Eosinophilic Esophagitis Risk Variant at 2p23 Dampens IL-13-Induced Calpain-14 Promoter Activity in a STAT6-Dependent Manner

Rationale: Eosinophilic esophagitis (EoE) is a chronic, food-driven, esophageal, inflammatory allergic disease. We have recently found that, in addition to genetic risk loci for allergic sensitization, EoE susceptibility is linked to a tissue-specific genetic factor(s) at 2p23, encoding the CAPN14 gene. In our initial studies we showed that CAPN14 is dynamically up-regulated as a function of EoE disease activity and after exposure of epithelial cells to IL-13, a critical regulator of esophageal inflammation in EoE. Patients with EoE and the 2p23 risk haplotype express decreased esophageal CAPN14.

Methods: We performed a replication and fine-mapping study of the 2p23 locus in an additional cohort of subjects with and without EoE. We used DNA affinity precipitation analysis and electromobility shift assays to identify proteins that differentially bound specific variants. Luciferase reporter assays were used to further define the IL-13 and genotype-dependent parts of the CAPN14 promoter.

Results: Using an independent genetic cohort, we replicated the 2p23 EoE-risk locus (rs76562819 p_meta<10^-18, Odds Ratio=1.98) and identified five genetic variants most likely to be causal. We identified the critical promoter elements of CAPN14 using promoter deletion constructs. We demonstrated STAT6 binding to the three putative binding sites in the promoter and first intron. Each of the three STAT6 elements were required for the 10-fold increase in IL-13 induced promoter activity and for the 50% reduction in genotype-dependent expression.

Conclusions: Our work establishes a candidate molecular mechanism for EoE disease etiology in which the risk variant rs76562819 at 2p23 dampens IL-13-induced calpain-14 promoter activity in a STAT6-dependent manner.