Proteomic applications in food allergy: food allergenomics

Study on the induced polymeric protein aggregation and immunoreactivity in biscuits enriched with peanut flour

This work deals with the study on the protein extractability of biscuits incurring different percentages of roasted peanut flour. The presence of two different flours influenced the rate of protein aggregation and protein extractability, according to the percentage of roasted peanut flour added to the formulation and assessing these features by testing the use of two buffers. Results showed that gluten network arrangement of biscuits was influenced by the flours mixture besides the baking, with possible different protein organizations. Protein extractability was affected, underlining a higher content of protein aggregates at high molecular weight especially with the addition of 20% of peanut flour, characterized by hydrophobic and reducible covalent bonds, as suggested by the higher extractability obtained with the buffer with chaotropic and reducing agents. These results suggested a possible induced supramolecular protein organization in these products, which could affect the immunoreactivity of the main allergens occurred in the formulation.

Allergy-associated biomarkers in early life identified by Omics techniques

The prevalence and severity of allergic diseases have increased over the last 30 years. Understanding the mechanisms responsible for these diseases is a major challenge in current allergology, as it is crucial for the transition towards precision medicine, which encompasses predictive, preventive, and personalized strategies. The urge to identify predictive biomarkers of allergy at early stages of life is crucial, especially in the context of major allergic diseases such as food allergy and atopic dermatitis. Identifying these biomarkers could enhance our understanding of the immature immune responses, improve allergy handling at early ages and pave the way for preventive and therapeutic approaches. This minireview aims to explore the relevance of three biomarker categories (proteome, microbiome, and metabolome) in early life. First, levels of some proteins emerge as potential indicators of mucosal health and metabolic status in certain allergic diseases. Second, bacterial taxonomy provides insight into the composition of the microbiota through high-throughput sequencing methods. Finally, metabolites, representing the end products of bacterial and host metabolic activity, serve as early indicators of changes in microbiota and host metabolism. This information could help to develop an extensive identification of biomarkers in AD and FA and their potential in translational personalized medicine in early life.

Proteogenomics in Cancer: Then and Now

For years, the paths of sequencing technologies and mass spectrometry have occurred in isolation, with each developing its own unique culture and expertise. These two technologies are crucial for inspecting complementary aspects of the molecular phenotype across the central dogma. Integrative multiomics strives to bridge the analysis gap among different fields to complete more comprehensive mechanisms of life events and diseases. Proteogenomics is one integrated multiomics field. Here in this review, we mainly summarize and discuss three aspects: workflow of proteogenomics, proteogenomics applications in cancer research, and the SWOT (Strengths, Weaknesses, Opportunities, Threats) analysis of proteogenomics in cancer research. In conclusion, proteogenomics has a promising future as it clarifies the functional consequences of many unannotated genomic abnormalities or noncanonical variants and identifies driver genes and novel therapeutic targets across cancers, which would substantially accelerate the development of precision oncology.

Hidden and Rare Food Allergens in Pediatric Age

In food allergy management, the avoidance of the allergen that caused the reaction plays a fundamental role. Nevertheless, that can be thwarted in case of accidental exposure to a rare or hidden allergen, causing the adoption of a monotonous diet and a consequent reduction in the quality of life of the patient and their family. The identification of a rare and hidden allergen is an important diagnostic challenge, taking into account that a significant proportion of all food reactions is in reality due to them. The aim of the present review is to provide the pediatric allergist an overview of the possible sources of rare and hidden food allergens, taking into consideration the routes of exposure to these potential allergens with the main examples published in the scientific literature and the distinction between types of direct or cross-contamination. The identification of the allergen responsible for the reaction and the provision of a dietary advice customized for the specific individual’s dietary habits is essential to improve quality of life of the familiar nucleus and to reduce the risk of further allergic reactions.

