Novel DNA methylation signatures of tobacco smoking with trans-ethnic effects

Colette Christiansen, Jordana Bell, Kerrin Small, Juan Castillo Fernandez, Julia El-Sayed Moustafa, Jane Maddock, Pei-Chien Tsai, Mariam Molokhia, Matthew Suderman, Chris Power, Caroline Relton, Andrew Wong, Diana Kuh, Alissa Goodman, G B Ploubidis, R Hardy, Arce Domingo-Relloso, Jennifer A Smith, Zhao Wei, Sharon L R KardiaKarin Haack, Shelley Cole, Maria Tellez-Plaza, Ana Navas-Acien

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Smoking remains one of the leading preventable causes of death. Smoking leaves a strong signature on the blood methylome as shown in multiple studies using the Infinium HumanMethylation450 BeadChip. Here, we explore novel blood methylation smoking signals on the Illumina MethylationEPIC BeadChip (EPIC) array, which , in addition, targets novel CpG-sites in enhancers.
Method: A smoking-methylation meta-analysis was carried out using EPIC DNA methylation profiles in 1,407 blood samples from four UK population-based cohorts, including the MRC National Survey for Health and Development (NSHD) or 1946 British birth cohort, the National Child Development Study (NCDS) or 1958 birth cohort, the 1970 British Cohort Study (BCS70), and the TwinsUK cohort (TwinsUK). The overall discovery sample included 269 current, 497 former and 643 never smokers. Replication was pursued in 3,425 trans-ethnic samples, including 2,325 American Indian individuals participating in the Strong Heart Study (SHS) in 1989-1991 and 1,100 African American participants in the Genetic Epidemiology Network of Arteriopathy Study (GENOA).
Results: Altogether 952 CpG-sites in 500 genes were differentially methylated between smokers and never-smokers after Bonferroni correction. There were 526 novel smoking-associated CpG-sites only profiled by the EPIC array, of which 486 (92%) replicated in a meta-analysis of the American Indian and African American samples. Novel CpG sites mapped both to genes containing previously identified smoking-methylation signals, and to 80 novel genes not previously linked to smoking, with the strongest novel signal in SLAMF7. Comparison of former vs. never smokers identified that 37 of these sites were persistently differentially methylated after cessation, where 16 represented novel signals only profiled by the EPIC array. We observed a depletion of smoking-associated signals in CpG-islands and an enrichment in enhancer regions, consistent with previous results.
Conclusion: This study identified novel smoking-associated signals as possible biomarkers of exposure to smoking and may help improve our understanding of smoking-related disease risk.
Original languageEnglish
JournalClinical Epigenetics
Publication statusAccepted/In press - 24 Jan 2021

Keywords

  • Epigenetics
  • Smoking

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