Esophageal microbiome in eosinophilic esophagitis

Eosinophilic esophagitis. The North against the South? A bio-economic-social mechanistic approach and clinical implications

Eosinophilic esophagitis is a chronic antigen-mediated disease characterized by esophageal symptoms, esophageal eosinophilia, and the absence of response to proton pump inhibitors. It is the most frequent cause of dysphagia and food impaction in adults. Its incidence and prevalence is very high in the developed countries (USA, Europe, Australia), where its connotation is that of an emerging epidemic. While studies have been published with large case series in the developed countries, those published in Latin America are small or consist of isolated case reports. The differences in the prevalence of the disease between the developed and developing regions are unknown. Genetic or racial causes have been cited. Nevertheless, the epidemic nature of the disease suggests that environmental causes are the most powerful. Based on the published hypotheses, as well as on epidemiologic studies, the present review discusses some of the possible causes of the disparity in the prevalence of eosinophilic esophagitis between the two types of countries. The 'hygiene hypothesis' is reviewed, together with the possible relation of Helicobacter pylori, intestinal parasites, and modifications of the esophageal microbiota in patients with eosinophilic esophagitis. In reference to studies conducted in the United States, the clinical behavior and progression of eosinophilic esophagitis in Hispanics is reviewed and a possible predominant phenotype in Mexican and other Latin American patients is discussed. Finally, based on the above, an algorithm for studying the disease in the Latin American countries is proposed.

Current concepts in eosinophilic esophagitis

Background

Eosinophilic esophagitis (EoE) is a disease entity first described in the 1990s, but showing an increasing incidence that is characterized clinically by esophageal dysfunction and histologically by a striking eosinophil infiltration.

Methods

This article discusses new aspects of the pathogenesis, symptoms, diagnosis, and treatment of EoE.

Results

EoE affects both children and adults and is frequently associated with atopic disease and IgE sensitization. Barrier dysfunction and T‑helper 2 inflammation are considered to be pathogenetically important factors. Recently, a proton pump inhibitor (PPI)-sensitive EoE subtype as well as an EoE-like disorder have been described.

Conclusion

Research in recent years has contributed to a better understanding of the disease spectrum and pathogenesis of EoE, including genetic dispositions, thereby laying the foundation for innovative treatment approaches.

Discovery and characterization of a novel humanized anti-IL-15 antibody and its relevance for the treatment of refractory celiac disease and eosinophilic esophagitis

Interleukin-15 (IL-15) is a critical regulator of immune responses, especially at mucosal interfaces within the gastro-intestinal tract. Here, we describe the discovery and characterization of a humanized antibody to IL-15. Data from its epitope and mode of action, cell biology and primate pharmacology, as well as translational studies in human samples and in vivo proof-of-concept experiments in mouse models demonstrate the therapeutic potential of this new antibody targeting IL-15 for refractory celiac disease and eosinophilic esophagitis.

Genetics of eosinophilic esophagitis

Eosinophilic esophagitis (EoE) is a chronic, allergic disease associated with marked mucosal eosinophil accumulation. EoE disease risk is multifactorial and includes environmental and genetic factors. This review will focus on the contribution of genetic variation to EoE risk, as well as the experimental tools and statistical methodology used to identify EoE risk loci. Specific disease-risk loci that are shared between EoE and other allergic diseases (TSLP, LRRC32) or unique to EoE (CAPN14), as well as Mendellian Disorders associated with EoE, will be reviewed in the context of the insight that they provide into the molecular pathoetiology of EoE. We will also discuss the clinical opportunities that genetic analyses provide in the form of decision support tools, molecular diagnostics, and novel therapeutic approaches.

The Esophageal and Gastric Microbiome in Health and Disease

The esophagus and stomach are host to their own population of bacteria, which differs in health and disease. Helicobacter pylori uniquely colonizes only gastric mucosa, but an increasing number of bacteria is now isolated from the gastric juice and gastric mucosa, including Lactobacillus. The presence of H pylori alters populations of other gastric bacteria with a marked reduction in diversity. Alterations in intragastric acidity may be the cause or the consequence of changes in the microbial populations of the stomach. Esophageal inflammation is associated with an altered microbiota in gastroesophageal reflux disease, Barrett's esophagus, eosinophilic esophagitis, and cancer.

