Eosinophilic Esophagitis: A Primary Disease of the Esophageal Mucosa

A multi-omic analysis reveals the esophageal dysbiosis as the predominant trait of eosinophilic esophagitis

BACKGROUND

Eosinophilic esophagitis (EoE) is a chronic immune-mediated rare disease, characterized by esophageal dysfunctions. It is likely to be primarily activated by food antigens and is classified as a chronic disease for most patients. Therefore, a deeper understanding of the pathogenetic mechanisms underlying EoE is needed to implement and improve therapeutic lines of intervention and ameliorate overall patient wellness.

METHODS

RNA-seq data of 18 different studies on EoE, downloaded from NCBI GEO with faster-qdump ( https://github.com/ncbi/sra-tools ), were batch-corrected and analyzed for transcriptomics and metatranscriptomics profiling as well as biological process functional enrichment. The EoE TaMMA web app was designed with plotly and dash. Tabula Sapiens raw data were downloaded from the UCSC Cell Browser. Esophageal single-cell raw data analysis was performed within the Automated Single-cell Analysis Pipeline. Single-cell data-driven bulk RNA-seq data deconvolution was performed with MuSiC and CIBERSORTx. Multi-omics integration was performed with MOFA.

RESULTS

The EoE TaMMA framework pointed out disease-specific molecular signatures, confirming its reliability in reanalyzing transcriptomic data, and providing new EoE-specific molecular markers including CXCL14, distinguishing EoE from gastroesophageal reflux disorder. EoE TaMMA also revealed microbiota dysbiosis as a predominant characteristic of EoE pathogenesis. Finally, the multi-omics analysis highlighted the presence of defined classes of microbial entities in subsets of patients that may participate in inducing the antigen-mediated response typical of EoE pathogenesis.

CONCLUSIONS

Our study showed that the complex EoE molecular network may be unraveled through advanced bioinformatics, integrating different components of the disease process into an omics-based network approach. This may implement EoE management and treatment in the coming years.

Viral Induced Effects on a Vulnerable Epithelium; Lessons Learned From Paediatric Asthma and Eosinophilic Oesophagitis

The epithelium is integral to the protection of many different biological systems and for the maintenance of biochemical homeostasis. Emerging evidence suggests that particular children have epithelial vulnerabilities leading to dysregulated barrier function and integrity, that resultantly contributes to disease pathogenesis. These epithelial vulnerabilities likely develop in utero or in early life due to various genetic, epigenetic and environmental factors. Although various epithelia are uniquely structured with specific function, prevalent allergic-type epithelial diseases in children potentially have common or parallel disease processes. These include inflammation and immune response dysregulation stemming from atypical epithelial barrier function and integrity. Two diseases where aetiology and pathogenesis are potentially linked to epithelial vulnerabilities include Paediatric Asthma and Eosinophilic Oesophagitis (EoE). For example, rhinovirus C (RV-C) is a known risk factor for paediatric asthma development and is known to disrupt respiratory epithelial barrier function causing acute inflammation. In addition, EoE, a prevalent atopic condition of the oesophageal epithelium, is characterised by similar innate immune and epithelial responses to viral injury. This review examines the current literature and identifies the gaps in the field defining viral-induced effects on a vulnerable respiratory epithelium and resulting chronic inflammation, drawing from knowledge generated in acute wheezing illness, paediatric asthma and EoE. Besides highlighting the importance of epithelial structure and barrier function in allergic disease pathogenesis regardless of specific epithelial sub-types, this review focuses on the importance of examining other parallel allergic-type disease processes that may uncover commonalities driving disease pathogenesis. This in turn may be beneficial in the development of common therapeutics for current clinical management and disease prevention in the future.

Sex Differences in Blood Transcriptional Profiles and Clinical Phenotypes in Pediatric Patients with Eosinophilic Esophagitis

BACKGROUND

Eosinophilic esophagitis (EoE) is an increasingly recognized, chronic inflammatory disease. Recent reports suggest clinical differences between males and females.

