RNA-sequencing identifies global transcriptional changes in peripheral CD4+ cells during active esophagitis and following epicutaneous immunotherapy in eosinophilic esophagitis.

Immunotherapy strategies have been studied for IgE-mediated food allergies but have not been studied for non-IgE mediated food allergy disorders, including eosinophilic esophagitis. We interrogated the transcriptional signatures of peripheral CD4+ cells isolated from pediatric eosinophilic esophagitis patients enrolled in a phase IIa clinical trial of milk-antigen epicutaneous immunotherapy. We analyzed differential expression in peripheral CD4+ cells before therapy in patients before and after milk-exclusion diet. RNA-sequencing analysis revealed that there were 244 differentially expressed genes in peripheral blood CD4+ cells of EoE patients consuming milk versus those eliminating it, and 129 DEGs in CD4+ cells isolated after EPIT versus after placebo (FDR<0.05). Gene set enrichment analysis identifies enrichment of hallmark interferon-a and -g response signatures in peripheral CD4+ T cells from EoE patients during active disease on a milk-containing diet. In post-EPIT therapy samples, our analysis identifies enrichment in T-cell receptor signaling, antigen presentation, costimulation, and cytokine signaling pathways. These data suggest a unique peripheral CD4+ T cell gene signature is present in EoE patients during active disease. We observe a distinct transcriptional profile post-EPIT therapy in EoE patients, suggesting that EPIT alters CD4+ responses in EoE patients. Peripheral blood samples were collected from 15 of 20 patients enrolled in in a clinical trial of milk antigen epicutaneous immunotherapy (EPIT) for EoE (PMID: 31100455). Samples were collected from three timepoints. (1) before therapy, on milk-containing diet (2) before therapy, on milk-avoidance diet (3) after EPIT or placebo therapy. CD4+ T cells were isolated from the peripheral blood samples using magnetic bead positive isolation. Total RNA was isolated and sequenced from isolated CD4+ cell population.