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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:S0002-9165(24)00342-3. [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] [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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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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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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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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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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6
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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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7
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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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8
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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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9
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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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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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11
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Hancock DB, Levy JL, Gaddis NC, Glasheen C, Saccone NL, Page GP, Bierut LJ, Kral AH, Johnson EO. Replication of ZNF804A gene variant associations with risk of heroin addiction. Genes Brain Behav 2015; 14:635-40. [PMID: 26382569 DOI: 10.1111/gbb.12254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/28/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022]
Abstract
Heroin addiction is heritable, but few specific genetic variants have been reproducibly associated with this disease. The zinc finger protein 804A (ZNF804A) gene is a biologically plausible susceptibility gene for heroin addiction, given its function as a transcription factor in human brain. Novel associations of two common ZNF804A single nucleotide polymorphisms (SNPs), rs7597593 and rs1344706, with heroin addiction have been reported in Han Chinese. Both SNPs have also been implicated for regulating ZNF804A expression in human brain, including the addiction-relevant dorsolateral prefrontal cortex. In this independent replication study, we tested the rs7597593 and rs1344706 SNP genotypes and their corresponding haplotypes for association with heroin addiction using cases drawn from the Urban Health Study and population controls: total N = 10 757 [7095 European Americans (EAs) and 3662 African Americans (AAs)]. We independently replicated both ZNF804A SNP associations in EAs: the rs7597593-T (P = 0.016) and rs1344706-A (P = 0.029) alleles both being associated with increased risk of heroin addiction, consistent with the prior report. Neither SNP was associated in AAs alone, but meta-analysis across both ancestry groups resulted in significant associations for rs1344706-A [P = 0.016, odds ratio (95% confidence interval) = 1.13 (1.02-1.25)] and its haplotype with rs7597593-T [P = 0.0067, odds ratio (95% confidence interval) = 1.16 (1.04-1.29)]. By showing consistent associations across independent studies and diverse ancestry groups, our study provides evidence that these two ZNF804A SNPs and their risk haplotype are among the few replicable genetic associations with heroin addiction.
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Affiliation(s)
- D B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, NC, USA
| | - J L Levy
- Research Computing Division, RTI International, Research Triangle Park, NC, USA
| | - N C Gaddis
- Research Computing Division, RTI International, Research Triangle Park, NC, USA
| | - C Glasheen
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, NC, USA
| | - N L Saccone
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - G P Page
- Fellow Program, Center for Genomics in Public Health and Medicine, RTI International, Atlanta, GA, USA
| | - L J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - A H Kral
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, San Francisco, CA, USA
| | - E O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
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12
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Hancock DB, Reginsson GW, Gaddis NC, Chen X, Saccone NL, Lutz SM, Qaiser B, Sherva R, Steinberg S, Zink F, Stacey SN, Glasheen C, Chen J, Gu F, Frederiksen BN, Loukola A, Gudbjartsson DF, Brüske I, Landi MT, Bickeböller H, Madden P, Farrer L, Kaprio J, Kranzler HR, Gelernter J, Baker TB, Kraft P, Amos CI, Caporaso NE, Hokanson JE, Bierut LJ, Thorgeirsson TE, Johnson EO, Stefansson K. Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence. Transl Psychiatry 2015; 5:e651. [PMID: 26440539 PMCID: PMC4930126 DOI: 10.1038/tp.2015.149] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [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: 06/26/2015] [Accepted: 08/19/2015] [Indexed: 01/04/2023] Open
Abstract
We conducted a 1000 Genomes-imputed genome-wide association study (GWAS) meta-analysis for nicotine dependence, defined by the Fagerström Test for Nicotine Dependence in 17 074 ever smokers from five European-ancestry samples. We followed up novel variants in 7469 ever smokers from five independent European-ancestry samples. We identified genome-wide significant association in the alpha-4 nicotinic receptor subunit (CHRNA4) gene on chromosome 20q13: lowest P=8.0 × 10(-9) across all the samples for rs2273500-C (frequency=0.15; odds ratio=1.12 and 95% confidence interval=1.08-1.17 for severe vs mild dependence). rs2273500-C, a splice site acceptor variant resulting in an alternate CHRNA4 transcript predicted to be targeted for nonsense-mediated decay, was associated with decreased CHRNA4 expression in physiologically normal human brains (lowest P=7.3 × 10(-4)). Importantly, rs2273500-C was associated with increased lung cancer risk (N=28 998, odds ratio=1.06 and 95% confidence interval=1.00-1.12), likely through its effect on smoking, as rs2273500-C was no longer associated with lung cancer after adjustment for smoking. Using criteria for smoking behavior that encompass more than the single 'cigarettes per day' item, we identified a common CHRNA4 variant with important regulatory properties that contributes to nicotine dependence and smoking-related consequences.