OBJECTIVE

To define the relevant molecular pathways that could be related to clinical phenotypes in children with EoE.

METHODS

We performed blood RNA expression analysis in children with newly diagnosed EoE and matched, healthy controls, and applied bioinformatics tools to define EoE host immune biosignatures. Questionnaires and medical records were used to characterize symptoms, esophagogastroduodenoscopy results, and treatment response.

RESULTS

Forty-one subjects (aged 2-17 years) were enrolled; the cohort consisted of 27 males and 14 females. Patients were randomly divided into a discovery cohort (21 EoE patients and 12 controls) that identified 544 significant differentially expressed transcripts (P ≤ .01; 1.25-fold change). Those 544 transcripts correctly classified most EoE patients in the validation cohort (n = 20) from healthy controls. Global transcriptional perturbation relative to healthy controls, Molecular Distance to Health scores were greater in EoE patients than controls (P = .003). When we analyzed subjects based on age and sex, males 13 years of age and older were more likely to have food impactions (P = .033) and to have higher endoscopic severity scores (P = .036). Separate group comparisons according to sex identified 294 differentially expressed transcripts in males and 643 transcripts in female EoE patients. Of those, 37 genes were shared and similarly expressed irrespective of sex.

CONCLUSIONS

Whole blood transcriptional analysis represents a promising noninvasive tool to assess activity of the immune/inflammatory response in children with EoE. Male and female EoE patients showed robust differences in gene expression suggesting distinct pathogenic endotypes.

The role of eosinophils in immunotherapy

PURPOSE OF REVIEW

The purpose of this review is to provide a brief discussion on the differential diagnosis for peripheral eosinophilia. We will then focus on targeted immunotherapies for atopic disease, their effects on absolute peripheral eosinophil counts, and use of peripheral eosinophils as a predictor of treatment response.

RECENT FINDINGS

In atopic disease, lower absolute peripheral eosinophil counts are typically associated with improved outcomes. Much of the current evidence on eosinophils as a biomarker comes from post-hoc analyses in therapeutic immunotherapy. While changes in eosinophilia were not the primary outcome of interest in many studies, some patterns did emerge. Cytolytic mAbs AK002 and benralizumab completely reduce peripheral and tissue eosinophil numbers. Dupilumab may have paradoxical transient eosinophilia despite observed clinical efficacy.

SUMMARY

Atopic inflammation is complex largely due to the various cytokines which affect eosinophils activation, proliferation, differentiation, and survival. This demonstrates the challenges of using peripheral eosinophilia alone as a biomarker for atopic disease activity. More attention should spotlight how different immunotherapy modalities affect eosinophil-driven responses.

The Role of Eosinophils in Immunotherapy

PURPOSE OF REVIEW

The purpose of this review is to provide a brief discussion on the differential diagnosis for peripheral eosinophilia. We will then focus on targeted immunotherapies for atopic disease, their effects on absolute peripheral eosinophil counts, and use of peripheral eosinophils as a predictor of treatment response.

RECENT FINDINGS

In atopic disease, lower absolute peripheral eosinophil counts are typically associated with improved outcomes. Much of the current evidence on eosinophils as a biomarker comes from post hoc analyses in therapeutic immunotherapy. While changes in eosinophilia were not the primary outcome of interest in many studies, some patterns did emerge. Cytolytic monoclonal antibodies AK002 and benralizumab completely reduce peripheral and tissue eosinophil numbers. Dupilumab may have paradoxical transient eosinophilia despite observed clinical efficacy. Atopic inflammation is complex largely due to the various cytokines which affect eosinophil activation, proliferation, differentiation, and survival. This demonstrates the challenges of using peripheral eosinophilia alone as a biomarker for atopic disease activity. More attention should spotlight how different immunotherapy modalities affect eosinophil-driven responses.

