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Principal Investigator: Melanie A Ruffner
Organization: CHILDREN'S HOSP OF PHILADELPHIA
Fiscal Year: 2024
Award: $185,328
Funding agency: National Institute of Allergy and Infectious Diseases
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.
Terms: <3-D><3-Dimensional><3D><Affect><Age><Air><Allergens><Allergic><Allergic to food><Allergy to food><Automobile Driving><B cell growth factor><B-Cell Differentiation Factor-1><B-Cell Growth Factor-1><B-Cell Growth Factor-I><B-Cell Proliferating Factor><B-Cell Stimulating Factor><B-Cell Stimulating Factor-1><B-Cell Stimulation Factor-1><B-Cell Stimulatory Factor-1><BCDF-1><BCGF><BCGF-1><BCSF 1><BSF-1><BSF1><Basal Cell Hyperplasia><Basal Transcription Factor><Basal transcription factor genes><Behavior><Binetrakin><Bio-Informatics><Bioinformatics><Biopsy><Blood Eosinophil><Body Tissues><Cell Body><Cell Communication and Signaling><Cell Function><Cell Physiology><Cell Process><Cell Signaling><Cell division><Cells><Cellular Function><Cellular Physiology><Cellular Process><ChIP Sequencing><ChIP assay><ChIP-seq><ChIPseq><Chemoattractants><Chemotactic Cytokines><Chemotactic Factors><Chemotaxins><Childhood><Chronic><DNA Sequence><Data><Disease><Disorder><Down-Regulation><Drug Targeting><Dysfunction><Environment><Eosinophilic Esophagitis><Eosinophilic Granulocyte><Eosinophilic Infiltrate><Eosinophilic Leukocyte><Epigenetic><Epigenetic Change><Epigenetic Mechanism><Epigenetic Process><Epithelial Cells><Epithelium><Esophageal mucous membrane><Esophagus><Exposure to><Expression Signature><Flow Cytofluorometries><Flow Cytofluorometry><Flow Cytometry><Flow Microfluorimetry><Flow Microfluorometry><Food Allergy><Food Hypersensitivity><Foundations><Functional disorder><Future><Gene Action Regulation><Gene Expression><Gene Expression Profile><Gene Expression Regulation><Gene Proteins><Gene Regulation><Gene Regulation Process><Gene Transcription><General Transcription Factor Gene><General Transcription Factors><Generalized Growth><Genes><Genetic Transcription><Genome><Goals><Growth><Heritability><Heterogeneity><Histologic><Histologically><Histones><Homologous Chemotactic Cytokines><Human><IL-13><IL-4><IL13><IL4 Protein><Immunoblotting><Immunofluorescence><Immunofluorescence Immunologic><Impairment><In Vitro><Inflammation><Inflammatory><Inflammatory Infiltrate><Intercrines><Interleukin-13><Interleukin-4><Interleukin-4 Precursor><Intracellular Communication and Signaling><Intracellular Space><Investigators><Liquid substance><Lymphocyte Stimulatory Factor 1><MCGF-2><Marrow Eosinophil><Mast Cell Growth Factor-2><Mediating><Medical><Mentors><Microbe><Modeling><Modern Man><Modification><Morbidity><Morbidity - disease rate><Mucosa><Mucosal Inflammation><Mucosal Tissue><Mucositis><Mucous Membrane><Occluding Junctions><Outcome Study><Pathogenesis><Pathway interactions><Patients><Persons><Phase><Phenotype><Physiopathology><Play><Population><Position><Positioning Attribute><Process><Protein Gene Products><Proteins><Quantitative RTPCR><Quantitative Reverse Transcriptase PCR><RNA Expression><Regulatory Pathway><Reproducibility><Research><Research Personnel><Researchers><Resolution><Risk><Role><SIS cytokines><Signal Pathway><Signal Transduction><Signal Transduction Systems><Signaling><Squamous Differentiation><Squamous Epithelium><Structural Protein><Structure><Subcellular Process><T-Cell Growth Factor 2><TIL4><TLR2><TLR2 gene><TLR2 receptor><Tight Junctions><Tissue Growth><Tissues><Toll-Like Receptor 2><Toll/Interleukin 1 Receptor-Like 4><Toll/Interleukin 1 Receptor-Like 4 Gene><Toll/Interleukin 1 Receptor-Like Protein 4><Training><Transcription><Transcription Factor Proto-Oncogene><Transcription factor genes><Translational Research><Translational Science><Up-Regulation><Upregulation><Western Blotting><Western Immunoblotting><Work><Zonula Occludens><ages><allergic airway epithelium inflammation><allergic airway inflammation><barrier to testing><biological signal transduction><career><chemoattractant cytokine><chemokine><chromatin immunoprecipitation><chromatin immunoprecipitation-sequencing><chromatin modification><compare to control><comparison control><complement chemotactic factor><cytokine><dietary><driving><eosinophil><eosinophilic inflammation><epigenetic regulation><epigenetically><esophageal mucosa><experience><flow cytophotometry><fluid><gene expression pattern><gene expression signature><gene locus><genetic locus><genomic location><genomic locus><global gene expression><global transcription profile><histone modification><hurdle to testing><improved><insight><liquid><microbial antigen><microorganism antigen><novel><obstacle to testing><ontogeny><pathophysiology><pathway><pediatric><programs><protein blotting><protein expression><qRTPCR><resolutions><scRNA-seq><single cell RNA-seq><single cell RNAseq><single cell expression profiling><single cell transcriptomic profiling><single-cell RNA sequencing><skills><social role><testing barrier><testing hurdle><testing obstacle><three dimensional><transcription factor><transcriptional profile><transcriptional signature><transcriptome><transcriptomics><translation research><translational investigation><unsupervised clustering>