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Kettunen J, Demirkan A, Würtz P, Draisma HHM, Haller T, Rawal R, Vaarhorst A, Kangas AJ, Lyytikäinen LP, Pirinen M, Pool R, Sarin AP, Soininen P, Tukiainen T, Wang Q, Tiainen M, Tynkkynen T, Amin N, Zeller T, Beekman M, Deelen J, van Dijk KW, Esko T, Hottenga JJ, van Leeuwen EM, Lehtimäki T, Mihailov E, Rose RJ, de Craen AJM, Gieger C, Kähönen M, Perola M, Blankenberg S, Savolainen MJ, Verhoeven A, Viikari J, Willemsen G, Boomsma DI, van Duijn CM, Eriksson J, Jula A, Järvelin MR, Kaprio J, Metspalu A, Raitakari O, Salomaa V, Slagboom PE, Waldenberger M, Ripatti S, Ala-Korpela M. Genome-wide study for circulating metabolites identifies 62 loci and reveals novel systemic effects of LPA. Nat Commun 2016; 7:11122. [PMID: 27005778 PMCID: PMC4814583 DOI: 10.1038/ncomms11122] [Citation(s) in RCA: 451] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 02/24/2016] [Indexed: 01/20/2023] Open
Abstract
Genome-wide association studies have identified numerous loci linked with complex
diseases, for which the molecular mechanisms remain largely unclear. Comprehensive
molecular profiling of circulating metabolites captures highly heritable traits,
which can help to uncover metabolic pathophysiology underlying established disease
variants. We conduct an extended genome-wide association study of genetic influences
on 123 circulating metabolic traits quantified by nuclear magnetic resonance
metabolomics from up to 24,925 individuals and identify eight novel loci for amino
acids, pyruvate and fatty acids. The LPA locus link with cardiovascular risk
exemplifies how detailed metabolic profiling may inform underlying aetiology via
extensive associations with very-low-density lipoprotein and triglyceride
metabolism. Genetic fine mapping and Mendelian randomization uncover wide-spread
causal effects of lipoprotein(a) on overall lipoprotein metabolism and we assess
potential pleiotropic consequences of genetically elevated lipoprotein(a) on diverse
morbidities via electronic health-care records. Our findings strengthen the argument
for safe LPA-targeted intervention to reduce cardiovascular risk. Circulating metabolites reflect human health and disease. Here,
Kettunen et al. perform a genome-wide association study on 123 circulating
metabolic traits and identify novel genetic loci influencing systemic metabolism. They
also link new molecular pathways with a known cardiovascular risk factor
Lp(a).
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Affiliation(s)
- Johannes Kettunen
- Computational Medicine, Faculty of Medicine, University of Oulu, PO Box 5000, 90014 Oulu, Finland.,National Institute for Health and Welfare, PO Box 30, FI-00271 Helsinki, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, Kuopio 70210, Finland.,Biocenter Oulu, University of Oulu, PO Box 5000, FI-90014 Oulu, Finland
| | - Ayşe Demirkan
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Peter Würtz
- Computational Medicine, Faculty of Medicine, University of Oulu, PO Box 5000, 90014 Oulu, Finland
| | - Harmen H M Draisma
- Department of Biological Psychology, VU University Amsterdam, Van der Boechorststraat 1, Room 2B-29, 1081 BT Amsterdam, The Netherlands.,EMGO Institute for Health and Care Research, Van der Boechorststraat 7, 1081BT Amsterdam, The Netherlands.,Neuroscience Campus Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Toomas Haller
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Anika Vaarhorst
- Department of Molecular Epidemiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Antti J Kangas
- Computational Medicine, Faculty of Medicine, University of Oulu, PO Box 5000, 90014 Oulu, Finland
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, Tampere University, Kalevantie 4, Tampere 33014, Finland
| | - Matti Pirinen
- Institute for Molecular Medicine (FIMM), University of Helsinki, Biomedicum 2, Tukholmankatu 8, Helsinki 00290, Finland
| | - René Pool
- Department of Biological Psychology, VU University Amsterdam, Van der Boechorststraat 1, Room 2B-29, 1081 BT Amsterdam, The Netherlands.,EMGO Institute for Health and Care Research, Van der Boechorststraat 7, 1081BT Amsterdam, The Netherlands
| | - Antti-Pekka Sarin
- National Institute for Health and Welfare, PO Box 30, FI-00271 Helsinki, Finland.,Institute for Molecular Medicine (FIMM), University of Helsinki, Biomedicum 2, Tukholmankatu 8, Helsinki 00290, Finland
| | - Pasi Soininen
- Computational Medicine, Faculty of Medicine, University of Oulu, PO Box 5000, 90014 Oulu, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, Kuopio 70210, Finland
| | - Taru Tukiainen
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 0330, Boston, Massachusetts 02115, USA
| | - Qin Wang
