrik K.E. Magnusson
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Elliot C. Nelson
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Markus M. Nöthen
- Institute of Human Genetics University of Bonn School of Medicine & University Hospital Bonn Bonn Germany
| | - Abraham A. Palmer
- Department of Psychiatry University of California San Diego La Jolla California USA
- Institute for Genomic Medicine University of California San Diego La Jolla California USA
| | - Brenda W.J.H. Penninx
- Department of Psychiatry, Amsterdam UMC VU University and GGZinGeest Amsterdam The Netherlands
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral Sciences, Henri Begleiter Neurodynamics Laboratory SUNY Downstate Medical Center Brooklyn New York USA
| | - John P. Rice
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim Heidelberg University Mannheim Germany
| | - Brien P. Riley
- Virginia Commonwealth University Alcohol Research Center Virginia Commonwealth University Richmond Virginia USA
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Richard J. Rose
- Department of Psychological & Brain Sciences Indiana University Bloomington Bloomington Indiana USA
| | - Pei‐Hong Shen
- Laboratory of Neurogenetics NIH/NIAAA Bethesda Maryland USA
| | - Judy Silberg
- Virginia Institute for Psychiatric and Behavioral Genetics Virginia Commonwealth University Richmond Virginia USA
- Department of Psychiatry Virginia Commonwealth University Richmond Virginia USA
| | - Michael C. Stallings
- Institute for Behavioral Genetics University of Colorado Boulder Boulder Colorado USA
| | - Ralph E. Tarter
- School of Pharmacy University of Pittsburgh Pittsburgh Pennsylvania USA
| | | | - Scott Vrieze
- Department of Psychology University of Minnesota Minneapolis Minnesota USA
| | - Tamara L. Wall
- Department of Psychiatry University of California San Diego La Jolla California USA
| | - John B. Whitfield
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health Yale University New Haven Connecticut USA
| | - Benjamin M. Neale
- Analytic and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston Massachusetts USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts USA
| | - Tracey D. Wade
- School of Psychology Flinders University Adelaide South Australia Australia
| | - Andrew C. Heath
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
| | - Grant W. Montgomery
- QIMR Berghofer Medical Research Institute Brisbane Queensland Australia
- Institute for Molecular Bioscience University of Queensland Brisbane Queensland Australia
- Queensland Brain Institute University of Queensland Brisbane Queensland Australia
| | | | - Patrick F. Sullivan
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Department of Genetics University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
| | - Jaakko Kaprio
- Department of Public Health University of Helsinki Helsinki Finland
- Institute for Molecular Medicine FIMM, HiLIFE University of Helsinki Helsinki Finland
| | - Gerome Breen
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience King's College London London UK
- National Institute for Health Research Biomedical Research Centre King's College London and South London and Maudsley National Health Service Trust London UK
| | - Joel Gelernter
- Department of Psychiatry, Division of Human Genetics Yale School of Medicine New Haven Connecticut USA
- Veterans Affairs Connecticut Healthcare System West Haven Connecticut USA
- Department of Genetics Yale School of Medicine New Haven Connecticut USA
- Department of Neuroscience Yale School of Medicine New Haven Connecticut USA
| | - Howard J. Edenberg
- Department of Biochemistry and Molecular Biology Indiana University School of Medicine Indianapolis Indiana USA
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana USA
| | - Cynthia M. Bulik
- Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
- Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden
- Department of Nutrition University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Arpana Agrawal
- Department of Psychiatry Washington University School of Medicine Saint Louis Missouri USA
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31
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Semick SA, Collado-Torres L, Markunas CA, Shin JH, Deep-Soboslay A, Tao R, Huestis M, Bierut LJ, Maher BS, Johnson EO, Hyde TM, Weinberger DR, Hancock DB, Kleinman JE, Jaffe AE. Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome. Mol Psychiatry 2020; 25:3267-3277. [PMID: 30131587 PMCID: PMC6438764 DOI: 10.1038/s41380-018-0223-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 01/05/2023]
Abstract
Cigarette smoking during pregnancy is a major public health concern. While there are well-described consequences in early child development, there is very little known about the effects of maternal smoking on human cortical biology during prenatal life. We therefore performed a genome-wide differential gene expression analysis using RNA sequencing (RNA-seq) on prenatal (N = 33; 16 smoking-exposed) as well as adult (N = 207; 57 active smokers) human postmortem prefrontal cortices. Smoking exposure during the prenatal period was directly associated with differential expression of 14 genes; in contrast, during adulthood, despite a much larger sample size, only two genes showed significant differential expression (FDR < 10%). Moreover, 1,315 genes showed significantly different exposure effects between maternal smoking during pregnancy and direct exposure in adulthood (FDR < 10%)-these differences were largely driven by prenatal differences that were enriched for pathways previously implicated in addiction and synaptic function. Furthermore, prenatal and age-dependent differentially expressed genes were enriched for genes implicated in non-syndromic autism spectrum disorder (ASD) and were differentially expressed as a set between patients with ASD and controls in postmortem cortical regions. These results underscore the enhanced sensitivity to the biological effect of smoking exposure in the developing brain and offer insight into how maternal smoking during pregnancy affects gene expression in the prenatal human cortex. They also begin to address the relationship between in utero exposure to smoking and the heightened risks for the subsequent development of neuropsychiatric disorders.
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Affiliation(s)
- Stephen A. Semick
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA,Center for Computational Biology, Johns Hopkins University,
Baltimore, MD, 21205, USA
| | - Christina A. Markunas
- Behavioral and Urban Health Program, Behavioral Health and
Criminal Justice Division, RTI International, Research Triangle Park, NC, 27709,
USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA
| | - Amy Deep-Soboslay
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA
| | - Ran Tao
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA
| | - Marilyn Huestis
- The Lambert Center for the Study of Medicinal Cannabis and
Hemp, Institute of Emerging Health Professions, Thomas Jefferson University,
Philadelphia, PA, USA
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of
Medicine, St. Louis, MO 63110, USA
| | - Brion S. Maher
- Department of Mental Health, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD, 21205, USA
| | - Eric O. Johnson
- Fellow Program and Behavioral Health and Criminal Justice
Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA,Department of Psychiatry and Behavioral Sciences, Johns
Hopkins School of Medicine, Baltimore, MD 21205, USA,Department of Neurology, Johns Hopkins School of Medicine,
Baltimore, MD, 21205, USA
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA,Department of Psychiatry and Behavioral Sciences, Johns
Hopkins School of Medicine, Baltimore, MD 21205, USA,Department of Neurology, Johns Hopkins School of Medicine,
Baltimore, MD, 21205, USA,Department of Neuroscience, Johns Hopkins School of
Medicine, Baltimore, MD, 21205, USA,McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Dana B. Hancock
- Behavioral and Urban Health Program, Behavioral Health and
Criminal Justice Division, RTI International, Research Triangle Park, NC, 27709,
USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA,Department of Psychiatry and Behavioral Sciences, Johns
Hopkins School of Medicine, Baltimore, MD 21205, USA,Contact: Lieber Institute for Brain Development,
855 N Wolfe St, Ste 300. Baltimore MD 21205. Ph: 1-410-955-1000
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA,Center for Computational Biology, Johns Hopkins University,
Baltimore, MD, 21205, USA,Department of Mental Health, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD, 21205, USA,McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins School of Medicine, Baltimore, MD 21205, USA,Department of Biostatistics, Johns Hopkins Bloomberg
School of Public Health, Baltimore, MD, 21205, USA,Contact: Lieber Institute for Brain Development, 855
N Wolfe St, Ste 300. Baltimore MD 21205. Ph: 1-410-955-1000
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32
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Johnson EC, Demontis D, Thorgeirsson TE, Walters RK, Polimanti R, Hatoum AS, Sanchez-Roige S, Paul SE, Wendt FR, Clarke TK, Lai D, Reginsson GW, Zhou H, He J, Baranger DAA, Gudbjartsson DF, Wedow R, Adkins DE, Adkins AE, Alexander J, Bacanu SA, Bigdeli TB, Boden J, Brown SA, Bucholz KK, Bybjerg-Grauholm J, Corley RP, Degenhardt L, Dick DM, Domingue BW, Fox L, Goate AM, Gordon SD, Hack LM, Hancock DB, Hartz SM, Hickie IB, Hougaard DM, Krauter K, Lind PA, McClintick JN, McQueen MB, Meyers JL, Montgomery GW, Mors O, Mortensen PB, Nordentoft M, Pearson JF, Peterson RE, Reynolds MD, Rice JP, Runarsdottir V, Saccone NL, Sherva R, Silberg JL, Tarter RE, Tyrfingsson T, Wall TL, Webb BT, Werge T, Wetherill L, Wright MJ, Zellers S, Adams MJ, Bierut LJ, Boardman JD, Copeland WE, Farrer LA, Foroud TM, Gillespie NA, Grucza RA, Harris KM, Heath AC, Hesselbrock V, Hewitt JK, Hopfer CJ, Horwood J, Iacono WG, Johnson EO, Kendler KS, Kennedy MA, Kranzler HR, Madden PAF, Maes HH, Maher BS, Martin NG, McGue M, McIntosh AM, Medland SE, Nelson EC, Porjesz B, Riley BP, Stallings MC, Vanyukov MM, Vrieze S, Davis LK, Bogdan R, Gelernter J, Edenberg HJ, Stefansson K, Børglum AD, Agrawal A. A large-scale genome-wide association study meta-analysis of cannabis use disorder. Lancet Psychiatry 2020; 7:1032-1045. [PMID: 33096046 PMCID: PMC7674631 DOI: 10.1016/s2215-0366(20)30339-4] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Variation in liability to cannabis use disorder has a strong genetic component (estimated twin and family heritability about 50-70%) and is associated with negative outcomes, including increased risk of psychopathology. The aim of the study was to conduct a large genome-wide association study (GWAS) to identify novel genetic variants associated with cannabis use disorder. METHODS To conduct this GWAS meta-analysis of cannabis use disorder and identify associations with genetic loci, we used samples from the Psychiatric Genomics Consortium Substance Use Disorders working group, iPSYCH, and deCODE (20 916 case samples, 363 116 control samples in total), contrasting cannabis use disorder cases with controls. To examine the genetic overlap between cannabis use disorder and 22 traits of interest (chosen because of previously published phenotypic correlations [eg, psychiatric disorders] or hypothesised associations [eg, chronotype] with cannabis use disorder), we used linkage disequilibrium score regression to calculate genetic correlations. FINDINGS We identified two genome-wide significant loci: a novel chromosome 7 locus (FOXP2, lead single-nucleotide polymorphism [SNP] rs7783012; odds ratio [OR] 1·11, 95% CI 1·07-1·15, p=1·84 × 10-9) and the previously identified chromosome 8 locus (near CHRNA2 and EPHX2, lead SNP rs4732724; OR 0·89, 95% CI 0·86-0·93, p=6·46 × 10-9). Cannabis use disorder and cannabis use were genetically correlated (rg 0·50, p=1·50 × 10-21), but they showed significantly different genetic correlations with 12 of the 22 traits we tested, suggesting at least partially different genetic underpinnings of cannabis use and cannabis use disorder. Cannabis use disorder was positively genetically correlated with other psychopathology, including ADHD, major depression, and schizophrenia. INTERPRETATION These findings support the theory that cannabis use disorder has shared genetic liability with other psychopathology, and there is a distinction between genetic liability to cannabis use and cannabis use disorder. FUNDING National Institute of Mental Health; National Institute on Alcohol Abuse and Alcoholism; National Institute on Drug Abuse; Center for Genomics and Personalized Medicine and the Centre for Integrative Sequencing; The European Commission, Horizon 2020; National Institute of Child Health and Human Development; Health Research Council of New Zealand; National Institute on Aging; Wellcome Trust Case Control Consortium; UK Research and Innovation Medical Research Council (UKRI MRC); The Brain & Behavior Research Foundation; National Institute on Deafness and Other Communication Disorders; Substance Abuse and Mental Health Services Administration (SAMHSA); National Institute of Biomedical Imaging and Bioengineering; National Health and Medical Research Council (NHMRC) Australia; Tobacco-Related Disease Research Program of the University of California; Families for Borderline Personality Disorder Research (Beth and Rob Elliott) 2018 NARSAD Young Investigator Grant; The National Child Health Research Foundation (Cure Kids); The Canterbury Medical Research Foundation; The New Zealand Lottery Grants Board; The University of Otago; The Carney Centre for Pharmacogenomics; The James Hume Bequest Fund; National Institutes of Health: Genes, Environment and Health Initiative; National Institutes of Health; National Cancer Institute; The William T Grant Foundation; Australian Research Council; The Virginia Tobacco Settlement Foundation; The VISN 1 and VISN 4 Mental Illness Research, Education, and Clinical Centers of the US Department of Veterans Affairs; The 5th Framework Programme (FP-5) GenomEUtwin Project; The Lundbeck Foundation; NIH-funded Shared Instrumentation Grant S10RR025141; Clinical Translational Sciences Award grants; National Institute of Neurological Disorders and Stroke; National Heart, Lung, and Blood Institute; National Institute of General Medical Sciences.
