Transcriptomic Genes Identified in Familial Eosinophilic Esophagitis

Background and Aims: Evidence for a genetic contribution to eosinophilic esophagitis (EoE) exists from family and genome-wide association studies. Extensive investigation into rare variants contributing to EoE has not been performed. The Aim is to evaluate families with multiple cases of EoE by genomic and transcriptomic sequencing to identify genes predisposing to EoE. Methods: We whole exome sequenced (WES) distant relative pairs (e.g., cousins) in extended EoE pedigrees and other affected relatives to identify rare, shared, potentially pathologic variants. Whole-transcriptome sequencing by RNA-Seq was performed in nuclear families with multiple EoE cases. We compared the overlap of genes from DNA and RNA sequencing for relevance to disease manifestations. Results: WES was performed in 50 familial cases in 21 EoE extended pedigrees. We observed 219 rare, candidate predisposition variants in 210 genes with complete sharing among all affected family members. Transcriptome sequencing was performed for 43 EoE cases in 18 nuclear kindreds, including 6 relatives without EoE. We observed 10,070 total differentially expressed genes compared to controls. We identified three genes (MUC16, ADGRE1, and TENM3) with evidence of rare variant sharing and differential gene expression among all affected family members. We identified 43 other genes with partial sharing of rare variants among affected family members and with differential gene expression. Several genes identified as prominent in EoE were also differentially expressed in unaffected relatives. Conclusions: Multiple genes related to immune response, barrier dysfunction, and cell adhesion were identified in familial EoE cases and unaffected family members supporting a genetic familial predisposition and a possible multi-hit background to disease pathophysiology. Overall design: We obtained leftover formalin-fixed, paraffin-embedded (FFPE) tissue blocks as the source for RNA; the FFPE tissue blocks were originally obtained for clinical diagnostic purposes. All included specimens were confirmed to meet diagnostic criteria for eosinophilic esophagitis (> 15 eosinophils/high power field for the esophageal biopsy specimen) as determined by pathologists. Individuals with a diagnosis of eosinophilic esophagitis (EoE) were selected from multiplex EoE families that included EoE cases who were 2-3 meioses apart (siblings, parent-offspring, and avuncular relationships) and included all known EoE cases in the family with esophageal FFPE specimens available. We also included unaffected family members who had no history of esophageal eosinophilia and had available esophageal biopsies that were devoid of eosinophils. All unaffected relatives were from nuclear families with at least two cases of EoE. Controls for RNA sequencing were obtained from individuals who had undergone esophageal biopsies and confirmed to have normal esophageal histology on pathology. Controls did not have autoimmune or eosinophilic disease and were not on immunosuppressive medications. Controls did not report a family history of eosinophilic disease.