Accuracy of digital mRNA profiling of oesophageal biopsies as a novel diagnostic approach to eosinophilic oesophagitis

Eosinophilic esophagitis and allergic susceptibility: A systematic review and meta-analysis

Background

Eosinophilic esophagitis (EoE) is a type 2 helper T (Th2) cell immune-mediated gastrointestinal disease. Accumulating evidence has supported allergic etiology as an underlying mechanism for EoE, but the magnitude of the correlation between EoE and atopy remains ambiguous. Hence, we performed a meta-analysis to evaluate and compare the rate of co-existing common atopic diseases between EoE and non-EoE patients.

Methods

We searched through electronic databases and reference lists of review articles for studies describing co-existing rates of atopic diseases in EoE and non-EoE patients. EoE was diagnosed based on clinical and pathological evaluations. Risk of bias was assessed using the modified Newcastle-Ottawa Scale. Random-effects models were used for analyses. Quantitative results were presented as odds ratio (OR) and 95% confidence interval (CI). Subgroup analyses and sensitivity analyses were performed to explore and to identify heterogeneity across studies. Publication bias was examined by Egger's test and visualized by funnel plots.

Results

Altogether, 27 studies containing 1831 cases and 2982 controls were enrolled. 57.2% of EoE patients had co-existing atopic disease. Patients with EoE were more likely to comorbid with atopic diseases (OR = 3.56, 95% CI: 2.27 to 5.59, I 2  = 78%), including asthma (OR = 2.43, 95% CI: 1.94 to 3.06, I 2  = 29%), allergic rhinitis (OR = 5.39, 95% CI: 3.29 to 8.84, I 2  = 78%), atopic dermatitis (OR = 2.46, 95% CI: 1.89 to 2.30, I 2  = 12%) and food allergy (OR = 4.93, 95% CI: 3.96 to 6.14, I 2  = 0%) than non-EoE controls. Heterogeneity sources were explored and identified via subgroup and sensitivity analyses, with the majority of subgroup estimates aligning with the primary findings. No significant publication bias was detected.

Conclusions

Our findings suggest that EoE patients are more likely to comorbid atopic diseases, favoring the allergic diathesis of EoE. Clinicians should be alert for EoE in allergic patients having upper gastrointestinal symptoms. However, the causality between EoE and atopic diseases was not revealed and remains to be explored.

A Distinct Esophageal mRNA Pattern Identifies Eosinophilic Esophagitis Patients With Food Impactions

Eosinophilic esophagitis (EoE), a Th2-type allergic immune disorder characterized by an eosinophil-rich esophageal immune infiltrate, is often associated with food impaction (FI) in pediatric patients but the molecular mechanisms underlying the development of this complication are not well understood. We aim to identify molecular pathways involved in the development of FI. Due to large variations in disease presentation, our analysis was further geared to find markers capable of distinguishing EoE patients that are prone to develop food impactions and thus expand an established medical algorithm for EoE by developing a secondary analysis that allows for the identification of patients with food impactions as a distinct patient population. To this end, mRNA patterns from esophageal biopsies of pediatric EoE patients presenting with and without food impactions were compared and machine learning techniques were employed to establish a diagnostic probability score to identify patients with food impactions (EoE+FI). Our analysis showed that EoE patients with food impaction were indistinguishable from other EoE patients based on their tissue eosinophil count, serum IgE levels, or the mRNA transcriptome-based p(EoE). Irrespectively, an additional analysis loop of the medical algorithm was able to separate EoE+FI patients and a composite FI-score was established that identified such patients with a sensitivity of 93% and a specificity of 100%. The esophageal mRNA pattern of EoE+FI patients was typified by lower expression levels of mast cell markers and Th2 associated transcripts, such as FCERIB, CPA3, CCL2, IL4, and IL5. Furthermore, lower expression levels of regulators of esophageal motility (NOS2 and HIF1A) were detected in EoE+FI. The EoE+FI -specific mRNA pattern indicates that impaired motility may be one underlying factor for the development of food impactions in pediatric patients. The availability of improved diagnostic tools such as a medical algorithm for EoE subpopulations will have a direct impact on clinical practice because such strategies can identify molecular inflammatory characteristics of individual EoE patients, which, in turn, will facilitate the development of individualized therapeutic approaches that target the relevant pathways affected in each patient.

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.

Developments in the field of allergy mechanisms in 2015 through the eyes of Clinical & Experimental Allergy

In the first of two papers we described the development in the field of allergy mechanisms as described by Clinical and Experimental Allergy in 2015. Experimental models of allergic disease, basic mechanisms, clinical mechanisms and allergens are all covered. A second paper will cover clinical aspects.

Spontaneous food allergy in Was-/- mice occurs independent of FcεRI-mediated mast cell activation

BACKGROUND

Food allergies are a growing health problem, and the development of therapies that prevent disease onset is limited by the lack of adjuvant-free experimental animal models. We compared allergic sensitization in patients with food allergy or Wiskott-Aldrich syndrome (WAS) and defined whether spontaneous disease in Was^-/- mice recapitulates the pathology of a conventional disease model and/or human food allergy.

METHODS

Comparative ImmunoCAP ISAC microarray was performed in patients with food allergy or WAS. Spontaneous food allergy in Was^-/- mice was compared to an adjuvant-based model in wild-type mice (WT-OVA/alum). Intestinal and systemic anaphylaxis was assessed, and the role of the high-affinity IgE Fc receptor (FcεRI) in allergic sensitization was evaluated using Was^-/- Fcer1a^-/- mice.

