DNA methylation of Th2 lineage determination genes at birth is associated with allergic outcomes in childhood

Abstract

Background: There is now increasing evidence that asthma and atopy originate in part in utero, with disease risk being associated with the altered epigenetic regulation of genes.

Objective and methods: To determine the relationship between variations in DNA methylation at birth and the development of allergic disease, we examined the methylation status of CpG loci within the promoter regions of Th1/2 lineage commitment genes (GATA3, IL-4, IL-4R, STAT4 and TBET) in umbilical cord DNA at birth in a cohort of infants from the Southampton Women's Survey (n = 696) who were later assessed for asthma, atopic eczema and atopy.

Results: We found that higher methylation of GATA3 CpGs -2211/-2209 at birth was associated with a reduced risk of asthma at ages 3 (median ratio [median methylation in asthma group/median methylation in non-asthma group] = 0.74, P = .006) and 6-7 (median ratio 0.90, P = .048) years. Furthermore, we demonstrated that the GATA3 CpG loci associated with later risk of asthma lie within a NF-κB binding site and that methylation here blocks transcription factor binding to the GATA3 promoter in the human Jurkat T-cell line. Associations between umbilical cord methylation of CpG loci within IL-4R with atopic eczema at 12 months (median ratio 1.02, P = .028), and TBET with atopy (median ratio 0.98, P = .017) at 6-7 years of age were also observed.

Conclusions and clinical relevance: Our findings provide further evidence of a developmental contribution to the risk of later allergic disorders and suggest that involvement of epigenetic mechanisms in childhood asthma is already demonstrable at birth.

Keywords: GATA3; Methylation; TBET; Th1/Th2; biomarkers.

Figure 1

A) Schematic diagram showing the promoter region of GATA3 and the location of the CpG sites measured. B/C) Methylation of GATA3 CpGs -2211/-2209 in umbilical cord at birth are associated with doctor diagnosed asthma incidence at 3 (B) and 6-7(C) years of age. Methylation has been divided into 4 equal groups according to rank; means and standard error means are plotted for each group.

Figure 2

Methylation at CpGs -2211/-2209 within a NFκB binding site blocks binding to the GATA3 promoter. Nuclear extract from the human Jurkat T cell line was incubated with a labelled probe covering CpGs -2211/-2209 and A) an increasing concentration of unmethylated or methylated competitor or B) with an increasing concentration an oligonucleotide containing the consensus NFκB binding site.