IL-13 involvement in eosinophilic esophagitis: transcriptome analysis
ABSTRACT: 3 eosinophilic esophagitis biopsies, cultured and stimulated with IL-13 : each of them was either left unstimulated or stimulated (100ng for 48h) We used microarray to uncover the IL-13-induced genes in esophageal epithelial cells of the esophagus Keywords: treated vs non treated Overall design: 3 biopsies from EE patients were obtained and primary epithelial cell were cultured and either left unstimulated or stimulated with IL-13 followed by RNA extraction and hybridization on Affymetrix microarrays.
Project description:3 eosinophilic esophagitis biopsies, cultured and stimulated with IL-13 : each of them was either left unstimulated or stimulated (100ng for 48h); We used microarray to uncover the IL-13-induced genes in esophageal epithelial cells of the esophagus Experiment Overall Design: 3 biopsies from EE patients were obtained and primary epithelial cell were cultured and either left unstimulated or stimulated with IL-13 followed by RNA extraction and hybridization on Affymetrix microarrays.
Project description:Despite the well-recognized role of IL-13–induced transcriptional responses in allergic inflammation, the epigenetic mechanisms driven by IL-13 have not been well defined. We interrogated the transcriptional and epigenetic signatures of IL-13-induced epithelial responses focusing on the chromatin activation marks H3K4me3, H3K9Ac, and H3K27Ac. ChIP-sequencing analysis revealed that IL-13–inducible genes were epigenetically poised for induction and continued to accumulate epigenetic changes in response to IL-13. By intersecting the transcriptome and the epigenome of the IL-13 response, we identified neurotrophic tyrosine kinase receptor 1 (NTRK1) as a major target of IL-13 in epithelial cells. Using eosinophilic esophagitis as a model system for human allergic inflammation, we found that NTRK1 was dramatically induced in inflamed esophageal biopsies, and downstream mediators of NTRK1 signaling were elevated in diseased tissue. The NTRK1 ligand nerve growth factor (NGF) was constitutively expressed in control and disease states, indicating that induction of the receptor by IL-13 limited pathway activation. In epithelial cells, NGF and IL-13 synergistically induced transcription and secretion of the key eosinophil chemoattractant CCL26 (eotaxin-3). In summary, we demonstrate that IL-13–mediated allergic responses are epigenetically driven and identify NTRK1 as a novel epigenetic and transcriptional target of IL-13 that uniquely contributes to allergic inflammation. Human esophageal epithelial cell line TE-7 was stimulated with IL-13 at 100 ng/ml for 2 hr, 6 hr and 24 hr and subjected to RNA-sequencing. In parallel, TE-7 cells were induced with IL-13 for 6 hr and subjected to ChIP-sequencing analysis for H3K4me3, H3K9Ac and H3K27Ac activating chromatin marks.
Project description:Nanostring nCounter Human miRNA assay (v1) of esophageal mucosal biopsies from children with eosinophilic esophagitis and controls Individual esophageal mucosal biopsies from children with eosinoniphilic esophagitis and controls were analysed for detection of microRNA
Project description:Significant recent progress has been made with understanding eosinophilic gastrointestinal disorders (EGIDs) yet most studies have focused on eosinophilic esophagitis (EoE). Herein, we aimed to provide fundamental information about the molecular characteristics of eosinophilic gastritis (EG). Overall design: RNA was isolated from gastric biopsies from control patients (n=5) and patients with EG (n=5) followed by hybridization on Affymetrix microarrays.
Project description:Eosinophilic esophagitis (EoE) is a T helper type 2 (TH2) cytokine-associated disease charaterized by eosinophil infiltration, epithelial cell hyperplasia and tissue remodeling. Recent studies have highlighted a major contribution for IL-13 in EoE pathogenesis. Paired immunoglobulin-like receptor (PIR)-B is a cell surface immune-inhibitory receptor that is expressed by eosinophils and postulated to regulate eosinophil development and migration. We report that Pirb is upregulated in the esophagus after inducible overexpression of IL-13 (CC10-IL13 Tg mice) and is overexpressed by esophageal eosinophils. CC10-IL13Tg/PirB-/- mice displayed increased esophageal eosinophilia and EoE pahtology, including epithelial cell thickening, fibrosis and angiogenesis, compared with CC10-IL13 Tg/PirB+/+ mice. Transcriptome analysis of primary Pirb+/+ and Prib-/- esophageal eosinophils revealed increased expression of transcripts associated with promoting tissue remodeling in Pirb-/- eosinophils including pro-fibrotic genes, genes promoting epithelial-to-mesenchymal transition (EMT) and genes associated with epithelial growth. These data identify PIR-B as a molecular checkpoint in IL-13-induced eosinophil accumulation and activation, which may serve as a novel target for future therapy in EoE. Overall design: 17 samples are analyzed in this experiment. The experiment was designed with 3 replicates for each treatment/genotype/tissue (Dox and no Dox/wildtype and knockout/bone marrow and esophagus), with the exception of the sample wildtype bone marrow no Dox where 1 replicate was dropped due to low hybridization signal. The no Dox and wildtype samples are controls for the treatment and background of the mice.
Project description:Serum from children with active and inactive treated eosinophilic esophagitis was analyzed for detection of microRNA Individual serum samples from children with eosinophilic esophagitis were analyzed for detection of microRNA. (n=5 for active EoE and n=5 for inactive EoE)
Project description:Aim of this study was to compare the effects of the lambda interferons IL-28A and IL-29 regarding transcriptional activation/repression of gene expression. For this purpose, the hepatic cell line Huh7 was stimulated with 100 ng/ml IL-28A or IL-29 for 6 hours or was left unstimulated. Then, gene expression of IL-28A or IL-29 treated cells was compared to expression in unstimulated cells
Project description:Idiopathic pulmonary arterial hypertension (IPAH) is characterized by medial hypertrophy due to pulmonary arterial smooth muscle cell (paSMC) hyperplasia. Interleukin (IL)-13 is a potent regulator of tissue fibrosis and remodelling, and its effects are dependent on the cell-type specific expression of the IL-13 receptor isotypes IL-4Rα, IL-13Rα1, and IL-13Rα2. In order to identify the possible mechanism how IL-13 can exert its antiproliferative effect on paSMC microarray analysis was performed. For this purpose paSMC were stimulated with IL-13(10ng/ml) for 2h and 6h, respectively and subjected to microarray analysis. Overall design: Comparison of stimulated versus unstimulated cells. 3 biological replicates, 2 time points