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Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing

Abstract

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 was 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 1607 significantly dysregulated transcripts (1096 upregulated, 511 downregulated). When clustered by raw expression levels, an abundance of immune cell-specific transcripts are highly induced in EoE but 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 BRAF-activated non-protein coding RNA (BANCR) was upregulated in EoE and induced in interleukin-13 (IL-13)–treated primary esophageal epithelial cells. Repression of BANCR significantly altered the expression of IL-13–induced proinflammatory genes. Together, these data comprise new potential biomarkers of EoE and demonstrate a novel role for lncRNAs in EoE and IL-13–associated responses.

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Acknowledgements

This work was supported in part by NIH U19 AI070235, NIH R01 DK076893, the PHS Grant P30 DK0789392 and the Campaign Urging Research for Eosinophilic Disease (CURED) Foundation, and the Angels for Eosinophilic Research Foundation. JDS was supported by the Thrasher Research Fund Early Career Award (NR-0171). We would like to thank Dr Anil Rustgi (University of Pennsylvania, Pennsylvania, PA, USA) for the EPC2-hTERT cell line and Dr Paul Khavari (Stanford University, Stanford, CA, USA) for supplying the BANCR shRNA lentiviral plasmids. We would also like to thank Shawna Hottinger for editorial assistance, all of the participating families and clinical research staff of the Cincinnati Center for Eosinophilic Disorders and members of the Division of Allergy and Immunology.

Author contributions

JDS, CB, BJA and MER were involved in study concept and design. JDS, KKC, CB, EMS and KAK were involved in data acquisition and/or sample preparation. MHC, JPA, PEP, VAM, AJP, SAK and JPK collected patient samples or provided histopathological analyses thereof. AJP, PJD and BJA performed computational analysis of RNA sequencing reads. JDS, AJP, PJD, RAK, BJA and MER were involved in data analysis and interpretation and the writing and critical revision of the manuscript. BJA and MER supervised the overall study.

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Correspondence to M E Rothenberg.

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MER is a consultant for Immune Therapeutics and has an equity interest in reslizumab (Teva Pharmaceuticals) and is a consultant for Immune Pharmaceuticals, Pluristem Pharmaceuticals, Novartis and Receptos. The remaining authors declare no conflict of interest.

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Sherrill, J., KC, K., Blanchard, C. et al. Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing. Genes Immun 15, 361–369 (2014). https://doi.org/10.1038/gene.2014.27

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