Food Allergen Specificity of Circulating T cells in Eosinophilic Esophagitis Patients

Eosinophilic esophagitis (EoE) is a chronic, T cell-mediated disease that is triggered by specific foods and results in progressive esophageal dysfunction. However, we have limited knowledge of the antigen specificity and TCR diversity of T cells in this condition. Identifying disease-causing antigen/TCR clonotypes in EoE patients will provide useful information to aid the development of novel diagnostic and therapeutic approaches. We isolated peripheral blood mononuclear cells from patients with EoE or healthy controls and cultured them in vitro in the absence or presence of five milk antigens. T cell expansion and type 2 cytokine production were measured. Single cell TCR sequencing with linked RNA sequencing was performed to examine clonotype expansion and transcriptional response in response to antigen stimulation. In contrast to peripheral CD4+ T cells from non-allergic controls, cells from patients with milk-triggered EoE divide and produce type 2 cytokines in response to milk stimulation. Single-cell TCR sequencing reveals milk-induced clonal expansion of T cell subsets, and identifies specific T cell clonotypes that are enriched upon milk stimulation. Milk-enriched T cell clonotypes shared transcriptional features with T cells from inflamed EoE esophageal mucosa. Food-specific T cells circulate in the blood of EoE patients, and are detectable after stimulation with food allergens. TCR repertoire analysis reveals expansion of CDR3s with high probability for allergen epitope specificity. This work improves our understanding of the pathophysiology of EoE, and is an important step towards developing efficient, definitive, and minimally invasive diagnostic tools for identification of EoE-causal foods.