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Dataset Information

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18 Citations

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Omics score: 37

Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing

ABSTRACT: We utilized RNA sequencing to expand and better define the molecular entities involved in the transcriptional programming within the eosphagus in eosinophilic esophagitis (EoE) Examination of differentially expressed genes from RNA sequencing data performed on esophageal biopsy specimen from 6 healthy controls and 10 patients with active EoE

ORGANISM(S): Homo sapiens

DISEASE(S): Normal,Eosinophilic Esophagitis

SUBMITTER: Marc E Rothenberg Joseph D Sherrill Marc Rothenberg

PROVIDER: E-GEOD-58640 | ArrayExpress | 2014-06-27

SECONDARY ACCESSION(S): SRP043388GSE58640PRJNA253059

REPOSITORIES: GEO, ArrayExpress, ENA

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	E-GEOD-58640.additional.1.zip	Other
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Publications

Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing.

Sherrill J D JD Kiran K C KC Blanchard C C Stucke E M EM Kemme K A KA Collins M H MH Abonia J P JP Putnam P E PE Mukkada V A VA Kaul A A Kocoshis S A SA Kushner J P JP Plassard A J AJ Karns R A RA Dexheimer P J PJ Aronow B J BJ Rothenberg M E ME

Genes and immunity 20140612 6

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 acti ...[more]

PMID: 24920534

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Eosinophilic esophagitis.

Project description:To review the understanding of the pathogenesis of eosinophilic esophagitis (EoE) and the role of the immune system in the disease process.Peer-reviewed articles on EoE from PubMed searching for "Eosinophilic Esophagitis and fibrosis" in the period of 1995 to 2013.Studies on the clinical and immunologic features, pathogenesis, and management of EoE.Recent work has revealed that thymic stromal lymphopoietin and basophil have an increased role in the pathogenesis of disease. Additional understanding on the role of fibrosis in EoE is emerging.The incidence of EoE is increasing like most atopic disease. Similar to other allergic diseases, EoE is treated with topical steroids and/or allergen avoidance.

2014-01-01 | S-EPMC4332835 | BioStudies

TaqMan microRNA array of human serum from children with eosinophilic esophagitis

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)

2014-09-01 | E-GEOD-55793 | ArrayExpress

The Salivary Microbiome Is Altered in Children With Eosinophilic Esophagitis and Correlates With Disease Activity.

Project description:OBJECTIVES:Eosinophilic esophagitis (EoE) is an allergen-mediated inflammatory disease affecting the esophagus. Although microbial communities may affect the host immune responses, little is known about the role of the microbiome in EoE. We compared the composition of the salivary microbiome in children with EoE with that of non-EoE controls to test the hypotheses that the salivary microbiome is altered in children with EoE and is associated with disease activity. METHODS:Saliva samples were collected from 26 children with EoE and 19 non-EoE controls comparable for age and ethnicity. The salivary microbiome was profiled using 16S rRNA gene sequencing. Disease activity was assessed using the Eosinophilic Esophagitis Endoscopic Reference Score and the Eosinophilic Esophagitis Histologic Scoring System (EoEHSS). RESULTS:A trend toward lower microbial richness and alpha diversity was noted in children with EoE. Although the overall salivary microbiome composition was similar between children with and without EoE, specific taxa such as Streptococcus (q value = 0.06) tended to be abundant in children with active EoE compared with non-EoE controls. Haemophilus was significantly abundant in children with active EoE compared with inactive EoE (q value = 0.0008) and increased with the increasing EoEHSS and Eosinophilic Esophagitis Histology Scoring System (q value = 5e-10). In addition, 4 broad salivary microbial communities correlated with the EoEHSS. DISCUSSION:The composition of the salivary microbiome community structure can be altered in children with EoE. A relative abundance of Haemophilus positively correlates with the disease activity. These findings indicate that perturbations in the salivary microbiome may have a role in EoE pathobiology and could serve as a noninvasive marker of disease activity.

2019-01-01 | S-EPMC6613866 | BioStudies

Prolonged Time to Diagnosis of Eosinophilic Esophagitis Despite Increasing Knowledge of the Disease.

