Evidence for novel tomato seed allergens: IgE-reactive legumin and vicilin proteins identified by multidimensional protein fractionation-mass spectrometry and in silico epitope modeling

EAACI Molecular Allergology User's Guide 2.0

Since the discovery of immunoglobulin E (IgE) as a mediator of allergic diseases in 1967, our knowledge about the immunological mechanisms of IgE-mediated allergies has remarkably increased. In addition to understanding the immune response and clinical symptoms, allergy diagnosis and management depend strongly on the precise identification of the elicitors of the IgE-mediated allergic reaction. In the past four decades, innovations in bioscience and technology have facilitated the identification and production of well-defined, highly pure molecules for component-resolved diagnosis (CRD), allowing a personalized diagnosis and management of the allergic disease for individual patients. The first edition of the "EAACI Molecular Allergology User's Guide" (MAUG) in 2016 rapidly became a key reference for clinicians, scientists, and interested readers with a background in allergology, immunology, biology, and medicine. Nevertheless, the field of molecular allergology is moving fast, and after 6 years, a new EAACI Taskforce was established to provide an updated document. The Molecular Allergology User's Guide 2.0 summarizes state-of-the-art information on allergen molecules, their clinical relevance, and their application in diagnostic algorithms for clinical practice. It is designed for both, clinicians and scientists, guiding health care professionals through the overwhelming list of different allergen molecules available for testing. Further, it provides diagnostic algorithms on the clinical relevance of allergenic molecules and gives an overview of their biology, the basic mechanisms of test formats, and the application of tests to measure allergen exposure.

Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato

The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.

Tomato Allergy: The Characterization of the Selected Allergens and Antioxidants of Tomato (Solanum lycopersicum)-A Review

Tomatoes are one of the most broadly produced and consumed crop plants. They are the source of health-promoting nutrients such as antioxidants, including ascorbic acid, polyphenols, or carotenoids. Despite the beneficial role of tomatoes in the daily diet, they have been confirmed as one of the most prevalent allergenic vegetables. Food allergies can cause many clinical symptoms, e.g., in the gastrointestinal tract, skin, and lungs, as well as anaphylactic shock. A huge amount of clinical research has been carried out to improve the understanding of the immunological mechanisms that lead to the lack of tolerance of food antigens, which can result in either immunoglobulin E (IgE)-mediated reactions or non-IgE-mediated reactions. Lifestyle and diet play an important role in triggering food allergies. Allergy to tomatoes is also linked to other allergies, such as grass pollen and latex allergy. Numerous attempts have been made to identify and characterize tomato allergens; however, the data available on the subject are not sufficient.

Component-Resolved Diagnosis in Food Allergies

Component-resolved diagnostics (CRD) in food allergies is an approach utilized to characterize the molecular components of each allergen involved in a specific IgE (sIgE)-mediated response. In the clinical practice, CRD can improve diagnostic accuracy and assist the physician in many aspects of the allergy work-up. CRD allows for discriminatory co-sensitization versus cross-sensitization phenomena and can be useful to stratify the clinical risk associated with a specific sensitization pattern, in addition to the oral food challenge (OFC). Despite this, there are still some unmet needs, such as the risk of over-prescribing unnecessary elimination diets and adrenaline auto-injectors. Moreover, up until now, none of the identified sIgE cutoff have shown a specificity and sensitivity profile as accurate as the OFC, which is the gold standard in diagnosing food allergies. In light of this, the aim of this review is to summarize the most relevant concepts in the field of CRD in food allergy and to provide a practical approach useful in clinical practice.