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Affiliation(s)
- D B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Research Division, Research Triangle Institute International, Research Triangle Park, NC, USA,Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Research Division, Research Triangle Institute International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA. E-mail:
| | | | - N C Gaddis
- Research Computing Division, Research Triangle Institute International, Research Triangle Park, NC, USA
| | - X Chen
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA,Nevada Institute of Personalized Medicine and Department of Psychology, University of Nevada, Las Vegas, NV, USA
| | - N L Saccone
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - S M Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - B Qaiser
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - R Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | | | - F Zink
- deCODE Genetics/Amgen, Reykjavik, Iceland
| | - S N Stacey
- deCODE Genetics/Amgen, Reykjavik, Iceland
| | - C Glasheen
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Research Division, Research Triangle Institute International, Research Triangle Park, NC, USA
| | - J Chen
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - 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
| | | | - A Loukola
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - I Brüske
- Institute of Epidemiology I, German Research Center for Environmental Health, Neuherberg, Germany
| | - 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
| | - H Bickeböller
- Department of Genetic Epidemiology, University of Göttingen—Georg-August University Göttingen, Göttingen, Germany
| | - P Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - L 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 Genetics and Genomics, 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 Kaprio
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland,National Institute for Health and Welfare, Helsinki, Finland,Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - H R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA,VISN 4 Mental Illness Research, Education and Clinical Center, Philadelphia VA Medical Center, Philadelphia, PA, 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 Neurobiology, Yale University School of Medicine, New Haven, CT, USA,VA CT Healthcare Center, Department of Psychiatry, West Haven, CT, USA
| | - T B Baker
- Center for Tobacco Research and Intervention, University of Wisconsin, Madison, WI, USA
| | - P Kraft
- Department of Epidemiology, Harvard University School of Public Health, Boston, MA, USA,Department of Biostatistics, Harvard University School of Public Health, Boston, MA, USA
| | - C I Amos
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA,Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanoven, NH, USA
| | - 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 School of Medicine, St. Louis, MO, USA
| | | | - E O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Research Division, Research Triangle Institute International, Research Triangle Park, NC, USA
| | - K Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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Hancock DB, Levy JL, Gaddis NC, Glasheen C, Saccone NL, Page GP, Hulse G, Wildenauer D, Kelty E, Schwab S, Degenhardt L, Martin NG, Montgomery GW, Attia J, Holliday EG, McEvoy M, Scott RJ, Bierut LJ, Nelson EC, Kral A, Johnson EO. Cis-Expression Quantitative Trait Loci Mapping Reveals Replicable Associations with Heroin Addiction in OPRM1. Biol Psychiatry 2015; 78:474-84. [PMID: 25744370 PMCID: PMC4519434 DOI: 10.1016/j.biopsych.2015.01.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [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: 10/13/2014] [Revised: 12/18/2014] [Accepted: 01/08/2015] [Indexed: 12/25/2022]
Abstract
BACKGROUND No opioid receptor, mu 1 (OPRM1) gene polymorphisms, including the functional single nucleotide polymorphism (SNP) rs1799971, have been conclusively associated with heroin/other opioid addiction, despite their biological plausibility. We used evidence of polymorphisms altering OPRM1 expression in normal human brain tissue to nominate and then test associations with heroin addiction. METHODS We tested 103 OPRM1 SNPs for association with OPRM1 messenger RNA expression in prefrontal cortex from 224 European Americans and African Americans of the BrainCloud cohort. We then tested the 16 putative cis-expression quantitative trait loci (cis-eQTL) SNPs for association with heroin addiction in the Urban Health Study and two replication cohorts, totaling 16,729 European Americans, African Americans, and Australians of European ancestry. RESULTS Four putative cis-eQTL SNPs were significantly associated with heroin addiction in the Urban Health Study (smallest p = 8.9 × 10(-5)): rs9478495, rs3778150, rs9384169, and rs562859. Rs3778150, located in OPRM1 intron 1, was significantly replicated (p = 6.3 × 10(-5)). Meta-analysis across all case-control cohorts resulted in p = 4.3 × 10(-8): the rs3778150-C allele (frequency = 16%-19%) being associated with increased heroin addiction risk. Importantly, the functional SNP allele rs1799971-A was associated with heroin addiction only in the presence of rs3778150-C (p = 1.48 × 10(-6) for rs1799971-A/rs3778150-C and p = .79 for rs1799971-A/rs3778150-T haplotypes). Lastly, replication was observed for six other intron 1 SNPs that had prior suggestive associations with heroin addiction (smallest p = 2.7 × 10(-8) for rs3823010). CONCLUSIONS Our findings show that common OPRM1 intron 1 SNPs have replicable associations with heroin addiction. The haplotype structure of rs3778150 and nearby SNPs may underlie the inconsistent associations between rs1799971 and heroin addiction.