Project description:Eosinophilic esophagitis (EoE) is a chronic condition characterized by eosinophilic-predominant inflammation and esophageal dysfunction.1,2 EoE represents a rapidly increasing cause of morbidity and a growing health problem.

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Managing eosinophilic esophagitis: challenges and solutions.

Project description:Eosinophilic esophagitis (EoE) is a chronic and progressive immune-mediated condition defined by symptoms of esophageal dysfunction and dense eosinophilic infiltration of the esophageal mucosa. Therapies consist of anti-eosinophilic medications and specialized diets aimed to decrease the progression of EoE and alleviate its symptoms, namely, dysphagia and food impaction. Assessing response to therapy remains challenging, as treatment end points are not well defined and currently consist of clinical, histologic, and endoscopic features. Newer validated measures may help standardize treatment end points. Emerging data support the use of maintenance therapy, which may reduce disease progression. Optimal dosages, delivery techniques, and duration of treatment need to be determined. When features of fibrostenosis develop, esophageal dilation is a safe and effective adjunctive strategy for improving symptoms. In EoE cases refractory to conventional treatments, newer therapies targeting inflammatory mediators and cytokines are on the horizon.

2016-01-01 | S-EPMC5033215 | BioStudies

Mechanisms of Disease of Eosinophilic Esophagitis.

Project description:Eosinophilic esophagitis (EoE) is a recently recognized inflammatory disease of the esophagus with clinical symptoms derived from esophageal dysfunction. The etiology of EoE is now being elucidated, and food hypersensitivity is emerging as the central cornerstone of disease pathogenesis. Herein, we present a thorough picture of the current clinical, pathologic, and molecular understanding of the disease with a focus on disease mechanisms.

2016-01-01 | S-EPMC4918086 | BioStudies

An Overview of the Diagnosis and Management of Eosinophilic Esophagitis.

Project description:Eosinophilic esophagitis (EoE) is a chronic inflammatory condition characterized by symptoms of esophageal dysfunction and eosinophilic infiltration of the esophageal mucosa. The diagnosis requires esophageal biopsies demonstrating at least 15 eosinophils per high-powered field following a course of high-dose proton pump inhibitors. Management of EoE consists of the three Ds: drugs, dietary therapy, and esophageal dilation. In this review, we discuss the epidemiology, pathogenesis, diagnosis, and treatment of EoE to include the role of emerging therapies.

2016-01-01 | S-EPMC4822098 | BioStudies

Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing.

Project description: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.

2014-01-01 | S-EPMC4156528 | BioStudies

Diet and Stress in Pediatric Eosinophilic Esophagitis.

Project description:Clinical experiences and recent studies suggest that eosinophilic esophagitis (EoE) has the potential to induce caregiver (CG) and child stress. The specific sources of CG EoE-related stress remain uncertain. To address this, we performed a survey of CGs and youth attending a patient with EoE education symposium that measured potential stressful elements in their daily life. Our results indicated that CGs experienced most stress associated with purchasing, preparation, and completion of meals. We conclude that providers should consider this in choosing therapeutic approaches for children with EoE.

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Recent discoveries and emerging therapeutics in eosinophilic esophagitis.

Project description:Eosinophilic esophagitis (EoE) is an allergy-mediated disease culminating in severe eosinophilic inflammation and dysfunction of the esophagus. This chronic disorder of the esophagus causes significant morbidity, poor quality of life, and complications involving fibrosis and esophageal remodeling. Overlapping features between EoE and gastroesophageal reflux disease (GERD) pose great challenges to differentiating the two conditions, although the two disorders are not mutually exclusive. Recent findings suggest that the confounding condition proton pump inhibitor - responsive esophageal eosinophilia (PPI-REE) is likely a subset of EoE. Since PPIs have therapeutic properties that can benefit EoE, PPIs should be considered as a therapeutic option for EoE rather than a diagnostic screen to differentiate GERD, PPI-REE, and EoE. Other current treatments include dietary therapy, corticosteroids, and dilation. Immunomodulators and biologic agents might have therapeutic value, and larger trials are needed to assess efficacy and safety. Understanding the pathophysiology of EoE is critical to the development of novel therapeutics.

2016-01-01 | S-EPMC4734951 | BioStudies

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