Assessing the Risk Factors for Refractory Eosinophilic Esophagitis in Children and Adults

Background

Up to one-third of the patients suffering from eosinophilic esophagitis (EoE) present a refractory form, as defined by nonresponsiveness in clinical, endoscopic, or histological assessment after first-line therapy. Several studies recently investigated which factors can influence the development of this disease, but very few analyzed the factors underlying refractory EoE.

Methods

Medical charts of patients affected by EoE were retrospectively evaluated. Phenotyping of patients was conducted according to demographic, clinical, histological, and treatment variables. Then, patients were divided into responder and nonresponder to therapy and distinguished among children and adults.

Results

Forty-five children and 35 adult EoE patients were included. In the pediatric population, female sex (p < 0.05) and a higher score of visual analogue scale (VAS) at the follow-up visit (p = 0.02) were significantly associated to the risk of refractory EoE. Among adults, statistical significance was reached for years of follow-up (p = 0.001), diagnostic delay (p = 0.03), use of antibiotics during infancy (p = 0.01), and food allergy (p = 0.04).

Conclusions

Our study highlighted female sex and a higher VAS score at the time of follow-up visits as risk factors for refractory EoE in children, while the risk factors in adults were identified as fewer years of follow-up, greater diagnostic delay, use of antibiotics during infancy, and food allergy.

An algorithm for the classification of mRNA patterns in eosinophilic esophagitis: Integration of machine learning

BACKGROUND

Diagnostic evaluation of eosinophilic esophagitis (EoE) remains difficult, particularly the assessment of the patient's allergic status.

OBJECTIVE

This study sought to establish an automated medical algorithm to assist in the evaluation of EoE.

METHODS

Machine learning techniques were used to establish a diagnostic probability score for EoE, p(EoE), based on esophageal mRNA transcript patterns from biopsies of patients with EoE, gastroesophageal reflux disease and controls. Dimensionality reduction in the training set established weighted factors, which were confirmed by immunohistochemistry. Following weighted factor analysis, p(EoE) was determined by random forest classification. Accuracy was tested in an external test set, and predictive power was assessed with equivocal patients. Esophageal IgE production was quantified with epsilon germ line (IGHE) transcripts and correlated with serum IgE and the T_h2-type mRNA profile to establish an IGHE score for tissue allergy.

RESULTS

In the primary analysis, a 3-class statistical model generated a p(EoE) score based on common characteristics of the inflammatory EoE profile. A p(EoE) ≥ 25 successfully identified EoE with high accuracy (sensitivity: 90.9%, specificity: 93.2%, area under the curve: 0.985) and improved diagnosis of equivocal cases by 84.6%. The p(EoE) changed in response to therapy. A secondary analysis loop in EoE patients defined an IGHE score of ≥37.5 for a patient subpopulation with increased esophageal allergic inflammation.

CONCLUSIONS

The development of intelligent data analysis from a machine learning perspective provides exciting opportunities to improve diagnostic precision and improve patient care in EoE. The p(EoE) and the IGHE score are steps toward the development of decision trees to define EoE subpopulations and, consequently, will facilitate individualized therapy.

The Journal of Allergy and Clinical Immunology: In Practice 2017 Year in Review

An impressive number of clinically impactful studies and reviews were published in The Journal of Allergy and Clinical Immunology: In Practice in 2017. As a service to our readers, the editors provide this Year in Review article to highlight and contextualize the advances published over the past year. We include information from articles on asthma, allergic rhinitis, rhinosinusitis, immunotherapy, atopic dermatitis, contact dermatitis, food allergy, anaphylaxis, drug hypersensitivity, urticarial/angioedema, eosinophilic disorders, and immunodeficiency. Within each topic, epidemiologic findings are presented, relevant aspects of prevention are described, and diagnostic and therapeutic advances are enumerated. Treatments discussed include behavioral therapy, allergen avoidance therapy, positive and negative effects of pharmacologic therapy, and various forms of immunologic and desensitization management. We hope this review will help readers consolidate and use this extensive and practical knowledge for the benefit of patients.