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Li S, Wong EM, Nguyen TL, Joo JHE, Stone J, Dite GS, Giles GG, Saffery R, Southey MC, Hopper JL. Causes of blood methylomic variation for middle-aged women measured by the HumanMethylation450 array. Epigenetics 2018; 12:973-981. [PMID: 29099274 DOI: 10.1080/15592294.2017.1384891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
To address the limitations in current classic twin/family research on the genetic and/or environmental causes of human methylomic variation, we measured blood DNA methylation for 479 women (mean age 56 years) including 66 monozygotic (MZ), 66 dizygotic (DZ) twin pairs and 215 sisters of twins, and 11 random technical duplicates using the HumanMethylation450 array. For each methylation site, we estimated the correlation for pairs of duplicates, MZ twins, DZ twins, and siblings, fitted variance component models by assuming the variation is explained by genetic factors, by shared and individual environmental factors, and by independent measurement error, and assessed the best fitting model. We found that the average (standard deviation) correlations for duplicate, MZ, DZ, and sibling pairs were 0.10 (0.35), 0.07 (0.21), -0.01 (0.14) and -0.04 (0.07). At the genome-wide significance level of 10-7, 93.3% of sites had no familial correlation, and 5.6%, 0.1%, and 0.2% of sites were correlated for MZ, DZ, and sibling pairs. For 86.4%, 6.9%, and 7.1% of sites, the best fitting model included measurement error only, a genetic component, and at least one environmental component. For the 13.6% of sites influenced by genetic and/or environmental factors, the average proportion of variance explained by environmental factors was greater than that explained by genetic factors (0.41 vs. 0.37, P value <10-15). Our results are consistent with, for middle-aged woman, blood methylomic variation measured by the HumanMethylation450 array being largely explained by measurement error, and more influenced by environmental factors than by genetic factors.
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Affiliation(s)
- Shuai Li
- a Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health , University of Melbourne , Parkville , Victoria , Australia
| | - Ee Ming Wong
- b Genetic Epidemiology Laboratory, Department of Pathology , University of Melbourne , Parkville , Victoria , Australia.,c Precision Medicine, School of Clinical Sciences at Monash Health , Monash University , Clayton , Victoria , Australia
| | - Tuong L Nguyen
- a Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health , University of Melbourne , Parkville , Victoria , Australia
| | - Ji-Hoon Eric Joo
- b Genetic Epidemiology Laboratory, Department of Pathology , University of Melbourne , Parkville , Victoria , Australia.,c Precision Medicine, School of Clinical Sciences at Monash Health , Monash University , Clayton , Victoria , Australia
| | - Jennifer Stone
- d Centre for Genetic Origins of Health and Disease , Curtin University and the University of Western Australia , Perth , Western Australia , Australia
| | - Gillian S Dite
- a Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health , University of Melbourne , Parkville , Victoria , Australia
| | - Graham G Giles
- a Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health , University of Melbourne , Parkville , Victoria , Australia.,e Cancer Epidemiology and Intelligence Division , Cancer Council Victoria , Melbourne , Victoria , Australia
| | - Richard Saffery
- f Murdoch Children's Research Institute , Royal Children's Hospital , Parkville , Victoria , Australia.,g Department of Paediatrics , University of Melbourne , Parkville , Victoria , Australia
| | - Melissa C Southey
- b Genetic Epidemiology Laboratory, Department of Pathology , University of Melbourne , Parkville , Victoria , Australia.,c Precision Medicine, School of Clinical Sciences at Monash Health , Monash University , Clayton , Victoria , Australia
| | - John L Hopper
- a Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health , University of Melbourne , Parkville , Victoria , Australia
