Methylomic markers of persistent childhood asthma: a longitudinal study of asthma-discordant monozygotic twins

Abstract

Background: Asthma is the most common chronic inflammatory disorder in children. The aetiology of asthma pathology is complex and highly heterogeneous, involving the interplay between genetic and environmental risk factors that is hypothesized to involve epigenetic processes. Our aim was to explore whether methylomic variation in early childhood is associated with discordance for asthma symptoms within monozygotic (MZ) twin pairs recruited from the Environmental Risk (E-Risk) longitudinal twin study. We also aimed to identify differences in DNA methylation that are associated with asthma that develops in childhood and persists into early adulthood as these may represent useful prognostic biomarkers.

Results: We examined genome-wide patterns of DNA methylation in buccal cell samples collected from 37 MZ twin pairs discordant for asthma at age 10. DNA methylation at individual CpG sites demonstrated significant variability within discordant MZ twin pairs with the top-ranked nominally significant differentially methylated position (DMP) located in the HGSNAT gene. We stratified our analysis by assessing DNA methylation differences in a sub-group of MZ twin pairs who remained persistently discordant for asthma at age 18. The top-ranked nominally significant DMP associated with persisting asthma is located in the vicinity of the HLX gene, which has been previously implicated in childhood asthma.

Conclusions: We identified DNA methylation differences associated with childhood asthma in peripheral DNA samples from discordant MZ twin pairs. Our data suggest that differences in DNA methylation associated with childhood asthma which persists into early adulthood are distinct from those associated with asthma which remits.

Keywords: Asthma; DNA methylation; Epigenetics; Monozygotic twins.

Fig. 1

Graphs showing the difference in DNA methylation (∆β) at age 10 between each pair of monozygotic (MZ) twins discordant for asthma (affected twin − unaffected co-twin) for each of the ten top-ranked differentially methylated positions (DMPs). Mean within-twin pair ∆β across all 37 MZ twin pairs is highlighted in red. Error bars represent the ±standard deviation. Consistent within-twin pair differences in DNA methylation at age 10 are observed across asthma-discordant MZ twin pairs at the top ten ranked differentially methylated positions

Fig. 2

a Graphs showing the difference in DNA methylation (∆β) at age 10 between each pair of monozygotic (MZ) twins persistently discordant (at ages 10 and 18) for asthma (affected twin − unaffected co-twin) for each of the ten top-ranked differential methylated positions (DMPs). Mean within-twin pair ∆β across all 13 MZ twin pairs is highlighted in red. Error bars represent the ±standard deviation. Consistent within-twin pair differences in DNA methylation are observed across persistently discordant MZ twin pairs at the ten top-ranked DMPs. b Graph showing average within-twin beta difference of (i) persistent-asthma-discordant MZ twins at age 10, (ii) asthma-remission sub-group (twins discordant for asthma at age 10 but the affected twin had remitted at 18, n = 20 twin pairs) and the age-matched concordant unaffected MZ twins (19 twin pairs). Average within-twin differences in DNA methylation are significantly larger at nine of the ten top-ranked DMPs in asthma-discordant twins compared to both the asthma-remission sub-group and twins concordant for no asthma. Between group comparisons of average within-twin beta differences were examined using a one-way ANOVA. ****P < 0.0001, ***P < 0.001, **P < 0.01, *P < 0.05

Fig. 3

A number of probes annotated to the HLX gene were significantly differentially methylated in persistent-asthma twins compared to their unaffected co-twin. Asthma-associated differentially methylated positions are highlighted in red. Green bars denote the location of annotated CpG islands. Of note, asthma-associated DMPs overlap known CpG islands downstream of the HLX gene. ∆β = mean within-twin beta difference