RESULTS

Polysensitization to food was detected in both WAS and food-allergic patients which was recapitulated in the Was^-/- model. Oral administration of ovalbumin (OVA) in Was^-/- mice induced low titers of OVA-specific IgE compared to the WT-OVA/alum model. Irrespectively, 79% of Was^-/- mice developed allergic diarrhea following oral OVA challenge. Systemic anaphylaxis occurred in Was^-/- mice (95%) with a mortality rate >50%. Spontaneous sensitization and intestinal allergy occurred independent of FcεRI expression on mast cells (MCs) and basophils.

CONCLUSIONS

Was^-/- mice provide a model of food allergy with the advantage of mimicking polysensitization and low food-antigen IgE titers as observed in humans with clinical food allergy. This model will facilitate studies on aberrant immune responses during spontaneous disease development. Our results imply that therapeutic targeting of the IgE/FcεRI activation cascade will not affect sensitization to food.

Eosinophilic esophagitis phenotypes: Ready for prime time?

Eosinophilic esophagitis (EoE) is one of the most common causes of reflux-like symptoms and feeding problems in children and food impaction and dysphagia in adults with a prevalence of 1:2500. Therapeutic options include diet, use of swallowed corticosteroids, or dilation. In the last several years, recent clinical and translational researches have identified some common and distinctive features, for example, the varying response to diet and medications. As EoE shares some characteristics with both asthma and inflammatory bowel disease, the advances in these fields suggest that various phenotypes may also exist in patients with EoE. Here, we provide a rationale for EoE phenotypes and provide some suggestions for potential phenotypes based on histology, molecular signature, response to therapy or dietary therapy.

A Gene Expression Panel is Accurate for Diagnosis and Monitoring Treatment of Eosinophilic Esophagitis in Adults

Objective:

Eosinophilic esophagitis (EoE) can be difficult to diagnose. We aimed to evaluate whether a gene expression score could differentiate adult EoE cases from non-EoE controls and to determine whether scores normalized after treatment for EoE.

Methods:

We analyzed prospectively collected esophageal biopsies from EoE patients (diagnosed as per consensus guidelines and after a proton pump inhibitor trial) and non-EoE controls. Gene expression for a previously constructed 94 gene panel was quantified for a single RNA-later preserved biopsy. For diagnosis, a summary expression score and the area under the receiver operating characteristic curve (AUC) were calculated. For treatment response (defined as <15 eosinophils per high-power field), pretreatment and posttreatment EoE samples were compared.

Results:

For 91 EoE cases and 174 controls, gene scores for EoE cases were lower than non-EoE controls (mean 198 vs. 420; P<0.001), with an AUC of 0.927. A score ≤263 yielded a positive predictive value=91% a score ≥349 yielded a negative predictive value=90% only 12% of subjects had an indeterminate score (264–348) by this classification scheme. For the 89 EoE cases with paired pretreatment and posttreatment samples, overall gene scores improved after treatment from 199 to 343 (P<0.001). This normalization was seen only in cases with histological response (202 vs. 425; P<0.001); scores were unchanged in non-responders (189 vs. 226; P=0.25).

Conclusions:

A gene expression score has high diagnostic utility for distinguishing EoE patients from non-EoE controls in adults and can be used in clinical algorithms. Because it is highly responsive to treatment, the test could be used to monitor disease status.

Eosinophilic esophagitis: published evidences for disease subtypes, indications for patient subpopulations, and how to translate patient observations to murine experimental models

Eosinophilic esophagitis (EoE) is a chronic inflammatory disorder of the esophagus and commonly classified as a Th2-type allergy. Major advances in our understanding of the EoE pathophysiology have recently been made, but clinicians struggle with highly unpredictable therapy responses indicative of phenotypic diversity within the patient population. Here, we summarize evidences for the existence of EoE subpopulations based on diverse inflammatory characteristics of the esophageal tissue in EoE. Additionally, clinical characteristics of EoE patients support the concept of disease subtypes. We conclude that clinical and experimental evidences indicate that EoE is an umbrella term for conditions that are unified by esophageal eosinophilia but that several disease subgroups with various inflammatory esophageal patterns and/or different clinical features exist. We further discuss strategies to study the pathophysiologic differences as observed in EoE patients in murine experimental EoE. Going forward, models of EoE that faithfully mimic EoE subentities as defined in humans will be essential because mechanistic studies on triggers which regulate the onset of diverse EoE subpopulations are not feasible in patients. Understanding how and why different EoE phenotypes develop will be a first and fundamental step to establish strategies that integrate individual variations of the EoE pathology into personalized therapy.

Recent research advances in eosinophilic esophagitis

PURPOSE OF REVIEW

Eosinophilic esophagitis (EoE) is a chronic allergic disease triggered by food allergens with an increasing prevalence. This review highlights recent research advances in EoE with a focus on the literature of the past 18 months.

RECENT FINDINGS

The incidence of EoE in the black population is higher than previously suggested. A novel locus spanning CAPN14 is associated with EoE. Diagnostic tests utilizing an analysis of EoE-specific transcriptome have been improved. Standardized EoE symptom score systems have been established. Treatment trials show the promise and limitations of allergen avoidance, antiinflammatory reagents, and anti-interleukin-13 antibodies. Insights into disease mechanisms highlight the role of invariant natural killer T cells and group 2 innate immune cells. Epithelial barrier protein desmoglein 1, bone morphogenetic protein antagonist follistatin, neurotrophic tyrosine kinase receptor type 1, and CAPN14 have been defined as new potential therapeutic targets in EoE as regulators of the inflammatory interleukin-13-axis. The role of IgG4 in the disease mechanisms has been suggested.

SUMMARY

Genetic predisposition influenced by environmental factors increases EoE susceptibility. Research identifying the critical events leading to allergen sensitization and the esophagus-specific responses that drive EoE is evolving, and will lead to a better understanding of EoE and new therapeutic approaches for the disease.