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Li S, Wong EM, Bui M, Nguyen TL, Joo JHE, Stone J, Dite GS, Dugué PA, Milne RL, Giles GG, Saffery R, Southey MC, Hopper JL. Inference about causation between body mass index and DNA methylation in blood from a twin family study. Int J Obes (Lond) 2018; 43:243-252. [PMID: 29777239 DOI: 10.1038/s41366-018-0103-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/19/2018] [Accepted: 04/04/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Several studies have reported DNA methylation in blood to be associated with body mass index (BMI), but few have investigated causal aspects of the association. We used a twin family design to assess this association at two life points and applied a novel analytical approach to appraise the evidence for causality. METHODS The methylation profile of DNA from peripheral blood was measured for 479 Australian women from 130 twin families. Linear regression was used to estimate the associations of DNA methylation at ~410,000 cytosine-guanine dinucleotides (CpGs), and of the average DNA methylation at ~20,000 genes, with current BMI, BMI at age 18-21 years, and the change between the two (BMI change). A novel regression-based methodology for twins, Inference about Causation through Examination of Familial Confounding (ICE FALCON), was used to assess causation. RESULTS At a 5% false discovery rate, nine, six and 12 CpGs at 24 loci were associated with current BMI, BMI at age 18-21 years and BMI change, respectively. The average DNA methylation of the BHLHE40 and SOCS3 loci was associated with current BMI, and of the PHGDH locus with BMI change. From the ICE FALCON analyses with BMI as the predictor and DNA methylation as the outcome, a woman's DNA methylation level was associated with her co-twin's BMI, and the association disappeared after conditioning on her own BMI, consistent with BMI causing DNA methylation. To the contrary, using DNA methylation as the predictor and BMI as the outcome, a woman's BMI was not associated with her co-twin's DNA methylation level, consistent with DNA methylation not causing BMI. CONCLUSION For middle-aged women, peripheral blood DNA methylation at several genomic locations is associated with current BMI, BMI at age 18-21 years and BMI change. Our study suggests that BMI has a causal effect on peripheral blood DNA methylation.
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Affiliation(s)
- Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Ee Ming Wong
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Ji-Hoon Eric Joo
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Jennifer Stone
- Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia, Perth, WA, Australia
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Pierre-Antoine Dugué
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.
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Li S, Wong EM, Dugué PA, McRae AF, Kim E, Joo JHE, Nguyen TL, Stone J, Dite GS, Armstrong NJ, Mather KA, Thalamuthu A, Wright MJ, Ames D, Milne RL, Craig JM, Saffery R, Montgomery GW, Song YM, Sung J, Spector TD, Sachdev PS, Giles GG, Southey MC, Hopper JL. Genome-wide average DNA methylation is determined in utero. Int J Epidemiol 2018. [PMID: 29518222 PMCID: PMC6005037 DOI: 10.1093/ije/dyy028] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Investigating the genetic and environmental causes of variation in genome-wide average DNA methylation (GWAM), a global methylation measure from the HumanMethylation450 array, might give a better understanding of genetic and environmental influences on methylation. METHODS We measured GWAM for 2299 individuals aged 0 to 90 years from seven twin and/or family studies. We estimated familial correlations, modelled correlations with cohabitation history and fitted variance components models for GWAM. RESULTS The correlation in GWAM for twin pairs was ∼0.8 at birth, decreased with age during adolescence and was constant at ∼0.4 throughout adulthood, with no evidence that twin pair correlations differed by zygosity. Non-twin first-degree relatives were correlated, from 0.17 [95% confidence interval (CI): 0.05-0.30] to 0.28 (95% CI: 0.08-0.48), except for middle-aged siblings (0.01, 95% CI: -0.10-0.12), and the correlation increased with time living together and decreased with time living apart. Spouse pairs were correlated in all studies, from 0.23 (95% CI: 0.3-0.43) to 0.31 (95% CI: 0.05-0.52), and the correlation increased with time living together. The variance explained by environmental factors shared by twins alone was 90% (95% CI: 74-95%) at birth, decreased in early life and plateaued at 28% (95% CI: 17-39%) in middle age and beyond. There was a cohabitation-related environmental component of variance. CONCLUSIONS GWAM is determined in utero by prenatal environmental factors, the effects of which persist throughout life. The variation of GWAM is also influenced by environmental factors shared by family members, as well as by individual-specific environmental factors.
