Proteomic analysis of wheat proteins recognized by IgE antibodies of allergic patients

Label-free quantitative proteomics to exploit the impact of sourdough fermentation on reducing wheat allergenic fractions

The microbial consortia of lactic acid bacteria and yeast of sourdough can partially degrade gluten subunits associated with wheat-related diseases. This study evaluated how sourdough fermentation interferes with wheat protein profiles and if it can be related to the reduction expression of allergenic proteins. Samples from five bread doughs (Saccharomyces cerevisiae -C1; chemical acidification -C2, and three sourdoughs formulations -S1, S2, and S3) were sequentially extracted, digested, and submitted to shotgun label-free proteomic analysis. Eight-five proteins were identified as allergenic, mainly belonging to gliadin fraction, including seven containing the 33-mer peptide sequence. The highest immunogenic potential was found in dough C1 and S3, while the least reactive group consisted of S1 and C2. The two folds down expression of an α-gliadin containing the 33-mer sequence corroborates this. This finding may indicate the role of organic acids produced by the microbiota sourdough type II during fermentation in changing the protein profile.

Plant Serpins: Potential Inhibitors of Serine and Cysteine Proteases with Multiple Functions

Plant serpins are a superfamily of protein inhibitors that have been continuously studied in different species and have great biotechnological potential. However, despite ongoing studies with these inhibitors, the biological role of this family in the plant kingdom has not yet been fully clarified. In order to obtain new insights into the potential of plant serpins, this study presents the first systematic review of the topic, whose main objective was to scrutinize the published literature to increase knowledge about this superfamily. Using keywords and the eligibility criteria defined in the protocol, we selected studies from the Scopus, PubMed, and Web of Science databases. According to the eligible studies, serpins inhibit different serine and non-serine proteases from plants, animals, and pathogens, and their expression is affected by biotic and abiotic stresses. Moreover, serpins like AtSerpin1, OSP-LRS, MtSer6, AtSRP4, AtSRP5, and MtPiI4, act in resistance and are involved in stress-induced cell death in the plant. Also, the system biology analysis demonstrates that serpins are related to proteolysis control, cell regulation, pollen development, catabolism, and protein dephosphorylation. The information systematized here contributes to the design of new studies of plant serpins, especially those aimed at exploring their biotechnological potential.

Immunoglobulin E-specific allergens against leaf in serum of dogs with clinical features of grass leaf allergy

BACKGROUND

Grass leaf has been suspected of causing immunoglobulin (Ig)E-mediated immediate hypersensitivity reactions in humans and dogs. However, most studies in this area are case-control studies without in vitro data showing the involvement of IgE in the reaction. Laboratory studies have demonstrated the reactivity to a 50-55 kDa protein with clinical signs immediately after contact with grass leaf material. The clinical findings of dogs with atopic-like dermatitis immediately after contact with grass leaf material suggest the involvement of grass leaves as the allergen source.

OBJECTIVES

This study was designed to test the IgE-reactivity of grass leaf proteins in dogs with clinical signs and positive scratch test results against grass leaf material.

MATERIALS AND METHODS

The serum of 41 patients with a history of allergy and suspected to grass leaf material was immunoblotted against grass leaf extracts from five suspected grass species. The IgE-positive blots were separated with 2D gel electrophoresis and analysed with mass spectrometry (MS). Commercially supplied proteins were used to validate immunoblot activity.

RESULTS

The serum of 25 dogs diagnosed with grass dermatitis had positive IgE-specific immunoblot against one or more grass leaf extracts. The MS data indicated a reactive band at 55 kDa to be beta-amylase or RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) large subunit (RbLS). All tested dog sera showed IgE-reactivity with beta-amylase and some with RbLS.

CONCLUSIONS AND CLINICAL RELEVANCE

Canines with clinical signs of grass-related dermatitis had IgE-reactivity against grass leaf proteins. Serum IgE-reactivity to beta-amylase and RuBisCO large subunit may indicate that these proteins act as allergens, possibly causing pruritus and skin lesions.

Proteomics as a promising biomarker in food authentication, quality and safety: A review

Adulteration and mislabeling have become a very common global malpractice in food industry. Especially foods of animal origin are prepared from plant sources and intentionally mislabeled. This type of mislabeling is an important concern in food safety as the replaced ingredients may cause a food allergy or toxicity to vulnerable consumers. Moreover, foodborne pathogens also pose a major threat to food safety. There is a dire need to develop strong analytical tools to deal with related issues. In this context, proteomics stands out as a promising tool used to report the aforementioned issues. The development in the field of omics has inimitable advantages in enabling the understanding of various biological fields especially in the discipline of food science. In this review, current applications and the role of proteomics in food authenticity, safety, and quality and food traceability are highlighted comprehensively. Additionally, the other components of proteomics have also been comprehensively described. Furthermore, this review will be helpful in the provision of new intuition into the use of proteomics in food analysis. Moreover, the pathogens in food can also be identified based on differences in their protein profiling. Conclusively, proteomics, an indicator of food properties, its origin, the processes applied to food, and its composition are also the limelight of this article.