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Affiliation(s)
- Dana B. Hancock
- Behavioral Health Epidemiology Program, Research Triangle Institute, Research Triangle Park, NC
| | - Joshua L. Levy
- Research Computing Division, RTI International, Research Triangle Park, NC
| | - Nathan C. Gaddis
- Research Computing Division, RTI International, Research Triangle Park, NC
| | - Cristie Glasheen
- Behavioral Health Epidemiology Program, Research Triangle Institute, Research Triangle Park, NC
| | - Nancy L. Saccone
- Department of Genetics, Washington University in St. Louis, St. Louis, MO
| | - Grier P. Page
- Center for Public Health Genomics, RTI International, Atlanta, GA
| | - Gary Hulse
- School of Psychiatry and Clinical Neurosciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Dieter Wildenauer
- School of Psychiatry and Clinical Neurosciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Erin Kelty
- School of Psychiatry and Clinical Neurosciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Sibylle Schwab
- Department of Psychiatry and Psychotherapy, University of Erlangen-Nuremberg, Erlangen, Germany,Faculty of Science, Medicine, and Health, University of Wollongong, Wollongong, Australia
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre, University of New South Wales, Sydney, Australia
| | - Nicholas G. Martin
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Grant W. Montgomery
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John Attia
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia,Clinical Research Design, IT and Statistical Support Unit, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Elizabeth G. Holliday
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia,Clinical Research Design, IT and Statistical Support Unit, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Mark McEvoy
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia,Public Health Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Rodney J. Scott
- Center for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia,School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia,Division of Genetics, Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - Laura J. Bierut
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO
| | - Elliot C. Nelson
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO
| | - Alex Kral
- Urban Health Program, Research Triangle Institute, San Francisco, CA
| | - Eric O. Johnson
- Behavioral Health Epidemiology Program, Research Triangle Institute, Research Triangle Park, NC
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14
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Hancock DB, Wang JC, Gaddis NC, Levy JL, Saccone NL, Stitzel JA, Goate A, Bierut LJ, Johnson EO. A multiancestry study identifies novel genetic associations with CHRNA5 methylation in human brain and risk of nicotine dependence. Hum Mol Genet 2015. [PMID: 26220977 DOI: 10.1093/hmg/ddv303] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Nicotine dependence is influenced by chromosome 15q25.1 single nucleotide polymorphisms (SNPs), including the missense SNP rs16969968 that alters function of the α5 nicotinic acetylcholine receptor (CHRNA5) and noncoding SNPs that regulate CHRNA5 mRNA expression. We tested for cis-methylation quantitative trait loci (cis-meQTLs) using SNP genotypes and DNA methylation levels measured across the IREB2-HYKK-PSMA4-CHRNA5-CHRNA3-CHRNB4 genes on chromosome 15q25.1 in the BrainCloud and Brain QTL cohorts [total N = 175 European-Americans and 65 African-Americans (AAs)]. We identified eight SNPs that were significantly associated with CHRNA5 methylation in prefrontal cortex: P ranging from 6.0 × 10(-10) to 5.6 × 10(-5). These SNP-methylation associations were also significant in frontal cortex, temporal cortex and pons: P ranging from 4.8 × 10(-12) to 3.4 × 10(-3). Of the eight cis-meQTL SNPs, only the intronic CHRNB4 SNP rs11636753 was associated with CHRNA5 methylation independently of the known SNP effects in prefrontal cortex, and it was the most significantly associated SNP with nicotine dependence across five independent cohorts (total N = 7858 European ancestry and 3238 AA participants): P = 6.7 × 10(-4), odds ratio (OR) [95% confidence interval (CI)] = 1.11 (1.05-1.18). The rs11636753 major allele (G) was associated with lower CHRNA5 DNA methylation, lower CHRNA5 mRNA expression and increased nicotine dependence risk. Haplotype analyses showed that rs11636753-G and the functional rs16969968-A alleles together increased risk of nicotine dependence more than each variant alone: P = 3.1 × 10(-12), OR (95% CI) = 1.32 (1.22-1.43). Our findings identify a novel regulatory SNP association with nicotine dependence and connect, for the first time, previously observed differences in CHRNA5 mRNA expression and nicotine dependence risk to underlying DNA methylation differences.
