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Tsaprouni LG, Yang TP, Bell J, Dick KJ, Kanoni S, Nisbet J, Viñuela A, Grundberg E, Nelson CP, Meduri E, Buil A, Cambien F, Hengstenberg C, Erdmann J, Schunkert H, Goodall AH, Ouwehand WH, Dermitzakis E, Spector TD, Samani NJ, Deloukas P. Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation. Epigenetics 2015; 9:1382-96. [PMID: 25424692 DOI: 10.4161/15592294.2014.969637] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [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: 12/17/2022] Open
Abstract
Smoking is a major risk factor in many diseases. Genome wide association studies have linked genes for nicotine dependence and smoking behavior to increased risk of cardiovascular, pulmonary, and malignant diseases. We conducted an epigenome wide association study in peripheral-blood DNA in 464 individuals (22 current smokers and 263 ex-smokers), using the Human Methylation 450 K array. Upon replication in an independent sample of 356 twins (41 current and 104 ex-smokers), we identified 30 probes in 15 distinct loci, all of which reached genome-wide significance in the combined analysis P < 5 × 10(-8). All but one probe (cg17024919) remained significant after adjusting for blood cell counts. We replicated all 9 known loci and found an independent signal at CPOX near GPR15. In addition, we found 6 new loci at PRSS23, AVPR1B, PSEN2, LINC00299, RPS6KA2, and KIAA0087. Most of the lead probes (13 out of 15) associated with cigarette smoking, overlapped regions of open chromatin (FAIRE and DNaseI hypersensitive sites) or/and H3K27Ac peaks (ENCODE data set), which mark regulatory elements. The effect of smoking on DNA methylation was partially reversible upon smoking cessation for longer than 3 months. We report the first statistically significant interaction between a SNP (rs2697768) and cigarette smoking on DNA methylation (cg03329539). We provide evidence that the metSNP for cg03329539 regulates expression of the CHRND gene located circa 95 Kb downstream of the methylation site. Our findings suggest the existence of dynamic, reversible site-specific methylation changes in response to cigarette smoking , which may contribute to the extended health risks associated with cigarette smoking.
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Key Words
- AHRR, aryl-hydrocarbon receptor repressor
- ALPP, alkaline phosphatase, placental
- AVPR1B, arginine vasopressin
- CHRND
- CHRND, cholinergic nicotinic receptor
- COPD, chronic obstructive pulmonary disease
- CPOX
- CPOX, coproporphyrinogen oxidase
- DNA methylation
- DNMT, DNA methyltransferase
- EWAS, epigenome wide association study
- FDR, false discovery rate
- GWAS, genome-wide association studies
- PRSS23, serine protease 23
- PSEN2, presenilin-2 gene
- RPS6KA2, ribosomal protein S6 kinase
- epigenome-wide screen
- gene network
- metQTL, methylation quantitative trait loci
- metQTLs
- rs2697768
- smoking
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Dick KJ, Nelson CP, Tsaprouni L, Sandling JK, Aïssi D, Wahl S, Meduri E, Morange PE, Gagnon F, Grallert H, Waldenberger M, Peters A, Erdmann J, Hengstenberg C, Cambien F, Goodall AH, Ouwehand WH, Schunkert H, Thompson JR, Spector TD, Gieger C, Trégouët DA, Deloukas P, Samani NJ. DNA methylation and body-mass index: a genome-wide analysis. Lancet 2014; 383:1990-8. [PMID: 24630777 DOI: 10.1016/s0140-6736(13)62674-4] [Citation(s) in RCA: 554] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Obesity is a major health problem that is determined by interactions between lifestyle and environmental and genetic factors. Although associations between several genetic variants and body-mass index (BMI) have been identified, little is known about epigenetic changes related to BMI. We undertook a genome-wide analysis of methylation at CpG sites in relation to BMI. METHODS 479 individuals of European origin recruited by the Cardiogenics Consortium formed our discovery cohort. We typed their whole-blood DNA with the Infinium HumanMethylation450 array. After quality control, methylation levels were tested for association with BMI. Methylation sites showing an association with BMI at a false discovery rate q value of 0·05 or less were taken forward for replication in a cohort of 339 unrelated white patients of northern European origin from the MARTHA cohort. Sites that remained significant in this primary replication cohort were tested in a second replication cohort of 1789 white patients of European origin from the KORA cohort. We examined whether methylation levels at identified sites also showed an association with BMI in DNA from adipose tissue (n=635) and skin (n=395) obtained from white female individuals participating in the MuTHER study. Finally, we examined the association of methylation at BMI-associated sites with genetic variants and with gene expression. FINDINGS 20 individuals from the discovery cohort were excluded from analyses after quality-control checks, leaving 459 participants. After adjustment for covariates, we identified an association (q value ≤0·05) between methylation at five probes across three different genes and BMI. The associations with three of these probes--cg22891070, cg27146050, and cg16672562, all of which are in intron 1 of HIF3A--were confirmed in both the primary and second replication cohorts. For every 0·1 increase in methylation β value at cg22891070, BMI was 3·6% (95% CI 2·4-4·9) higher in the discovery cohort, 2·7% (1·2-4·2) higher in the primary replication cohort, and 0·8% (0·2-1·4) higher in the second replication cohort. For the MuTHER cohort, methylation at cg22891070 was associated with BMI in adipose tissue (p=1·72 × 10(-5)) but not in skin (p=0·882). We observed a significant inverse correlation (p=0·005) between methylation at cg22891070 and expression of one HIF3A gene-expression probe in adipose tissue. Two single nucleotide polymorphisms--rs8102595 and rs3826795--had independent associations with methylation at cg22891070 in all cohorts. However, these single nucleotide polymorphisms were not significantly associated with BMI. INTERPRETATION Increased BMI in adults of European origin is associated with increased methylation at the HIF3A locus in blood cells and in adipose tissue. Our findings suggest that perturbation of hypoxia inducible transcription factor pathways could have an important role in the response to increased weight in people. FUNDING The European Commission, National Institute for Health Research, British Heart Foundation, and Wellcome Trust.