Wheat amylase/trypsin inhibitors (ATIs): occurrence, function and health aspects

Amylase/trypsin inhibitors (ATIs) are widely consumed in cereal-based foods and have been implicated in adverse reactions to wheat exposure, such as respiratory and food allergy, and intestinal responses associated with coeliac disease and non-coeliac wheat sensitivity. ATIs occur in multiple isoforms which differ in the amounts present in different types of wheat (including ancient and modern ones). Measuring ATIs and their isoforms is an analytical challenge as is their isolation for use in studies addressing their potential effects on the human body. ATI isoforms differ in their spectrum of bioactive effects in the human gastrointestinal (GI), which may include enzyme inhibition, inflammation and immune responses and of which much is not known. Similarly, although modifications during food processing (exposure to heat, moisture, salt, acid, fermentation) may affect their structure and activity as shown in vitro, it is important to relate these changes to effects that may present in the GI tract. Finally, much of our knowledge of their potential biological effects is based on studies in vitro and in animal models. Validation by human studies using processed foods as commonly consumed is warranted. We conclude that more detailed understanding of these factors may allow the effects of ATIs on human health to be better understood and when possible, to be ameliorated, for example by innovative food processing. We therefore review in short our current knowledge of these proteins, focusing on features which relate to their biological activity and identifying gaps in our knowledge and research priorities.

Wheat ATIs: Characteristics and Role in Human Disease

Amylase/trypsin-inhibitors (ATIs) comprise about 2-4% of the total wheat grain proteins and may contribute to natural defense against pests and pathogens. However, they are currently among the most widely studied wheat components because of their proposed role in adverse reactions to wheat consumption in humans. ATIs have long been known to contribute to IgE-mediated allergy (notably Bakers' asthma), but interest has increased since 2012 when they were shown to be able to trigger the innate immune system, with attention focused on their role in coeliac disease which affects about 1% of the population and, more recently, in non-coeliac wheat sensitivity which may affect up to 10% of the population. This has led to studies of their structure, inhibitory properties, genetics, control of expression, behavior during processing, effects on human adverse reactions to wheat and, most recently, strategies to modify their expression in the plant using gene editing. We therefore present an integrated account of this range of research, identifying inconsistencies, and gaps in our knowledge and identifying future research needs. Note  This paper is the outcome of an invited international ATI expert meeting held in Amsterdam, February 3-5 2020.

Quantitative Label-Free Comparison of the Metabolic Protein Fraction in Old and Modern Italian Wheat Genotypes by a Shotgun Approach

Wheat represents one of the most important cereals for mankind. However, since wheat proteins are also the causative agent of several adverse reactions, during the last decades, consumers have shown an increasing interest in the old wheat genotypes, which are generally perceived as more "natural" and healthier than the modern ones. Comparison of nutritional value for modern and old wheat genotypes is still controversial, and to evaluate the real impact of these foods on human health comparative experiments involving old and modern genotypes are desirable. The nutritional quality of grain is correlated with its proteomic composition that depends on the interplay between the genetic characteristics of the plant and external factors related to the environment. We report here the label-free shotgun quantitative comparison of the metabolic protein fractions of two old Sicilian landraces (Russello and Timilia) and the modern variety Simeto, from the 2010-2011 and 2011-2012 growing seasons. The overall results show that Timilia presents the major differences with respect to the other two genotypes investigated. These differences may be related to different defense mechanisms and some other peculiar properties of these genotypes. On the other hand, our results confirm previous results leading to the conclusion that with respect to a nutritional value evaluation, there is a substantial equivalence between old and modern wheat genotypes. Data are available via ProteomeXchange with identifier <PXD024204>.

Deciphering the immunogenic potential of wheat flour: a reference map of the salt-soluble proteome from the U.S. wheat Butte 86

Background

Within the complex wheat flour proteome, the gluten proteins have attracted most of the attention because of their importance in determining the functional properties of wheat flour doughs and their roles in human health conditions such as celiac disease and food allergies. However, certain non-gluten proteins also trigger immunological responses but may be present in flour in low amounts or obscured by the more abundant gluten proteins in two-dimensional gels of total protein preparations.

Methods

Non-gluten proteins were preferentially extracted from the flour with a dilute salt solution and separated by two-dimensional gel electrophoresis. Proteins in 173 gel spots were identified by tandem mass spectrometry after cleavage with trypsin or chymotrypsin. Transgenic wheat lines in which specific groups of gluten proteins were suppressed by RNA interference were used to estimate the amount of carry-over of gluten proteins in the salt-soluble protein fraction.

Results

Fifty-seven different types of non-gluten proteins were identified, including 14 types that are known or suspected immunogenic proteins. The predominant proteins in 18 gel spots were gluten proteins. Some of these also contained non-gluten proteins. Analysis of the salt-soluble proteins from a transgenic line in which omega-1,2 gliadins were eliminated by RNA interference indicated that certain omega-1,2 gliadins were present in large amounts in the salt-soluble fraction and obscured relatively small amounts of beta-amylase and protein disulfide isomerase. In comparison, analysis of a transgenic line in which alpha gliadins were absent revealed that glyceraldehyde-3 phosphate dehydrogenase was a moderately abundant protein that co-migrated with several alpha gliadins.

Conclusions

In this study, we constructed a proteomic map of the non-gluten protein fraction of wheat flour from the US wheat Butte 86 that complements a proteomic map of the total flour proteins developed previously for the same cultivar. Knowing the identities of low abundance proteins in the flour as well as proteins that are hidden by some of the major gluten proteins on two-dimensional gels is critical for studies aimed at assessing the immunogenic potential of wheat flour and determining which wheat proteins that should be targeted in future gene editing experiments to reduce the immunogenic potential of wheat flour.