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Affiliation(s)
- Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA.
| | - Ditte Demontis
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | | | - Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renato Polimanti
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Alexander S Hatoum
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA; Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sarah E Paul
- Department of Psychological and Brain Sciences, Washington University in Saint Louis, St. Louis, MO, USA
| | - Frank R Wendt
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Toni-Kim Clarke
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Hang Zhou
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - June He
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - David A A Baranger
- Department of Psychiatry, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Daniel F Gudbjartsson
- Statistics Department, Reykjavik, Iceland; School of Engineering and Natural Sciences, Iceland University, Reykjavik, Iceland
| | - Robbee Wedow
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel E Adkins
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA; Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Amy E Adkins
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA; Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Jeffry Alexander
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Silviu-Alin Bacanu
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Joseph Boden
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Sandra A Brown
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA; Department of Psychology and Office of Research Affairs, University of California San Diego, La Jolla, CA, USA
| | - Kathleen K Bucholz
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Department for Congenital Disorders, Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Robin P Corley
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Danielle M Dick
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA; Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Benjamin W Domingue
- Stanford University Graduate School of Education, Stanford University, Stanford, CA, USA
| | - Louis Fox
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Alison M Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott D Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Laura M Hack
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Durham, NC, USA
| | - Sarah M Hartz
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Ian B Hickie
- Brain and Mind Centre, University of Sydney, Sydney, Australia
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Department for Congenital Disorders, Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Kenneth Krauter
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA; University of Colorado Boulder, Boulder, CO, USA
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Jacquelyn L Meyers
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA; Henri Begleiter Neurodynamics Laboratory, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, QLD, Australia
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Psychosis Research Unit, Aarhus University Hospital, Aarhus, Denmark
| | - Preben B Mortensen
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark; Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand; Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Roseann E Peterson
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | | | - John P Rice
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | | | - Nancy L Saccone
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA; Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Judy L Silberg
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA; Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Ralph E Tarter
- School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Tamara L Wall
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Bradley T Webb
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, and Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Margaret J Wright
- Queensland Brain Institute, University of Queensland, QLD, Australia
| | - Stephanie Zellers
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Jason D Boardman
- Institute of Behavioral Science and Department of Sociology, University of Colorado Boulder, Boulder, CO, USA
| | - William E Copeland
- Department of Psychiatry, University of Vermont Medical Center, Burlington, VT, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Tatiana M Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nathan A Gillespie
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Richard A Grucza
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Kathleen Mullan Harris
- Department of Sociology, and The Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Victor Hesselbrock
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
| | - John K Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Christian J Hopfer
- Department of Psychiatry, University of Colorado Denver, Aurora, CO, USA
| | - John Horwood
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - William G Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Durham, NC, USA
| | - Kenneth S Kendler
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Henry R Kranzler
- Center for Studies of Addiction, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; VISN 4 MIRECC, Crescenz VAMC, Philadelphia, PA, USA
| | - Pamela A F Madden
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Hermine H Maes
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA; Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Brion S Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Matthew McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | | | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Elliot C Nelson
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA; Henri Begleiter Neurodynamics Laboratory, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Brien P Riley
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Michael C Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | | | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Lea K Davis
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Psychiatry and Behavioral Sciences, and Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ryan Bogdan
- Department of Psychological and Brain Sciences, Washington University in Saint Louis, St. Louis, MO, USA
| | - Joel Gelernter
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Department of Genetics, and Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Anders D Børglum
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
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Quach BC, Bray MJ, Gaddis NC, Liu M, Palviainen T, Minica CC, Zellers S, Sherva R, Aliev F, Nothnagel M, Young KA, Marks JA, Young H, Carnes MU, Guo Y, Waldrop A, Sey NYA, Landi MT, McNeil DW, Drichel D, Farrer LA, Markunas CA, Vink JM, Hottenga JJ, Iacono WG, Kranzler HR, Saccone NL, Neale MC, Madden P, Rietschel M, Marazita ML, McGue M, Won H, Winterer G, Grucza R, Dick DM, Gelernter J, Caporaso NE, Baker TB, Boomsma DI, Kaprio J, Hokanson JE, Vrieze S, Bierut LJ, Johnson EO, Hancock DB. Expanding the genetic architecture of nicotine dependence and its shared genetics with multiple traits. Nat Commun 2020; 11:5562. [PMID: 33144568 PMCID: PMC7642344 DOI: 10.1038/s41467-020-19265-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
Cigarette smoking is the leading cause of preventable morbidity and mortality. Genetic variation contributes to initiation, regular smoking, nicotine dependence, and cessation. We present a Fagerström Test for Nicotine Dependence (FTND)-based genome-wide association study in 58,000 European or African ancestry smokers. We observe five genome-wide significant loci, including previously unreported loci MAGI2/GNAI1 (rs2714700) and TENM2 (rs1862416), and extend loci reported for other smoking traits to nicotine dependence. Using the heaviness of smoking index from UK Biobank (N = 33,791), rs2714700 is consistently associated; rs1862416 is not associated, likely reflecting nicotine dependence features not captured by the heaviness of smoking index. Both variants influence nearby gene expression (rs2714700/MAGI2-AS3 in hippocampus; rs1862416/TENM2 in lung), and expression of genes spanning nicotine dependence-associated variants is enriched in cerebellum. Nicotine dependence (SNP-based heritability = 8.6%) is genetically correlated with 18 other smoking traits (rg = 0.40-1.09) and co-morbidities. Our results highlight nicotine dependence-specific loci, emphasizing the FTND as a composite phenotype that expands genetic knowledge of smoking.
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Affiliation(s)
- Bryan C Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Michael J Bray
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Nathan C Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290, Helsinki, Finland
| | - Camelia C Minica
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - Stephanie Zellers
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, 02118, USA
| | - Fazil Aliev
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Faculty of Business, Karabuk University, 78050, Kılavuzlar/Karabük Merkez/Karabük, Turkey
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, 50931, Köln, Germany
- University Hospital Cologne, 50931, Köln, Germany
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jesse A Marks
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Hannah Young
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Megan U Carnes
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Yuelong Guo
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
- GeneCentric Therapeutics, Research Triangle Park, NC, 27709, USA
| | - Alex Waldrop
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Nancy Y A Sey
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Maria T Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, 20892, USA
| | - Daniel W McNeil
- Department of Psychology, West Virginia University, Morgantown, WV, 26505, USA
- Department of Dental Practice and Rural Health, West Virginia University, Morgantown, WV, 26505, USA
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, 50931, Köln, Germany
- University Hospital Cologne, 50931, Köln, Germany
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, 02118, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Christina A Markunas
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Jacqueline M Vink
- Behavioural Science Institute, Radboud University, 6500 HE, Nijmegen, The Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - William G Iacono
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- VISN 4 MIRECC, Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Nancy L Saccone
- Department of Genetics, Washington University, St. Louis, MO, 63130, USA
- Division of Biostatistics, Washington University, St. Louis, MO, 63130, USA
| | - Michael C Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Pamela Madden
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, 68159, Mannheim, Germany
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Matthew McGue
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Georg Winterer
- Experimental & Clinical Research Center, Department of Anesthesiology and Operative Intensive Care Medicine, Charité - University Medicine Berlin, 10117, Berlin, Germany
| | - Richard Grucza
- Departments of Family and Community Medicine and Health and Clinical Outcomes Research, Saint Louis University, St. Louis, MO, 63130, USA
| | - Danielle M Dick
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Psychiatry, VA CT Healthcare Center, West Haven, CT, 06511, USA
| | - Neil E Caporaso
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, 20892, USA
| | - Timothy B Baker
- Center for Tobacco Research and Intervention, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Scott Vrieze
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
- Fellow Program, RTI International, Research Triangle Park, NC, 27709, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA.
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34
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Chen J, Loukola A, Gillespie NA, Peterson R, Jia P, Riley B, Maes H, Dick DM, Kendler KS, Damaj MI, Miles MF, Zhao Z, Li MD, Vink JM, Minica CC, Willemsen G, Boomsma DI, Qaiser B, Madden PAF, Korhonen T, Jousilahti P, Hällfors J, Gelernter J, Kranzler HR, Sherva R, Farrer L, Maher B, Vanyukov M, Taylor M, Ware JJ, Munafò MR, Lutz SM, Hokanson JE, Gu F, Landi MT, Caporaso NE, Hancock DB, Gaddis NC, Baker TB, Bierut LJ, Johnson EO, Chenoweth M, Lerman C, Tyndale R, Kaprio J, Chen X. Genome-Wide Meta-Analyses of FTND and TTFC Phenotypes. Nicotine Tob Res 2020; 22:900-909. [PMID: 31294817 DOI: 10.1093/ntr/ntz099] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022]
Abstract
INTRODUCTION FTND (Fagerstrӧm test for nicotine dependence) and TTFC (time to smoke first cigarette in the morning) are common measures of nicotine dependence (ND). However, genome-wide meta-analysis for these phenotypes has not been reported. METHODS Genome-wide meta-analyses for FTND (N = 19,431) and TTFC (N = 18,567) phenotypes were conducted for adult smokers of European ancestry from 14 independent cohorts. RESULTS We found that SORBS2 on 4q35 (p = 4.05 × 10-8), BG182718 on 11q22 (p = 1.02 × 10-8), and AA333164 on 14q21 (p = 4.11 × 10-9) were associated with TTFC phenotype. We attempted replication of leading candidates with independent samples (FTND, N = 7010 and TTFC, N = 10 061), however, due to limited power of the replication samples, the replication of these new loci did not reach significance. In gene-based analyses, COPB2 was found associated with FTND phenotype, and TFCP2L1, RELN, and INO80C were associated with TTFC phenotype. In pathway and network analyses, we found that the interconnected interactions among the endocytosis, regulation of actin cytoskeleton, axon guidance, MAPK signaling, and chemokine signaling pathways were involved in ND. CONCLUSIONS Our analyses identified several promising candidates for both FTND and TTFC phenotypes, and further verification of these candidates was necessary. Candidates supported by both FTND and TTFC (CHRNA4, THSD7B, RBFOX1, and ZNF804A) were associated with addiction to alcohol, cocaine, and heroin, and were associated with autism and schizophrenia. We also identified novel pathways involved in cigarette smoking. The pathway interactions highlighted the importance of receptor recycling and internalization in ND. IMPLICATIONS Understanding the genetic architecture of cigarette smoking and ND is critical to develop effective prevention and treatment. Our study identified novel candidates and biological pathways involved in FTND and TTFC phenotypes, and this will facilitate further investigation of these candidates and pathways.