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Affiliation(s)
- Katherine J Dick
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Loukia Tsaprouni
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK; ISPAR Institute, University of Bedforshire, Bedford, UK
| | - Johanna K Sandling
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK; Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dylan Aïssi
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1166, F-75013, Paris, France; INSERM, UMR_S 1166, F-75013, Paris, France; ICAN Institute for Cardiometabolism And Nutrition, F-75013, Paris, France
| | - Simone Wahl
- German Center for Diabetes Research, Neuherberg, Germany; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Eshwar Meduri
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - France Gagnon
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Harald Grallert
- German Center for Diabetes Research, Neuherberg, Germany; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; German Centre for Cardiovascular Research, Munich Heart Alliance, Munich, Germany
| | - Jeanette Erdmann
- Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Lübeck, Germany; German Centre for Cardiovascular Research, Hamburg/Kiel/Lübeck, Germany
| | - Christian Hengstenberg
- German Centre for Cardiovascular Research, Munich Heart Alliance, Munich, Germany; Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Francois Cambien
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1166, F-75013, Paris, France; INSERM, UMR_S 1166, F-75013, Paris, France; ICAN Institute for Cardiometabolism And Nutrition, F-75013, Paris, France
| | - Alison H Goodall
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Willem H Ouwehand
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK; Department of Haematology, University of Cambridge, Cambridge, UK; National Health Service Blood and Transplant, Cambridge, UK
| | - Heribert Schunkert
- German Centre for Cardiovascular Research, Munich Heart Alliance, Munich, Germany; Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - John R Thompson
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - David-Alexandre Trégouët
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1166, F-75013, Paris, France; INSERM, UMR_S 1166, F-75013, Paris, France; ICAN Institute for Cardiometabolism And Nutrition, F-75013, Paris, France
| | - Panos Deloukas
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK; William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK; Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK.
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Auer-Grumbach M, Olschewski A, Papić L, Kremer H, McEntagart ME, Uhrig S, Fischer C, Fröhlich E, Bálint Z, Tang B, Strohmaier H, Lochmüller H, Schlotter-Weigel B, Senderek J, Krebs A, Dick KJ, Petty R, Longman C, Anderson NE, Padberg GW, Schelhaas HJ, van Ravenswaaij-Arts CMA, Pieber TR, Crosby AH, Guelly C. Alterations in the ankyrin domain of TRPV4 cause congenital distal SMA, scapuloperoneal SMA and HMSN2C. Nat Genet 2009; 42:160-4. [PMID: 20037588 DOI: 10.1038/ng.508] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 10/15/2009] [Indexed: 11/10/2022]
Abstract
Spinal muscular atrophies (SMA, also known as hereditary motor neuropathies) and hereditary motor and sensory neuropathies (HMSN) are clinically and genetically heterogeneous disorders of the peripheral nervous system. Here we report that mutations in the TRPV4 gene cause congenital distal SMA, scapuloperoneal SMA, HMSN 2C. We identified three missense substitutions (R269H, R315W and R316C) affecting the intracellular N-terminal ankyrin domain of the TRPV4 ion channel in five families. Expression of mutant TRPV4 constructs in cells from the HeLa line revealed diminished surface localization of mutant proteins. In addition, TRPV4-regulated Ca(2+) influx was substantially reduced even after stimulation with 4alphaPDD, a TRPV4 channel-specific agonist, and with hypo-osmotic solution. In summary, we describe a new hereditary channelopathy caused by mutations in TRPV4 and present evidence that the resulting substitutions in the N-terminal ankyrin domain affect channel maturation, leading to reduced surface expression of functional TRPV4 channels.
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