EAACI Molecular Allergology User's Guide

The availability of allergen molecules ('components') from several protein families has advanced our understanding of immunoglobulin E (IgE)-mediated responses and enabled 'component-resolved diagnosis' (CRD). The European Academy of Allergy and Clinical Immunology (EAACI) Molecular Allergology User's Guide (MAUG) provides comprehensive information on important allergens and describes the diagnostic options using CRD. Part A of the EAACI MAUG introduces allergen molecules, families, composition of extracts, databases, and diagnostic IgE, skin, and basophil tests. Singleplex and multiplex IgE assays with components improve both sensitivity for low-abundance allergens and analytical specificity; IgE to individual allergens can yield information on clinical risks and distinguish cross-reactivity from true primary sensitization. Part B discusses the clinical and molecular aspects of IgE-mediated allergies to foods (including nuts, seeds, legumes, fruits, vegetables, cereal grains, milk, egg, meat, fish, and shellfish), inhalants (pollen, mold spores, mites, and animal dander), and Hymenoptera venom. Diagnostic algorithms and short case histories provide useful information for the clinical workup of allergic individuals targeted for CRD. Part C covers protein families containing ubiquitous, highly cross-reactive panallergens from plant (lipid transfer proteins, polcalcins, PR-10, profilins) and animal sources (lipocalins, parvalbumins, serum albumins, tropomyosins) and explains their diagnostic and clinical utility. Part D lists 100 important allergen molecules. In conclusion, IgE-mediated reactions and allergic diseases, including allergic rhinoconjunctivitis, asthma, food reactions, and insect sting reactions, are discussed from a novel molecular perspective. The EAACI MAUG documents the rapid progression of molecular allergology from basic research to its integration into clinical practice, a quantum leap in the management of allergic patients.

Crystal structure of the vicilin from Solanum melongena reveals existence of different anionic ligands in structurally similar pockets

Crystal structure of a vicilin, SM80.1, was determined towards exploring its possible physiological functions. The protein was purified from Solanum melongena by combination of ammonium sulphate fractionation and size exclusion chromatography. Structure was determined ab initio at resolution of 1.5 Å by X-ray crystallography showing the three-dimensional topology of the trimeric protein. Each monomer of SM80.1 consists of two similar domains with hydrophobic binding pocket and each accommodating different ligands, i.e. acetate and pyroglutamate. The relatively high stability of these independent anionic ligands in similar pockets indicated a strict requirement of stabilization by hydrogen bonds with the charged residues, suggesting a degree of plasticity within the binding pocket. Comparison of SM80.1 structure with those of other 7S vicilins indicated conservation of putative binding pocket for anionic ligands. Here we propose the possibility of trapping of these ligands in the protein for their requirement in the metabolic processes.

Purification, identification and preliminary crystallographic studies of an allergenic protein from Solanum melongena

Solanum melongena (eggplant), a member of the Solanaceae family, is a widely cultivated vegetable crop and is commonly used as a food throughout the world. Allergic reactions caused by members of this family are well known. However, mechanistic analyses to understand their molecular basis have not been adequately explored. In order to address this issue, the 7S vicilin protein (SM80.1) of size 45 kDa was purified from seeds of S. melongena by ammonium sulfate fractionation and size-exclusion chromatography. Significant homology of SM80.1 to an allergy-related protein from S. lycopersicum was identified through a BLAST search. Crystallization attempts with purified protein using the hanging-drop vapour-diffusion method led to hexagonal-shaped crystals. The crystals diffracted to 2.21 Å resolution and belonged to space group P6322, with unit-cell parameters a = 117.9, c = 123.5 Å.

Proteomics-based allergen analysis in plants

Plants may trigger hypersensitivity reactions when individuals with allergies consume foods derived from plant materials or inhale plant pollen. As each plant food or pollen contains multiple allergens, proteomics is a powerful tool to detect the allergens present. Allergen-targeted proteomics, termed allergenomics, has been used for comprehensive identification and/or quantification of plant allergens, because it is a simple and inexpensive tool for rapid detection of proteins that bind to IgE. There are increasing numbers of reports on the applications of allergenomics. In this review, we outline some of the applications of proteomics, including: (i) identification of novel allergens, (ii) allergic diagnoses, (iii) quantification of allergens, and (iv) natural diversity of allergens, and finally discuss (v) the use of allergenomics for safety assessment of genetically modified (GM) plants.