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Affiliation(s)
- Jingchun Chen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
| | - Anu Loukola
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Nathan A Gillespie
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Roseann Peterson
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Peilin Jia
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX
| | - Brien Riley
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Hermine Maes
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Daniella M Dick
- Department of Psychology, Virginia Commonwealth University, Richmond, VA
| | - Kenneth S Kendler
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - M Imad Damaj
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA
| | - Michael F Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA
| | - Zhongming Zhao
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX
| | - Ming D Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jacqueline M Vink
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Behavioural Science Institute, Radboud University, Nijmegen, the Netherlands
| | - Camelia C Minica
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Neuroscience Campus Amsterdam, the Netherlands.,EMGO+ Institute for Health and Care Research, VU Medical Center, Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Neuroscience Campus Amsterdam, the Netherlands.,EMGO+ Institute for Health and Care Research, VU Medical Center, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Neuroscience Campus Amsterdam, the Netherlands.,EMGO+ Institute for Health and Care Research, VU Medical Center, Amsterdam, the Netherlands
| | - Beenish Qaiser
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Tellervo Korhonen
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Finland
| | | | - Jenni Hällfors
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Joel Gelernter
- Department of Psychiatry, Yale University, New Haven, CT
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
| | - Richard Sherva
- Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Lindsay Farrer
- Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Brion Maher
- Department of Mental Health, Johns Hopkins University, Baltimore, MD
| | - Michael Vanyukov
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Michelle Taylor
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, BS, UK
| | - Jenifer J Ware
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, BS, UK
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, BS, UK
| | - Sharon M Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - John E Hokanson
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Fangyi Gu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD
| | - Maria T Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD
| | - Neil E Caporaso
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD
| | - Dana B Hancock
- Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC
| | - Nathan C Gaddis
- Research Computing Division, RTI International, Research Triangle Park, NC
| | - Timothy B Baker
- Center for Tobacco Research and Intervention, University of Wisconsin, Madison, WI
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO
| | - Eric O Johnson
- Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC.,Fellow Program, RTI International, Research Triangle Park, NC
| | - Meghan Chenoweth
- Centre for Addiction and Mental Health, and Departments of Pharmacology and Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Caryn Lerman
- Center for Interdisciplinary Research on Nicotine Addiction, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
| | - Rachel Tyndale
- Centre for Addiction and Mental Health, and Departments of Pharmacology and Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Xiangning Chen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV.,Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA.,Department of Psychology, University of Nevada Las Vegas, Las Vegas, NV
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Shu C, Justice AC, Zhang X, Marconi VC, Hancock DB, Johnson EO, Xu K. DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population. Epigenetics 2020; 16:741-753. [PMID: 33092459 PMCID: PMC8216205 DOI: 10.1080/15592294.2020.1824097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background: With the improved life expectancy of people living with HIV (PLWH), identifying vulnerable subpopulations at high mortality risk is important. Evidences showed that DNA methylation (DNAm) is associated with mortality in non-HIV populations. Here, we established a panel of DNAm biomarkers that can predict mortality risk among PLWH. Methods: 1,081 HIV-positive participants from the Veterans Ageing Cohort Study (VACS) were divided into training (N = 460), validation (N = 114), and testing (N = 507) sets. VACS index was used as a measure of mortality risk among PLWH. Model training and fine-tuning were conducted using the ensemble method in the training and validation sets and prediction performance was assessed in the testing set. The survival analysis comparing the predicted high and low mortality risk groups and the Gene Ontology enrichment analysis of the predictive CpG sites were performed. Results: We selected a panel of 393 CpGs for the ensemble prediction model that showed excellent performance in predicting high mortality risk with an auROC of 0.809 (95%CI: 0.767,0.851) and a balanced accuracy of 0.653 (95%CI: 0.611, 0.693) in the testing set. The high mortality risk group was significantly associated with 10-year mortality (hazard ratio = 1.79, p = 4E-05) compared with low risk group. These 393 CpGs were located in 280 genes enriched in immune and inflammation response pathways. Conclusions: We identified a panel of DNAm features associated with mortality risk in PLWH. These DNAm features may serve as predictive biomarkers for mortality risk among PLWH. Abbreviations: AUC: Area Under Curve; CI: Confidence interval; DMR: differentially methylated region; DNA: Deoxyribonucleic acid; DNAm: DNA methylation; DAVID: Database for Annotation, Visualization, and Integrated Discovery; EWA: epigenome-wide association; FDR: False discovery rate; FWER: Family-wise error rate; GLMNET: elastic-net-regularized generalized linear models; GO: Gene ontology; HIV: Human immunodeficiency virus; HM450K: Human Methylation 450 K BeadChip; k-NN: k-nearest neighbours; NK: Natural killer; PC: Principal component; PLWH: people living with HIV; QC: Quality control; SVM: Support Vector Machines; VACS: Veterans Ageing Cohort Study; XGBoost: Extreme Gradient Boosting Tree
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Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- Connecticut Veteran Healthcare System, West Haven, CT, USA.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Vincent C Marconi
- Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
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Bray MJ, Chen LS, Fox L, Hancock DB, Culverhouse RC, Hartz SM, Johnson EO, Liu M, McKay JD, Saccone NL, Hokanson JE, Vrieze SI, Tyndale RF, Baker TB, Bierut LJ. Dissecting the genetic overlap of smoking behaviors, lung cancer, and chronic obstructive pulmonary disease: A focus on nicotinic receptors and nicotine metabolizing enzyme. Genet Epidemiol 2020; 44:748-758. [PMID: 32803792 PMCID: PMC7793026 DOI: 10.1002/gepi.22331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/14/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022]
Abstract
Smoking is a major contributor to lung cancer and chronic obstructive pulmonary disease (COPD). Two of the strongest genetic associations of smoking-related phenotypes are the chromosomal regions 15q25.1, encompassing the nicotinic acetylcholine receptor subunit genes CHRNA5-CHRNA3-CHRNB4, and 19q13.2, encompassing the nicotine metabolizing gene CYP2A6. In this study, we examined genetic relations between cigarettes smoked per day, smoking cessation, lung cancer, and COPD. Data consisted of genome-wide association study summary results. Genetic correlations were estimated using linkage disequilibrium score regression software. For each pair of outcomes, z-score-z-score (ZZ) plots were generated. Overall, heavier smoking and decreased smoking cessation showed positive genetic associations with increased lung cancer and COPD risk. The chromosomal region 19q13.2, however, showed a different correlational pattern. For example, the effect allele-C of the sentinel SNP (rs56113850) within CYP2A6 was associated with an increased risk of heavier smoking (z-score = 19.2; p = 1.10 × 10-81 ), lung cancer (z-score = 8.91; p = 5.02 × 10-19 ), and COPD (z-score = 4.04; p = 5.40 × 10-5 ). Surprisingly, this allele-C (rs56113850) was associated with increased smoking cessation (z-score = -8.17; p = 2.52 × 10-26 ). This inverse relationship highlights the need for additional investigation to determine how CYP2A6 variation could increase smoking cessation while also increasing the risk of lung cancer and COPD likely through increased cigarettes smoked per day.
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Affiliation(s)
- Michael J. Bray
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
- The Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Louis Fox
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Dana B. Hancock
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division, RTI International, Research Triangle Park, NC
| | - Robert C. Culverhouse
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO
| | - Sarah M. Hartz
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Eric O. Johnson
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division, RTI International, Research Triangle Park, NC
- Fellow Program, RTI International, Research Triangle Park, NC
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota, Minnesota, MN
| | - James D. McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Nancy L. Saccone
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - John E. Hokanson
- Department of Epidemiology, University of Colorado, Denver, Aurora, CO
| | - Scott I. Vrieze
- Department of Psychology, University of Minnesota, Minnesota, MN
| | - Rachel F. Tyndale
- Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Timothy B. Baker
- Center for Tobacco Research and Intervention, University of Wisconsin, School of Medicine and Public Health, Madison, WI
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
- The Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
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Shu C, Justice AC, Zhang X, Wang Z, Hancock DB, Johnson EO, Xu K. DNA methylation mediates the effect of cocaine use on HIV severity. Clin Epigenetics 2020; 12:140. [PMID: 32928285 PMCID: PMC7491141 DOI: 10.1186/s13148-020-00934-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background Cocaine use accelerates human immunodeficiency virus (HIV) progression and worsens HIV outcomes. We assessed whether DNA methylation in blood mediates the association between cocaine use and HIV severity in a veteran population. Methods We analyzed 1435 HIV-positive participants from the Veterans Aging Cohort Study Biomarker Cohort (VACS-BC). HIV severity was measured by the Veteran Aging Cohort Study (VACS) index. We assessed the effect of cocaine use on VACS index and mortality among the HIV-positive participants. We selected candidate mediators that were associated with both persistent cocaine use and VACS index by epigenome-wide association (EWA) scans at a liberal p value cutoff of 0.001. Mediation analysis of the candidate CpG sites between cocaine’s effect and the VACS index was conducted, and the joint mediation effect of multiple CpGs was estimated. A two-step epigenetic Mendelian randomization (MR) analysis was conducted as validation. Results More frequent cocaine use was significantly associated with a higher VACS index (β = 1.00, p = 2.7E−04), and cocaine use increased the risk of 10-year mortality (hazard ratio = 1.10, p = 0.011) with adjustment for confounding factors. Fifteen candidate mediator CpGs were selected from the EWA scan. Twelve of these CpGs showed significant mediation effects, with each explaining 11.3–29.5% of the variation. The mediation effects for 3 of the 12 CpGs were validated by the two-step epigenetic MR analysis. The joint mediation effect of the 12 CpGs accounted for 47.2% of cocaine’s effect on HIV severity. Genes harboring these 12 CpGs are involved in the antiviral response (IFIT3, IFITM1, NLRC5, PLSCR1, PARP9) and HIV progression (CX3CR1, MX1). Conclusions We identified 12 DNA methylation CpG sites that appear to play a mediation role in the association between cocaine use and HIV severity.
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Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- Connecticut Veteran Healthcare System, West Haven, CT, USA.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA. .,Connecticut Veteran Healthcare System, West Haven, CT, USA.
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Polimanti R, Walters RK, Johnson EC, McClintick JN, Adkins AE, Adkins DE, Bacanu SA, Bierut LJ, Bigdeli TB, Brown S, Bucholz KK, Copeland WE, Costello EJ, Degenhardt L, Farrer LA, Foroud TM, Fox L, Goate AM, Grucza R, Hack LM, Hancock DB, Hartz SM, Heath AC, Hewitt JK, Hopfer CJ, Johnson EO, Kendler KS, Kranzler HR, Krauter K, Lai D, Madden PAF, Martin NG, Maes HH, Nelson EC, Peterson RE, Porjesz B, Riley BP, Saccone N, Stallings M, Wall TL, Webb BT, Wetherill L, Edenberg HJ, Agrawal A, Gelernter J. Leveraging genome-wide data to investigate differences between opioid use vs. opioid dependence in 41,176 individuals from the Psychiatric Genomics Consortium. Mol Psychiatry 2020; 25:1673-1687. [PMID: 32099098 PMCID: PMC7392789 DOI: 10.1038/s41380-020-0677-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/15/2020] [Accepted: 01/30/2020] [Indexed: 01/17/2023]
Abstract
To provide insights into the biology of opioid dependence (OD) and opioid use (i.e., exposure, OE), we completed a genome-wide analysis comparing 4503 OD cases, 4173 opioid-exposed controls, and 32,500 opioid-unexposed controls, including participants of European and African descent (EUR and AFR, respectively). Among the variants identified, rs9291211 was associated with OE (exposed vs. unexposed controls; EUR z = -5.39, p = 7.2 × 10-8). This variant regulates the transcriptomic profiles of SLC30A9 and BEND4 in multiple brain tissues and was previously associated with depression, alcohol consumption, and neuroticism. A phenome-wide scan of rs9291211 in the UK Biobank (N > 360,000) found association of this variant with propensity to use dietary supplements (p = 1.68 × 10-8). With respect to the same OE phenotype in the gene-based analysis, we identified SDCCAG8 (EUR + AFR z = 4.69, p = 10-6), which was previously associated with educational attainment, risk-taking behaviors, and schizophrenia. In addition, rs201123820 showed a genome-wide significant difference between OD cases and unexposed controls (AFR z = 5.55, p = 2.9 × 10-8) and a significant association with musculoskeletal disorders in the UK Biobank (p = 4.88 × 10-7). A polygenic risk score (PRS) based on a GWAS of risk-tolerance (n = 466,571) was positively associated with OD (OD vs. unexposed controls, p = 8.1 × 10-5; OD cases vs. exposed controls, p = 0.054) and OE (exposed vs. unexposed controls, p = 3.6 × 10-5). A PRS based on a GWAS of neuroticism (n = 390,278) was positively associated with OD (OD vs. unexposed controls, p = 3.2 × 10-5; OD vs. exposed controls, p = 0.002) but not with OE (p = 0.67). Our analyses highlight the difference between dependence and exposure and the importance of considering the definition of controls in studies of addiction.