Scientific Opinion related to a notification from Lyckeby Starch AB on barley starch to be used in the manufacturing of several foods as ingredient, of the food additive modified starch and of glucose syrups pursuant to Article 21(2) of Regulation (EU) No 1169/2011 - for permanent exemption from labelling

Following a request from the European Commission, the EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA) was asked to deliver a scientific opinion on barley starch to be used in the manufacturing of several foods as ingredient, of the food additive modified starch and of glucose syrups pursuant to Article 21(2) of Regulation (EU) No 1169/2011, as notified by Lyckeby Starch AB. The applicant provided information on the manufacturing process and data on the content of total protein, gluten and allergenic proteins in barley starch. The applicant also performed IgE-binding in vitro tests, which were considered inconclusive by the Panel. No human intervention studies with barley starch or food products thereof were provided by the applicant, except for a DBPCFC with barley starch hydrolysate in cereal allergic individuals. The Panel notes that glucose syrups based on barley have been already exempted from allergen labelling as per Annex II of Regulation (EU) No 1169/2011 and that the current application is for the exemption from labelling of all foods manufactured from barley starch. In all the scenarios considered for the anticipated intake, the calculated total protein intake from barley starch was above the MED/MOED for wheat (expressed in mg of wheat protein) in adults (10 mg) and children (2 mg). The Panel concludes that the data available are insufficient to conclude on the likelihood of adverse allergic reactions in cereal-allergic individuals upon consumption of barley starch under the conditions of use proposed by the applicant, and that the consumption of foodstuffs produced from barley starch as starting (raw) material or foodstuffs containing barley starch as an ingredient is unlikely to cause an adverse reaction in individuals with coeliac disease who are not allergic to cereals, provided that the value of gluten for 'gluten-free' foods (20 mg/kg) is not exceeded.

Occurrence of serum antibodies against wheat alpha-amylase inhibitor 0.19 in celiac disease

The alcohol-soluble fraction of wheat gluten (gliadins) induces in genetically susceptible individuals immunologically mediated celiac disease (CLD). However, gliadins and related cereal proteins are not unique foodstuff targets of CLD patients´ immune system. Non-gluten wheat alpha-amylase inhibitor 0.19 (AAI 0.19) has been found to be capable of activating human monocyte-derived dendritic cells and inducing pro-inflammatory status in intestinal mucosa of patients with celiac disease (CLD). The possible contribution of this reactivity in incomplete remission of CLD patients on a gluten-free diet (GFD) is matter of contention. In an attempt to characterize the antigenicity of AAI 0.19 in patients with active CLD, patients on a GFD and healthy controls we developed ELISA employing wheat recombinant AAI 0.19. Using this test we revealed a significant (P<0.001) elevation of IgA anti-AAI 0.19 antibodies (Ab) in patients with active CLD (12 out of 30 patients were seropositive) but also in CLD patients on a GFD (15/46), in contrast to healthy controls (2/59). Anti-AAI 0.19 IgG Ab levels were increased (P<0.001) only in patients with active CLD (14/30) in contrast to the controls. Interestingly, the levels of anti-AAI 0.19 IgG Ab were decreased in CLD patients on a GFD (P<0.001, 1/46) compared to the controls (1/59). Notably, 20 out of 30 patients with active CLD were positive either for IgA or for IgG anti-AAI 0.19 Ab. Thus, the majority of CLD patients developed a robust IgA and IgG Ab response against AAI 0.19. These findings may contribute to the broadening of the knowledge about CLD pathogenesis.

Detecting Allergens From Black Tiger Shrimp Penaeus monodon That Can Bind and Cross-link IgE by ELISA, Western Blot, and a Humanized Rat Basophilic Leukemia Reporter Cell Line RS-ATL8

Background

Black tiger shrimp Penaeus monodon is one of the common causes of shellfish allergy that is increasing worldwide. One of the important problems in the management of shellfish allergy is the lack of accurate diagnostic assay because the biological and immunological properties of allergens in black tiger shrimp have not been well characterized. This study aims to detect proteins with the ability to bind and cross-link immunoglobulin E (IgE) from black tiger shrimp by enzyme-linked immunosorbent assay (ELISA), Western blot, and a humanized rat basophilic leukemia reporter cell line RS-ATL8.

Methods

Sera from shrimp allergic subjects were subjected to ELISA and Western blots using raw or cooked shrimp extract as antigens. Pooled sera were used to sensitize the RS-ATL8 reporter cell line and cells were activated by shrimp extract. Eluted protein extracts separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) were tested on the RS-ATL8 cell line and subjected to mass spectrometry to identify potential candidate allergens.

Results

Allergic sera reacted stronger to raw shrimp extract than cooked shrimp extract (P=0.009). Western blot demonstrated that major IgE reactivity protein bands were at 32–39 kDa and 91–230 kDa in both raw and cooked shrimp extracts. The eluted protein bands at the molecular weight of 38 and 115 kDa from raw shrimp extract induced IgE cross-linking as assayed by the RS-ATL8 cell line. These protein bands were subjected to mass spectrometry for analysis. Ubiquitin-activating enzyme and crustacyanin were identified as potential candidate novel shrimp allergens.

Conclusions

The RS-ATL8 reporter cell line can be used to identify potential new shrimp allergens that can functionally cross-link IgE and induce mast cell degranulation.