BIOLOGICAL SIGNIFICANCE

Recently, the number of allergic patients is increasing. Therefore, a comprehensive analysis of allergens (allergenomics) in plants is highly important for not only risk assessment of food plants but also diagnosis of allergic symptoms. In this manuscript, we reviewed the recent progress of allergenomics for identification, quantification and profiling of allergens. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Foodomics: MS-based strategies in modern food science and nutrition

Modern research in food science and nutrition is moving from classical methodologies to advanced analytical strategies in which MS-based techniques play a crucial role. In this context, Foodomics has been recently defined as a new discipline that studies food and nutrition domains through the application of advanced omics technologies in which MS techniques are considered indispensable. Applications of Foodomics include the genomic, transcriptomic, proteomic, and/or metabolomic study of foods for compound profiling, authenticity, and/or biomarker-detection related to food quality or safety; the development of new transgenic foods, food contaminants, and whole toxicity studies; new investigations on food bioactivity, food effects on human health, etc. This review work does not intend to provide an exhaustive revision of the many works published so far on food analysis using MS techniques. The aim of the present work is to provide an overview of the different MS-based strategies that have been (or can be) applied in the new field of Foodomics, discussing their advantages and drawbacks. Besides, some ideas about the foreseen development and applications of MS-techniques in this new discipline are also provided.

Tomato allergy: impact of genotype and environmental factors on the biological response

BACKGROUND

Food allergies are increasing in the European population. At present the onset of symptoms can be avoided only by elimination of a particular fruit or vegetable from the diet. A new approach is to develop hypoallergenic food products. This study characterises the allergenic potential of tomatoes, considering cultivation conditions, developmental stages and genotypes, in order to identify hypoallergenic fruits.

RESULTS

Patients with a history of tomato allergy were recruited for skin allergy tests. Tomatoes carrying distinct genotypes were grown under various cultivation conditions and harvested at different maturation stages. Cultivation conditions (nitrogen fertilisation, light exposure and plant nutrition) did not affect the skin reactivity in tomato-allergic patients. However, skin reactivity was significantly lower when using green-unripe compared with red-ripe tomatoes and when using landrace cultivars compared with cultivars bred for use in organic horticulture.

CONCLUSION

Depending on their genetic background and maturity level, some tomato cultivars elicit positive reactions in tomato-allergic patients in the skin allergy test. This novel finding should pave the way for the development of tomatoes with reduced allergenicity to relieve sufferers of tomato allergy.

Molecular diagnosis of fruit and vegetable allergy

PURPOSE OF REVIEW

The purpose of this paper is to review and discuss studies on molecular diagnosis in fruit and vegetable allergy.

RECENT FINDINGS

Celeriac, carrot and tomato are the most prevalent allergenic vegetables, whereas fruit allergy is mainly induced by apple, peach and kiwi. Component-resolved molecular diagnosis has been recently applied in two well-defined patient groups with kiwifruit and celeriac allergy, respectively. In kiwifruit allergy Act d 1 and Act d 3 were identified as potential marker allergens for severe symptoms. For celeriac allergy, however, such markers are still missing. In both studies component-resolved molecular diagnosis approach improved in particular sensitivity compared to extract-based diagnostic test assays.

SUMMARY

Food and vegetable allergy can be acquired both via a direct sensitization over the gastrointestinal tract and via a primary sensitization to pollen or latex. The diagnosis of fruit and vegetable allergy in birch pollen-sensitized patients should not be excluded on a negative IgE testing to extracts. Bet v 1-related allergens are often under-represented in extracts. Few recombinant allergens derived from fruits and vegetables are nowadays commercially available and facilitate diagnosis of fruit and vegetable allergies.

Allergenic activity of different tomato cultivars in tomato allergic subjects

BACKGROUND

Tomatoes (Solanum lycopersicum) are consumed worldwide and their amount of consumption is associated with the prevalence of tomato allergy. Therefore, identification of tomato cultivars with reduced allergenicity would potentially increase the quality of life of affected subjects.

OBJECTIVE

In this study, we examined the allergenic and biological activity of two different tomato cultivars in tomato allergic subjects.

METHODS

Twenty-five subjects with tomato allergy were identified using double-blind, placebo-controlled food challenges (DBPCFC). We applied skin prick test (SPT) and further DBPCFC to investigate the clinical differences between two tomato cultivars ('Reisetomate' and 'Matina'). To examine the molecular basis of allergenic activity, immunoblotting and basophil activation test (BAT) were performed.

RESULTS

The cultivar 'Reisetomate' induced significantly less positive skin reactions (P = 0.045) and elicited fewer symptoms after oral challenge compared with 'Matina' (P = 0.047). Molecular assessment revealed that IgE-binding profiles were variable on an interindividual basis, but no major differences between 'Reisetomate' and 'Matina' were detectable. In contrast, BAT underpinned the clinical differences evoked by the different tomato cultivars and showed a left-shift of the dose-response curve obtained for 'Matina' extract (P = 0.046).