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Affiliation(s)
- Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Amy E Adkins
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA
| | - Daniel E Adkins
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Silviu-Alin Bacanu
- Virginia Commonwealth University Alcohol Research Center, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Sandra Brown
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Kathleen K Bucholz
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - William E Copeland
- Department of Psychiatry, University of Vermont Medical Center, Burlington, VT, USA
| | - E Jane Costello
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Tatiana M Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Louis Fox
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alison M Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Richard Grucza
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Laura M Hack
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Dana B Hancock
- Center for Omics Discovery and Epidemiology, RTI International, Research Triangle Park, NC, USA
| | - Sarah M Hartz
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - John K Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Christian J Hopfer
- Department of Psychiatry, University of Colorado Denver, Aurora, CO, USA
| | - Eric O Johnson
- Center for Omics Discovery and Epidemiology, RTI International, Research Triangle Park, NC, USA
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Henry R Kranzler
- Center for Studies of Addiction, University of Pennsylvania Perelman School of Medicine, VISN 4 MIRECC, Crescenz VAMC, Philadelphia, PA, USA
| | - Kenneth Krauter
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Pamela A F Madden
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | | | - Hermine H Maes
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Elliot C Nelson
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Roseann E Peterson
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral Sciences, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Brien P Riley
- Virginia Commonwealth University Alcohol Research Center, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Nancy Saccone
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Michael Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Tamara L Wall
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Bradley T Webb
- Virginia Commonwealth University Alcohol Research Center, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA.
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Saccone NL, Emery LS, Sofer T, Gogarten SM, Becker DM, Bottinger EP, Chen LS, Culverhouse RC, Duan W, Hancock DB, Hosgood HD, Johnson EO, Loos RJF, Louie T, Papanicolaou G, Perreira KM, Rodriquez EJ, Schurmann C, Stilp AM, Szpiro AA, Talavera GA, Taylor KD, Thrasher JF, Yanek LR, Laurie CC, Pérez-Stable EJ, Bierut LJ, Kaplan RC. Genome-Wide Association Study of Heavy Smoking and Daily/Nondaily Smoking in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Nicotine Tob Res 2019; 20:448-457. [PMID: 28520984 DOI: 10.1093/ntr/ntx107] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/11/2017] [Indexed: 02/07/2023]
Abstract
Introduction Genetic variants associated with nicotine dependence have previously been identified, primarily in European-ancestry populations. No genome-wide association studies (GWAS) have been reported for smoking behaviors in Hispanics/Latinos in the United States and Latin America, who are of mixed ancestry with European, African, and American Indigenous components. Methods We examined genetic associations with smoking behaviors in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) (N = 12 741 with smoking data, 5119 ever-smokers), using ~2.3 million genotyped variants imputed to the 1000 Genomes Project phase 3. Mixed logistic regression models accounted for population structure, sampling, relatedness, sex, and age. Results The known region of CHRNA5, which encodes the α5 cholinergic nicotinic receptor subunit, was associated with heavy smoking at genome-wide significance (p ≤ 5 × 10-8) in a comparison of 1929 ever-smokers reporting cigarettes per day (CPD) > 10 versus 3156 reporting CPD ≤ 10. The functional variant rs16969968 in CHRNA5 had a p value of 2.20 × 10-7 and odds ratio (OR) of 1.32 for the minor allele (A); its minor allele frequency was 0.22 overall and similar across Hispanic/Latino background groups (Central American = 0.17; South American = 0.19; Mexican = 0.18; Puerto Rican = 0.22; Cuban = 0.29; Dominican = 0.19). CHRNA4 on chromosome 20 attained p < 10-4, supporting prior findings in non-Hispanics. For nondaily smoking, which is prevalent in Hispanic/Latino smokers, compared to daily smoking, loci on chromosomes 2 and 4 achieved genome-wide significance; replication attempts were limited by small Hispanic/Latino sample sizes. Conclusions Associations of nicotinic receptor gene variants with smoking, first reported in non-Hispanic European-ancestry populations, generalized to Hispanics/Latinos despite different patterns of smoking behavior. Implications We conducted the first large-scale genome-wide association study (GWAS) of smoking behavior in a US Hispanic/Latino cohort, and the first GWAS of daily/nondaily smoking in any population. Results show that the region of the nicotinic receptor subunit gene CHRNA5, which in non-Hispanic European-ancestry smokers has been associated with heavy smoking as well as cessation and treatment efficacy, is also significantly associated with heavy smoking in this Hispanic/Latino cohort. The results are an important addition to understanding the impact of genetic variants in understudied Hispanic/Latino smokers.
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Affiliation(s)
- Nancy L Saccone
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Leslie S Emery
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA
| | | | - Diane M Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Erwin P Bottinger
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | | | - Weimin Duan
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Dana B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC
| | - H Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
| | - Eric O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA
| | - George Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Krista M Perreira
- Department of Public Policy, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Erik J Rodriquez
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.,Division of General Internal Medicine, University of California, San Francisco, San Francisco, CA
| | - Claudia Schurmann
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Adam A Szpiro
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Gregory A Talavera
- Graduate School of Public Health, San Diego State University, San Diego, CA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - James F Thrasher
- Department of Health Promotion, Education and Behavior, University of South Carolina, Columbia, SC
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Eliseo J Pérez-Stable
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
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Xu J, Gaddis NC, Bartz TM, Hou R, Manichaikul AW, Pankratz N, Smith AV, Sun F, Terzikhan N, Markunas CA, Patchen BK, Schu M, Beydoun MA, Brusselle GG, Eiriksdottir G, Zhou X, Wood AC, Graff M, Harris TB, Ikram MA, Jacobs DR, Launer LJ, Lemaitre RN, O’Connor GT, Oelsner EC, Psaty BM, Vasan RS, Rohde RR, Rich SS, Rotter JI, Seshadri S, Smith LJ, Tiemeier H, Tsai MY, Uitterlinden AG, Voruganti VS, Xu H, Zilhão NR, Fornage M, Zillikens MC, London SJ, Barr RG, Dupuis J, Gharib SA, Gudnason V, Lahousse L, North KE, Steffen LM, Cassano PA, Hancock DB. Omega-3 Fatty Acids and Genome-Wide Interaction Analyses Reveal DPP10-Pulmonary Function Association. Am J Respir Crit Care Med 2019; 199:631-642. [PMID: 30199657 PMCID: PMC6396866 DOI: 10.1164/rccm.201802-0304oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/07/2018] [Indexed: 12/18/2022] Open
Abstract
RATIONALE Omega-3 polyunsaturated fatty acids (n-3 PUFAs) have anti-inflammatory properties that could benefit adults with comprised pulmonary health. OBJECTIVE To investigate n-3 PUFA associations with spirometric measures of pulmonary function tests (PFTs) and determine underlying genetic susceptibility. METHODS Associations of n-3 PUFA biomarkers (α-linolenic acid, eicosapentaenoic acid, docosapentaenoic acid [DPA], and docosahexaenoic acid [DHA]) were evaluated with PFTs (FEV1, FVC, and FEV1/FVC) in meta-analyses across seven cohorts from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (N = 16,134 of European or African ancestry). PFT-associated n-3 PUFAs were carried forward to genome-wide interaction analyses in the four largest cohorts (N = 11,962) and replicated in one cohort (N = 1,687). Cohort-specific results were combined using joint 2 degree-of-freedom (2df) meta-analyses of SNP associations and their interactions with n-3 PUFAs. RESULTS DPA and DHA were positively associated with FEV1 and FVC (P < 0.025), with evidence for effect modification by smoking and by sex. Genome-wide analyses identified a novel association of rs11693320-an intronic DPP10 SNP-with FVC when incorporating an interaction with DHA, and the finding was replicated (P2df = 9.4 × 10-9 across discovery and replication cohorts). The rs11693320-A allele (frequency, ∼80%) was associated with lower FVC (PSNP = 2.1 × 10-9; βSNP = -161.0 ml), and the association was attenuated by higher DHA levels (PSNP×DHA interaction = 2.1 × 10-7; βSNP×DHA interaction = 36.2 ml). CONCLUSIONS We corroborated beneficial effects of n-3 PUFAs on pulmonary function. By modeling genome-wide n-3 PUFA interactions, we identified a novel DPP10 SNP association with FVC that was not detectable in much larger studies ignoring this interaction.
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Affiliation(s)
- Jiayi Xu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
| | | | - Traci M. Bartz
- Department of Biostatistics
- Cardiovascular Health Research Unit
| | - Ruixue Hou
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
| | - Ani W. Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | | | - Albert V. Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Fangui Sun
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Natalie Terzikhan
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Epidemiology
| | - Christina A. Markunas
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division, and
| | - Bonnie K. Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
| | - Matthew Schu
- Genomics in Public Health and Medicine Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, North Carolina
| | - May A. Beydoun
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Guy G. Brusselle
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Epidemiology
- Department of Respiratory Medicine
| | | | - Xia Zhou
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota
| | - Alexis C. Wood
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, Texas
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Tamara B. Harris
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | | | - David R. Jacobs
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota
| | - Lenore J. Launer
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | | | | | | | - Bruce M. Psaty
- Cardiovascular Health Research Unit
- Department of Medicine
- Department of Epidemiology
- Department of Health Services, and
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Ramachandran S. Vasan
- Division of Cardiology and Preventive Medicine, Department of Medicine, and
- Boston University’s and NHLBI’s Framingham Heart Study, Framingham, Massachusetts
| | - Rebecca R. Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor–UCLA Medical Center, Torrance, California
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Glenn Biggs Institute of Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, Texas
| | - Lewis J. Smith
- Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Henning Tiemeier
- Department of Epidemiology
- Department of Psychiatry
- Department of Child and Adolescent Psychiatry, and
| | | | | | - V. Saroja Voruganti
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | | | - Myriam Fornage
- Institute of Molecular Medicine and
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | - M. Carola Zillikens
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Genomics Initiative–sponsored Netherlands Consortium for Healthy Aging, Leiden, the Netherlands
| | - Stephanie J. London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina
| | - R. Graham Barr
- Department of Medicine, Columbia University, New York, New York
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Sina A. Gharib
- Department of Medicine
- Center for Lung Biology, University of Washington, Seattle, Washington
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Lies Lahousse
- Department of Epidemiology
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lyn M. Steffen
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medical College, New York, New York
| | - Dana B. Hancock
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division, and
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Walters RK, Polimanti R, Johnson EC, McClintick JN, Adams MJ, Adkins AE, Aliev F, Bacanu SA, Batzler A, Bertelsen S, Biernacka JM, Bigdeli TB, Chen LS, Clarke TK, Chou YL, Degenhardt F, Docherty AR, Edwards AC, Fontanillas P, Foo JC, Fox L, Frank J, Giegling I, Gordon S, Hack LM, Hartmann AM, Hartz SM, Heilmann-Heimbach S, Herms S, Hodgkinson C, Hoffmann P, Jan Hottenga J, Kennedy MA, Alanne-Kinnunen M, Konte B, Lahti J, Lahti-Pulkkinen M, Lai D, Ligthart L, Loukola A, Maher BS, Mbarek H, McIntosh AM, McQueen MB, Meyers JL, Milaneschi Y, Palviainen T, Pearson JF, Peterson RE, Ripatti S, Ryu E, Saccone NL, Salvatore JE, Sanchez-Roige S, Schwandt M, Sherva R, Streit F, Strohmaier J, Thomas N, Wang JC, Webb BT, Wedow R, Wetherill L, Wills AG, Boardman JD, Chen D, Choi DS, Copeland WE, Culverhouse RC, Dahmen N, Degenhardt L, Domingue BW, Elson SL, Frye MA, Gäbel W, Hayward C, Ising M, Keyes M, Kiefer F, Kramer J, Kuperman S, Lucae S, Lynskey MT, Maier W, Mann K, Männistö S, Müller-Myhsok B, Murray AD, Nurnberger JI, Palotie A, Preuss U, Räikkönen K, Reynolds MD, Ridinger M, Scherbaum N, Schuckit MA, Soyka M, Treutlein J, Witt S, Wodarz N, Zill P, Adkins DE, Boden JM, Boomsma DI, Bierut LJ, Brown SA, Bucholz KK, Cichon S, Costello EJ, de Wit H, Diazgranados N, Dick DM, Eriksson JG, Farrer LA, Foroud TM, Gillespie NA, Goate AM, Goldman D, Grucza RA, Hancock DB, Harris KM, Heath AC, Hesselbrock V, Hewitt JK, Hopfer CJ, Horwood J, Iacono W, Johnson EO, Kaprio JA, Karpyak VM, Kendler KS, Kranzler HR, Krauter K, Lichtenstein P, Lind PA, McGue M, MacKillop J, Madden PAF, Maes HH, Magnusson P, Martin NG, Medland SE, Montgomery GW, Nelson EC, Nöthen MM, Palmer AA, Pedersen NL, Penninx BWJH, Porjesz B, Rice JP, Rietschel M, Riley BP, Rose R, Rujescu D, Shen PH, Silberg J, Stallings MC, Tarter RE, Vanyukov MM, Vrieze S, Wall TL, Whitfield JB, Zhao H, Neale BM, Gelernter J, Edenberg HJ, Agrawal A. Transancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders. Nat Neurosci 2018; 21:1656-1669. [PMID: 30482948 PMCID: PMC6430207 DOI: 10.1038/s41593-018-0275-1] [Citation(s) in RCA: 367] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 10/12/2018] [Indexed: 01/21/2023]
Abstract
Liability to alcohol dependence (AD) is heritable, but little is known about its complex polygenic architecture or its genetic relationship with other disorders. To discover loci associated with AD and characterize the relationship between AD and other psychiatric and behavioral outcomes, we carried out the largest genome-wide association study to date of DSM-IV-diagnosed AD. Genome-wide data on 14,904 individuals with AD and 37,944 controls from 28 case-control and family-based studies were meta-analyzed, stratified by genetic ancestry (European, n = 46,568; African, n = 6,280). Independent, genome-wide significant effects of different ADH1B variants were identified in European (rs1229984; P = 9.8 × 10-13) and African ancestries (rs2066702; P = 2.2 × 10-9). Significant genetic correlations were observed with 17 phenotypes, including schizophrenia, attention deficit-hyperactivity disorder, depression, and use of cigarettes and cannabis. The genetic underpinnings of AD only partially overlap with those for alcohol consumption, underscoring the genetic distinction between pathological and nonpathological drinking behaviors.
