Rationale: Currently patients with eosinophilic esophagitis (EoE) are treated empirically to resolve esophageal eosinophilia. Our objective was to compare gene expression profiles in EoE patients at baseline and after treatment to characterize transcriptional phenotypes and identify molecular pathways involved in the disease.
Methods: We collected blood samples at baseline and after 6-8 weeks of treatment from EoE patients treated with cow’s milk elimination diet or swallowed fluticasone. We extracted RNA and analyzed whole genome expression using Illumina Beadstation, GeneSpring software and a modular transcriptional analysis tool.
Results: We compared 20 age-matched healthy controls with 40 EoE patients at baseline. Thirty patients were also studied after treatment. Among EoE patients, 159 genes were differentially expressed with a minimum of two-fold expression change compared with healthy controls. By comparison with controls, EoE patients had over expression of genes involved in cell cycle and inflammation and under expression of cytotoxic/NK cell and platelets/red blood cell related genes. In EoE treated patients, a high proportion of cytotoxic/NK cell genes were over expressed. Although the signature was faint, hierarchical clustering revealed two groups of EoE patients with distinct transcriptional profiles.
Conclusions: EoE patients showed differences in gene expression patterns compared with healthy controls that are modified following treatment suggesting that they may be functionally significant. Further studies are needed to understand the significance of two distinct groups of EoE patients.