An IgE-associated polymorphism in STAT6 alters NF-κB binding, STAT6 promoter activity, and mRNA expression

Background: The IL-4/IL-13 pathway is central for IgE regulation. Signal transducer and activator of transcription 6 (STAT6) is the major transcription factor within this pathway. STAT6 polymorphisms were recently associated with elevated total IgE levels in a genome-wide association study. Objective: This study aimed to assess biological mechanisms by which an IgE-associated genetic variation in STAT6 may potentially influence gene expression. Methods: STAT6 intron 2 carrying either the wild-type C or the polymorphic T allele of the putatively causal single nucleotide polymorphism rs324011 was cloned into STAT6 promoter vectors to investigate their influence on STAT6 promoter activity by in vitro luciferase assays. Transcription factor binding depending on rs324011 was examined by electrophoretic mobility shift assays in Jurkat T cells and primary CD4(+) T cells. Allele-specific STAT6 gene expression of 3 splice variants was studied ex vivo by real-time PCR in 239 individuals. Results: STAT6 intron 2 acts as a silencer regulatory element. The polymorphic T allele at rs324011 (in linkage disequilibrium with the genome-wide association signal and consistently associated with elevated IgE levels in 3 previous studies) increases STAT6 promoter activity significantly in vitro (P < .00001) and gene expression of STAT6 splice variants ex vivo (P < .01) compared with the wild-type C allele. These effects correlate with the creation of a novel, T-allele-specific binding site for the transcription factor nuclear factor-kappa B in T cells. Conclusion: The consistently replicated effects of genetic variance in STAT6 on IgE regulation may be explained in part by allele-specific alterations in nuclear factor-kappa B binding at rs324011 and consecutive changes in STAT6 gene expression. (J Allergy Clin Immunol 2009; 124: 583-9.)