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Affiliation(s)
- Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine and Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - Emma C Johnson
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mark J Adams
- University of Edinburgh, Division of Psychiatry, Edinburgh, UK
| | - Amy E Adkins
- Department of Psychology & College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Fazil Aliev
- Virginia Commonwealth University, Department of Psychology, Richmond, VA, USA
| | - Silviu-Alin Bacanu
- Virginia Commonwealth University Alcohol Research Center; Virginia Institute for Psychiatric and Behavioral Genetics; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Anthony Batzler
- Mayo Clinic, Psychiatric Genomics and Pharmacogenomics Program, Rochester, MN, USA
| | - Sarah Bertelsen
- Icahn School of Medicine at Mount Sinai, Department of Neuroscience, New York, NY, USA
| | - Joanna M Biernacka
- Mayo Clinic, Department of Health Sciences Research, and Department of Psychiatry and Psychology, Rochester, MN, USA
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Li-Shiun Chen
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Toni-Kim Clarke
- University of Edinburgh, Division of Psychiatry, Edinburgh, UK
| | - Yi-Ling Chou
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn; and Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Anna R Docherty
- University of Utah, Department of Psychiatry, Salt Lake City, UT, USA
| | - Alexis C Edwards
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | | | - Jerome C Foo
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Louis Fox
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ina Giegling
- Martin-Luther-University Halle-Wittenberg, Department of Psychiatry, Psychotherapy and Psychosomatics, Halle, Germany
| | - Scott Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Laura M Hack
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Annette M Hartmann
- Martin-Luther-University Halle-Wittenberg, Department of Psychiatry, Psychotherapy and Psychosomatics, Halle, Germany
| | - Sarah M Hartz
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn; and Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn; and Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Per Hoffmann
- Institute of Human Genetics, University of Bonn; and Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Mervi Alanne-Kinnunen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Bettina Konte
- Martin-Luther-University Halle-Wittenberg, Department of Psychiatry, Psychotherapy and Psychosomatics, Halle, Germany
| | - Jari Lahti
- Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | | | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lannie Ligthart
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Brion S Maher
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hamdi Mbarek
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andrew M McIntosh
- University of Edinburgh, Division of Psychiatry, Centre for Cognitive Ageing and Cognitive Epidemiology, Edinburgh, UK
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Jacquelyn L Meyers
- Henri Begleiter Neurodynamics Laboratory, Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health Research Institute, VU University Medical Center/GGz inGeest, Amsterdam, The Netherlands
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Roseann E Peterson
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | - Samuli Ripatti
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Euijung Ryu
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN, USA
| | - Nancy L Saccone
- Washington University School of Medicine, Department of Genetics, St. Louis, MO, USA
| | - Jessica E Salvatore
- Virginia Commonwealth University, Department of Psychology, Richmond, VA, USA
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | - Sandra Sanchez-Roige
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
| | | | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nathaniel Thomas
- Department of Psychology & College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Jen-Chyong Wang
- Icahn School of Medicine at Mount Sinai, Department of Neuroscience, New York, NY, USA
| | - Bradley T Webb
- Virginia Commonwealth University Alcohol Research Center; Virginia Institute for Psychiatric and Behavioral Genetics; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Robbee Wedow
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Sociology, Harvard University, Cambridge, MA, USA
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Amanda G Wills
- University of Colorado School of Medicine, Department of Pharmacology, Aurora, CO, USA
| | - Jason D Boardman
- Institute of Behavioral Science and Department of Sociology, University of Colorado, Boulder, CO, USA
| | - Danfeng Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Doo-Sup Choi
- Mayo Clinic, Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, USA
| | - William E Copeland
- Duke University Medical Center, Department of Psychiatry and Behavioral Sciences, Durham, NC, USA
| | - Robert C Culverhouse
- Washington University School of Medicine, Department of Medicine and Division of Biostatistics, St. Louis, MO, USA
| | - Norbert Dahmen
- Department of Psychiatry, University of Mainz, Mainz, Germany
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | | | | | - Mark A Frye
- Mayo Clinic, Department of Psychiatry and Psychology, Rochester, MN, USA
| | - Wolfgang Gäbel
- Department of Psychiatry and Psychotherapy, University of Düsseldorf, Düsseldorf, Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Marcus Ising
- Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Margaret Keyes
- University of Minnesota, Department of Psychology, Minneapolis, MN, USA
| | - Falk Kiefer
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - John Kramer
- University of Iowa Roy J and Lucille A Carver College of Medicine, Department of Psychiatry, Iowa City, IA, USA
| | - Samuel Kuperman
- University of Iowa Roy J and Lucille A Carver College of Medicine, Department of Psychiatry, Iowa City, IA, USA
| | | | - Michael T Lynskey
- Addictions Department, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Wolfgang Maier
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | - Karl Mann
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | | | - Bertram Müller-Myhsok
- Department of Statistical Genetics, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Alison D Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - John I Nurnberger
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Medicine, Department of Neurology and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Ulrich Preuss
- Martin-Luther-University Halle-Wittenberg, Department of Psychiatry, Psychotherapy and Psychosomatics, Halle, Germany
- Vitos Hospital Herborn, Department of Psychiatry and Psychotherapy, Herborn, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | | | - Monika Ridinger
- Department of Psychiatry and Psychotherapy, University of Regensburg Psychiatric Health Care Aargau, Regensburg, Germany
| | - Norbert Scherbaum
- LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Department of Addictive Behaviour and Addiction Medicine, Medical Faculty, University of Duisburg-Essen, Duisburg, Germany
| | - Marc A Schuckit
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
| | - Michael Soyka
- Medical Park Chiemseeblick in Bernau-Felden, Chiemsee, Germany
- Psychiatric Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stephanie Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Norbert Wodarz
- Department of Psychiatry and Psychotherapy, University of Regensburg, Regensburg, Germany
| | - Peter Zill
- Psychiatric Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Daniel E Adkins
- University of Utah, Department of Psychiatry, Salt Lake City, UT, USA
- University of Utah, Department of Sociology, Salt Lake City, UT, USA
| | | | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Laura J Bierut
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Sandra A Brown
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
- University of California, San Diego School of Medicine, Department of Psychology, San Diego, CA, USA
| | - Kathleen K Bucholz
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Sven Cichon
- Human Genomics Research Group, Department of Biomedicine, University of Basel Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - E Jane Costello
- Duke University Medical Center, Department of Psychiatry and Behavioral Sciences, Durham, NC, USA
| | | | | | - Danielle M Dick
- Department of Psychology & College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, and National Institute for Health and Welfare, Helsinki, Finland
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
- Departments of Neurology, Ophthalmology, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - Tatiana M Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nathan A Gillespie
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | - Alison M Goate
- Icahn School of Medicine at Mount Sinai, Department of Neuroscience, New York, NY, USA
| | - David Goldman
- NIH/NIAAA, Laboratory of Neurogenetics, Bethesda, MD, USA
- NIH/NIAAA, Office of the Clinical Director, Bethesda, MD, USA
| | - Richard A Grucza
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Dana B Hancock
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division, RTI International, Research Triangle Park, NC, USA
| | - Kathleen Mullan Harris
- Department of Sociology and Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew C Heath
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Victor Hesselbrock
- University of Connecticut School of Medicine, Department of Psychiatry, Farmington, CT, USA
| | - John K Hewitt
- University of Colorado Boulder, Institute for Behavioral Genetics, Boulder, CO, USA
| | | | | | - William Iacono
- University of Minnesota, Department of Psychology, Minneapolis, MN, USA
| | - Eric O Johnson
- RTI International, Fellows Program, Research Triangle Park, NC, USA
| | - Jaakko A Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Victor M Karpyak
- Mayo Clinic, Department of Psychiatry and Psychology, Rochester, MN, USA
| | - Kenneth S Kendler
- Virginia Commonwealth University Alcohol Research Center; Virginia Institute for Psychiatric and Behavioral Genetics; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Henry R Kranzler
- University of Pennsylvania Perelman School of Medicine, Center for Studies of Addiction, Department of Psychiatry and VISN 4 MIRECC, Crescenz VAMC, Philadelphia, PA, USA
| | - Kenneth Krauter
- University of Colorado Boulder, Department of Molecular, Cellular, and Developmental Biology, Boulder, CO, USA
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Instituet, Stockholm, Sweden
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matt McGue
- University of Minnesota, Department of Psychology, Minneapolis, MN, USA
| | - James MacKillop
- Peter Boris Centre for Addictions Research, McMaster University/St. Joseph's Healthcare Hamilton; Michael G. DeGroote Centre for Medicinal Cannabis Research, Hamilton, Ontario, Canada
| | - Pamela A F Madden
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Hermine H Maes
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Patrik Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Instituet, Stockholm, Sweden
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Grant W Montgomery
- The Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Elliot C Nelson
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Abraham A Palmer
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
- University of California San Diego, Institute for Genomic Medicine, San Diego, CA, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Instituet, Stockholm, Sweden
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health Research Institute, VU University Medical Center/GGz inGeest, Amsterdam, The Netherlands
| | - Bernice Porjesz
- Henri Begleiter Neurodynamics Laboratory, Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - John P Rice
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Brien P Riley
- Virginia Commonwealth University Alcohol Research Center; Virginia Institute for Psychiatric and Behavioral Genetics; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Richard Rose
- Department of Psychological & Brain Sciences, Indiana University Bloomington, Bloomington, IN, USA
| | - Dan Rujescu
- Martin-Luther-University Halle-Wittenberg, Department of Psychiatry, Psychotherapy and Psychosomatics, Halle, Germany
| | - Pei-Hong Shen
- NIH/NIAAA, Laboratory of Neurogenetics, Bethesda, MD, USA
| | - Judy Silberg
- Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | - Michael C Stallings
- University of Colorado Boulder, Institute for Behavioral Genetics, Boulder, CO, USA
| | - Ralph E Tarter
- University of Pittsburgh, School of Pharmacy, Pittsburgh, PA, USA
| | | | - Scott Vrieze
- University of Minnesota, Department of Psychology, Minneapolis, MN, USA
| | - Tamara L Wall
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
| | - John B Whitfield
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joel Gelernter
- Departments of Psychiatry, Genetics, and Neuroscience, Yale University School of Medicine, Veterans Affairs Connecticut Healthcare System, New Haven, CT, USA.