Biomarkers in oral immunotherapy

Food allergy (FA) is a global health problem that affects a large population, and thus effective treatment is highly desirable. Oral immunotherapy (OIT) has been showing reasonable efficacy and favorable safety in most FA subjects. Dependable biomarkers are needed for treatment assessment and outcome prediction during OIT. Several immunological indicators have been used as biomarkers in OIT, such as skin prick tests, basophil and mast cell reactivity, T cell and B cell responses, allergen-specific antibody levels, and cytokines. Other novel indicators also could be potential biomarkers. In this review, we discuss and assess the application of various immunological indicators as biomarkers for OIT.

Mass Spectrometry as a Crucial Analytical Basis for Omics Sciences

This review is devoted to the consideration of mass spectrometric platforms as applied to omics sciences. The most significant attention is paid to omics related to life sciences (genomics, proteomics, meta-bolomics, lipidomics, glycomics, plantomics, etc.). Mass spectrometric approaches to solving the problems of petroleomics, polymeromics, foodomics, humeomics, and exosomics, related to inorganic sciences, are also discussed. The review comparatively presents the advantages of various principles of separation and mass spectral techniques, complementary derivatization, used to obtain large arrays of various structural and quantitative information in the mentioned omics sciences.

Food Allergies: An Example of Translational Research

Food allergies have been rising in prevalence since the 1990s, imposing substantial physical, psychosocial, and economic burdens on affected patients and their families. Until recently, the only therapy for food allergy was strict avoidance of the allergenic food. Recent advances in translational studies, however, have led to insights into allergic sensitization and tolerance. This article provides an overview of cutting-edge research into food allergy and immune tolerance mechanisms utilizing mouse models, human studies, and systems biology approaches. This research is being translated and implemented in the clinical setting to improve diagnosis and reduce food allergy's public health burden.

Proteomic and Bioinformatic Investigations of Heat-Treated Anisakis simplex Third-Stage Larvae

Anisakis simplex third-stage larvae are the main source of hidden allergens in marine fish products. Some Anisakis allergens are thermostable and, even highly processed, could cause hypersensitivity reactions. However, Anisakis proteome has not been studied under autoclaving conditions of 121 °C for 60 min, which is an important process in the food industry. The aim of the study was the identification and characterization of allergens, potential allergens, and other proteins of heat-treated A. simplex larvae. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to identify 470 proteins, including allergens-Ani s 1, Ani s 2, Ani s 3, Ani s 4, Ani s 5-and 13 potential allergens that were mainly homologs of Anisakis spp., Ascaris spp., and Acari allergens. Ani s 2, Ani s 3, Ani s 5, and three possible allergens were found among the top 25 most abundant proteins. The computational analysis allowed us to detect allergen epitopes, assign protein families, and domains as well as to annotate the localization of proteins. The predicted 3D models of proteins revealed similarities between potential allergens and homologous allergens. Despite the partial degradation of heated A. simplex antigens, their immunoreactivity with anti-A. simplex IgG antibodies was confirmed using a Western blot. In conclusion, identified epitopes of allergenic peptides highlighted that the occurrence of Anisakis proteins in thermally processed fish products could be a potential allergic hazard. Further studies are necessary to confirm the IgE immunoreactivity and thermostability of identified proteins.