Eosinophils, probiotics, and the microbiome

There is currently substantial interest in the therapeutic properties of probiotic microorganisms as recent research suggests that oral administration of specific bacterial strains may reduce inflammation and alter the nature of endogenous microflora in the gastrointestinal tract. Eosinophils are multifunctional tissue leukocytes, prominent among the resident cells of the gastrointestinal mucosa that promote local immunity. Recent studies with genetically altered mice indicate that eosinophils not only participate in maintaining gut homeostasis, but that the absence of eosinophils may have significant impact on the nature of the endogenous gut microflora and responses to gut pathogens, notably Clostridium difficile Furthermore, in human subjects, there is an intriguing relationship between eosinophils, allergic inflammation, and the nature of the lung microflora, notably a distinct association between eosinophil infiltration and detection of bacteria of the phylum Actinobacteria. Among topics for future research, it will be important to determine whether homeostatic mechanisms involve direct interactions between eosinophils and bacteria or whether they involve primarily eosinophil-mediated responses to cytokine signaling in the local microenvironment. Likewise, although is it clear that eosinophils can and do interact with bacteria in vivo, their ability to discern between pathogenic and probiotic species in various settings remains to be explored.

Microbiome and its impact on gastrointestinal atopy

The prevalence of allergic conditions has continuously increased in the last few decades in Westernized countries. A dysbiotic gut microbiome may play an important role in the development of allergic diseases. Genetic, environmental, and dietary factors may alter the commensal microbiota leading to inflammatory dysregulation of homeostasis. Murine and human studies have begun to elucidate the role of the microbiota in the pathogenesis of atopic diseases including asthma, atopic dermatitis, and food allergies. However, the role of the microbiome in most eosinophilic gastrointestinal diseases (EGIDs) is not yet known. This review provides an overview of what is currently known about the development of tolerance from both molecular and clinical standpoints. We also look at the gut-specific microbiome and its role in atopic conditions with the hope of applying this knowledge to the understanding, prevention, and treatment of EGIDs, particularly EoE.

The oesophageal microbiome: an unexplored link in obesity-associated oesophageal adenocarcinoma

The influence of diets rich in saturated fats and simple sugars on the intestinal microbiota plays a central role in obesity. Being overweight or obese predisposes individuals to several diseases including oesophageal adenocarcinoma (OAC), which develops through a cascade of events starting with gastro-oesophageal reflux disease, progressing to Barrett's oesophagus (BO), and then OAC. A range of mechanisms for the increased risk of OAC in obese individuals have been proposed; however, a role for the oesophageal microbiota has been largely ignored. This is despite the fact that it is clear that the composition of the oesophageal microbiota shifts with the development of OAC. Given the well-established impact that unhealthy diets have on the intestinal microbiota, it is plausible that exposure to unhealthy foods, and the ensuing obesity, would result in an imbalance in the oesophageal microbiota. It is also likely that these changes may mimic the changes observed in the intestinal microbiota (i.e. increase in short-chain fatty acid (SCFA) producers and bile acid biosynthesis). The modulation of SCFAs and bile acids in the oesophagus by diet could promote the transdifferentiation from squamous to intestinal-like columnar cells observed in BO, given that intestinal cells proliferate in the presence of SCFAs.

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.