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Arpana Agrawal
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA.
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Xu J, Bartz TM, Chittoor G, Eiriksdottir G, Manichaikul AW, Sun F, Terzikhan N, Zhou X, Booth SL, Brusselle GG, de Boer IH, Fornage M, Frazier-Wood AC, Graff M, Gudnason V, Harris TB, Hofman A, Hou R, Houston DK, Jacobs Jr DR, Kritchevsky SB, Latourelle J, Lemaitre RN, Lutsey PL, Connor GO, Oelsner EC, Pankow JS, Psaty BM, Rohde RR, Rich SS, Rotter JI, Smith LJ, Stricker BH, Voruganti VS, Wang TJ, Zillikens MC, Barr RG, Dupuis J, Gharib SA, Lahousse L, London SJ, North KE, Smith AV, Steffen LM, Hancock DB, Cassano PA. Meta-analysis across Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium provides evidence for an association of serum vitamin D with pulmonary function. Br J Nutr 2018; 120:1159-1170. [PMID: 30205856 PMCID: PMC6263170 DOI: 10.1017/s0007114518002180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The role that vitamin D plays in pulmonary function remains uncertain. Epidemiological studies reported mixed findings for serum 25-hydroxyvitamin D (25(OH)D)-pulmonary function association. We conducted the largest cross-sectional meta-analysis of the 25(OH)D-pulmonary function association to date, based on nine European ancestry (EA) cohorts (n 22 838) and five African ancestry (AA) cohorts (n 4290) in the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium. Data were analysed using linear models by cohort and ancestry. Effect modification by smoking status (current/former/never) was tested. Results were combined using fixed-effects meta-analysis. Mean serum 25(OH)D was 68 (sd 29) nmol/l for EA and 49 (sd 21) nmol/l for AA. For each 1 nmol/l higher 25(OH)D, forced expiratory volume in the 1st second (FEV1) was higher by 1·1 ml in EA (95 % CI 0·9, 1·3; P<0·0001) and 1·8 ml (95 % CI 1·1, 2·5; P<0·0001) in AA (P race difference=0·06), and forced vital capacity (FVC) was higher by 1·3 ml in EA (95 % CI 1·0, 1·6; P<0·0001) and 1·5 ml (95 % CI 0·8, 2·3; P=0·0001) in AA (P race difference=0·56). Among EA, the 25(OH)D-FVC association was stronger in smokers: per 1 nmol/l higher 25(OH)D, FVC was higher by 1·7 ml (95 % CI 1·1, 2·3) for current smokers and 1·7 ml (95 % CI 1·2, 2·1) for former smokers, compared with 0·8 ml (95 % CI 0·4, 1·2) for never smokers. In summary, the 25(OH)D associations with FEV1 and FVC were positive in both ancestries. In EA, a stronger association was observed for smokers compared with never smokers, which supports the importance of vitamin D in vulnerable populations.
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Affiliation(s)
- Jiayi Xu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States
| | - Traci M. Bartz
- Department of Biostatistics, University of Washington, Seattle, Washington, United States
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States
| | - Geetha Chittoor
- Department of Biomedical and Translational Informatics, Geisinger, Danville, Pennsylvania, United States
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | | | - Ani W. Manichaikul
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Fangui Sun
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States
| | - Natalie Terzikhan
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Xia Zhou
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Sarah L. Booth
- Jean Mayer-U.S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, United States
| | - Guy G. Brusselle
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ian H. de Boer
- Department of Medicine, University of Washington, Seattle, Washington, United States
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States
| | - Alexis C. Frazier-Wood
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, Texas, United States
| | - Mariaelisa Graff
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging, Leiden, the Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Ruixue Hou
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina, United States
| | - Denise K. Houston
- Sticht Center on Aging, Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United State
| | - David R. Jacobs Jr
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Stephen B. Kritchevsky
- Sticht Center on Aging, Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United State
| | - Jeanne Latourelle
- The Pulmonary Center, Department of Medicine, Boston University, Boston, Massachusetts, United State
- Department of Neurology, Boston University, Boston, Massachusetts, United States
| | - Rozenn N. Lemaitre
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States
- Department of Medicine, University of Washington, Seattle, Washington, United States
| | - Pamela L. Lutsey
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - George O. Connor
- The Pulmonary Center, Department of Medicine, Boston University, Boston, Massachusetts, United State
| | | | - James S. Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States
- Department of Medicine, University of Washington, Seattle, Washington, United States
- Department of Epidemiology, University of Washington, Seattle, Washington, United States
- Department of Health Services, University of Washington, Seattle, Washington, United States
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, United States
| | - Rebecca R. Rohde
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, California, United States
| | - Lewis J. Smith
- Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Bruno H. Stricker
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging, Leiden, the Netherlands
| | - V. Saroja Voruganti
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina, United States
| | - Thomas J. Wang
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States
| | - M. Carola Zillikens
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging, Leiden, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - R. Graham Barr
- Department of Medicine, Columbia University, New York, New York, United States
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States
| | - Sina A. Gharib
- Department of Medicine, University of Washington, Seattle, Washington, United States
- Center for Lung Biology, University of Washington, Seattle, Washington, United States
| | - Lies Lahousse
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Stephanie J. London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States
| | - Kari E. North
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Albert V. Smith
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Lyn M. Steffen
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Dana B. Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, North Carolina, United States
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States
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43
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Hancock DB, Guo Y, Reginsson GW, Gaddis NC, Lutz SM, Sherva R, Loukola A, Minica CC, Markunas CA, Han Y, Young KA, Gudbjartsson DF, Gu F, McNeil DW, Qaiser B, Glasheen C, Olson S, Landi MT, Madden PAF, Farrer LA, Vink J, Saccone NL, Neale MC, Kranzler HR, McKay J, Hung RJ, Amos CI, Marazita ML, Boomsma DI, Baker TB, Gelernter J, Kaprio J, Caporaso NE, Thorgeirsson TE, Hokanson JE, Bierut LJ, Stefansson K, Johnson EO. Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence. Mol Psychiatry 2018; 23:1911-1919. [PMID: 28972577 PMCID: PMC5882602 DOI: 10.1038/mp.2017.193] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 11/09/2022]
Abstract
Cigarette smoking is a leading cause of preventable mortality worldwide. Nicotine dependence, which reduces the likelihood of quitting smoking, is a heritable trait with firmly established associations with sequence variants in nicotine acetylcholine receptor genes and at other loci. To search for additional loci, we conducted a genome-wide association study (GWAS) meta-analysis of nicotine dependence, totaling 38,602 smokers (28,677 Europeans/European Americans and 9925 African Americans) across 15 studies. In this largest-ever GWAS meta-analysis for nicotine dependence and the largest-ever cross-ancestry GWAS meta-analysis for any smoking phenotype, we reconfirmed the well-known CHRNA5-CHRNA3-CHRNB4 genes and further yielded a novel association in the DNA methyltransferase gene DNMT3B. The intronic DNMT3B rs910083-C allele (frequency=44-77%) was associated with increased risk of nicotine dependence at P=3.7 × 10-8 (odds ratio (OR)=1.06 and 95% confidence interval (CI)=1.04-1.07 for severe vs mild dependence). The association was independently confirmed in the UK Biobank (N=48,931) using heavy vs never smoking as a proxy phenotype (P=3.6 × 10-4, OR=1.05, and 95% CI=1.02-1.08). Rs910083-C is also associated with increased risk of squamous cell lung carcinoma in the International Lung Cancer Consortium (N=60,586, meta-analysis P=0.0095, OR=1.05, and 95% CI=1.01-1.09). Moreover, rs910083-C was implicated as a cis-methylation quantitative trait locus (QTL) variant associated with higher DNMT3B methylation in fetal brain (N=166, P=2.3 × 10-26) and a cis-expression QTL variant associated with higher DNMT3B expression in adult cerebellum from the Genotype-Tissue Expression project (N=103, P=3.0 × 10-6) and the independent Brain eQTL Almanac (N=134, P=0.028). This novel DNMT3B cis-acting QTL variant highlights the importance of genetically influenced regulation in brain on the risks of nicotine dependence, heavy smoking and consequent lung cancer.
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Affiliation(s)
- D B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA.
| | - Y Guo
- Center for Genomics in Public Health and Medicine, RTI International, Research Triangle Park, NC, USA
| | | | - N C Gaddis
- Research Computing Division, RTI International, Research Triangle Park, NC, USA
| | - S M Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - R Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - A Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - C C Minica
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - C A Markunas
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
| | - Y Han
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - K A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - D F Gudbjartsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - F Gu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
| | - D W McNeil
- Department of Psychology, West Virginia University, Morgantown, WV, USA
- Department of Dental Practice and Rural Health, West Virginia University, Morgantown, WV, USA
| | - B Qaiser
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - C Glasheen
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
| | - S Olson
- Public Health Informatics Program, eHealth, Quality and Analytics Division, RTI International, Research Triangle Park, NC, USA
| | - M T Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
| | - P A F Madden
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - L A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - J Vink
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - N L Saccone
- Department of Genetics, Washington University, St. Louis, MO, USA
| | - M C Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - H R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Crescenz VA Medical Center, Philadelphia, PA, USA
| | - J McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - R J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, ON, Canada
| | - C I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - M L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - D I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - T B Baker
- Center for Tobacco Research and Intervention, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - J Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- VA CT Healthcare Center, Department of Psychiatry, West Haven, CT, USA
| | - J Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - N E Caporaso
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
| | | | - J E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - L J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | | | - E O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
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Glasheen C, Johnson EO, Saccone NL, Lutz SM, Baker TB, McNeil DW, Marazita ML, Hokanson JE, Bierut LJ, Hancock DB. Is the Fagerström test for nicotine dependence invariant across secular trends in smoking? A question for cross-birth cohort analysis of nicotine dependence. Drug Alcohol Depend 2018; 185:127-132. [PMID: 29438887 PMCID: PMC5889733 DOI: 10.1016/j.drugalcdep.2017.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 11/17/2022]
Abstract
BACKGROUND The Fagerström Test for Nicotine Dependence (FTND), a derivation of the Fagerström Tolerance Questionnaire, was first published in 1991. The FTND remains one of the most widely used measures of nicotine dependence for studying genetic and epidemiological risk factors and the likelihood of smoking cessation. However, it is unclear whether secular trends in patterns of smoking alter the psychometric properties of the FTND and its interpretation. METHODS We examined measurement invariance in the lifetime and current FTND scores across birth cohorts using participants drawn from six study samples (N = 13,775). RESULTS We found significant (p < 0.05) measurement non-invariance in means and factor loadings of most FTND items by birth cohort, but effect sizes, ranging from r2 = 0.0001 to r2 = 0.0035, indicated that less than 0.5% of the model variance was explained by the measurement non-invariance for each factor loading. To assess its impact, we regressed the lifetime FTND latent variable on well-established factors associated with nicotine dependence (quitting smoking and the nicotinic acetylcholine receptor gene [CHRNA5] variant rs16969968, separately), and we observed that the regression coefficients were unchanged between models with and without adjustment for measurement non-invariance. CONCLUSIONS These findings suggest that possible FTND non-invariance that occurs across study samples of various birth years has a negligible impact on study results.
