Interferon-γ signaling in eosinophilic esophagitis has implications for epithelial barrier function and programmed cell death
Authors: Lal Megha , Burk Caitlin M. , Gautam Ravi , Mrozek Zoe , Trachsel Tina , Beers Jarad , Carroll Margaret C. , Morgan Duncan M. , Muir Amanda B. , Shreffler Wayne G. , Ruffner Melanie A. 
Published: January 2024

ABSTRACTObjectiveEosinophilic esophagitis (EoE) is a chronic esophageal inflammatory disorder characterized by eosinophil-rich mucosal inflammation and tissue remodeling. Transcriptional profiling of esophageal biopsies has previously revealed upregulation of type I and II interferon (IFN) response genes. We aim to unravel interactions between immune and epithelial cells and examine functional significance in esophageal epithelial cells.DesignWe investigated epithelial gene expression from EoE patients using single-cell RNA sequencing and a confirmatory bulk RNA-sequencing experiment of isolated epithelial cells. The functional impact of interferon signaling on epithelial cells was investigated usingin vitroorganoid models.ResultsWe observe upregulation of interferon response signature genes (ISGs) in the esophageal epithelium during active EoE compared to other cell types, single-cell data, and pathway analyses, identified upregulation in ISGs in epithelial cells isolated from EoE patients. Using an esophageal organoid and air-liquid interface models, we demonstrate that IFN-γ stimulation triggered disruption of esophageal epithelial differentiation, barrier integrity, and induced apoptosis via caspase upregulation. We show that an increase in cleaved caspase-3 is seen in EoE tissue and identify interferon gamma (IFNG) expression predominantly in a cluster of majority-CD8+ T cells with high expression ofCD69andFOS.ConclusionThese findings offer insight into the interplay between immune and epithelial cells in EoE. Our data illustrate the relevance of several IFN-γ-mediated mechanisms on epithelial function in the esophagus, which have the potential to impact epithelial function during inflammatory conditions.Key MessagesWhat is already known about this topic:The transcriptome of esophageal biopsy tissue reproducibly distinguishes eosinophilic esophagitis from histologically normal tissue, with evidence of mixed inflammatory signals.Interferon response signature genes are elevated in EoE biopsy tissue compared to controls, suggesting T1 in addition to T2 cytokine signaling within EoE mucosa.What this study adds:We observe reproducible, robust upregulation of interferon signature genes in esophageal epithelium, and we confirm that esophageal epithelium expresses functional IFN-a and IFN-γ receptors.IFN-γ treatment of epithelial organoids has several detrimental effects, including decreased proliferation, organoid formation, and increased caspase activation.Analysis of single-cell RNA-sequencing data from of EoE biopsy tissue during active disease and remission identified that a CD8+ population expressing high levels ofFOS, ITGAE, and ITGA1expresses high levels ofIFNGHow this study might affect research, practice, or policy:We identify esophageal epithelium as the cellular source for interferon response gene signature in EoE and a CD8+ tissue-resident memory T-cell population was the main source ofIFNG.Further mechanistic studies are required to identify how non-T2 signaling mechanisms like IFN-γ signaling contribute to EoE pathogenesis, and if this pathway can be targeted as an adjunctive therapy for EoE.