The esophageal microbiota in health and disease

The esophageal mucosa is among the sites colonized by human microbiota, the complex microbial ecosystem that colonizes various body surfaces and is increasingly recognized to play roles in several physiological and pathological processes. Our understanding of the composition of the esophageal microbiota in health and disease is challenged by the need for invasive sampling procedures and by the dynamic nature of the esophageal environment and remains limited in comparison with the information available for other body sites. Members of the genus Streptococcus appear to be the major components of the microbiota of the healthy esophagus, although the presence of several other taxa has also been reported. Dysbiosis, consisting of enrichment in some Gram-negative taxa (including Veillonella, Prevotella, Haemophilus, Neisseria, Campylobacter, and Fusobacterium), has been reported in association with gastroesophageal reflux disease and is hypothesized to contribute to the evolution of this condition toward Barrett's esophagus (which is the most common esophageal precancerous lesion) and, eventually, adenocarcinoma. Some Campylobacter species (mostly C. concisus) are also putatively involved in the progression of disease toward adenocarcinoma. However, variable findings have recently been reported in additional studies. Causative relationships between dysbiosis or specific bacterial species and esophageal diseases remain controversial and warrant further investigations.

The Immunologic Mechanisms of Eosinophilic Esophagitis

Eosinophilic esophagitis (EoE) is a chronic allergic inflammatory disease that is triggered by food and/or environmental allergens and is characterized by a clinical and pathologic phenotype of progressive esophageal dysfunction due to tissue inflammation and fibrosis. EoE is suspected in patients with painful swallowing, among other symptoms, and is diagnosed by the presence of 15 or more eosinophils per high-power field in one or more of at least four esophageal biopsy specimens. The prevalence of EoE is increasing and has now reached rates similar to those of other chronic gastrointestinal disorders such as Crohn's disease. In recent years, our understanding of the immunologic mechanisms underlying this condition has grown considerably. Thanks to new genetic, molecular, cellular, animal, and translational studies, we can now postulate a detailed pathway by which exposure to allergens results in a complex and coordinated type 2 inflammatory cascade that, if not intervened upon, can result in pain on swallowing, esophageal strictures, and food impaction. Here, we review the most recent research in this field to synthesize and summarize our current understanding of this complex and important disease.

Eosinophilic esophagitis is characterized by a non-IgE-mediated food hypersensitivity

Eosinophilic esophagitis (EoE) is a chronic disease characterized clinically by symptoms of esophageal dysfunction and histologically by eosinophil-predominant inflammation. EoE is frequently associated with concomitant atopic diseases and immunoglobulin E (IgE) sensitization to food allergens in children as well as to aeroallergens and cross-reactive plant allergen components in adults. Patients with EoE respond well to elemental and empirical food elimination diets. Recent research has, however, indicated that the pathogenesis of EoE is distinct from IgE-mediated food allergy. In this review, we discuss the individual roles of epithelial barrier defects, dysregulated innate and adaptive immune responses, and of microbiota in the pathogenesis of EoE. Although food has been recognized as a trigger factor of EoE, the mechanism by which it initiates or facilitates eosinophilic inflammation appears to be largely independent of IgE and needs to be further investigated. Understanding the pathogenic role of food in EoE is a prerequisite for the development of specific diagnostic tools and targeted therapeutic procedures.

Zero-inflated negative binomial mixed model: an application to two microbial organisms important in oesophagitis

Altered microbial communities are thought to play an important role in eosinophilic oesophagitis, an allergic inflammatory condition of the oesophagus. Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. However, these data consist of non-negative, highly skewed sequence counts with a large proportion of zeros. In addition, hierarchical study designs are often performed with repeated measurements or multiple samples collected from the same subject, thus requiring approaches to account for within-subject variation, yet only a small number of microbiota studies have applied hierarchical regression models. In this paper, we describe and illustrate the use of a hierarchical regression-based approach to evaluate multiple factors for a small number of organisms individually. More specifically, the zero-inflated negative binomial mixed model with random effects in both the count and zero-inflated parts is applied to evaluate associations with disease state while adjusting for potential confounders for two organisms of interest from a study of human microbiota sequence data in oesophagitis.

The efficacy of step-down therapy in adult patients with proton pump inhibitor-responsive oesophageal eosinophilia

BACKGROUND

Proton pump inhibitor-responsive oesophageal eosinophilia (PPI-REE) is common in patients with suspected eosinophilic oesophagitis (EoE). However, the long-term efficacy of PPIs and the best maintenance doses are yet to be defined.