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Affiliation(s)
- Cristie Glasheen
- Behavioral Health and Criminal Justice Division, Behavioral and Urban Health Program, RTI International, Research Triangle Park, NC, USA.
| | - Eric O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
| | - Nancy L Saccone
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Sharon M Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Timothy B Baker
- Center for Tobacco Research and Intervention, University of Wisconsin, Madison, WI, USA
| | - Daniel W McNeil
- Department of Psychology, Department of Dental Practice and Rural Health, West Virginia University, Morgantown, WV, USA
| | - Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO,USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Dana B Hancock
- Behavioral Health and Criminal Justice Division, Behavioral and Urban Health Program, RTI International, Research Triangle Park, NC, USA
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Abstract
PURPOSE OF REVIEW With the advent of the genome-wide association study (GWAS), our understanding of the genetics of addiction has made significant strides forward. Here, we summarize genetic loci containing variants identified at genome-wide statistical significance (P < 5 × 10-8) and independently replicated, review evidence of functional or regulatory effects for GWAS-identified variants, and outline multi-omics approaches to enhance discovery and characterize addiction loci. RECENT FINDINGS Replicable GWAS findings span 11 genetic loci for smoking, eight loci for alcohol, and two loci for illicit drugs combined and include missense functional variants and noncoding variants with regulatory effects in human brain tissues traditionally viewed as addiction-relevant (e.g., prefrontal cortex [PFC]) and, more recently, tissues often overlooked (e.g., cerebellum). GWAS analyses have discovered several novel, replicable variants contributing to addiction. Using larger sample sizes from harmonized datasets and new approaches to integrate GWAS with multiple 'omics data across human brain tissues holds great promise to significantly advance our understanding of the biology underlying addiction.
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Affiliation(s)
- Dana B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, 3040 East Cornwallis Road, P. O. Box 12194, Research Triangle Park, NC, 27709, USA.
| | - Christina A Markunas
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, 3040 East Cornwallis Road, P. O. Box 12194, Research Triangle Park, NC, 27709, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Eric O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
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Hartz SM, Horton A, Oehlert M, Carey CE, Agrawal A, Bogdan R, Chen LS, Hancock DB, Johnson EO, Pato C, Pato M, Rice JP, Bierut LJ. Association Between Substance Use Disorder and Polygenic Liability to Schizophrenia. Biol Psychiatry 2017; 82:709-715. [PMID: 28739213 PMCID: PMC5643224 DOI: 10.1016/j.biopsych.2017.04.020] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/19/2017] [Accepted: 04/30/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND There are high levels of comorbidity between schizophrenia and substance use disorder, but little is known about the genetic etiology of this comorbidity. METHODS We tested the hypothesis that shared genetic liability contributes to the high rates of comorbidity between schizophrenia and substance use disorder. To do this, polygenic risk scores for schizophrenia derived from a large meta-analysis by the Psychiatric Genomics Consortium were computed in three substance use disorder datasets: the Collaborative Genetic Study of Nicotine Dependence (ascertained for tobacco use disorder; n = 918 cases; 988 control subjects), the Collaborative Study on the Genetics of Alcoholism (ascertained for alcohol use disorder; n = 643 cases; 384 control subjects), and the Family Study of Cocaine Dependence (ascertained for cocaine use disorder; n = 210 cases; 317 control subjects). Phenotypes were harmonized across the three datasets and standardized analyses were performed. Genome-wide genotypes were imputed to the 1000 Genomes reference panel. RESULTS In each individual dataset and in the mega-analysis, strong associations were observed between any substance use disorder diagnosis and the polygenic risk score for schizophrenia (mega-analysis pseudo-R2 range 0.8-3.7%; minimum p = 4 × 10-23). CONCLUSIONS These results suggest that comorbidity between schizophrenia and substance use disorder is partially attributable to shared polygenic liability. This shared liability is most consistent with a general risk for substance use disorder rather than specific risks for individual substance use disorders and adds to increasing evidence of a blurred boundary between schizophrenia and substance use disorder.
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Affiliation(s)
| | - Amy Horton
- Washington University in St. Louis, MO, USA
| | - Mary Oehlert
- VA Eastern Kansas Health Care System, Leavenworth, KS, USA,The University of Kansas Medical Center, Kansas City, KS, USA
| | | | | | | | | | | | | | - Carlos Pato
- SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Michele Pato
- SUNY Downstate Medical Center, Brooklyn, NY, USA
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47
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McKay JD, Hung RJ, Han Y, Zong X, Carreras-Torres R, Christiani DC, Caporaso NE, Johansson M, Xiao X, Li Y, Byun J, Dunning A, Pooley KA, Qian DC, Ji X, Liu G, Timofeeva MN, Bojesen SE, Wu X, Le Marchand L, Albanes D, Bickeböller H, Aldrich MC, Bush WS, Tardon A, Rennert G, Teare MD, Field JK, Kiemeney LA, Lazarus P, Haugen A, Lam S, Schabath MB, Andrew AS, Shen H, Hong YC, Yuan JM, Bertazzi PA, Pesatori AC, Ye Y, Diao N, Su L, Zhang R, Brhane Y, Leighl N, Johansen JS, Mellemgaard A, Saliba W, Haiman CA, Wilkens LR, Fernandez-Somoano A, Fernandez-Tardon G, van der Heijden HF, Kim JH, Dai J, Hu Z, Davies MPA, Marcus MW, Brunnström H, Manjer J, Melander O, Muller DC, Overvad K, Trichopoulou A, Tumino R, Doherty JA, Barnett MP, Chen C, Goodman GE, Cox A, Taylor F, Woll P, Brüske I, Wichmann HE, Manz J, Muley TR, Risch A, Rosenberger A, Grankvist K, Johansson M, Shepherd FA, Tsao MS, Arnold SM, Haura EB, Bolca C, Holcatova I, Janout V, Kontic M, Lissowska J, Mukeria A, Ognjanovic S, Orlowski TM, Scelo G, Swiatkowska B, Zaridze D, Bakke P, Skaug V, Zienolddiny S, Duell EJ, Butler LM, Koh WP, Gao YT, Houlston RS, McLaughlin J, Stevens VL, Joubert P, Lamontagne M, Nickle DC, Obeidat M, Timens W, Zhu B, Song L, Kachuri L, Artigas MS, Tobin MD, Wain LV, Rafnar T, Thorgeirsson TE, Reginsson GW, Stefansson K, Hancock DB, Bierut LJ, Spitz MR, Gaddis NC, Lutz SM, Gu F, Johnson EO, Kamal A, Pikielny C, Zhu D, Lindströem S, Jiang X, Tyndale RF, Chenevix-Trench G, Beesley J, Bossé Y, Chanock S, Brennan P, Landi MT, Amos CI. Large-scale association analysis identifies new lung cancer susceptibility loci and heterogeneity in genetic susceptibility across histological subtypes. Nat Genet 2017; 49:1126-1132. [PMID: 28604730 PMCID: PMC5510465 DOI: 10.1038/ng.3892] [Citation(s) in RCA: 365] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 05/10/2017] [Indexed: 12/15/2022]
Abstract
Although several lung cancer susceptibility loci have been identified, much of the heritability for lung cancer remains unexplained. Here 14,803 cases and 12,262 controls of European descent were genotyped on the OncoArray and combined with existing data for an aggregated genome-wide association study (GWAS) analysis of lung cancer in 29,266 cases and 56,450 controls. We identified 18 susceptibility loci achieving genome-wide significance, including 10 new loci. The new loci highlight the striking heterogeneity in genetic susceptibility across the histological subtypes of lung cancer, with four loci associated with lung cancer overall and six loci associated with lung adenocarcinoma. Gene expression quantitative trait locus (eQTL) analysis in 1,425 normal lung tissue samples highlights RNASET2, SECISBP2L and NRG1 as candidate genes. Other loci include genes such as a cholinergic nicotinic receptor, CHRNA2, and the telomere-related genes OFBC1 and RTEL1. Further exploration of the target genes will continue to provide new insights into the etiology of lung cancer.
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Affiliation(s)
- James D. McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | - Younghun Han
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Xuchen Zong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | | | - David C. Christiani
- Department of Environmental Health, Harvard TH Chan School of Public Health, and Massachusetts General Hospital/Harvard Medical School, Boston, MA. 02115
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Yafang Li
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Jinyoung Byun
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Alison Dunning
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Karen A. Pooley
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - David C. Qian
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Xuemei Ji
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Geoffrey Liu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | - Maria N. Timofeeva
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Stig E. Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen, Denmark
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Germany
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center
| | - William S. Bush
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, OH
| | - Adonina Tardon
- University of Oviedo and CIBERESP, Faculty of Medicine, Campus del Cristo s/n, 33006 Oviedo, Spain
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - M. Dawn Teare
- School of Health and Related Research, University of Sheffield, England, UK
| | - John K. Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | | | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, Washington, USA
| | - Aage Haugen
- National Institute of Occupational Health, Oslo, Norway
| | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, Canada
| | - Matthew B. Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | | | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- University of Pittsburgh Cancer Institute, Pittsburgh, USA
| | - Pier Alberto Bertazzi
- Department of Preventive Medicine, IRCCS Foundation Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health – DISCCO, University of Milan, Milan, Italy
| | - Angela C. Pesatori
- Department of Clinical Sciences and Community Health – DISCCO, University of Milan, Milan, Italy
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Nancy Diao
- Department of Environmental Health, Harvard TH Chan School of Public Health, and Massachusetts General Hospital/Harvard Medical School, Boston, MA. 02115
| | - Li Su
- Department of Environmental Health, Harvard TH Chan School of Public Health, and Massachusetts General Hospital/Harvard Medical School, Boston, MA. 02115
| | - Ruyang Zhang
- Department of Environmental Health, Harvard TH Chan School of Public Health, and Massachusetts General Hospital/Harvard Medical School, Boston, MA. 02115
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | - Natasha Leighl
- University Health Network- The Princess Margaret Cancer Centre, Toronto, CA
| | - Jakob S. Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Anders Mellemgaard
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Walid Saliba
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Ana Fernandez-Somoano
- University of Oviedo and CIBERESP, Faculty of Medicine, Campus del Cristo s/n, 33006 Oviedo, Spain
| | | | | | - Jin Hee Kim
- Department of Integrative Bioscience & Biotechnology, Sejong University, Gwangjin-gu, Seoul, Republic of Korea
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Michael PA Davies
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael W. Marcus
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | | | - Jonas Manjer
- Faculty of Medicine, Lund University, Lund, Sweden
| | | | - David C. Muller
- School of Public Health, St Mary’s Campus, Imperial College London, UK
| | - Kim Overvad
- Section for Epidemiology, Department of Public Health, Aarhus University, Denmark
| | | | - Rosario Tumino
- Tumino. Molecular and Nutritional Epidemiology Unit CSPO (Cancer Research and Prevention Centre), Scientific Institute of Tuscany, Florence, Italy
| | - Jennifer A. Doherty
- Department of Epidemiology, Geisel School of Medicine, Hanover, NH
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Huntsman Cancer Institute, 2000 Circle of Hope, Salt Lake City, UT 84112
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Matt P. Barnett
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chu Chen
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Angela Cox
- Department of Oncology, University of Sheffield, Sheffield, UK
| | - Fiona Taylor
- Department of Oncology, University of Sheffield, Sheffield, UK
| | - Penella Woll
- Department of Oncology, University of Sheffield, Sheffield, UK
| | - Irene Brüske
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - H.-Erich Wichmann
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Germany
| | - Judith Manz
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas R. Muley
- Thoraxklinik at University Hospital Heidelberg
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany
| | - Angela Risch
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Thoraxklinik at University Hospital Heidelberg
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
- University of Salzburg and Cancer Cluster Salzburg, Austria
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Germany
| | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | | | | | - Susanne M. Arnold
- University of Kentucky, Markey Cancer Center, Lexington, Kentucky, USA
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Ciprian Bolca
- Institute of Pneumology “Marius Nasta”, Bucharest, Romania
| | - Ivana Holcatova
- 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Milica Kontic
- Clinical Center of Serbia, Belgrade. School of Medicine, University of Belgrade
| | - Jolanta Lissowska
- M. Sklodowska-Curie Cancer Center, Institute of Oncology, Warsaw, Poland
| | - Anush Mukeria
- Department of Epidemiology and Prevention, Russian N.N.Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Simona Ognjanovic
- International Organization for Cancer Prevention and Research, Belgrade, Serbia
| | - Tadeusz M. Orlowski
- Department of Surgery, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Ghislaine Scelo
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz, Poland
| | - David Zaridze
- Department of Epidemiology and Prevention, Russian N.N.Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Vidar Skaug
- National Institute of Occupational Health, Oslo, Norway
| | | | - Eric J. Duell
- Unit of Nutrition and Cancer, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | | | - Woon-Puay Koh
- Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, China
| | | | | | | | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Maxime Lamontagne
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
| | - David C. Nickle