- Computational Medicine, Faculty of Medicine, University of Oulu, PO Box 5000, 90014 Oulu, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, Kuopio 70210, Finland
| | - Mika Tiainen
- Computational Medicine, Faculty of Medicine, University of Oulu, PO Box 5000, 90014 Oulu, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, Kuopio 70210, Finland
| | - Tuulia Tynkkynen
- Computational Medicine, Faculty of Medicine, University of Oulu, PO Box 5000, 90014 Oulu, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, Kuopio 70210, Finland
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Tanja Zeller
- German Center for Cardiovascular Research (DZHK e.V.), Partner Site Hamburg/Lübeck/Kiel, Martinistraße 52, 20246 Hamburg, Germany.,University Heart Center Hamburg, Clinic of general and interventional Cardiology, Martinistraße 52, 20246 Hamburg, Germany
| | - Marian Beekman
- Department of Molecular Epidemiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.,Department of Endocrinology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, Van der Boechorststraat 1, Room 2B-29, 1081 BT Amsterdam, The Netherlands.,EMGO Institute for Health and Care Research, Van der Boechorststraat 7, 1081BT Amsterdam, The Netherlands
| | - Elisabeth M van Leeuwen
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, Tampere University, Kalevantie 4, Tampere 33014, Finland
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Richard J Rose
- Department of Public Health, Hjelt Institute, University of Helsinki, PO Box 41 Mannerheimintie 172, Helsinki 00014, Finland.,Department of Psychological and Brain Sciences, Indiana University, 1101 E 10th Street, Bloomington, Indiana 47405, USA
| | - Anton J M de Craen
- Department of Geriatrics and Gerontology, Leiden University Medical Center, Postzone C7-Q, PO Box 9600, 2300RC Leiden, The Netherlands
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere, University Hospital, PO Box 2000, FIN-33521 Tampere, Finland
| | - Markus Perola
- National Institute for Health and Welfare, PO Box 30, FI-00271 Helsinki, Finland.,Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia.,Institute for Molecular Medicine (FIMM), University of Helsinki, Biomedicum 2, Tukholmankatu 8, Helsinki 00290, Finland
| | - Stefan Blankenberg
- German Center for Cardiovascular Research (DZHK e.V.), Partner Site Hamburg/Lübeck/Kiel, Martinistraße 52, 20246 Hamburg, Germany.,University Heart Center Hamburg, Clinic of general and interventional Cardiology, Martinistraße 52, 20246 Hamburg, Germany
| | - Markku J Savolainen
- Biocenter Oulu, University of Oulu, PO Box 5000, FI-90014 Oulu, Finland.,Medical Research Center, Internal Medicine, Oulu University Hospital, University of Oulu, Aapistie 5A, Oulu FI-90220, Finland
| | - Aswin Verhoeven
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Jorma Viikari
- Department of Medicine, University of Turku and Turku University Hospital, PB 52, 20521 Turku, Finland
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Van der Boechorststraat 1, Room 2B-29, 1081 BT Amsterdam, The Netherlands.,EMGO Institute for Health and Care Research, Van der Boechorststraat 7, 1081BT Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Van der Boechorststraat 1, Room 2B-29, 1081 BT Amsterdam, The Netherlands.,EMGO Institute for Health and Care Research, Van der Boechorststraat 7, 1081BT Amsterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Johan Eriksson
- National Institute for Health and Welfare, PO Box 30, FI-00271 Helsinki, Finland.,Department of General Practice and Primary Health Care, University of Helsinki, PL 20, Tukholmankatu 8B, Helsinki 00029, Finland.,Folkhälsan Research Centre, Helsingfors Universitet, PB 63, Helsinki 00014, Finland
| | - Antti Jula
- National Institute for Health and Welfare, PO Box 30, FI-00271 Helsinki, Finland
| | - Marjo-Riitta Järvelin
- Biocenter Oulu, University of Oulu, PO Box 5000, FI-90014 Oulu, Finland.,Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London SW7 2AZ, UK.,Center for Life Course and Systems Epidemiology, Faculty of Medicine, University of Oulu, PL 5000, 90014 Oulu, Finland.,Unit of Primary Care, Oulu University Hospital, P.O. Box 20, OYS, Oulu 90029, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine (FIMM), University of Helsinki, Biomedicum 2, Tukholmankatu 8, Helsinki 00290, Finland.,Department of Public Health, Hjelt Institute, University of Helsinki, PO Box 41 Mannerheimintie 172, Helsinki 00014, Finland.,Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, PO Box 30 (Mannerheimintie 166), Helsinki 00300, Finland
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Kiinamyllynkatu 4-8, Turku 20521, Finland.,Department of Clinical Physiology, Turku University Hospital, Kiinamyllynkatu 4-8, Turku 20521, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, PO Box 30, FI-00271 Helsinki, Finland