Comparative proteomic analysis of two transgenic low-gliadin wheat lines and non-transgenic wheat control

Gluten proteins are major determinants of the bread making quality of wheat, but also of important wheat-related disorders, including coeliac disease (CD), and allergies. We carried out a proteomic study using the total grain proteins from two low-gliadin wheat lines, obtained by RNAi, and the untransformed wild type as reference. The impact of silencing on both target and on non-target proteins was evaluated. Because of the great protein complexity, we performed separate analyses of four kernel protein fractions: gliadins and glutenin subunits, and metabolic and CM-like proteins, by using a classical 2D electrophoresis gel based approach followed by RP-HPLC/nESI-MS/MS. As a result of the strong down-regulation of gliadins, the HMW-GS, metabolic and chloroform/methanol soluble proteins were over-accumulated in the transgenic lines, especially in the line D793, which showed the highest silencing of gliadins. Basing on these data, and considering that metabolic proteins and chloroform/methanol soluble proteins (CM-like), such as the α-amylase/trypsin inhibitor family, β-amylase and serpins, were related to wheat allergens, further in vivo analysis will be needed, especially those related to clinical trials in controlled patients, to determine if these lines could be used for food preparation for celiac or other gluten intolerant groups.

BIOLOGICAL SIGNIFICANCE

Several enteropathies and allergies are related to wheat proteins. Biotechnological techniques such as genetic transformation and RNA interference have allowed the silencing of gliadin genes, providing lines with very low gliadin content in the grains. We report a proteomic-based approach to characterize two low-gliadin transgenic wheat lines obtained by RNAi technology. These lines harbor the same silencing fragment, but driven by two different endosperm specific promoters (γ-gliadin and D-hordein). The comprehensive proteome analysis of these transgenic lines, by combining two-dimensional electrophoresis and RP-HPLC/nESI-MS/MS, provided a large number of spots differentially expressed between the control and the transgenic lines. Hence, the results of this study will facilitate further safety evaluation of these transgenic lines.

Wheat protein recognition pattern in tolerant and allergic children

BACKGROUND

Wheat is one of the most common food allergens in early childhood. In contrast to other food allergies, wheat-specific IgE correlates badly with clinical symptoms and relevant components have been identified mostly for wheat-depended exercise-induced anaphylaxis. Moreover, a high percentage of patients present with immediate type symptoms but wheat-specific IgE cannot be detected with commercial available systems.

OBJECTIVE

We addressed the question whether the IgE recognition pattern between wheat allergic (WA) and clinically tolerant (WT) children differs in order to identify individual proteins useful for component-resolved diagnostics.

METHODS

Sera of 106 children with suspected wheat allergy, of whom 44 children had clinical relevant wheat allergy and 62 were tolerant upon oral food challenge, were analyzed for wheat-specific IgE using the ImmunoCap system as well as immunoblots against water and salt soluble, and water-insoluble protein fractions. 40 randomly selected sera were analyzed for specific IgE to ω5-gliadin.

RESULTS

Sixty-three percent of the WT and 86% of the WA children were sensitized to wheat with >0.35 kUA /l in ImmunoCAP analysis. We could confirm the role of α-, ß-, γ-, and ω-gliadins, and LMW glutenin subunits as major allergens and found also IgE binding to a broad spectrum of water- and salt-soluble protein bands. It is of great importance that wheat allergic and tolerant patients showed IgE binding to the same protein bands. WT and WA did not significantly differ in levels of ω5-gliadin-specific IgE.

CONCLUSIONS & CLINICAL RELEVANCE

Children with challenge proven clinical relevant food allergy and tolerant ones had a similar spectrum of IgE binding to the same protein bands. These findings imply that component-resolved diagnostics might not be helpful in the diagnostic work-up of wheat allergy.

Common food allergens and their IgE-binding epitopes

Food allergy is an adverse immune response to certain kinds of food. Although any food can cause allergic reactions, chicken egg, cow's milk, wheat, shellfish, fruit, and buckwheat account for 75% of food allergies in Japan. Allergen-specific immunoglobulin E (IgE) antibodies play a pivotal role in the development of food allergy. Recent advances in molecular biological techniques have enabled the efficient analysis of food allergens. As a result, many food allergens have been identified, and their molecular structure and IgE-binding epitopes have also been identified. Studies of allergens have demonstrated that IgE antibodies specific to allergen components and/or the peptide epitopes are good indicators for the identification of patients with food allergy, prediction of clinical severity and development of tolerance. In this review, we summarize our current knowledge regarding the allergens and IgE epitopes in the well-researched allergies to chicken egg, cow's milk, wheat, shrimp, and peanut.

A Grounded Guide to Gluten: How Modern Genotypes and Processing Impact Wheat Sensitivity

The role of wheat, and particularly of gluten protein, in our diet has recently been scrutinized. This article provides a summary of the main pathologies related to wheat in the human body, including celiac disease, wheat allergy, nonceliac wheat sensitivity, fructose malabsorption, and irritable bowel syndrome. Differences in reactivity are discussed for ancient, heritage, and modern wheats. Due to large variability among species and genotypes, it might be feasible to select wheat varieties with lower amounts and fewer types of reactive prolamins and fructans. Einkorn is promising for producing fewer immunotoxic effects in a number of celiac research studies. Additionally, the impact of wheat processing methods on wheat sensitivity is reviewed. Research indicates that germination and fermentation technologies can effectively alter certain immunoreactive components. For individuals with wheat sensitivity, less-reactive wheat products can slow down disease development and improve quality of life. While research has not proven causation in the increase in wheat sensitivity over the last decades, modern wheat processing may have increased exposure to immunoreactive compounds. More research is necessary to understand the influence of modern wheat cultivars on epidemiological change.

Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms

In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.

