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

Abstract

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.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 years 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.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] change 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.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.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Differentially methylated DNA regions in early childhood wheezing: An epigenome‐wide study using saliva

“…One of the limitations of our study is the fact that the time se- Findings from previous studies suggest that the associations observed between DNA methylation and asthma are largely driven by eosinophils 22,23 that are known to be involved in airway inflammation present in T-helper 2-type asthmatic phenotypes. 38 However, we used a quite robust method for cell composition adjustment and we believe that the differences observed in PM20D1 are not likely to be driven by eosinophil count.…”

“…In fact, the magnitude of the associations for wheezing and asthma candidate CpGs identified in several previous EWAS was also small. 22,23,31 As the power of our exploratory EWAS was relatively low, we used a more powerful approach that allowed us to identify a wheezing-related differentially methylated region located in PM20D1 gene. This gene codes peptidase M20 domain-containing one enzyme that regulates production of N-fatty-acyl amino acids, which are a large family of more than 70 endogenous signalling molecules involved in pain and inflammation regulation, and their metabolites are important mediators of chronic airway inflammation in asthma.…”

“…However, various studies identified asthma-and wheezing-related epigenetic marks in several tissues, including nasal and buccal epithelium, whole peripheral blood, cord blood, as well as in mononuclear cells from cord and peripheral blood. [17][18][19][20][21][22][23][24]39 While blood may be valuable for studying common immunologic processes, nasal and saliva epithelia, being probably closer to the methylation status of the bronchial mucosa than blood or cord blood DNA methylation, are likely better surrogate tissues for studies focused on local inflammation and environmental influences in asthma. These two tissues are also easily accessible and appear to reflect pathologic changes in the airways during asthma development.…”

“…Several previous studies reported associations with childhood wheezing and asthma of DNA methylation changes at a number of single methylation sites and differentially methylated regions (DMRs). [17][18][19][20][21][22][23][24] A large cross-sectional EWAS of childhood asthma conducted within the MeDALL consortium identified an altered peripheral blood DNA methylation at 35 CpG sites; most of the associations were with school-age asthma, while only one CpG site was associated with asthma at preschool age. 23 Importantly, all the associations were largely attenuated, but persisted, following adjustment for eosinophil count.…”

Role of early life immune regulation in asthma development

“…Interestingly, also gender-specific methylation structures were found, as CpG hypermethylation of the receptor tyrosine kinase AXL in newborns blood was associated with wheeze at age 6 especially in girls [56]. Epigenome-wide association studies (EWAS) revealed consistently hypomethylated signatures driven by higher numbers of eosinophil, a granular cell type that is known to be centrally involved in allergic inflammatory processes [57]. Moreover, low methylation and subsequent overexpression of T-cell developmental genes including runt-related transcription factor 3 (RUNX3) and T-cell immunoreceptor with Ig and Immunoreceptor tyrosine-based inhibitory motif (ITIM) domains (TIGIT) have been demonstrated in asthmatics [58].…”