Optimization of Protein Extraction Method for 2DE Proteomics of Goat's Milk

Two-dimensional electrophoretic (2DE)-based proteomics remains a powerful tool for allergenomic analysis of goat’s milk but requires effective extraction of proteins to accurately profile the overall causative allergens. However, there are several current issues with goat’s milk allergenomic analysis, and among these are the absence of established standardized extraction method for goat’s milk proteomes and the complexity of goat’s milk matrix that may hamper the efficacy of protein extraction. This study aimed to evaluate the efficacies of three different protein extraction methods, qualitatively and quantitatively, for the 2DE-proteomics, using milk from two commercial dairy goats in Malaysia, Saanen, and Jamnapari. Goat’s milk samples from both breeds were extracted by using three different methods: a milk dilution in urea/thiourea based buffer (Method A), a triphasic separation protocol in methanol/chloroform solution (Method B), and a dilution in sulfite-based buffer (Method C). The efficacies of the extraction methods were assessed further by performing the protein concentration assay and 1D and 2D SDS-PAGE profiling, as well as identifying proteins by MALDI-TOF/TOF MS/MS. The results showed that method A recovered the highest amount of proteins (72.68% for Saanen and 71.25% for Jamnapari) and produced the highest number of protein spots (199 ± 16.1 and 267 ± 10.6 total spots for Saanen and Jamnapari, respectively) with superior gel resolution and minimal streaking. Six milk protein spots from both breeds were identified based on the positive peptide mass fingerprinting matches with ruminant milk proteins from public databases, using the Mascot software. These results attest to the fitness of the optimized protein extraction protocol, method A, for 2DE proteomic and future allergenomic analysis of the goat’s milk.

Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges

Asthma is a common condition caused by immune and respiratory dysfunction, and it is often linked to allergy. A systems perspective may prove helpful in unravelling the complexity of asthma and allergy. Our aim is to give an overview of systems biology approaches used in allergy and asthma research. Specifically, we describe recent "omic"-level findings, and examine how these findings have been systematically integrated to generate further insight.Current research suggests that allergy is driven by genetic and epigenetic factors, in concert with environmental factors such as microbiome and diet, leading to early-life disturbance in immunological development and disruption of balance within key immuno-inflammatory pathways. Variation in inherited susceptibility and exposures causes heterogeneity in manifestations of asthma and other allergic diseases. Machine learning approaches are being used to explore this heterogeneity, and to probe the pathophysiological patterns or "endotypes" that correlate with subphenotypes of asthma and allergy. Mathematical models are being built based on genomic, transcriptomic and proteomic data to predict or discriminate disease phenotypes, and to describe the biomolecular networks behind asthma.The use of systems biology in allergy and asthma research is rapidly growing, and has so far yielded fruitful results. However, the scale and multidisciplinary nature of this research means that it is accompanied by new challenges. Ultimately, it is hoped that systems medicine, with its integration of omics data into clinical practice, can pave the way to more precise, personalised and effective management of asthma.

Food allergomics based on high-throughput and bioinformatics technologies

Food allergy is a serious food safety problem worldwide, and the investigation of food allergens is the foundation of preventing and treating them, but relevant knowledge is far from sufficient. With the advent of the "big data era", it has been possible to investigate food allergens by high-throughput methods, proposing the concept of allergomics. Allergomics is the discipline studying the repertoire of allergens, which has relatively higher throughput and is faster and more sensitive than conventional methods. This review introduces the basis of allergomics and summarizes its major strategies and applications. Particularly, strategies based on immunoblotting, phage display, allergen microarray, and bioinformatics are reviewed in detail, and the advantages and limitations of each strategy are discussed. Finally, further development of allergomics is predicted. This provides basic theories and recent advances in food allergomics research, which could be insightful for both food allergy research and practical applications.

