Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing

Eosinophilic esophagitis (EoE) is an allergic inflammatory disorder of the esophagus that is compounded by genetic predisposition and hypersensitivity to environmental antigens. Using high-density oligonucleotide expression chips, a disease-specific esophageal transcript signature was identified and shown to be largely reversible with therapy. In an effort to expand the molecular signature of EoE, we performed RNA sequencing on esophageal biopsies from healthy controls and patients with active EoE and identified a total of 1 607 significantly dysregulated transcripts (1 096 upregulated, 511 downregulated). When clustered by raw expression levels, an abundance of immune-cell specific transcripts that are highly induced in EoE are expressed at low (or undetectable) levels in healthy controls. Moreover, 66% of the gene signature identified by RNA sequencing was previously unrecognized in the EoE transcript signature by microarray-based expression profiling and included several long non-coding RNAs (lncRNA), an emerging class of transcriptional regulators. The lncRNA BANCR was upregulated in EoE and induced in IL-13–treated primary esophageal epithelial cells. Repression of BANCR significantly altered the expression of IL-13–induced pro-inflammatory genes. Together, these data comprise new potential biomarkers of EoE and demonstrate a novel role for lncRNAs in EoE and IL-13–associated responses.