Epigenetic regulation of esophageal epithelial barrier function in eosinophilic esophagitis

PROJECT SUMMARY The proposed research explores the mechanisms of epithelial barrier dysfunction in eosinophilic esophagitis (EoE). During its active disease phase, EoE is characterized by Th2-type, eosinophil-rich inflammation with high levels of IL-13, IL-4 and chemoattractant chemokines. There is a growing appreciation that epithelial dysfunction in active EoE may play an equally important role as the inflammatory component due to sensitization to allergens and exposure to microbes. Additionally, data suggests that for many patients, epithelial dysfunction persists during inactive EoE when therapy has cleared the inflammatory infiltrate. The mechanism of persistent epithelial dysfunction is poorly understood. However, we and others have observed a reproducible, dysregulated gene expression pattern during active EoE with aberrant expression of epithelial structural proteins. We show that epithelial cells from EoE patients maintain aspects of this dysregulated gene expression pattern when grown in a neutral culture environment. This suggests that epigenetic mechanisms maintain these gene expression patterns in EoE epithelium in the absence of inflammation. Notably, in vitro IL-13 treatment of control epithelial cells replicates similar aspects of the EoE mucosal transcriptome, suggesting a specific role for this Th2 cytokine in the epithelial barrier dysfunction of EoE. IL-13-associated epigenetic alteration of epithelial function has been shown in several types of epithelium but the affected loci and functional implications in the esophagus are unclear. The hypothesis of this proposal is that IL-13 induces epigenetic changes in the esophageal epithelium of patients with EoE, leading to persistent epithelial dysfunction. The work will leverage access to a training team with expertise in epigenetics, transcriptomics and bioinformatics is uniquely situated to work with a pediatric population of EoE patients. Aim 1 will use a three dimensional air-liquid interface model of esophageal squamous epithelium to determine if chronic in vitro exposure to IL-13 treatment induces epigenetic changes and barrier dysfunction in primary epithelium from non-EoE control patients. The goal of this aim is to identify if IL-13 treatment is associated with alterations in histone marks and gene expression changes in genes known to affect barrier function. Aim 2 will use biopsy tissue from patients with and without EoE to examine changes in histone marks and gene expression in the esophageal epithelium. The goal of this aim is to identify and localize a set of epithelial genes with persistently dysregulated expression in active and inactive EoE (when compared to control patients). The outcome of these studies will inform the understanding of esophageal epithelial barrier dysfunction and EoE disease persistence, and provide the basis for the applicant’s first R01 submission. The overarching goal of the research strategy and training plan in this proposal is to develop the candidate into an independent investigator leading a robust research program that utilizes research and analysis skills in epigenetics, transcriptomics and bioinformatics in the field of non-IgE mediated food allergies.

PROJECT SUMMARY The proposed research explores the mechanisms of epithelial barrier dysfunction in eosinophilic esophagitis (EoE). During its active disease phase, EoE is characterized by Th2-type, eosinophil-rich inflammation with high levels of IL-13, IL-4 and chemoattractant chemokines. There is a growing appreciation that epithelial dysfunction in active EoE may play an equally important role as the inflammatory component due to sensitization to allergens and exposure to microbes. Additionally, data suggests that for many patients, epithelial dysfunction persists during inactive EoE when therapy has cleared the inflammatory infiltrate. The mechanism of persistent epithelial dysfunction is poorly understood. However, we and others have observed a reproducible, dysregulated gene expression pattern during active EoE with aberrant expression of epithelial structural proteins. We show that epithelial cells from EoE patients maintain aspects of this dysregulated gene expression pattern when grown in a neutral culture environment. This suggests that epigenetic mechanisms maintain these gene expression patterns in EoE epithelium in the absence of inflammation. Notably, in vitro IL-13 treatment of control epithelial cells replicates similar aspects of the EoE mucosal transcriptome, suggesting a specific role for this Th2 cytokine in the epithelial barrier dysfunction of EoE. IL-13-associated epigenetic alteration of epithelial function has been shown in several types of epithelium but the affected loci and functional implications in the esophagus are unclear. The hypothesis of this proposal is that IL-13 induces epigenetic changes in the esophageal epithelium of patients with EoE, leading to persistent epithelial dysfunction. The work will leverage access to a training team with expertise in epigenetics, transcriptomics and bioinformatics is uniquely situated to work with a pediatric population of EoE patients. Aim 1 will use a three dimensional air-liquid interface model of esophageal squamous epithelium to determine if chronic in vitro exposure to IL-13 treatment induces epigenetic changes and barrier dysfunction in primary epithelium from non-EoE control patients. The goal of this aim is to identify if IL-13 treatment is associated with alterations in histone marks and gene expression changes in genes known to affect barrier function. Aim 2 will use biopsy tissue from patients with and without EoE to examine changes in histone marks and gene expression in the esophageal epithelium. The goal of this aim is to identify and localize a set of epithelial genes with persistently dysregulated expression in active and inactive EoE (when compared to control patients). The outcome of these studies will inform the understanding of esophageal epithelial barrier dysfunction and EoE disease persistence, and provide the basis for the applicant’s first R01 submission. The overarching goal of the research strategy and training plan in this proposal is to develop the candidate into an independent investigator leading a robust research program that utilizes research and analysis skills in epigenetics, transcriptomics and bioinformatics in the field of non-IgE mediated food allergies.