AllerBase: a comprehensive allergen knowledgebase

Allergic diseases represent a major health concern worldwide due to steady rise in their prevalence leading to increased disease burden. The field of allergy research has witnessed significant progress and the focus of studies has shifted to molecular level. Vast amounts of data for allergens are archived in allergen databases, which cover diverse aspects of allergens and allergenicity with varying degrees of completeness. Users are required to refer to multiple databases including general purpose immunological databases to obtain relevant data of allergens. AllerBase, a relational database, has been developed with the objective of integrating protein allergens and related data from prevailing bioinformatics resources and published literature. AllerBase is a manually curated comprehensive knowledgebase of experimentally validated allergens where various attributes of allergenicity are made available on a single platform. Links to sequences, structures and immunological data are provided, where available, for all allergens. Data for specific features such as IgE-binding epitopes, IgE cross-reactivity and IgE antibodies are curated and archived. Bibliographic data reporting assays used for experimental characterization of allergens are compiled and processed using text mining approach. AllerBase, thus provides enhanced coverage of data with high granularity. The database can be browsed by category of allergens, epitopes or antibodies. It can also be queried using various attributes such as allergen name, isoallergens/variants, taxonomic level, source organism, sequences, structures, epitopes, antibodies and cross-reactive allergens. AllerBase also provides interface for sequence-based analyses and visualization of structure/epitope which can be used as a framework for translational research. A Completeness Index has been devised to indicate the availability of data on nine attributes for every allergen. This index will also serve as a pointer to identify allergen-specific areas of further research. AllerBase can be used to understand various aspects of allergy and allergenicity at molecular level and to design anti-allergy therapeutics.

Database URL:http://bioinfo.net.in/AllerBase/Home.html

Overview of the Commonly Used Methods for Food Allergens

Food allergy has become a major public health problem worldwide. In the past two decades, development in molecular biology and immunology has led to many new techniques that had improved traditional methods in the food allergy field. These methods greatly facilitate identification, characterization, and quantification of food allergen and are certainly leading to better diagnostics and therapeutics for food allergic diseases. Here we review methods commonly used for food allergens.

2D-Electrophoresis and Immunoblotting in Food Allergy

Two-dimensional polyacrylamide gel electrophoresis (2DE) and Western immunoblotting have proven to be invaluable and fundamental techniques for comprehensive characterization of food allergens. Here, we describe and discuss detailed protocols used in our studies on identification of allergenic proteins in shrimp, sesame, hazelnut, and pistachio.

Targeted proteomics: Current status and future perspectives for quantification of food allergens

Allergen levels in fresh and processed foods can vary dynamically. As different sources of foods can cause different types of allergic reactions, the food industry and regulatory bodies urgently require reliable detection and absolute quantitation methods for allergen detection in complex food products to effectively safeguard the food-allergic population. Recent advances of targeted proteomic technologies namely multiple-reaction monitoring (MRM) mass spectrometry (MS) coupled with isotope-labeled internal standard, also known as AQUA peptides offers absolute quantitation of food allergens even at 10ppb level in a multiplex fashion. However, development of successful AQUA-MRM assay relies on a number of pre and post MS criteria. In this review, we briefly describe how allergen levels could potentially change in plant and animal based foods, necessitating the development of a high throughput multiplexed allergen quantification methodology for successful AQUA-MRM assay. We also propose some future strategies that could provide better management of food allergy.

BIOLOGICAL SIGNIFICANCE

Given the rapid increases of food allergenicity, it has become imperative to know absolute allergen levels in foods. This essential information could be the most effective means of protecting humans suffering from allergies. In this review, we emphasize the significance of the absolute quantitation of food allergens using AQUA-MRM approach and discuss the likely critical steps for successful assay development.

Proteomics in food: Quality, safety, microbes, and allergens

Food safety and quality and their associated risks pose a major concern worldwide regarding not only the relative economical losses but also the potential danger to consumer's health. Customer's confidence in the integrity of the food supply could be hampered by inappropriate food safety measures. A lack of measures and reliable assays to evaluate and maintain a good control of food characteristics may affect the food industry economy and shatter consumer confidence. It is imperative to create and to establish fast and reliable analytical methods that allow a good and rapid analysis of food products during the whole food chain. Proteomics can represent a powerful tool to address this issue, due to its proven excellent quantitative and qualitative drawbacks in protein analysis. This review illustrates the applications of proteomics in the past few years in food science focusing on food of animal origin with some brief hints on other types. Aim of this review is to highlight the importance of this science as a valuable tool to assess food quality and safety. Emphasis is also posed in food processing, allergies, and possible contaminants like bacteria, fungi, and other pathogens.