AIM

To evaluate the durability of the response to PPI therapy after tapering PPI doses in PPI-REE patients.

METHODS

Prospective study conducted on PPI-REE patients. Upon complete remission on high-dose PPI therapy (omeprazole 40 mg b.d. for 8 weeks), PPI doses were tapered followed by an endoscopic procedure after each dose reduction. The primary outcomes were sustained clinical and histological remission (<15 eos/HPF) after decreasing PPI doses.

RESULTS

From a total of 121 patients with suspected EoE, 40 (33%) achieved complete remission on high-dose PPIs and were given a diagnosis of PPI-REE. No patient in histological remission showed symptom relapse, but half of patients with relapsing oesophageal inflammation were in clinical remission. After reduction to omeprazole 40 mg once daily, 38/31 (81%) remained in complete remission. Among these latter patients, 15/18 (83%) were kept in remission with omeprazole 20 mg once daily. As for side effects, only asymptomatic hypertransaminasemia and oesophageal candidiasis were observed in two patients while receiving high doses of omeprazole.

CONCLUSIONS

Most PPI-responsive oesophageal eosinophilia patients show sustained clinical and histological remission with daily PPI doses equal to or below 40 mg of omeprazole. As adverse effects only appeared with the highest dose of omeprazole, it would be advisable to individualise the dose of PPIs for each patient, lowering it to the minimum capable of maintaining the disease controlled.

Update on food allergy

Food allergies are a global health issue with increasing prevalence. Allergic reactions can range from mild local symptoms to severe anaphylactic reactions. Significant progress has been made in diagnostic tools such as component-resolved diagnostics and its impact on risk stratification as well as in therapeutic approaches including biologicals. However, a cure for food allergy has not yet been achieved and patients and their families are forced to alter eating habits and social engagements, impacting their quality of life. New technologies and improved in vitro and in vivo models will advance our knowledge of the pathogenesis of food allergies and multicenter-multinational cohort studies will elucidate interactions between genetic background, lifestyle, and environmental factors. This review focuses on new insights and developments in the field of food allergy and summarizes recently published articles.

Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives

Next-generation sequencing (NGS) technologies have greatly impacted on every field of molecular research mainly because they reduce costs and increase throughput of DNA sequencing. These features, together with the technology's flexibility, have opened the way to a variety of applications including the study of the molecular basis of human diseases. Several analytical approaches have been developed to selectively enrich regions of interest from the whole genome in order to identify germinal and/or somatic sequence variants and to study DNA methylation. These approaches are now widely used in research, and they are already being used in routine molecular diagnostics. However, some issues are still controversial, namely, standardization of methods, data analysis and storage, and ethical aspects. Besides providing an overview of the NGS-based approaches most frequently used to study the molecular basis of human diseases at DNA level, we discuss the principal challenges and applications of NGS in the field of human genomics.

Allergic mechanisms of Eosinophilic oesophagitis

Eosinophilic oesophagitis (EoE) is characterized by oesophageal dysfunction and oesophageal eosinophilia refractory to proton-pump-inhibitor treatment. EoE is a food allergy, as elimination of food trigger(s) abrogates the disease, while trigger reintroduction causes recurrence. The allergic mechanism of EoE involves both IgE and non-IgE processes. There is a break in oral tolerance, the immune mechanism allowing enteric exposure to food and micro-organisms without causing deleterious immune responses. Changes in life-style, alterations in gut flora and use of antibiotics may be increasing disease prevalence. Mouse models of EoE and human studies revealed the role of regulatory T-cells and iNKT-cells in the pathogenesis. Th2-cytokines like IL-4, IL-5 and IL-13, and other cytokines like TGFβ and TSLP are involved, but perhaps no one cytokine is critically important for driving the disease. Control of EoE may require a pharmaceutical approach that blocks more than one target in the Th2-inflammatory pathway.