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Affiliation(s)
- Dana B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division,
| | - Jen-Chyong Wang
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | | | - Jerry A Stitzel
- Department of Integrative Physiology, University of Colorado, Boulder, CO 80309, USA
| | - Alison Goate
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, USA and
| | - Eric O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division, Research Triangle Institute (RTI) International, Research Triangle Park, NC 27709, USA
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15
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Johnson EO, Hancock DB, Gaddis NC, Levy JL, Page G, Novak SP, Glasheen C, Saccone NL, Rice JP, Moreau MP, Doheny KF, Romm JM, Brooks AI, Kral AH. Correction: Novel Genetic Locus Implicated for HIV-1 Acquisition with Putative Regulatory Links to HIV Replication and Infectivity: A Genome-Wide Association Study. PLoS One 2015; 10:e0129671. [PMID: 26023777 PMCID: PMC4448994 DOI: 10.1371/journal.pone.0129671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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16
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Johnson EO, Hancock DB, Gaddis NC, Levy JL, Page G, Novak SP, Glasheen C, Saccone NL, Rice JP, Moreau MP, Doheny KF, Romm JM, Brooks AI, Aouizerat BE, Bierut LJ, Kral AH. Novel genetic locus implicated for HIV-1 acquisition with putative regulatory links to HIV replication and infectivity: a genome-wide association study. PLoS One 2015; 10:e0118149. [PMID: 25786224 PMCID: PMC4364715 DOI: 10.1371/journal.pone.0118149] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 06/05/2014] [Accepted: 01/05/2015] [Indexed: 11/18/2022] Open
Abstract
Fifty percent of variability in HIV-1 susceptibility is attributable to host genetics. Thus identifying genetic associations is essential to understanding pathogenesis of HIV-1 and important for targeting drug development. To date, however, CCR5 remains the only gene conclusively associated with HIV acquisition. To identify novel host genetic determinants of HIV-1 acquisition, we conducted a genome-wide association study among a high-risk sample of 3,136 injection drug users (IDUs) from the Urban Health Study (UHS). In addition to being IDUs, HIV- controls were frequency-matched to cases on environmental exposures to enhance detection of genetic effects. We tested independent replication in the Women’s Interagency HIV Study (N=2,533). We also examined publicly available gene expression data to link SNPs associated with HIV acquisition to known mechanisms affecting HIV replication/infectivity. Analysis of the UHS nominated eight genetic regions for replication testing. SNP rs4878712 in FRMPD1 met multiple testing correction for independent replication (P=1.38x10-4), although the UHS-WIHS meta-analysis p-value did not reach genome-wide significance (P=4.47x10-7 vs. P<5.0x10-8) Gene expression analyses provided promising biological support for the protective G allele at rs4878712 lowering risk of HIV: (1) the G allele was associated with reduced expression of FBXO10 (r=-0.49, P=6.9x10-5); (2) FBXO10 is a component of the Skp1-Cul1-F-box protein E3 ubiquitin ligase complex that targets Bcl-2 protein for degradation; (3) lower FBXO10 expression was associated with higher BCL2 expression (r=-0.49, P=8x10-5); (4) higher basal levels of Bcl-2 are known to reduce HIV replication and infectivity in human and animal in vitro studies. These results suggest new potential biological pathways by which host genetics affect susceptibility to HIV upon exposure for follow-up in subsequent studies.
