Epigenetic signatures of starting and stopping smoking

Daniel L. McCartney; Anna J. Stevenson; Robert F. Hillary; Rosie M. Walker; Mairead L. Bermingham; Stewart W. Morris; Toni Kim Clarke; Archie Campbell; Alison D. Murray; Heather C. Whalley; David J. Porteous; Peter M. Visscher; Andrew M. McIntosh; Kathryn L. Evans; Ian J. Deary; Riccardo E. Marioni

doi:10.1016/j.ebiom.2018.10.051

Epigenetic signatures of starting and stopping smoking

Daniel L. McCartney, Anna J. Stevenson, Robert F. Hillary, Rosie M. Walker, Mairead L. Bermingham, Stewart W. Morris, Toni Kim Clarke, Archie Campbell, Alison D. Murray, Heather C. Whalley, David J. Porteous, Peter M. Visscher, Andrew M. McIntosh, Kathryn L. Evans, Ian J. Deary, Riccardo E. Marioni^* (Corresponding Author)

^*Corresponding author for this work

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Abstract

Background: Multiple studies have made robust associations between differential DNA methylation and exposure to cigarette smoke. But whether a DNA methylation phenotype is established immediately upon exposure, or only after prolonged exposure is less well–established. Here, we assess DNA methylation patterns from peripheral blood samples in current smokers in response to dose and duration of exposure, along with the effects of smoking cessation on DNA methylation in former smokers. Methods: Dimensionality reduction was applied to DNA methylation data at 90 previously identified smoking–associated CpG sites for over 4900 individuals in the Generation Scotland cohort. K–means clustering was performed to identify clusters associated with current and never smoker status based on these methylation patterns. Cluster assignments were assessed with respect to duration of exposure in current smokers (years as a smoker), time since smoking cessation in former smokers (years), and dose (cigarettes per day). Findings: Two clusters were specified, corresponding to never smokers (97·5% of whom were assigned to Cluster 1) and current smokers (81·1% of whom were assigned to Cluster 2). The exposure time point from which >50% of current smokers were assigned to the smoker–enriched cluster varied between 5 and 9 years in heavier smokers and between 15 and 19 years in lighter smokers. Low–dose former smokers were more likely to be assigned to the never smoker–enriched cluster in the first year following cessation. In contrast, a period of at least two years was required before the majority of former high–dose smokers were assigned to the never smoker–enriched cluster. Interpretation: Our findings suggest that smoking–associated DNA methylation changes are a result of prolonged exposure to cigarette smoke, and can be reversed following cessation. The length of time in which these signatures are established and recovered is dose dependent. Should DNA methylation–based signatures of smoking status be predictive of smoking–related health outcomes, our findings may provide an additional criterion on which to stratify risk.

Original language	English
Pages (from-to)	214-220
Number of pages	7
Journal	EBioMedicine
Volume	37
Early online date	30 Oct 2018
DOIs	https://doi.org/10.1016/j.ebiom.2018.10.051
Publication status	Published - Nov 2018

Bibliographical note

Acknowledgements: This work was supported by Alzheimer's Research UK Major Project Grant [ARUK–PG2017B–10]. Generation Scotland received core funding from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006]. We are grateful to all the families who took part, the general practitioners and the Scottish School of Primary Care for their help in recruiting them, and the whole Generation Scotland team, which includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses. Genotyping of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” (STRADL) [104036/Z/14/Z]. DNA methylation data collection was funded by the Wellcome Trust Strategic Award [10436/Z/14/Z]. The research was conducted in The University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology (CCACE), part of the cross–council Lifelong Health and Wellbeing Initiative [MR/K026992/1]; funding from the Biotechnology and Biological Sciences Research Council (BBSRC) and Medical Research Council (MRC) is gratefully acknowledged. CCACE supports Ian Deary, with some additional support from Dementias Platform UK [MR/L015382/1]. HCW is supported by a JMAS SIM fellowship from the Royal College of Physicians of Edinburgh. AMM and HCW have received support from the Sackler Institute

Keywords

DNA methylation
Epidemiology
Epigenetics
Smoking

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10.1016/j.ebiom.2018.10.051Licence: CC BY

Epigenetic signatures of starting and stopping smoking
© 2018 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Final published version, 1.19 MBLicence: CC BY

