(4x) Clonally Expanded, GPR15-Expressing Effector Th2 Cells Are Associated with Eosinophilic Esophagitis

Eosinophilic esophagitis (EoE) is an allergic disorder characterized by the recruitment of eosinophils to the esophagus, resulting in chronic esophageal inflammation. Clinically, EoE often manifests as an antigen-specific disease, in which exposure to specific food allergens triggers esophageal inflammation, but evidence for an antigen-specific adaptive immune response in EoE is lacking. In addition, while EoE is known to involve tissue-resident Th2 cells that produce the cytokines IL-5 and IL-13, much of the available transcriptomic and genomic data place the dysfunction of the esophageal epithelium, rather than the adaptive immune system, at the center of disease pathogenesis. Ultimately, the full set of mechanisms through which Th2 cells are recruited to the esophagus and generate chronic esophageal inflammation and organ-wide dysfunction, as well as the antigen specificities of these cells, remain unknown.

In this work, we utilized single-cell RNA and T cell receptor (TCR) sequencing to analyze over 60,000 single cells from the esophageal biopsies, duodenal biopsies, and peripheral blood of patients with EoE. We identified a population of pathogenic effector Th2 (peTh2) cells present in the esophageal biopsies of patients with active disease that exhibited clonal expansion, suggesting antigen-specific activation, and expressed unique gene signatures associated with the synthesis of eicosanoids. Eicosanoids and cytokines synthesized by tissue-resident Th2 cells were predicted to directly recruit and activate esophagus-resident eosinophils and other allergic mediators, such as mast cells. In the peripheral blood, a subset of CRTH2+ memory CD4+ T cells also expressed a peTh2 phenotype. These cells also exhibited clonal expansion as well as convergence of TCR sequences, indicating that these cells are expanded in response to a defined set of antigens. Shared clonotypes were detected between tissue-resident and peripheral peTh2 cells, and the esophagus-homing receptor GPR15 was upregulated by peripheral peTh2 clonotypes that were also detected in the esophagus. Lastly, peTh2 cells and GPR15+ cells were enriched among milk-reactive CD4+ T cells in patients with milk-triggered disease, suggesting that peTh2 cells in EoE are an expanded, food antigen-specific population with enhanced esophagus homing potential. These results provide important insight into the role of conventional antigen-specific Th2 cells in the pathogenesis of EoE and illustrate how single-cell profiling of human biopsy samples can elucidate the mechanisms of immunological disease.