Genome‐Wide Blood DNA Methylation Profiling in Birch Pollen Allergic Patients Undergoing Allergen‐Specific Immunotherapy

ABSTRACT Background Until now, no study has investigated the impact of allergen immunotherapy (AIT) on genome‐wide DNA methylation in a longitudinal set‐up. Herein, we investigated whether differences in DNA methylation occur in birch pollen allergic patients undergoing 6 months of birch pollen AIT, assessed alterations in methylation‐based blood cell type composition, and correlated DNA methylation to serological AIT biomarkers. Methods We performed genome‐wide DNA‐methylation analysis on bisulfite‐converted DNA derived from whole blood samples of 16 birch pollen‐allergic patients (pre–/post‐birch pollen AIT) and 15 placebo (pre‐/post‐placebo treatment). Results Our analysis identified cg22187251, located within a regulatory region upstream of the glucosaminyl (N‐acetyl) transferase 2 ( GCNT2 ) gene and cg22336863 upstream of the transcription start site of actin binding rho activating protein ( ABRA ), as hypermethylated. Functional assays revealed that these regions exhibit methylation‐dependent promoter and enhancer activities. We identified differentially methylated positions within the HLA gene complex, and an AIT‐specific increase of CD8+ T cell populations accompanied by a decrease in natural killer (NK) cell proportion. Strong to moderate correlations with clinical biomarkers (such as specific IgG 4 ) were observed for 42% of the top 100 differentially methylated positions. Conclusion GCNT2 and ABRA are implicated in Rho‐signaling, a pathway involved in Th2 differentiation. GCNT2 modulates the SMAD‐dependent TGF‐β pathway, indicating a role in mediating AIT‐induced immunotolerance. This is the first longitudinal study investigating DNA methylation changes induced by birch pollen AIT.