Specific nongluten proteins of wheat are novel target antigens in celiac disease humoral response

While the antigenic specificity and pathogenic relevance of immunologic reactivity to gluten in celiac disease have been extensively researched, the immune response to nongluten proteins of wheat has not been characterized. We aimed to investigate the level and molecular specificity of antibody response to wheat nongluten proteins in celiac disease. Serum samples from patients and controls were screened for IgG and IgA antibody reactivity to a nongluten protein extract from the wheat cultivar Triticum aestivum Butte 86. Antibodies were further analyzed for reactivity to specific nongluten proteins by two-dimensional gel electrophoresis and immunoblotting. Immunoreactive molecules were identified by tandem mass spectrometry. Compared with healthy controls, patients exhibited significantly higher levels of antibody reactivity to nongluten proteins. The main immunoreactive nongluten antibody target proteins were identified as serpins, purinins, α-amylase/protease inhibitors, globulins, and farinins. Assessment of reactivity toward purified recombinant proteins further confirmed the presence of antibody response to specific antigens. The results demonstrate that, in addition to the well-recognized immune reaction to gluten, celiac disease is associated with a robust humoral response directed at a specific subset of the nongluten proteins of wheat.

Next generation of food allergen quantification using mass spectrometric systems

Food allergies are increasing worldwide and becoming a public health concern. Food legislation requires detailed declarations of potential allergens in food products and therefore an increased capability to analyze for the presence of food allergens. Currently, antibody-based methods are mainly utilized to quantify allergens; however, these methods have several disadvantages. Recently, mass spectrometry (MS) techniques have been developed and applied to food allergen analysis. At present, 46 allergens from 11 different food sources have been characterized using different MS approaches and some specific signature peptides have been published. However, quantification of allergens using MS is not routinely employed. This review compares the different aspects of food allergen quantification using advanced MS techniques including multiple reaction monitoring. The latter provides low limits of quantification for multiple allergens in simple or complex food matrices, while being robust and reproducible. This review provides an overview of current approaches to analyze food allergens, with specific focus on MS systems and applications.

Immunoproteomics analysis of food allergens

Immunoblot-coupled proteomics based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), namely, immunoproteomics, has been used for comprehensive identification of food allergens, because it is a simple and inexpensive tool for rapid identification of several IgE-binding proteins. In this section, we describe our protocols for identification of food allergens using immunoproteomics and discuss a few technical points in detail.

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.

How much does transgenesis affect wheat allergenicity?: Assessment in two GM lines over-expressing endogenous genes

Wheat kernel albumins/globulins (A/G) and gluten proteins are responsible for baker's asthma and food allergy in atopic subjects. Although no commercial genetically modified wheats are currently being grown, they are under study and the allergenicity of GM products is a major concern. In order to establish the expected and unexpected effects of genetic transformation on allergenicity and also to carry out a safety assessment of genetic transformation, two GM wheat lines (bread and pasta wheat) transformed with endogenous genes were compared to their untransformed counterparts (wt), first by an allergenomic approach, and second, using ELISA with sera from patients suffering from food allergy to wheat and baker's asthma. The 2D immunoblots performed on sera from patients suffering from food allergy and baker's asthma on the A/G fraction of the four lines (two GM and two wt) revealed comparable IgE-binding profiles. A total of 109 IgE-binding spots were analyzed by mass spectrometry, and most of the proteins identified had already been described as allergens or potential allergens. Only two IgE-binding proteins were specific to one GM line. The concentration of specific IgE against the A/G fractions of GM wheat lines and their wt genotypes differed for some sera.

BIOLOGICAL SIGNIFICANCE

The originality of our paper is to relate the transformation of wheat lines with their potential allergenicity using patient sera, such focus has never been done before in wheat and should be of interest to the researches working in this field. Another interesting point of this paper is the study of two types of allergies (respiratory and food) on two wheat genotypes and their GM which reveals that some allergens already known in respiratory allergy could be involved in children suffering from wheat food allergy. In this paper we used a classical 2D proteomic analysis and the protein identifications were performed by mass spectrometry after spot picking and in gel trypsin hydrolysis. Concerning the LC-MS/MS analyses classical software and parameters were used as described in Material and methods. We worked on wheat which is actually not fully sequenced that was a difficulty; we therefore searched against two databanks (proteins and ESTs) in order to compare the results. Moreover all proteins reported in our paper were identified with at least three unique peptides. The identified proteins were checked for their potential allergenicity. In order to have a best interpretation of protein identified in terms of potential allergens, BLAST alignments were performed by using an allergen databank (SDAP). This allows the determination of the cross-reactivity of these identified proteins with known allergens of other species and also the prediction of a potential allergenicity.

Molecular and immunological characterization of wheat Serpin (Tri a 33)

SCOPE

Several wheat proteins are responsible for food and respiratory allergies. Due to their large polymorphism, the allergenic potential of a number of them has not yet been precisely established. The aim of this work was to perform a thorough assessment of serpin (Tri a 33) allergenicity.

METHODS AND RESULTS

Recombinant wheat Serpin-Z2B isoform (rSerpin-Z2B) was expressed in Escherichia coli. Synchrotron radiation circular dichroism data indicated that the recombinant serpin contains slightly more β-strands than α-helix structures. IgE reactivity of sera from 103 patients with food allergy and 29 patients with Baker's asthma was evaluated using ELISA, a model of basophil activation and linear epitope mapping (Pepscan). Twenty percent of patients with food allergy to wheat and 31% of those with Baker's asthma displayed rSerpin-Z2B-specific IgE in ELISA. The protein was able to induce IgE-dependent basophil degranulation. The Pepscan experiment identified four regions involved in IgE binding to serpin. Heating the protein induced its irreversible denaturation and impaired IgE binding, revealing the predominance of conformational epitopes.

CONCLUSION

This study confirms wheat serpin allergenicity and shows that recombinant serpin may be a marker of a broad spectrum of sensitization to wheat proteins.

