A Deep Intronic Polymorphism at 9q21.11 Contributes to the Risk of Atopic Dermatitis Through Methylation-Regulated Expression of Tight Junction Protein 2.

Background and objective: Atopic dermatitis (AD) is a chronic inflammatory itchy skin condition. Genome- and epigenome-wide association studies provide insights into genetic susceptibility and the pathogenesis of potential underlying disease. This study sought to functionally characterize an AD-associated single-nucleotide polymorphism (SNP) located deep intronic of the tight junction protein 2 (TJP2) gene (9q21.11 locus), identified through a genome-wide association study (GWAS).

Methods: The association between the 9q21.11 locus (rs7872806) and AD was identified through a GWAS of 956 cases and 723 controls. TJP2 expression in peripheral blood mononuclear cells (PBMCs) was assessed against the rs7872806 genotype. Allele-specific methylation was evaluated at CpG sites 10 kb up- and down-stream of the 9q21.11 locus. The effect of DNA methylation on TJP2 expression was validated via in vitro methylation and 5-aza-2'-deoxycytidine-induced transcriptional activation studies. Transepidermal water loss (TEWL) measurements were used to determine skin barrier function.

Results: The major allele "G" of rs7872806 was found to increase the risk of AD by 2.64-fold (adjusted P value, 2.40 × 10-18; OR, 0.38) and was associated with increased methylation levels at the cg13920460 site (P<.001) and lower TJP2 expression in PBMCs (Pearson P=1.09 × 10-6, Pearson R, -0.313, P<.001). Inhibition of methylation by 5-aza-2'-deoxycytidine increased TJP2 promoter activity by up to 85%. Elimination of the cg13920460 methylation site increased expression by approximately 25%. The major allele of rs7872806 was also found to be associated with increased TEWL (P<.001).

Conclusion: Epigenetic influence at CpG site cg13920460 is associated with rs7872806 located deep intronic at 9q21.11. The SNP confers susceptibility to AD by altering TJP2 expression and promoting TEWL.