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Affiliation(s)
- Eric O. Johnson
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
- * E-mail:
| | - Dana B. Hancock
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Nathan C. Gaddis
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Joshua L. Levy
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Grier Page
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Scott P. Novak
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Cristie Glasheen
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Nancy L. Saccone
- Washington University School of Medicine, St. Louis, MO, United States of America
| | - John P. Rice
- Washington University School of Medicine, St. Louis, MO, United States of America
| | - Michael P. Moreau
- Rutgers University Cell and DNA Repository (RUCDR), Piscataway, NJ, United States of America
| | - Kimberly F. Doheny
- Center for Inherited Disease Research (CIDR), Johns Hopkins University, Baltimore, MD, United States of America
| | - Jane M. Romm
- Center for Inherited Disease Research (CIDR), Johns Hopkins University, Baltimore, MD, United States of America
| | - Andrew I. Brooks
- Rutgers University Cell and DNA Repository (RUCDR), Piscataway, NJ, United States of America
| | - Bradley E. Aouizerat
- School of Nursing, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States of America
| | - Laura J. Bierut
- Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alex H. Kral
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
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17
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Johnson EO, Hancock DB, Levy JL, Gaddis NC, Saccone NL, Bierut LJ, Page GP. Imputation across genotyping arrays for genome-wide association studies: assessment of bias and a correction strategy. Hum Genet 2013; 132:509-22. [PMID: 23334152 DOI: 10.1007/s00439-013-1266-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 01/07/2013] [Indexed: 12/20/2022]
Abstract
A great promise of publicly sharing genome-wide association data is the potential to create composite sets of controls. However, studies often use different genotyping arrays, and imputation to a common set of SNPs has shown substantial bias: a problem which has no broadly applicable solution. Based on the idea that using differing genotyped SNP sets as inputs creates differential imputation errors and thus bias in the composite set of controls, we examined the degree to which each of the following occurs: (1) imputation based on the union of genotyped SNPs (i.e., SNPs available on one or more arrays) results in bias, as evidenced by spurious associations (type 1 error) between imputed genotypes and arbitrarily assigned case/control status; (2) imputation based on the intersection of genotyped SNPs (i.e., SNPs available on all arrays) does not evidence such bias; and (3) imputation quality varies by the size of the intersection of genotyped SNP sets. Imputations were conducted in European Americans and African Americans with reference to HapMap phase II and III data. Imputation based on the union of genotyped SNPs across the Illumina 1M and 550v3 arrays showed spurious associations for 0.2 % of SNPs: ~2,000 false positives per million SNPs imputed. Biases remained problematic for very similar arrays (550v1 vs. 550v3) and were substantial for dissimilar arrays (Illumina 1M vs. Affymetrix 6.0). In all instances, imputing based on the intersection of genotyped SNPs (as few as 30 % of the total SNPs genotyped) eliminated such bias while still achieving good imputation quality.
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Affiliation(s)
- Eric O Johnson
- Behavioral Health Epidemiology Program, RTI International, 3040 Cornwallis Road, PO Box 12194, Research Triangle Park, NC 27709-12194, USA.
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18
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Hancock DB, Levy JL, Gaddis NC, Bierut LJ, Saccone NL, Page GP, Johnson EO. Assessment of genotype imputation performance using 1000 Genomes in African American studies. PLoS One 2012; 7:e50610. [PMID: 23226329 PMCID: PMC3511547 DOI: 10.1371/journal.pone.0050610] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [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] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/26/2012] [Indexed: 11/19/2022] Open
Abstract
Genotype imputation, used in genome-wide association studies to expand coverage of single nucleotide polymorphisms (SNPs), has performed poorly in African Americans compared to less admixed populations. Overall, imputation has typically relied on HapMap reference haplotype panels from Africans (YRI), European Americans (CEU), and Asians (CHB/JPT). The 1000 Genomes project offers a wider range of reference populations, such as African Americans (ASW), but their imputation performance has had limited evaluation. Using 595 African Americans genotyped on Illumina's HumanHap550v3 BeadChip, we compared imputation results from four software programs (IMPUTE2, BEAGLE, MaCH, and MaCH-Admix) and three reference panels consisting of different combinations of 1000 Genomes populations (February 2012 release): (1) 3 specifically selected populations (YRI, CEU, and ASW); (2) 8 populations of diverse African (AFR) or European (AFR) descent; and (3) all 14 available populations (ALL). Based on chromosome 22, we calculated three performance metrics: (1) concordance (percentage of masked genotyped SNPs with imputed and true genotype agreement); (2) imputation quality score (IQS; concordance adjusted for chance agreement, which is particularly informative for low minor allele frequency [MAF] SNPs); and (3) average r2hat (estimated correlation between the imputed and true genotypes, for all imputed SNPs). Across the reference panels, IMPUTE2 and MaCH had the highest concordance (91%-93%), but IMPUTE2 had the highest IQS (81%-83%) and average r2hat (0.68 using YRI+ASW+CEU, 0.62 using AFR+EUR, and 0.55 using ALL). Imputation quality for most programs was reduced by the addition of more distantly related reference populations, due entirely to the introduction of low frequency SNPs (MAF≤2%) that are monomorphic in the more closely related panels. While imputation was optimized by using IMPUTE2 with reference to the ALL panel (average r2hat = 0.86 for SNPs with MAF>2%), use of the ALL panel for African American studies requires careful interpretation of the population specificity and imputation quality of low frequency SNPs.
