Profound loss of esophageal tissue differentiation in patients with eosinophilic esophagitis

Abstract

Background A key question in the allergy field is to understand how tissue specific disease is manifested. Eosinophilic esophagitis (EoE) is an emerging tissue specific allergic disease whose pathogenesis remains unclear. Objective Herein, we tested the hypothesis that a defect in tissue specific esophageal genes is an integral part of EoE pathogenesis. Methods We interrogated the pattern of expression of esophagus-specific signature genes derived from the Human Protein Atlas in the EoE transcriptome and in EPC2 esophageal epithelial cells. Western blot and immunofluorescence were used for evaluating expression of esophageal proteins in control and active EoE biopsies. Whole-exome sequencing (WES) was performed to identify mutations in esophagus-specific genes. Results We found that ~39% of the esophagus-specific transcripts were altered in EoE, with ~90% being downregulated. The majority of transcriptional changes observed in esophagus-specific genes were reproduced in vitro in esophageal epithelial cells differentiated in the presence of IL-13. Functional enrichment analysis revealed keratinization and differentiation as the most affected biological processes, and identified IL-1 cytokines and serine peptidase inhibitors (SERPINs) as the most dysregulated esophagus-specific protein families in EoE. Accordingly, EoE biopsies evidenced a profound loss of tissue differentiation, decreased expression of keratin 4 and cornulin and elevated expression of keratin 5 and 14. Whole-exome sequencing of 33 unrelated EoE cases revealed 39 rare mutations in 18 esophagus-specific differentially expressed genes. Conclusions A tissue-centered analysis has revealed a profound loss of esophageal tissue differentiation (identity) as an integral and specific part of the pathophysiology of EoE, and implicated protease- and IL-1–related activities as putative central pathways in disease pathogenesis.

Genetics of eosinophilic esophagitis

“…Strikingly 39 rare genetic variants in 18 genes were identified in this study, and this preliminary analysis indicates enrichment in gene in epithelial differentiation. 85 …”

“…EoE co-occurs with several Mendelian and non-Mendelian disorders (Table 2 and refs 85,86). For example, EoE is enriched in patients with hypermobility-associated connective-tissue disorders including Loeys-Dietz syndrome (also known as Marfan syndrome type II) 88 and the hypermobility variant of Ehlers-Danlos syndrome.…”

Novel immunologic mechanisms in eosinophilic esophagitis

“…Moreover, a substantial number of genes specifically expressed in the esophagus are dysregulated in EoE; of these, a striking majority are downregulated, suggesting a profound loss of esophageal tissue identity. This includes dysregulation of epithelial differentiation genes (e.g., keratins, cornulin) but also additional classes of genes likely involved in maintaining esophageal tissue integrity such as proteases, protease inhibitors, and IL-1 family members [19 •• ]. These significant alterations in esophageal epithelial structure likely contribute to the initiation and propagation of EoE and constitute a mechanism accounting for the tissue specificity of the disease.…”

“…Remarkably, certain genetic loci associated with increased EoE risk (e.g., FLG , CAPN14 ) [17,20 •• ,21 • ] encode proteins that mediate epithelial barrier function [22,23]. Furthermore, certain rare, damaging genetic variants observed in affected individuals exhibiting a familial pattern of EoE inheritance occur in esophagus-specific genes [19 •• ]. Certain Mendelian diseases associated with squamous epithelial cell barrier defects exhibit EoE (e.g., Netherton’s Syndrome [ SPINK5 ] and severe atopy syndrome associated with metabolic wasting [SAM syndrome] [ DSG1 , DSP ]) [24,25,26].…”

Synaptopodin is upregulated by IL-13 in eosinophilic esophagitis and regulates esophageal epithelial cell motility and barrier integrity

“…EoE pathogenesis is driven by IL-13-mediated transcriptional responses of the esophageal epithelium (7,8), which are collectively improved by steroids (9). Structural and transcriptional changes observed in the inflamed epithelium in biopsies from patients with EoE can be recapitulated in vitro by treating esophageal epithelial cells with IL-13 (10)(11)(12)(13). IL-13 is thought to mediate these responses through epigenetic changes, including elevated levels of histone acetylation and decreased DNA methylation in the promoters of critical mediators, such as eotaxin 3 (also known as CCL26), CAPN14, and NTRK1 (14)(15)(16).…”