RNA Sequencing if Esophageal Tissues During Food Elimination and Reintroduction Reveals Novel Findings Regarding the Early Pathogenesis of EoE - PROJECT ABSTRACT Eosinophilic Esophagitis (EoE) is a morbid, highly inflammatory condition of the esophagus, increasingly diagnosed in both children and adults, resulting in substantial healthcare burden for patients and payors. Due to the need for invasive upper endoscopies for diagnosis, the disease is not identified for years after the onset of symptoms. Yet, identifying and controlling the disease early in its development would provide a means to personalize therapy and reduce complications. Our long-term goal is to detect and characterize the early epithelial signals which precede the development of persistent, chronic EoE, identifying biomarkers of early disease, in order to reduce the burden of this morbid, inflammatory process. The overall objective for this application is to characterize the molecular pathways responsible for disease initiation, differentiating them from those that are responsible for the maintenance and persistence of inflammation over years. Our central hypothesis is that the initiation of EoE involves specific reversible (preventable) epithelial signals which propagate and perpetuate a robust, complex, inflammatory reaction leading to diffuse esophageal inflammation, fibrosis, narrowing, and life-altering symptoms of choking, food impactions, and food/social aversion. Our rationale stems from our discovery that specific pathways are differentially regulated within esophageal tissues during food elimination/reintroduction diets. The central hypothesis will be tested by pursuing two specific aims: (1) to differentiate RNA signatures responsible for the initiation of EoE (acute EoE) from those involved in persistent, longstanding inflammation (chronic EoE);and (2) to identify the specific epithelial and immune pathways which precede the onset of robust, diffuse esophageal eosinophilia. Under the Aim 1, the RNA signatures from paired biopsies taken prior to food elimination (“chronic” EoE) and after recurrence of EoE during reintroduction of trigger foods (“acute” disease phase) within patients will be compared to differentiate the processes involved in disease initiation and disease persistence. For the Aim 2, tissues from patients who resolved their EoE with food elimination diet and subsequently demonstrated “patchy” recurrence of disease upon trigger food reintroduction (i.e. obvious eosinophilic inflammation and endoscopic signs of EoE interspersed with normal-appearing tissue) will undergo spatial transcriptome sequencing to localize and decipher the cellular contributions involved in disease recurrence. The proposed research is innovative in its study of human samples to thoroughly categorize early changes involved in disease initiation. This study of early transcriptional signals capitalizes on biopsies performed during food elimination/reintroduction diets which remove and then expose patients to the antigenic stimulus – essentially recreating a scenario which mimics disease genesis. The significance of the research lies in the identification of new biomarkers and eventual interventions/therapies for early stages of EoE. Collectively, our observations should inform future investigation into early markers of disease and the development of pre-emptive therapies to prevent disease progression.