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Affiliation(s)
- Dana B Hancock
- Behavioral Health Epidemiology Program, Research Triangle Institute International, Research Triangle Park, North Carolina, United States of America.
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19
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Abstract
In the past decade, Caenorhabditis elegans has been used to dissect several genetic pathways involved in immunity; however, little is known about transcription factors that regulate the expression of immune effectors. C. elegans does not appear to have a functional homolog of the key immune transcription factor NF-κB. Here we show that that the intestinal GATA transcription factor ELT-2 is required for both immunity to Salmonella enterica and expression of a C-type lectin gene, clec-67, which is expressed in the intestinal cells and is a good marker of S. enterica infection. We also found that ELT-2 is required for immunity to Pseudomonas aeruginosa, Enterococcus faecalis, and Cryptococcus neoformans. Lack of immune inhibition by DAF-2, which negatively regulates the FOXO transcription factor DAF-16, rescues the hypersusceptibility to pathogens phenotype of elt-2(RNAi) animals. Our results indicate that ELT-2 is part of a multi-pathogen defense pathway that regulates innate immunity independently of the DAF-2/DAF-16 signaling pathway.
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20
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Gaddis NC, Sheehy AM, Ahmad KM, Swanson CM, Bishop KN, Beer BE, Marx PA, Gao F, Bibollet-Ruche F, Hahn BH, Malim MH. Further investigation of simian immunodeficiency virus Vif function in human cells. J Virol 2004; 78:12041-6. [PMID: 15479843 PMCID: PMC523299 DOI: 10.1128/jvi.78.21.12041-12046.2004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primate lentivirus Vif proteins function by suppressing the antiviral activity of the cell-encoded apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like (APOBEC) proteins APOBEC3G and APOBEC3F. It has been hypothesized that species-specific susceptibilities of APOBEC proteins to Vif proteins may help govern the transmission of primate lentiviruses to new host species. Consistent with this view and with previous results, we report that the Vif proteins of several diverse simian immunodeficiency viruses (SIVs) that are not known to infect humans are not effective inhibitors of human APOBEC3G or APOBEC3F when assessed in transient-transfection experiments. Unexpectedly, this lack of SIV Vif function did not prevent the replication of two vif-deficient SIVs (SIVtan and SIVmnd1; isolated from tantalus monkeys and mandrills, respectively) in a human T-cell line, HUT78, that expresses both APOBEC 3G and APOBEC3F, a finding which demonstrates that some SIVs are partially resistant to the antiretroviral effects of these enzymes irrespective of Vif function. Additional virus replication studies also revealed that the Vif protein of SIVtan is, in fact, active in human T cells, as it substantially enhanced the replication of its cognate virus and human immunodeficiency virus type 1. In sum, we now consider it improbable that species-specific restrictions to SIV Vif function can explain the lack of human infection with certain SIVs. Instead, our data reveal that the species-specific modulation of Vif function is more complex than previously envisioned and that additional (as-yet-unidentified) viral or host factors may be involved in regulating this dynamic interaction between host and pathogen.
