Epigenome-wide association study of asthma and wheeze in childhood and adolescence

Clin Epigenetics. 2017 Oct 13;9:112. doi: 10.1186/s13148-017-0414-7. eCollection 2017.


Background: Asthma heritability has only been partially explained by genetic variants and is known to be sensitive to environmental factors, implicating epigenetic modifications such as DNA methylation in its pathogenesis.

Methods: Using data collected in the Avon Longitudinal Study of Parents and Children (ALSPAC), we assessed associations of asthma and wheeze with DNA methylation at 7.5 and 16.5 years, at over 450,000 CpG sites in DNA from the peripheral blood of approx. 1000 participants. We used Mendelian randomization (MR), a method of causal inference that uses genetic variants as instrumental variables, to infer the direction of association between DNA methylation and asthma.

Results: We identified 302 CpGs associated with current asthma status (FDR-adjusted P value < 0.05) and 445 with current wheeze status at 7.5 years, with substantial overlap between the two. Genes annotated to the 302 associated CpGs were enriched for pathways related to movement of cellular/subcellular components, locomotion, interleukin-4 production and eosinophil migration. All associations attenuated when adjusted for eosinophil and neutrophil cell count estimates. At 16.5 years, two sites were associated with current asthma after adjustment for cell counts. The CpGs mapped to the AP2A2 and IL5RA genes, with a - 2.32 [95% CI - 1.47, - 3.18] and - 2.49 [95% CI - 1.56, - 3.43] difference in percentage methylation in asthma cases respectively. Two-sample bi-directional MR indicated a causal effect of asthma on DNA methylation at several CpG sites at 7.5 years. However, associations did not persist after adjustment for multiple testing. There was no evidence of a causal effect of asthma on DNA methylation at either of the two CpG sites at 16.5 years.

Conclusion: The majority of observed associations are driven by higher eosinophil cell counts in asthma cases, acting as an intermediate phenotype, with important implications for future studies of DNA methylation in atopic diseases.

Keywords: ALSPAC; Asthma; DNA methylation; Longitudinal; Mendelian randomization; Wheeze.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Protein Complex 2 / genetics
  • Adaptor Protein Complex alpha Subunits / genetics
  • Adolescent
  • Asthma / genetics*
  • Asthma / immunology
  • Blood Cell Count
  • Child
  • CpG Islands
  • DNA Methylation*
  • Eosinophils / cytology
  • Epigenomics / methods*
  • Female
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study / methods*
  • Humans
  • Interleukin-5 Receptor alpha Subunit / genetics
  • Longitudinal Studies
  • Male
  • Neutrophils / cytology
  • Respiratory Sounds / genetics*
  • Respiratory Sounds / immunology


  • Adaptor Protein Complex 2
  • Adaptor Protein Complex alpha Subunits
  • IL5RA protein, human
  • Interleukin-5 Receptor alpha Subunit
  • adaptor protein complex 2, alpha 2 subunit