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Samuli Ripatti
- National Institute for Health and Welfare, PO Box 30, FI-00271 Helsinki, Finland.,Institute for Molecular Medicine (FIMM), University of Helsinki, Biomedicum 2, Tukholmankatu 8, Helsinki 00290, Finland.,Department of Public Health, Hjelt Institute, University of Helsinki, PO Box 41 Mannerheimintie 172, Helsinki 00014, Finland.,Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu, PO Box 5000, 90014 Oulu, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, Kuopio 70210, Finland.,Biocenter Oulu, University of Oulu, PO Box 5000, FI-90014 Oulu, Finland.,Oulu University Hospital, Kajaanintie 50, Oulu 90220, Finland.,Computational Medicine, School of Social and Community Medicine, University of Bristol, Senate House, Tyndall Avenue, Bristol, Bristol BS8 1TH, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, Bristol BS8 1TH, UK
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55
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Loukola A, Buchwald J, Gupta R, Palviainen T, Hällfors J, Tikkanen E, Korhonen T, Ollikainen M, Sarin AP, Ripatti S, Lehtimäki T, Raitakari O, Salomaa V, Rose RJ, Tyndale RF, Kaprio J. A Genome-Wide Association Study of a Biomarker of Nicotine Metabolism. PLoS Genet 2015; 11:e1005498. [PMID: 26407342 PMCID: PMC4583245 DOI: 10.1371/journal.pgen.1005498] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/14/2015] [Indexed: 11/25/2022] Open
Abstract
Individuals with fast nicotine metabolism typically smoke more and thus have a greater risk for smoking-induced diseases. Further, the efficacy of smoking cessation pharmacotherapy is dependent on the rate of nicotine metabolism. Our objective was to use nicotine metabolite ratio (NMR), an established biomarker of nicotine metabolism rate, in a genome-wide association study (GWAS) to identify novel genetic variants influencing nicotine metabolism. A heritability estimate of 0.81 (95% CI 0.70-0.88) was obtained for NMR using monozygotic and dizygotic twins of the FinnTwin cohort. We performed a GWAS in cotinine-verified current smokers of three Finnish cohorts (FinnTwin, Young Finns Study, FINRISK2007), followed by a meta-analysis of 1518 subjects, and annotated the genome-wide significant SNPs with methylation quantitative loci (meQTL) analyses. We detected association on 19q13 with 719 SNPs exceeding genome-wide significance within a 4.2 Mb region. The strongest evidence for association emerged for CYP2A6 (min p = 5.77E-86, in intron 4), the main metabolic enzyme for nicotine. Other interesting genes with genome-wide significant signals included CYP2B6, CYP2A7, EGLN2, and NUMBL. Conditional analyses revealed three independent signals on 19q13, all located within or in the immediate vicinity of CYP2A6. A genetic risk score constructed using the independent signals showed association with smoking quantity (p = 0.0019) in two independent Finnish samples. Our meQTL results showed that methylation values of 16 CpG sites within the region are affected by genotypes of the genome-wide significant SNPs, and according to causal inference test, for some of the SNPs the effect on NMR is mediated through methylation. To our knowledge, this is the first GWAS on NMR. Our results enclose three independent novel signals on 19q13.2. The detected CYP2A6 variants explain a strikingly large fraction of variance (up to 31%) in NMR in these study samples. Further, we provide evidence for plausible epigenetic mechanisms influencing NMR.
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Affiliation(s)
- Anu Loukola
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jadwiga Buchwald
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Richa Gupta
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Teemu Palviainen
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jenni Hällfors
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Emmi Tikkanen
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Tellervo Korhonen
- Department of Public Health, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Miina Ollikainen
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Samuli Ripatti
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
| | - Olli Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Richard J. Rose
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, Indiana, United States of America
| | - Rachel F. Tyndale
- Campbell Family Mental Health Research Institute, CAMH, and Departments of Pharmacology & Toxicology and Psychiatry, University of Toronto, Toronto, Canada
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
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