Follow-up functional studies on a risk variant for atopic dermatitis on chromosome 11q13.5 identified by genome-wide association studies
Final Report Abstract
Genome-wide association studies (GWAS) have been successful in the identification of common single nucleotide polymorphisms (SNPs) associated with complex traits and common diseases. However, one of the greatest challenges in the “post-GWAS” era is to identify the causal variants underlying association signals and to understand their biological consequences. Thus, comprehensive fine-mapping of loci and functional studies are needed in order to refine the signals. Within the scope of the funded project, our functional approach first characterized the functionality of common variants at the widely replicated AD-risk locus on chromosome 11q13.5. We identified the transcriptional impact of the GWAS lead SNP rs7927894 risk allele in whole blood, demonstrating decreased mRNA expression levels of LRRC32 encoding glycoprotein A repetitions predominantly (GARP), a receptor on human regulatory Tcells that binds and activates latent TGF-beta. In skin samples, however, no rs7927894-dependent allelic imbalance neither on LRRC32 transcripts nor C11orf30 expression levels was observed using allele-specific expression analysis. Further, we demonstrated a proxy SNP (rs2155219) together with rs34455012indel and rs11236797C>A influences LRRC32 promoter activity and showed impact of the rs2155219 risk allele on SP1 transcription factor binding. Second, the low-frequency LRRC32 missense variant rs79525962 identified through targeted resequencing was shown to influence posttranslational effects of LRRC32. Overexpression assays in CD4+CD25- T cells showed a significant reduction in surface expression together with intracellular retention of the mutated protein that may possibly result in disturbed TGF-beta signaling. These downstream effects will have to be examined in more detail in follow-up projects. Together, our results indicate that both common and infrequent variants underlie the association signal for AD on chromosome 11q13.5, and that LRRC32/GARP is the causal gene affected.