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Affiliation(s)
- Shuai Li
- Centre for Epidemiology and Biostatistics
| | - Ee Ming Wong
- Genetic Epidemiology Laboratory, University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, Monash University, Clayton, VIC, Australia
| | - Pierre-Antoine Dugué
- Centre for Epidemiology and Biostatistics.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Allan F McRae
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - Eunae Kim
- Complex Disease and Genome Epidemiology Branch, Department of Public Health Science, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Ji-Hoon Eric Joo
- Genetic Epidemiology Laboratory, University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, Monash University, Clayton, VIC, Australia
| | | | - Jennifer Stone
- Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia, Perth, WA, Australia
| | | | | | - Karen A Mather
- Centre for Healthy Brain Ageing (CHeBA), University of New South Wales, Sydney, NSW, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing (CHeBA), University of New South Wales, Sydney, NSW, Australia
| | - Margaret J Wright
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - David Ames
- National Ageing Research Institute and University of Melbourne Academic Unit for Psychiatry of Old Age, Parkville, VIC, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Jeffrey M Craig
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Richard Saffery
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Yun-Mi Song
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Joohon Sung
- Complex Disease and Genome Epidemiology Branch, Department of Public Health Science, School of Public Health, Seoul National University, Seoul, Republic of Korea.,Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing (CHeBA), University of New South Wales, Sydney, NSW, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, Monash University, Clayton, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics.,Complex Disease and Genome Epidemiology Branch, Department of Public Health Science, School of Public Health, Seoul National University, Seoul, Republic of Korea.,Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
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Li S, Wong EM, Bui M, Nguyen TL, Joo JHE, Stone J, Dite GS, Giles GG, Saffery R, Southey MC, Hopper JL. Causal effect of smoking on DNA methylation in peripheral blood: a twin and family study. Clin Epigenetics 2018; 10:18. [PMID: 29456763 PMCID: PMC5810186 DOI: 10.1186/s13148-018-0452-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/01/2018] [Indexed: 11/10/2022] Open
Abstract
Background Smoking has been reported to be associated with peripheral blood DNA methylation, but the causal aspects of the association have rarely been investigated. We aimed to investigate the association and underlying causation between smoking and blood methylation. Methods The methylation profile of DNA from the peripheral blood, collected as dried blood spots stored on Guthrie cards, was measured for 479 Australian women including 66 monozygotic twin pairs, 66 dizygotic twin pairs, and 215 sisters of twins from 130 twin families using the Infinium HumanMethylation450K BeadChip array. Linear regression was used to estimate associations between methylation at ~ 410,000 cytosine-guanine dinucleotides (CpGs) and smoking status. A regression-based methodology for twins, Inference about Causation through Examination of Familial Confounding (ICE FALCON), was used to assess putative causation. Results At a 5% false discovery rate, 39 CpGs located at 27 loci, including previously reported AHRR, F2RL3, 2q37.1 and 6p21.33, were found to be differentially methylated across never, former and current smokers. For all 39 CpG sites, current smokers had the lowest methylation level. Our study provides the first replication for two previously reported CpG sites, cg06226150 (SLC2A4RG) and cg21733098 (12q24.32). From the ICE FALCON analysis with smoking status as the predictor and methylation score as the outcome, a woman’s methylation score was associated with her co-twin’s smoking status, and the association attenuated towards the null conditioning on her own smoking status, consistent with smoking status causing changes in methylation. To the contrary, using methylation score as the predictor and smoking status as the outcome, a woman’s smoking status was not associated with her co-twin’s methylation score, consistent with changes in methylation not causing smoking status. Conclusions For middle-aged women, peripheral blood DNA methylation at several genomic locations is associated with smoking. Our study suggests that smoking has a causal effect on peripheral blood DNA methylation, but not vice versa. Electronic supplementary material The online version of this article (10.1186/s13148-018-0452-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuai Li
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia
| | - Ee Ming Wong
- 2Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria Australia.,3Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria Australia
| | - Minh Bui
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia
| | - Tuong L Nguyen
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia
| | - Ji-Hoon Eric Joo
- 2Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria Australia.,3Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria Australia
| | - Jennifer Stone
- 4Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia, Perth, Western Australia Australia
| | - Gillian S Dite
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia
| | - Graham G Giles
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia.,5Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
| | - Richard Saffery
- 6Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria Australia.,7Department of Paediatrics, University of Melbourne, Parkville, Victoria Australia
| | - Melissa C Southey
- 2Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria Australia.,3Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria Australia
| | - John L Hopper
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia
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Saffery R, Morley R, Carlin JB, Joo JHE, Ollikainen M, Novakovic B, Andronikos R, Li X, Loke YJ, Carson N, Wallace EM, Umstad MP, Permezel M, Galati JC, Craig JM. Cohort profile: The peri/post-natal epigenetic twins study. Int J Epidemiol 2011; 41:55-61. [PMID: 22422448 DOI: 10.1093/ije/dyr140] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Richard Saffery
- Cancer and Disease Epigenetics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
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