Mass spectrometry in the proteome analysis of mature cereal kernels

In the last decade, the improved performance and versatility of the mass spectrometers together with the increasing availability of gene and genomic sequence database, led the mass spectrometry to become an indispensable tool for either protein and proteome analyses in cereals. Mass spectrometric works on prolamins have rapidly evolved from the determination of the molecular masses of proteins to the proteomic approaches aimed to a large-scale protein identification and study of functional and regulatory aspects of proteins. Mass spectrometry coupled with electrophoresis, chromatographic methods, and bioinformatics tools is currently making significant contributions to a better knowledge of the composition and structure of the cereal proteins and their structure-function relationships. Results obtained using mass spectrometry, including characterization of prolamins, investigation of the gluten toxicity for coeliac patients, identification of proteins responsible of cereal allergies, determination of the protein pattern and its modification under environmental or stress effects, investigation of genetically modified varieties by proteomic approaches, are summarized here, to illustrate current trends, analytical troubles and challenges, and suggest possible future perspectives.

Exposure to respirable flour dust and gliadin in wheat flour mills

OBJECTIVES

The aim of this study was to determine the concentrations of respirable flour dusts and gliadin as well as gliadin-specific serum antibodies in exposed workers of Hamadan wheat flour mill factories.

METHODS

Blood samples from 95 exposed workers and 80 air samples from flour packing, husk packing, flour production and wheat unloading areas were collected. Respirable flour dust density was measured by a gravimetric method, and dust gliadin concentration as well as serum antibodies were determined by enzyme-linked immunosorbent assays.

RESULTS

The Time-weighted average (TWA) flour dust density was higher in all factories (1.56-4.68 mg/m(3)) compared with the threshold limit value (0.5 mg/m(3)) of ACGIH and showed a positive correlation with the gliadin concentration (p<0.05). Additionally, the respirable dust and gliadin concentrations were significantly higher at flour packing workstations compare with the other work areas. Moreover, the mean serum gliadin-specific IgA and IgG and total IgE antibodies were remarkably higher in exposed mill workers compared with the controls (p<0.05).

CONCLUSION

We clearly demonstrated that workers in Hamadan flour mills are in exposed to a hazardous level of respirable flour dust, receiving the highest level of dust and gliadin in flour packing areas. Furthermore, dust-exposed workers showed upper levels of serum antibodies indicating exposure to higher amounts of allergens than controls.

Multiple wheat flour allergens and cross-reactive carbohydrate determinants bind IgE in baker's asthma

BACKGROUND

Several wheat flour allergens relevant to baker's asthma have been identified in the last 25 years. The aim of this study was to determine the frequency of sensitization to these allergens in German bakers.

METHODS

Using recombinant DNA technology, the following wheat flour allergens were cloned, expressed in Escherichia coli and purified: five subunits of the wheat α-amylase inhibitors (WTAI-CM1, WTAI-CM2, WTAI-CM3, WDAI-0.19 and WMAI-0.28), thioredoxin, thiol reductase or 1-cys-peroxiredoxin homologues, triosephosphate-isomerase, αβ-gliadin, serpin, glyceraldehyde-3-phosphate-dehydrogenase, a nonspecific lipid transfer protein (nsLTP), dehydrin, profilin and peroxidase. In addition, ImmunoCAPs with the recombinant allergen ω-5-gliadin and two cross-reactive carbohydrate determinants (CCDs), horse radish peroxidase (HRP) and the N-glycan of bromelain (MUXF), were used. Specific IgE was measured in wheat flour-positive sera from 40 German bakers with work-related asthma/rhinitis and 10 controls with pollinosis.

RESULTS

Thirty bakers (75%) had IgE to at least one of the 19 single allergens. Most frequent was IgE to WDAI-0.19, HRP and MUXF (25% each), followed by WTAI-CM1 (20%), thiol reductase (16%), WTAI-CM3 (15%), WTAI-CM2 and thioredoxin (12.5%), WMAI-28, triosephosphate-isomerase, αβ-gliadin (10%), 1-cys-peroxiredoxin (7.5%), dehydrin, serpin, glyceraldehyde-3-phosphate-dehydrogenase (5%), ω-5-gliadin, nsLTP and profilin (2.5%). Fifteen bakers (38%) had IgE to any α-amylase inhibitor and 12 (30%) to at least one CCD. The controls reacted exclusively to CCDs (80%), profilin (60%), thioredoxin (30%), triosephosphate isomerase and nsLTP (10%).

CONCLUSIONS

The single allergen sensitization profiles obtained with 17 recombinant wheat flour allergens and two CCDs revealed no major allergen for German bakers. The highest frequencies were found for α-amylase inhibitors and CCDs.

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.

Nutriproteomics: technologies and applications for identification and quantification of biomarkers and ingredients

Nutrition refers to the process by which a living organism ingests and digests food and uses the nutrients therein for growth, tissue maintenance and all other functions essential to life. Food components interact with our body at molecular, cellular, organ and system level. Nutrients come in complex mixtures, in which the presence and concentration of single compounds as well as their interactions with other compounds and the food matrix influence their bioavailability and bioefficacy. Traditionally, nutrition research mainly concentrated on supplying nutrients of quality to nourish populations and on preventing specific nutrient deficiencies. More recently, it investigates health-related aspects of individual ingredients or of complete diets, in view of health promotion, performance optimisation, disease prevention and risk assessment. This review focuses on proteins and peptides, their role as nutrients and biomarkers and on the technologies developed for their analysis. In the first part of this review, we provide insights into the way proteins are currently characterised and analysed using classical and emerging proteomic approaches. The scope of the second part is to review major applications of proteomics to nutrition, from characterisation of food proteins and peptides, via investigation of health-related food benefits to understanding disease-related mechanisms.