- Merck Research Laboratories, Genetics and Pharmacogenomics, Boston, MA, USA
| | - Ma’en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Wim Timens
- University of Groningen, Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, The Netherlands
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Linda Kachuri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - SpiroMeta Consortium
- SpiroMeta Consortium see Supplemental Materials for full list of participating members
| | | | | | | | | | - Dana B. Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, North Carolina, USA
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Nathan C. Gaddis
- Research Computing Division, RTI International, Research Triangle Park, North Carolina, USA
| | - Sharon M. Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Fangyi Gu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Eric O. Johnson
- Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, North Carolina, USA
| | - Ahsan Kamal
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Claudio Pikielny
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Dakai Zhu
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Sara Lindströem
- Department of Epidemiology, University of Washington, 1959 NE Pacific Street, Health Sciences Bldg., F-247B, Box 357236, Seattle, WA 98195
| | - Xia Jiang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115
| | - Rachel F. Tyndale
- Departments of Pharmacology and Toxicology & Psychiatry, Toronto, Ontario, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | | | - Jonathan Beesley
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
- Department of Molecular Medicine, Laval University, Québec, Canada
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
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48
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Aschard H, Tobin MD, Hancock DB, Skurnik D, Sood A, James A, Vernon Smith A, Manichaikul AW, Campbell A, Prins BP, Hayward C, Loth DW, Porteous DJ, Strachan DP, Zeggini E, O’Connor GT, Brusselle GG, Boezen HM, Schulz H, Deary IJ, Hall IP, Rudan I, Kaprio J, Wilson JF, Wilk JB, Huffman JE, Hua Zhao J, de Jong K, Lyytikäinen LP, Wain LV, Jarvelin MR, Kähönen M, Fornage M, Polasek O, Cassano PA, Barr RG, Rawal R, Harris SE, Gharib SA, Enroth S, Heckbert SR, Lehtimäki T, Gyllensten U, Jackson VE, Gudnason V, Tang W, Dupuis J, Soler Artigas M, Joshi AD, London SJ, Kraft P. Evidence for large-scale gene-by-smoking interaction effects on pulmonary function. Int J Epidemiol 2017; 46:894-904. [PMID: 28082375 PMCID: PMC5837518 DOI: 10.1093/ije/dyw318] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2016] [Indexed: 01/23/2023] Open
Abstract
Background Smoking is the strongest environmental risk factor for reduced pulmonary function. The genetic component of various pulmonary traits has also been demonstrated, and at least 26 loci have been reproducibly associated with either FEV 1 (forced expiratory volume in 1 second) or FEV 1 /FVC (FEV 1 /forced vital capacity). Although the main effects of smoking and genetic loci are well established, the question of potential gene-by-smoking interaction effect remains unanswered. The aim of the present study was to assess, using a genetic risk score approach, whether the effect of these 26 loci on pulmonary function is influenced by smoking. Methods We evaluated the interaction between smoking exposure, considered as either ever vs never or pack-years, and a 26-single nucleotide polymorphisms (SNPs) genetic risk score in relation to FEV 1 or FEV 1 /FVC in 50 047 participants of European ancestry from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) and SpiroMeta consortia. Results We identified an interaction ( βint = -0.036, 95% confidence interval, -0.040 to -0.032, P = 0.00057) between an unweighted 26 SNP genetic risk score and smoking status (ever/never) on the FEV 1 /FVC ratio. In interpreting this interaction, we showed that the genetic risk of falling below the FEV /FVC threshold used to diagnose chronic obstructive pulmonary disease is higher among ever smokers than among never smokers. A replication analysis in two independent datasets, although not statistically significant, showed a similar trend in the interaction effect. Conclusions This study highlights the benefit of using genetic risk scores for identifying interactions missed when studying individual SNPs and shows, for the first time, that persons with the highest genetic risk for low FEV 1 /FVC may be more susceptible to the deleterious effects of smoking.
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Affiliation(s)
- Hugues Aschard
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA,Program in Genetic Epidemiology and Statistical Genetics, Harvard TH Chan School of Public Health, Boston, MA, USA,Corresponding author. Department of Epidemiology, Harvard School of Public Health, Building 2, Room 205, 665 Huntington Avenue, Boston, MA 02115, USA. E-mail:
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK,National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Dana B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Research Division, Research Triangle Institute (RTI) International, Research Triangle Park, NC, USA
| | - David Skurnik
- Division of Infectious Diseases, Brigham and Women Hospital, Harvard Medical School, Boston, MA, USA
| | - Akshay Sood
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Alan James
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia,School of Medicine and Pharmacology, University of Western Australia, Crawley, Australia
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur, Iceland,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA,Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, VA, USA
| | - Archie Campbell
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK,Generation Scotland, Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - Bram P Prins
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Daan W Loth
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - David J Porteous
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK,Generation Scotland, Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - David P Strachan
- Population Health Research Institute, St George’s University of London, London, UK
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - George T O’Connor
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA,The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Guy G Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands,Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium,Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Ian P Hall
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, Finland,Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland,National Institute for Health and Welfare, Department of Health, Helsinki, Finland
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Jemma B Wilk
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
| | - Jennifer E Huffman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK,Institute of Metabolic Science, Biomedical Campus, Cambridge, UK
| | - Kim de Jong
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland,Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK,National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC–PHE Centre for Environment & Health, School of Public Health, Imperial College London, UK,Center for Life Course Epidemiology, Faculty of Medicine, University of Oulu, Oulu, Finland,Biocenter Oulu, University of Oulu, Oulu, Finland,Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ozren Polasek
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK,Faculty of Medicine, University of Split, Split, Croatia
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA,Department of Healthcare Policy and Research, Weill Cornell Medical College, NY, NY, USA
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University Medical Center
| | - Rajesh Rawal
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sarah E Harris
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Sina A Gharib
- Computational Medicine Core at Center for Lung Biology, Division of Pulmonary & Critical Care Medicine, University of Washington, Seattle, WA,Cardiovascular Health Research Unit and Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Uppsala, Sweden
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland,Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Uppsala, Sweden
| | | | - Victoria E Jackson
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA,Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
| | - Josée Dupuis
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Amit D Joshi
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA,Program in Genetic Epidemiology and Statistical Genetics, Harvard TH Chan School of Public Health, Boston, MA, USA,Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA. Human Services, Research Triangle Park, NC, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA,Program in Genetic Epidemiology and Statistical Genetics, Harvard TH Chan School of Public Health, Boston, MA, USA
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49
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Markunas CA, Johnson EO, Hancock DB. Comprehensive evaluation of disease- and trait-specific enrichment for eight functional elements among GWAS-identified variants. Hum Genet 2017; 136:911-919. [PMID: 28567521 DOI: 10.1007/s00439-017-1815-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/22/2017] [Indexed: 01/17/2023]
Abstract
Genome-wide association study (GWAS)-identified variants are enriched for functional elements. However, we have limited knowledge of how functional enrichment may differ by disease/trait and tissue type. We tested a broad set of eight functional elements for enrichment among GWAS-identified SNPs (p < 5×10-8) from the NHGRI-EBI Catalog across seven disease/trait categories: cancer, cardiovascular disease, diabetes, autoimmune disease, psychiatric disease, neurological disease, and anthropometric traits. SNPs were annotated using HaploReg for the eight functional elements across any tissue: DNase sites, expression quantitative trait loci (eQTL), sequence conservation, enhancers, promoters, missense variants, sequence motifs, and protein binding sites. In addition, tissue-specific annotations were considered for brain vs. blood. Disease/trait SNPs were compared to a control set of 4809 SNPs matched to the GWAS SNPs (N = 1639) on allele frequency, gene density, distance to nearest gene, and linkage disequilibrium at ~3:1 ratio. Enrichment analyses were conducted using logistic regression, with Bonferroni correction. Overall, a significant enrichment was observed for all functional elements, except sequence motifs. Missense SNPs showed the strongest magnitude of enrichment. eQTLs were the only functional element significantly enriched across all diseases/traits. Magnitudes of enrichment were generally similar across diseases/traits, where enrichment was statistically significant. Blood vs. brain tissue effects on enrichment were dependent on disease/trait and functional element (e.g., cardiovascular disease: eQTLs P TissueDifference = 1.28 × 10-6 vs. enhancers P TissueDifference = 0.94). Identifying disease/trait-relevant functional elements and tissue types could provide new insight into the underlying biology, by guiding a priori GWAS analyses (e.g., brain enhancer elements for psychiatric disease) or facilitating post hoc interpretation.
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Affiliation(s)
- Christina A Markunas
- Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA.
| | - Eric O Johnson
- Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA.,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Dana B Hancock
- Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
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50
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Johnson EO, Hancock DB, Levy JL, Gaddis NC, Page GP, Glasheen C, Saccone NL, Bierut LJ, Kral AH. KAT2B polymorphism identified for drug abuse in African Americans with regulatory links to drug abuse pathways in human prefrontal cortex. Addict Biol 2016. [PMID: 26202629 DOI: 10.1111/adb.12286] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Drug abuse is a common and heritable set of disorders, but the underlying genetic factors are largely unknown. We conducted genome-wide association studies of drug abuse using 7 million imputed single nucleotide polymorphisms (SNPs) and insertions/deletions in African Americans (AAs; n = 3742) and European Americans (EAs; n = 6845). Cases were drawn from the Urban Health Study of street-recruited people, who injected drugs and reported abusing opioids, cocaine, marijuana, stimulants and/or other drugs 10 or more times in the past 30 days, and were compared with population controls. Independent replication testing was conducted in 755 AAs and 1131 EAs from the Genetic Association Information Network. An intronic SNP (rs9829896) in the K(lysine) acetyltransferase 2B (KAT2B) gene was significantly associated with drug abuse in AAs (P = 4.63 × 10-8 ) and independently replicated in AAs (P = 0.0019). The rs9829896-C allele (frequency = 12%) had odds ratios of 0.68 and 0.53 across the AA cohorts: meta-analysis P = 3.93 × 10-10 . Rs9829896-C was not associated with drug abuse across the EA cohorts: frequency = 36% and meta-analysis P = 0.12. Using dorsolateral prefrontal cortex data from the BrainCloud cohort, we found that rs9829896-C was associated with reduced KAT2B expression in AAs (n = 113, P = 0.050) but not EAs (n = 110, P = 0.39). KAT2B encodes a transcriptional regulator in the cyclic adenosine monophosphate and dopamine signaling pathways, and rs9829896-C was associated with expression of genes in these pathways: reduced CREBBP expression (P = 0.011) and increased OPRM1 expression (P = 0.016), both in AAs only. Our study identified the KAT2B SNP rs9829896 as having novel and biologically plausible associations with drug abuse and gene expression in AAs but not EAs, suggesting ancestry-specific effects.
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Affiliation(s)
- Eric O. Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division; RTI International; Research Triangle Park NC USA
| | - Dana B. Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division; RTI International; Research Triangle Park NC USA
| | - Joshua L. Levy
- Research Computing Division; RTI International; Research Triangle Park NC USA
| | - Nathan C. Gaddis
- Research Computing Division; RTI International; Research Triangle Park NC USA
| | - Grier P. Page
- Fellow Program, Center for Genomics in Public Health and Medicine, and Genomics, Statistical Genetics, and Environmental Research Program; RTI International; Atlanta GA USA
| | - Cristie Glasheen
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division; RTI International; Research Triangle Park NC USA
| | - Nancy L. Saccone
- Department of Genetics; Washington University School of Medicine; St. Louis MO USA
| | - Laura J. Bierut
- Department of Psychiatry; Washington University School of Medicine; St. Louis MO USA
| | - Alex H. Kral
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division; RTI International; San Francisco CA USA
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