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

Abstract

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.

Epigenome‐wide association studies in asthma: A systematic review

“…Differences in study power and discovered methylation sites were also noted between the two studies, possibly due to differences in samples (peripheral blood mononuclear cells vs whole blood). 38 Reese et al also reported differential methylation in genes related to immune functions.…”

“…Thirteen CpGs detected in Xu et al were replicated in the study by Reese et al (seven genome-wide significant, six nominally significant). 33 CpGs annotated to the IL5RA gene, a gene where differential methylation was first associated with asthma by Arathimos et al, were also replicated by Reese et al 33,38 We compared the available data from CpGs in three blood stud- 32,34 In blood studies, 41…”

“…Yang et al 35 CpGs were associated with asthma; however, the associations did not remain significant after adjustment for cell counts and multiple testing. 38 One limitation in the study was the use of questionnaires to assess asthma, subjecting the outcome to potential misreporting. 45 The study also highlighted that eosinophils seem to be the main driver of differential DNA methylation (on average 18% difference in methylation levels between asthmatics and non-asthmatics in eosinophils) seen in whole blood samples, which is likely to have a significant effect on asthma phenotype.…”

“…ZFPM1 (Top locus)(FDR-adjusted P value < 0.05) the use of questionnaires filled by the subjects' mother to assess asthma by Arathimos et al, a method prone to recall bias) or the use of a calendar of history of events in Murphy et al) 29,38. …”

“…HumanMethylation450k beadchip was used in 11 studies,,29,[31][32][33][34][35]38,40 the Methylated CpG Island Recovery Assay (MIRA)chip and Illumina GoldenGate Methylation Cancer Panel I were used in one study each 36,41. Xu et al31 also used Iplex genotyping method in the validation and replication phases.…”