A new approach to the isolation and characterization of wheat flour allergens

BACKGROUND

The incidence of food allergy to wheat is increasing. Its diagnosis depends on the purity of major allergens and their inclusion in tests. Isolation and characterization of wheat allergens are therefore of utmost importance.

OBJECTIVE

To purify and identify wheat flour allergens most frequently recognized by patients' IgE antibodies and to study their allergenicity.

METHODS

Water/salt-soluble extracts from wheat flour were prepared and separated using a combination of ultrafiltration, isoelectric focusing and liquid chromatography. Purified proteins were analysed by immunoblotting using pooled sera from patients with atopic dermatitis who possessed IgE specific to wheat. Wheat proteins found to bind IgE were subsequently identified by matrix-assisted laser desorption/ionisation-time of flight mass spectrometry. The frequency and intensity of IgE binding of isolated proteins were tested using individual sera from patients and controls.

RESULTS

We developed a procedure that allows isolation of wheat allergens from natural sources. Twenty-seven potential wheat allergens have been successfully identified; of these, the following seven are newly reported in food allergy: endogenous α-amylase/subtilisin inhibitor, trypsin/α-amylase inhibitor (AAI) CMX1/CMX3, thaumatin-like protein (TLP), xylanase inhibitor protein-1, β-glucosidase, class II chitinase and 26 kDa endochitinase. TLP and wheatwin were shown to activate patients' basophils to a similar extent as two well-known allergens, lipid transfer protein (Tri a 14) and AAI 0.19 (Tri a 28.0101).

CONCLUSION AND CLINICAL RELEVANCE

Our new approach enables the isolation of water/salt-soluble wheat allergens in their native form in amounts sufficient both for biological testing (in vivo and in vitro) and for physicochemical characterization. Such studies will lead to a more detailed knowledge of allergenicity of wheat proteins and to improved accuracy of diagnostic tests.

Proteomic analysis in allergy and intolerance to wheat products

Owing to its extensive use in the human diet, wheat is among the most common causes of food-related allergies and intolerances. Allergies to wheat are provoked by ingestion, inhalation or contact with either the soluble or the insoluble gluten proteins in wheat. Gluten proteins, and particularly the gliadin fraction, are also the main factor triggering celiac disease, a common enteropathy induced by ingestion of wheat gluten proteins and related prolamins from oat, rye and barley in genetically susceptible individuals. The role of gliadin and of its derived peptides in eliciting the adverse reactions in celiac disease are still far from being completely explained. Owing to its unique pathogenesis, celiac disease is widely investigated as a model immunogenetic disorder. The structural characterization of the injuring agents, the gluten proteins, assumes a particular significance in order to deepen the understanding of the events that trigger this and similar diseases at the molecular level. Recent developments in proteomics have provided an important contribution to the understanding of several basic aspects of wheat protein-related diseases. These include: the identification of gluten fractions and derived peptides involved in wheat allergy and intolerance, including celiac disease, and the elucidation of their mechanism of toxicity; the development and validation of sensitive and specific methods for detecting trace amounts of gluten proteins in gluten-free foods for intolerant patients; and the formulation of completely new substitute foods and ingredients to replace the gluten-based ones. In this article, the main aspects of current and prospective applications of mass spectrometry and proteomic technologies to the structural characterization of gluten proteins and derived peptides are critically presented, with a focus on issues related to their detection, identification and quantification, which are relevant to the biochemical, immunological and toxicological aspects of wheat intolerance.

Assessment of allergenicity of diploid and hexaploid wheat genotypes: identification of allergens in the albumin/globulin fraction

Wheat is an important part of the daily diet of millions of people. However, this staple food is also responsible for food allergies. Ancient cultivars of wheat are gaining interest today but nothing is known about their allergenicity. Many wheat proteins have been reported as causative food allergens, including some prolamin-type gluten proteins, and salt soluble proteins of the albumin/globulin (A/G) type. The objective of this work is to obtain information about the allergenicity of the salt soluble A/G fraction of an ancient diploid cultivar compared with a standard hexaploid bread wheat cultivar using 20 sera from patients with wheat allergy. Differences in the IgE reactivity of sera towards the two genotypes were quantified by ELISA. Qualitative differences in IgE-binding proteins were searched after 1D or 2D electrophoresis. For most of the sera, the concentration in A/G specific IgE was higher for the hexaploid T. aestivum (cv Récital) than for the diploid T. monococcum (cv Engrain). The analysis of 2D spots revealed by immunoblotting leads to the identification by mass spectrometry of 39 IgE-binding proteins, some of them unknown until now as wheat allergens. Numerous allergens were identified, differences observed between Engrain and Récital will be discussed.

Identification of sole parvalbumin as a major allergen: study of cross-reactivity between parvalbumins in a Spanish fish-allergic population

BACKGROUND

Fish allergy is becoming an important health problem in Spain, a country with the third highest level of fish consumption after Japan and Portugal. The most common fish allergens are parvalbumins. In our area, the most widely consumed fish species are lean, such as whiff (Lepidorhombus whiffiagonis) and sole (Solea solea). Adverse reactions to fish are usually related to these species, a fact that is largely unknown to allergists in other countries.

OBJECTIVE

The aim of this study was to identify and purify the major allergen implicated in allergic response to sole and evaluate the IgE cross-reactivity of purified parvalbumins from whiff and sole, which are phylogenetically close, and more distant species (i.e. cod and salmon).

