The nuts and bolts of omics for the clinical allergist

Gut Microbiome Proteomics in Food Allergies

Food allergies (FA) have dramatically increased in recent years, particularly in developed countries. It is currently well-established that food tolerance requires the strict maintenance of a specific microbial consortium in the gastrointestinal (GI) tract microbiome as alterations in the gut microbiota can lead to dysbiosis, causing inflammation and pathogenic intestinal conditions that result in the development of FA. Although there is currently not enough knowledge to fully understand how the interactions between gut microbiota, host responses and the environment cause food allergies, recent advances in '-omics' technologies (i.e., proteomics, genomics, metabolomics) and in approaches involving systems biology suggest future headways that would finally allow the scientific understanding of the relationship between gut microbiome and FA. This review summarizes the current knowledge in the field of FA and insights into the future advances that will be achieved by applying proteomic techniques to study the GI tract microbiome in the field of FA and their medical treatment. Metaproteomics, a proteomics experimental approach of great interest in the study of GI tract microbiota, aims to analyze and identify all the proteins in complex environmental microbial communities; with shotgun proteomics, which uses liquid chromatography (LC) for separation and tandem mass spectrometry (MS/MS) for analysis, as it is the most promising technique in this field.

Allergic Rhinitis: What Do We Know About Allergen-Specific Immunotherapy?

Allergic rhinitis (AR) is an IgE-mediated disease that is characterized by Th2 joint inflammation. Allergen-specific immunotherapy (AIT) is indicated for AR when symptoms remain uncontrolled despite medication and allergen avoidance. AIT is considered to have been effective if it alleviated allergic symptoms, decreased medication use, improved the quality of life even after treatment cessation, and prevented the progression of AR to asthma and the onset of new sensitization. AIT can be administered subcutaneously or sublingually, and novel routes are still being developed, such as intra-lymphatically and epicutaneously. AIT aims at inducing allergen tolerance through modification of innate and adaptive immunologic responses. The main mechanism of AIT is control of type 2 inflammatory cells through induction of various functional regulatory cells such as regulatory T cells (Tregs), follicular T cells (Tfr), B cells (Bregs), dendritic cells (DCregs), innate lymphoid cells (IL-10⁺ ILCs), and natural killer cells (NKregs). However, AIT has a number of disadvantages: the long treatment period required to achieve greater efficacy, high cost, systemic allergic reactions, and the absence of a biomarker for predicting treatment responders. Currently, adjunctive therapies, vaccine adjuvants, and novel vaccine technologies are being studied to overcome the problems associated with AIT. This review presents an updated overview of AIT, with a special focus on AR.

A severity grading system of food-induced acute allergic reactions to avoid the delay of epinephrine administration

BACKGROUND

Substantial discrepancies among anaphylaxis severity scores may delay epinephrine administration.

OBJECTIVE

The study aims to develop a transparent severity grading system of food-induced acute allergic reactions with a decision model for epinephrine use.

METHODS

The natural course of 315 acute food-induced allergic reactions in children hospitalized at the Allergology department between May 2016 and July 2019 owing to follow-up treatment and allergy diagnostics was evaluated. The severity of episodes was classified according to the 5 most accepted grading systems. The interrater reliability of classification between anaphylaxis severity scores was assessed. All symptoms were grouped into a heat map according to their real-life incidence and clinical relevance. Based on the heat map analysis, a severity grading system of food-induced acute allergic reactions in children with the epinephrine administration decision model was created.

RESULTS

Data from 259 food-induced anaphylaxis episodes in 157 children were included in the analysis. Comparing the grading systems, we observed a 24.7% to 70.2% disagreement between severity scores. The heat map illustrated a strong association between 29 symptoms and their categorization. A new severity grading system was developed and a 2-stage decision model was proposed: "epinephrine yes" (any rapidly progressing symptoms, even mild ones or from 1 organ system; any symptoms from more than 1 organ system; or every grade of anaphylaxis), and "epinephrine available and prepared to use" (nonprogressing mild systemic allergic reaction from 1 system area only; no anaphylaxis).

CONCLUSION

A new severity grading system of food-induced acute allergic reactions in children could serve as a clinical tool for health care professionals to avoid epinephrine administration delay.

Impact of Altered Gut Microbiota and Its Metabolites in Cystic Fibrosis

Cystic fibrosis (CF) is the most common lethal, multisystemic genetic disorder in Caucasians. Mutations in the gene encoding the cystic fibrosis transmembrane regulator (CFTR) protein are responsible for impairment of epithelial anionic transport, leading to impaired fluid regulation and pH imbalance across multiple organs. Gastrointestinal (GI) manifestations in CF may begin in utero and continue throughout the life, resulting in a chronic state of an altered intestinal milieu. Inherent dysfunction of CFTR leads to dysbiosis of the gut. This state of dysbiosis is further perpetuated by acquired factors such as use of antibiotics for recurrent pulmonary exacerbations. Since the gastrointestinal microbiome and their metabolites play a vital role in nutrition, metabolic, inflammatory, and immune functions, the gut dysbiosis will in turn impact various manifestations of CF-both GI and extra-GI. This review focuses on the consequences of gut dysbiosis and its metabolic implications on CF disease and possible ways to restore homeostasis.

Biomarkers for diagnosis and prediction of therapy responses in allergic diseases and asthma

Modern health care requires a proactive and individualized response to diseases, combining precision diagnosis and personalized treatment. Accordingly, the approach to patients with allergic diseases encompasses novel developments in the area of personalized medicine, disease phenotyping and endotyping, and the development and application of reliable biomarkers. A detailed clinical history and physical examination followed by the detection of IgE immunoreactivity against specific allergens still represents the state of the art. However, nowadays, further emphasis focuses on the optimization of diagnostic and therapeutic standards and a large number of studies have been investigating the biomarkers of allergic diseases, including asthma, atopic dermatitis, allergic rhinitis, food allergy, urticaria and anaphylaxis. Various biomarkers have been developed by omics technologies, some of which lead to a better classification of distinct phenotypes or endotypes. The introduction of biologicals to clinical practice increases the need for biomarkers for patient selection, prediction of outcomes and monitoring, to allow for an adequate choice of the duration of these costly and long‐lasting therapies. Escalating healthcare costs together with questions about the efficacy of the current management of allergic diseases require further development of a biomarker‐driven approach. Here, we review biomarkers in diagnosis and treatment of asthma, atopic dermatitis, allergic rhinitis, viral infections, chronic rhinosinusitis, food allergy, drug hypersensitivity and allergen immunotherapy with a special emphasis on specific IgE, the microbiome and the epithelial barrier. In addition, EAACI guidelines on biologicals are discussed within the perspective of biomarkers.

Precision health: A pragmatic approach to understanding and addressing key factors in autoimmune diseases

The past decade has witnessed a significant paradigm shift in the clinical approach to autoimmune diseases, lead primarily by initiatives in precision medicine, precision health and precision public health initiatives. An understanding and pragmatic implementation of these approaches require an understanding of the drivers, gaps and limitations of precision medicine. Gaining the trust of the public and patients is paramount but understanding that technologies such as artificial intelligences and machine learning still require context that can only be provided by human input or what is called augmented machine learning. The role of genomics, the microbiome and proteomics, such as autoantibody testing, requires continuing refinement through research and pragmatic approaches to their use in applied precision medicine.