CONCLUSIONS AND CLINICAL RELEVANCE

Tomato cultivars promote a distinct clinical reactivity in tomato allergic subjects, demonstrated using SPT, DBPCFC and BAT. The molecular background for these differences could not be clarified, as the IgE-binding profiles did not reveal significant alterations. This might be due to instabilities of physicochemical sensitive proteins and/or different isoform expression of allergens.

The frontiers of mass spectrometry-based techniques in food allergenomics

In the last years proteomic science has started to provide an important contribution to the disclosure of basic aspects of food-related diseases. Among these, the identification of proteins involved in food allergy and their mechanism of activation of toxicity. Elucidation of these key issues requires the integration of clinical, immunological, genomic and proteomic approaches. These combined research efforts are aimed to obtain structural and functional information to assist the development of novel, more reliable and powerful diagnostic protocols alternative to the currently available procedures, mainly based on food challenge tests. Another crucial aspect related to food allergy is the need for methods to detect trace amounts of allergenic proteins in foods. Mass spectrometry is the only non-immunological method for high-specificity and high-sensitivity detection of allergens in foods. Nowadays, once provided the appropriate sample handling and the correct operative conditions, qualitative and quantitative determination of allergens in foods and ingredients can be efficiently obtained by MALDI-TOF-MS and LC-MS/MS methods, with limits of detection and quantification in the low-ppb range. The availability of accurate and fast alternatives to immunological ELISA tests may also enable the development of novel therapeutic strategies and food processing technologies to aid patients with food allergy or intolerance, and to support allergen labelling and certification processes, all issues where the role of proteomic science is emerging.

Reduction of cross-reactive carbohydrate determinants in plant foodstuff: elucidation of clinical relevance and implications for allergy diagnosis

BACKGROUND

A longstanding debate in allergy is whether or not specific immunoglobulin-E antibodies (sIgE), recognizing cross-reactive carbohydrate determinants (CCD), are able to elicit clinical symptoms. In pollen and food allergy, ≥20% of patients display in-vitro CCD reactivity based on presence of α1,3-fucose and/or β1,2-xylose residues on N-glycans of plant (xylose/fucose) and insect (fucose) glycoproteins. Because the allergenicity of tomato glycoallergen Lyc e 2 was ascribed to N-glycan chains alone, this study aimed at evaluating clinical relevance of CCD-reduced foodstuff in patients with carbohydrate-specific IgE (CCD-sIgE).

METHODOLOGY/PRINCIPAL FINDINGS

Tomato and/or potato plants with stable reduction of Lyc e 2 (tomato) or CCD formation in general were obtained via RNA interference, and gene-silencing was confirmed by immunoblot analyses. Two different CCD-positive patient groups were compared: one with tomato and/or potato food allergy and another with hymenoptera-venom allergy (the latter to distinguish between CCD- and peptide-specific reactions in the food-allergic group). Non-allergic and CCD-negative food-allergic patients served as controls for immunoblot, basophil activation, and ImmunoCAP analyses. Basophil activation tests (BAT) revealed that Lyc e 2 is no key player among other tomato (glyco)allergens. CCD-positive patients showed decreased (re)activity with CCD-reduced foodstuff, most obvious in the hymenoptera venom-allergic but less in the food-allergic group, suggesting that in-vivo reactivity is primarily based on peptide- and not CCD-sIgE. Peptide epitopes remained unaffected in CCD-reduced plants, because CCD-negative patient sera showed reactivity similar to wild-type. In-house-made ImmunoCAPs, applied to investigate feasibility in routine diagnosis, confirmed BAT results at the sIgE level.

CONCLUSIONS/SIGNIFICANCE

CCD-positive hymenoptera venom-allergic patients (control group) showed basophil activation despite no allergic symptoms towards tomato and potato. Therefore, this proof-of-principle study demonstrates feasibility of CCD-reduced foodstuff to minimize 'false-positive results' in routine serum tests. Despite confirming low clinical relevance of CCD antibodies, we identified one patient with ambiguous in-vitro results, indicating need for further component-resolved diagnosis.