Our study shows that prior allergen sensitization is associated with increased DNA methylation of the repetitive element Alu in a cohort of elderly men. No associations with allergic disease were observed for LINE-1. Hypermethylation of DNA from sensitized individuals suggests a potential underlying epigenetic mechanism for altered immune response in allergic disease. Although a considerable amount of epigenetic programming occurs during fetal development [27
], the association between increased Alu methylation and allergen sensitization in this older population suggests that epigenetic changes in later life may also be relevant for allergy. Epigenetic modifications in adulthood may occur as a result of the aging process, or due to environmental exposures. In this cohort, aging [28
], lead exposure [29
], air pollution [30
] and smoking [31
] have all been associated with a decrease in methylation of repetitive elements in DNA. In contrast, dietary consumption of methyl donors may increase DNA methylation levels, potentially leading to an increased risk of allergic disease. Human and animal studies of prenatal exposures have shown a link between consumption of high levels of folate during pregnancy and increased risk of allergies and asthma in offspring [6
]. Folate consumption was not associated with DNA methylation in this cohort. However, data on folate supplementation and DNA methylation in humans is mixed [32
], and the relationship between methyl donor consumption, allergies, and asthma in adults requires further study.
While prior allergen sensitization was associated with increased Alu methylation in this cohort, we did not find similar effects for total IgE levels or methacholine responsiveness. Total IgE as a marker of allergen sensitization is much less specific than skin prick testing, which could explain why we did not observe an effect for this predictor. Methacholine response showed a minimal overlap with sensitization, with only 20% of responders demonstrating sensitization to at least one allergen. This limited overlap may explain why a concomitant association was not detected for methacholine responsiveness and Alu methylation. An alternative explanation may relate to statistical power. Our sample size was larger for subjects with skin prick test data (n=605), as compared to the number subjects with IgE measurement (n=469) or methacholine responsiveness (n=423).
Since epigenetic patterns may be influenced by cell populations, we adjusted for percent eosinophils, which were elevated in subjects with allergen sensitization. The relationship between prior allergen sensitization and DNA methylation remained unchanged after adjustment for % eosinophils. While sensitization to any allergen was significantly associated with increased methylation of Alu, multiple regression models examining individual specific allergies showed tree sensitization as the strongest predictor.
Methylation of repetitive DNA sequences like Alu and LINE-1 may serve as a broad indicator of global DNA methylation (with potential implications for groups of specific genes involved in allergy, like those in T-cell differentiation and adaptive immunity), or the repetitive elements themselves may alter immune function in a way that influences allergy. While the majority of Alu copies are hypermethylated and therefore inactive, hypomethylation (as a result of vitamin B deficiency, treatment with medications such as 5-azacytidine, procainamide and hydralazine, or toxin exposure), results in transcription of Alu elements [18
]. Transcripts of this transposon derived DNA are perceived as ‘foreign’ to the immune system, and may have immune stimulatory capabilities. Additionally, the unmethylated CpG rich Alu DNA fragments could potentially mimic the effects of bacterial CpG rich motifs, which are known to prime Th1 response, suppress IgE production, and initiate the release of the cytokines IL-12 and IFN-γ [35
While this study showed a clear association between allergen sensitization and increased DNA methylation, there were some study limitations. The allergen sensitization data in the cohort was collected several years prior to DNA methylation data, therefore we were not able to assess the association between current allergen sensitization and DNA methylation. While sensitization to tree allergen seemed to drive the relationship between current allergen sensitization and methylation, the number of subjects within this subgroup was relatively small. Also, our analysis was limited to older, predominantly white men. Lastly, although methylation of repetitive elements may represent epigenetic modifications in a large portion of the genome, the significance of these epigenetic markers can be difficult to interpret.
In summary, this study suggests that increased methylation of repetitive elements may be associated with allergen sensitization, but not asthma, in this cohort. Future work is needed to identify potential underlying mechanisms for these relationships.