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McCartney, D. L., Stevenson, A. J., Hillary, R. F., Walker, R. M., Bermingham, M. L., Morris, S. W., Clarke, T. K., Campbell, A., Murray, A. D., Whalley, H. C., Porteous, D. J., Visscher, P. M., McIntosh, A. M., Evans, K. L., Deary, I. J., & Marioni, R. E. (2018). Epigenetic signatures of starting and stopping smoking. EBioMedicine, 37, 214-220. https://doi.org/10.1016/j.ebiom.2018.10.051

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title = "Epigenetic signatures of starting and stopping smoking",

abstract = "Background: Multiple studies have made robust associations between differential DNA methylation and exposure to cigarette smoke. But whether a DNA methylation phenotype is established immediately upon exposure, or only after prolonged exposure is less well–established. Here, we assess DNA methylation patterns from peripheral blood samples in current smokers in response to dose and duration of exposure, along with the effects of smoking cessation on DNA methylation in former smokers. Methods: Dimensionality reduction was applied to DNA methylation data at 90 previously identified smoking–associated CpG sites for over 4900 individuals in the Generation Scotland cohort. K–means clustering was performed to identify clusters associated with current and never smoker status based on these methylation patterns. Cluster assignments were assessed with respect to duration of exposure in current smokers (years as a smoker), time since smoking cessation in former smokers (years), and dose (cigarettes per day). Findings: Two clusters were specified, corresponding to never smokers (97·5% of whom were assigned to Cluster 1) and current smokers (81·1% of whom were assigned to Cluster 2). The exposure time point from which >50% of current smokers were assigned to the smoker–enriched cluster varied between 5 and 9 years in heavier smokers and between 15 and 19 years in lighter smokers. Low–dose former smokers were more likely to be assigned to the never smoker–enriched cluster in the first year following cessation. In contrast, a period of at least two years was required before the majority of former high–dose smokers were assigned to the never smoker–enriched cluster. Interpretation: Our findings suggest that smoking–associated DNA methylation changes are a result of prolonged exposure to cigarette smoke, and can be reversed following cessation. The length of time in which these signatures are established and recovered is dose dependent. Should DNA methylation–based signatures of smoking status be predictive of smoking–related health outcomes, our findings may provide an additional criterion on which to stratify risk.",

keywords = "DNA methylation, Epidemiology, Epigenetics, Smoking",

author = "McCartney, {Daniel L.} and Stevenson, {Anna J.} and Hillary, {Robert F.} and Walker, {Rosie M.} and Bermingham, {Mairead L.} and Morris, {Stewart W.} and Clarke, {Toni Kim} and Archie Campbell and Murray, {Alison D.} and Whalley, {Heather C.} and Porteous, {David J.} and Visscher, {Peter M.} and McIntosh, {Andrew M.} and Evans, {Kathryn L.} and Deary, {Ian J.} and Marioni, {Riccardo E.}",

note = "Acknowledgements: This work was supported by Alzheimer's Research UK Major Project Grant [ARUK–PG2017B–10]. Generation Scotland received core funding from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006]. We are grateful to all the families who took part, the general practitioners and the Scottish School of Primary Care for their help in recruiting them, and the whole Generation Scotland team, which includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses. Genotyping of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” (STRADL) [104036/Z/14/Z]. DNA methylation data collection was funded by the Wellcome Trust Strategic Award [10436/Z/14/Z]. The research was conducted in The University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology (CCACE), part of the cross–council Lifelong Health and Wellbeing Initiative [MR/K026992/1]; funding from the Biotechnology and Biological Sciences Research Council (BBSRC) and Medical Research Council (MRC) is gratefully acknowledged. CCACE supports Ian Deary, with some additional support from Dementias Platform UK [MR/L015382/1]. HCW is supported by a JMAS SIM fellowship from the Royal College of Physicians of Edinburgh. AMM and HCW have received support from the Sackler Institute",

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AU - McCartney, Daniel L.

AU - Stevenson, Anna J.

AU - Hillary, Robert F.

AU - Walker, Rosie M.

AU - Bermingham, Mairead L.

AU - Morris, Stewart W.

AU - Clarke, Toni Kim

AU - Campbell, Archie

AU - Murray, Alison D.

AU - Whalley, Heather C.

AU - Porteous, David J.

AU - Visscher, Peter M.

AU - McIntosh, Andrew M.

AU - Evans, Kathryn L.

AU - Deary, Ian J.

AU - Marioni, Riccardo E.