METHODS

Eighteen Spanish fish-allergic patients with a positive history of type I allergy to fish were recruited from the clinic. Total protein extracts and purified parvalbumins from whiff and sole were tested for their IgE-binding properties by combining two-dimensional Western blotting and mass spectrometry. The extent of cross-reactivity between these parvalbumins along with cod and salmon parvalbumins was investigated by IgE ELISA inhibition assay.

RESULTS

An IgE-binding spot of approximately 14 kDa was identified as parvalbumin and confirmed as a major allergen in sole extract, which is recognized by almost 70% of the patients. Whiff parvalbumin was recognized by 83.4% of the patients. High cross-reactivity was determined for all purified parvalbumins by IgE inhibition assay.

CONCLUSIONS AND CLINICAL RELEVANCE

Sole and whiff parvalbumin were confirmed as major allergens. The parvalbumins of sole, whiff, cod and salmon were highly cross-reactive, thus suggesting a high amino acid sequence identity between them.

Proteome mining for novel IgE-binding proteins from the German cockroach (Blattella germanica) and allergen profiling of patients

Although cockroaches are known to produce allergens that can cause IgE-mediated hypersensitivity reactions, including perennial rhinitis and asthma, the various cockroach allergens have not yet been fully studied. Many proteins from the German cockroach show high IgE reactivity, but have never been comprehensively characterized. To identify these potential allergens, proteins were separated by 2-DE and IgE-binding proteins were analyzed by nanoLC-MS/MS or N-terminal sequencing analysis. Using a combination of proteomic techniques and bioinformatic allergen database analysis, we identified a total of ten new B. germanica IgE-binding proteins. Of these, aldolase, arginine kinase, enolase, Hsp70, triosephosphate isomerase, and vitellogenin have been reported as allergens in species other than B. germanica. Analysis of the Food Allergy Research and Resource Program allergen database indicated that arginine kinase, enolase, and triosephosphate isomerase showed significant potential cross-reactivity with other related allergens. This study revealed that vitellogenin is an important novel B. germanica allergen. Personalized profiling and reactivity of IgE Abs against the panel of IgE-binding proteins varied between cockroach-allergic individuals. These findings make it possible to monitor the individual IgE reactivity profile of each patient and facilitate personalized immunotherapies for German cockroach allergy disorders.

Liquid chromatography and mass spectrometry in food allergen detection

Food allergy is an important issue in the field of food safety because of the hazards for affected persons and the hygiene requirements and legal regulations imposed on the food industry. Consumer protection and law enforcement require suitable analytical techniques for the detection of allergens in foods. Immunological methods are currently preferred; however, confirmatory alternatives are needed. The determination of allergenic proteins by liquid chromatography and mass spectrometry has greatly advanced in recent years, and gel-free allergenomics is becoming a routinely used approach for the identification and quantitation of food allergens. The present review provides a brief overview of the principles of proteomic procedures, various chromatographic set ups, and mass spectrometry instrumentation used in allergenomics. A compendium of published liquid chromatography methods, proteomic analyses, typical marker peptides, and quantitative assays for 14 main allergy-causing foods is also included.

Identification of IgE-reactive proteins in patients with wheat protein contact dermatitis

BACKGROUND

Wheat protein and its derivatives can cause protein contact dermatitis (PCD), which mainly occurs in bakers. Few studies have attempted to identify the allergens responsible for wheat PCD.

OBJECTIVES

The aim of this study was to identify allergenic wheat proteins in patients with wheat PCD.

METHODS

Water-soluble and water-insoluble wheat flour proteins were separated by 1- or 2-dimensional gel electrophoresis. IgE-binding proteins were detected by immunoblotting with sera from 3 wheat PCD patients and identified by N-terminal amino acid sequence analysis. The IgE-binding proteins were recombinantly expressed in Escherichia coli and tested against patients' sera.

RESULTS

IgE antibodies from the patients' sera reacted with water-soluble proteins rather than water-insoluble proteins, and the 2-dimensional electrophoresis and immunoblotting produced individual IgE-binding patterns. Analysis of the N-terminal amino acid sequence of the IgE-binding proteins from the 2-dimensional gel led to the identification of three glycoproteins, wheat 27-kDa allergen, peroxidase, and purple acid phosphatase. No specific IgE antibodies to their non-glycosylated recombinant proteins were observed.

CONCLUSIONS

We identified wheat 27-kDa allergen, peroxidase and purple acid phosphatase as candidate allergens for wheat PCD. Our results suggest that glycan moieties in these proteins are involved in IgE binding.

Two-dimensional electrophoresis and IgE-mediated food allergy

Food allergy is recognized as one of the major health concerns. It is estimated that ca. 4% of the population is affected by food allergenic disorders. Food allergies are defined as IgE-mediated hypersensitivity reactions. Foods such as peanuts, tree nuts, wheat, soy, cow's milk, egg, fish and shellfish are regarded as responsible for the majority of reactions. The ubiquitous presence of allergens in the human foods coupled with an increased awareness of food allergies warrants to undertake appropriate preventive measures for protecting sensitive consumers from unwanted exposure to offending food allergens. 2-DE followed by immunoblotting and identification of IgE-reactive proteins, as a proteomic approach to identify new allergens in foods, are reviewed. Specific examples of identification of allergens in foods and beverages by using 2-DE and IgE are described. Protein profiling using 2-DE and allergens detection by IgE has become a powerful method for analyzing changes of allergens content in complex matrix during food processing.