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Affiliation(s)
- Nathan C Gaddis
- Department of Microbiology, University of Pennsylvania, Philadelphia, USA
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21
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Sheehy AM, Gaddis NC, Malim MH. The antiretroviral enzyme APOBEC3G is degraded by the proteasome in response to HIV-1 Vif. Nat Med 2003; 9:1404-7. [PMID: 14528300 DOI: 10.1038/nm945] [Citation(s) in RCA: 777] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2003] [Accepted: 09/15/2003] [Indexed: 12/18/2022]
Abstract
The human protein apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like-3G (APOBEC3G), also known as CEM-15, mediates a newly described form of innate resistance to retroviral infection by catalyzing the deamination of deoxycytidine to deoxyuridine in viral cDNA replication intermediates. Because DNA deamination takes place after virus entry into target cells, APOBEC3G function is dependent on its association with the viral nucleoprotein complexes that synthesize cDNA and must therefore be incorporated into virions as they assemble in infected cells. Here we show that the HIV-1 virion infectivity factor (Vif) protein protects the virus from APOBEC3G-mediated inactivation by preventing its incorporation into progeny virions, thus allowing the ensuing infection to proceed without DNA deamination. In addition to helping exclude APOBEC3G from nascent virions, Vif also removes APOBEC3G from virus-producing cells by inducing its ubiquitination and subsequent degradation by the proteasome. Our findings indicate that pharmacologic strategies aimed at stabilizing APOBEC3G in HIV-1 infected cells should be explored as potential HIV/AIDS therapeutics.
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Affiliation(s)
- Ann M Sheehy
- Department of Infectious Diseases, Guy's, King's and St. Thomas' School of Medicine, King's College London, London, SE1 9RT, UK
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22
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Gaddis NC, Chertova E, Sheehy AM, Henderson LE, Malim MH. Comprehensive investigation of the molecular defect in vif-deficient human immunodeficiency virus type 1 virions. J Virol 2003; 77:5810-20. [PMID: 12719574 PMCID: PMC154025 DOI: 10.1128/jvi.77.10.5810-5820.2003] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [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] [Indexed: 01/06/2023] Open
Abstract
Replication of human immunodeficiency virus type 1 (HIV-1) in primary blood lymphocytes, certain T-cell lines (nonpermissive cells), and most likely in vivo is highly dependent on the virally encoded Vif protein. Evidence suggests that Vif acts late in the viral life cycle during assembly, budding, and/or maturation to counteract the antiviral activity of the CEM15 protein and possibly other antiviral factors. Because HIV-1 virions produced in the absence of Vif are severely restricted at a postentry, preintegration step of infection, it is presumed that such virions differ from wild-type virions in some way. In the present study, we established a protocol for producing large quantities of vif-deficient HIV-1 (HIV-1/Delta vif) from an acute infection of nonpermissive T cells and performed a thorough examination of the defect in these virions. Aside from the expected lack of Vif, we observed no apparent abnormalities in the packaging, modification, processing, or function of proteins in Delta vif virions. In addition, we found no consistent defect in the ability of Delta vif virions to perform intravirion reverse transcription under a variety of assay conditions, suggesting that the reverse transcription complexes in these particles can behave normally under cell-free conditions. Consistent with this finding, neither the placement of the primer tRNA3Lys nor its ability to promote reverse transcription in an in vitro assay was affected by a lack of Vif. Based on the inability of this comprehensive analysis to uncover molecular defects in Delta vif virions, we speculate that such defects are likely to be subtle and/or rare.
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Affiliation(s)
- Nathan C Gaddis
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Abstract
Viruses have developed diverse non-immune strategies to counteract host-mediated mechanisms that confer resistance to infection. The Vif (virion infectivity factor) proteins are encoded by primate immunodeficiency viruses, most notably human immunodeficiency virus-1 (HIV-1). These proteins are potent regulators of virus infection and replication and are consequently essential for pathogenic infections in vivo. HIV-1 Vif seems to be required during the late stages of virus production for the suppression of an innate antiviral phenotype that resides in human T lymphocytes. Thus, in the absence of Vif, expression of this phenotype renders progeny virions non-infectious. Here, we describe a unique cellular gene, CEM15, whose transient or stable expression in cells that do not normally express CEM15 recreates this phenotype, but whose antiviral action is overcome by the presence of Vif. Because the Vif:CEM15 regulatory circuit is critical for HIV-1 replication, perturbing the circuit may be a promising target for future HIV/AIDS therapies.