N1 - Acknowledgements: This work was supported by Alzheimer's Research UK Major Project Grant [ARUK–PG2017B–10]. Generation Scotland received core funding from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006]. We are grateful to all the families who took part, the general practitioners and the Scottish School of Primary Care for their help in recruiting them, and the whole Generation Scotland team, which includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses. Genotyping of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” (STRADL) [104036/Z/14/Z]. DNA methylation data collection was funded by the Wellcome Trust Strategic Award [10436/Z/14/Z]. The research was conducted in The University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology (CCACE), part of the cross–council Lifelong Health and Wellbeing Initiative [MR/K026992/1]; funding from the Biotechnology and Biological Sciences Research Council (BBSRC) and Medical Research Council (MRC) is gratefully acknowledged. CCACE supports Ian Deary, with some additional support from Dementias Platform UK [MR/L015382/1]. HCW is supported by a JMAS SIM fellowship from the Royal College of Physicians of Edinburgh. AMM and HCW have received support from the Sackler Institute

PY - 2018/11

Y1 - 2018/11

N2 - Background: Multiple studies have made robust associations between differential DNA methylation and exposure to cigarette smoke. But whether a DNA methylation phenotype is established immediately upon exposure, or only after prolonged exposure is less well–established. Here, we assess DNA methylation patterns from peripheral blood samples in current smokers in response to dose and duration of exposure, along with the effects of smoking cessation on DNA methylation in former smokers. Methods: Dimensionality reduction was applied to DNA methylation data at 90 previously identified smoking–associated CpG sites for over 4900 individuals in the Generation Scotland cohort. K–means clustering was performed to identify clusters associated with current and never smoker status based on these methylation patterns. Cluster assignments were assessed with respect to duration of exposure in current smokers (years as a smoker), time since smoking cessation in former smokers (years), and dose (cigarettes per day). Findings: Two clusters were specified, corresponding to never smokers (97·5% of whom were assigned to Cluster 1) and current smokers (81·1% of whom were assigned to Cluster 2). The exposure time point from which >50% of current smokers were assigned to the smoker–enriched cluster varied between 5 and 9 years in heavier smokers and between 15 and 19 years in lighter smokers. Low–dose former smokers were more likely to be assigned to the never smoker–enriched cluster in the first year following cessation. In contrast, a period of at least two years was required before the majority of former high–dose smokers were assigned to the never smoker–enriched cluster. Interpretation: Our findings suggest that smoking–associated DNA methylation changes are a result of prolonged exposure to cigarette smoke, and can be reversed following cessation. The length of time in which these signatures are established and recovered is dose dependent. Should DNA methylation–based signatures of smoking status be predictive of smoking–related health outcomes, our findings may provide an additional criterion on which to stratify risk.

AB - Background: Multiple studies have made robust associations between differential DNA methylation and exposure to cigarette smoke. But whether a DNA methylation phenotype is established immediately upon exposure, or only after prolonged exposure is less well–established. Here, we assess DNA methylation patterns from peripheral blood samples in current smokers in response to dose and duration of exposure, along with the effects of smoking cessation on DNA methylation in former smokers. Methods: Dimensionality reduction was applied to DNA methylation data at 90 previously identified smoking–associated CpG sites for over 4900 individuals in the Generation Scotland cohort. K–means clustering was performed to identify clusters associated with current and never smoker status based on these methylation patterns. Cluster assignments were assessed with respect to duration of exposure in current smokers (years as a smoker), time since smoking cessation in former smokers (years), and dose (cigarettes per day). Findings: Two clusters were specified, corresponding to never smokers (97·5% of whom were assigned to Cluster 1) and current smokers (81·1% of whom were assigned to Cluster 2). The exposure time point from which >50% of current smokers were assigned to the smoker–enriched cluster varied between 5 and 9 years in heavier smokers and between 15 and 19 years in lighter smokers. Low–dose former smokers were more likely to be assigned to the never smoker–enriched cluster in the first year following cessation. In contrast, a period of at least two years was required before the majority of former high–dose smokers were assigned to the never smoker–enriched cluster. Interpretation: Our findings suggest that smoking–associated DNA methylation changes are a result of prolonged exposure to cigarette smoke, and can be reversed following cessation. The length of time in which these signatures are established and recovered is dose dependent. Should DNA methylation–based signatures of smoking status be predictive of smoking–related health outcomes, our findings may provide an additional criterion on which to stratify risk.

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Epigenetic signatures of starting and stopping smoking

Abstract

Bibliographical note

Keywords

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