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Affiliation(s)
- Ann M Sheehy
- Department of Microbiology, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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24
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Alexander L, Weiskopf E, Greenough TC, Gaddis NC, Auerbach MR, Malim MH, O'Brien SJ, Walker BD, Sullivan JL, Desrosiers RC. Unusual polymorphisms in human immunodeficiency virus type 1 associated with nonprogressive infection. J Virol 2000; 74:4361-76. [PMID: 10756051 PMCID: PMC111953 DOI: 10.1128/jvi.74.9.4361-4376.2000] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.5] [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] [Indexed: 02/01/2023] Open
Abstract
Factors accounting for long-term nonprogression may include infection with an attenuated strain of human immunodeficiency virus type 1 (HIV-1), genetic polymorphisms in the host, and virus-specific immune responses. In this study, we examined eight individuals with nonprogressing or slowly progressing HIV-1 infection, none of whom were homozygous for host-specific polymorphisms (CCR5-Delta32, CCR2-64I, and SDF-1-3'A) which have been associated with slower disease progression. HIV-1 was recovered from seven of the eight, and recovered virus was used for sequencing the full-length HIV-1 genome; full-length HIV-1 genome sequences from the eighth were determined following amplification of viral sequences directly from peripheral blood mononuclear cells (PBMC). Longitudinal studies of one individual with HIV-1 that consistently exhibited a slow/low growth phenotype revealed a single amino acid deletion in a conserved region of the gp41 transmembrane protein that was not seen in any of 131 envelope sequences in the Los Alamos HIV-1 sequence database. Genetic analysis also revealed that five of the eight individuals harbored HIV-1 with unusual 1- or 2-amino-acid deletions in the Gag sequence compared to subgroup B Gag consensus sequences. These deletions in Gag have either never been observed previously or are extremely rare in the database. Three individuals had deletions in Nef, and one had a 4-amino-acid insertion in Vpu. The unusual polymorphisms in Gag, Env, and Nef described here were also found in stored PBMC samples taken 3 to 11 years prior to, or in one case 4 years subsequent to, the time of sampling for the original sequencing. In all, seven of the eight individuals exhibited one or more unusual polymorphisms; a total of 13 unusual polymorphisms were documented in these seven individuals. These polymorphisms may have been present from the time of initial infection or may have appeared in response to immune surveillance or other selective pressures. Our results indicate that unusual, difficult-to-revert polymorphisms in HIV-1 can be found associated with slow progression or nonprogression in a majority of such cases.
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MESH Headings
- Amino Acid Sequence
- Animals
- Cells, Cultured
- Chemokine CXCL12
- Chemokines, CXC/genetics
- Disease Progression
- Gene Products, gag/metabolism
- Gene Products, nef/genetics
- Gene Products, nef/physiology
- Gene Products, vpr/metabolism
- Genotype
- HIV Infections/physiopathology
- HIV Infections/virology
- HIV-1/classification
- HIV-1/genetics
- HIV-1/growth & development
- HIV-1/immunology
- HLA Antigens/classification
- HLA Antigens/genetics
- Haplotypes
- Humans
- Macaca mulatta
- Molecular Sequence Data
- Polymorphism, Genetic
- Receptors, CCR2
- Receptors, CCR5/genetics
- Receptors, Chemokine
- Receptors, Cytokine/genetics
- Sequence Homology, Amino Acid
- Simian Immunodeficiency Virus/genetics
- Simian Immunodeficiency Virus/physiology
- gag Gene Products, Human Immunodeficiency Virus
- nef Gene Products, Human Immunodeficiency Virus
- vpr Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- L Alexander
- New England Regional Primate Research Center, Harvard Medical School, Southborough, Massachusetts 01772, USA
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25
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Abstract
Animal cells have developed many ways to suppress viral replication, and viruses have evolved diverse strategies to resist these. Here we provide evidence that the virion infectivity factor protein of human immunodeficiency virus type 1 (HIV-1) functions to counteract a newly discovered activity in human cells that otherwise inhibits virus replication. This anti-viral phenotype is shown by human T cells, the principal in vivo targets for HIV-1, and, based on our present understanding of virion infectivity factor action, is presumed to act by interfering with a late step(s) in the virus life cycle. These observations indicate that the inhibition of virion infectivity factor function in vivo may prevent HIV-1 replication by 'unmasking' an innate anti-viral phenotype.
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Affiliation(s)
- J H Simon
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia 19104-6148, USA
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