Protein allergenicity assessment of foods produced through agricultural biotechnology

Food buffering capacity: quantification methods and its importance in digestion and health

Understanding the influence of food properties on buffering capacity will have an impact on gastric secretions and breakdown during digestion.

AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes

AlgPred 2.0 is a web server developed for predicting allergenic proteins and allergenic regions in a protein. It is an updated version of AlgPred developed in 2006. The dataset used for training, testing and validation consists of 10 075 allergens and 10 075 non-allergens. In addition, 10 451 experimentally validated immunoglobulin E (IgE) epitopes were used to identify antigenic regions in a protein. All models were trained on 80% of data called training dataset, and the performance of models was evaluated using 5-fold cross-validation technique. The performance of the final model trained on the training dataset was evaluated on 20% of data called validation dataset; no two proteins in any two sets have more than 40% similarity. First, a Basic Local Alignment Search Tool (BLAST) search has been performed against the dataset, and allergens were predicted based on the level of similarity with known allergens. Second, IgE epitopes obtained from the IEDB database were searched in the dataset to predict allergens based on their presence in a protein. Third, motif-based approaches like multiple EM for motif elicitation/motif alignment and search tool have been used to predict allergens. Fourth, allergen prediction models have been developed using a wide range of machine learning techniques. Finally, the ensemble approach has been used for predicting allergenic protein by combining prediction scores of different approaches. Our best model achieved maximum performance in terms of area under receiver operating characteristic curve 0.98 with Matthew's correlation coefficient 0.85 on the validation dataset. A web server AlgPred 2.0 has been developed that allows the prediction of allergens, mapping of IgE epitope, motif search and BLAST search (https://webs.iiitd.edu.in/raghava/algpred2/).

Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin

To what extent do structural and biophysical features of food allergen proteins distinguish them from other proteins in our diet? Invertebrate tropomyosins (Tpms) as a class are considered "pan-allergens," inducing food allergy to shellfish and respiratory allergy to dust mites. Vertebrate Tpms are not known to elicit allergy or cross-reactivity, despite their high structural similarity and sequence identity to invertebrate homologs. We expect allergens are sufficiently stable against gastrointestinal proteases to survive for immune sensitization in the intestines, and that proteolytic stability will correlate with thermodynamic stability. Thermal denaturation of shrimp Tpm shows that it is more stable than non-allergen vertebrate Tpm. Shrimp Tpm is also more resistant to digestion. Molecular dynamics uncover local dynamics that select epitopes and global differences in flexibility between shrimp and pig Tpm that discriminate allergens from non-allergens. Molecular determinants of allergenicity depend not only on sequence but on contributions of protein structure and dynamics.

Approaches to assess IgE mediated allergy risks (sensitization and cross-reactivity) from new or modified dietary proteins

The development and introduction of new dietary protein sources has the potential to improve food supply sustainability. Understanding the potential allergenicity of these new or modified proteins is crucial to ensure protection of public health. Exposure to new proteins may result in de novo sensitization, with or without clinical allergy, or clinical reactions through cross-reactivity. In this paper we review the potential of current methodologies (in silico, in vitro degradation, in vitro IgE binding, animal models and clinical studies) to address these outcomes for risk assessment purposes for new proteins, and especially to identify and characterise the risk of sensitization for IgE mediated allergy from oral exposure. Existing tools and tests are capable of assessing potential crossreactivity. However, there are few possibilities to assess the hazard due to de novo sensitization. The only methods available are in vivo models, but many limitations exist to use them for assessing risk. We conclude that there is a need to understand which criteria adequately define allergenicity for risk assessment purposes, and from these criteria develop a more suitable battery of tests to distinguish between proteins of high and low allergenicity, which can then be applied to assess new proteins with unknown risks.

Allergenic potential of novel proteins - What can we learn from animal production?

Currently, risk assessment of the allergenic potential of novel proteins relies heavily on evaluating protein digestibility under normal conditions based on the theory that allergens are more resistant to gastrointestinal digestion than non-allergens. There is also proposed guidance for expanded in vitro digestibility assay conditions to include vulnerable sub-populations. One of the underlying rationales for the expanded guidance is that current in vitro assays do not accurately replicate the range of physiological conditions. Animal scientists have long sought to predict protein and amino acid digestibility for precision nutrition. Monogastric production animals, especially swine, have gastrointestinal systems similar to humans, and evaluating potential allergen digestibility in this context may be beneficial. Currently, there is no compelling evidence that the mechanisms sometimes postulated to be associated with allergenic sensitization, e.g. antacid modification of stomach pH, are valid among production animals. Furthermore, examples are provided where non-biologically representative assays are better at predicting protein and amino acid digestibility compared with those designed to mimic in vivo conditions. Greater emphasis should be made to align in vitro assessments with in vivo data.

Peptidomics of an in vitro digested α-Gal carrying protein revealed IgE-reactive peptides

The mammalian carbohydrate galactose-α1,3-galactose (α-Gal) causes a novel form of food allergy, red meat allergy, where patients experience severe allergic reactions several hours after red meat consumption. Here we explored gastric digestion of α-Gal glycoproteins using an in vitro model. Bovine thyroglobulin (BTG), a typical α-Gal carrying glycoprotein, was digested with pepsin. The resulting peptides were characterised by SDS PAGE, immunoblot and ImmunoCAP using sera from 20 red meat allergic patients. During pepsinolysis of BTG, a wide range of peptide bands was observed of which 14 to 17 kDa peptides remained stable throughout the gastric phase. The presence of the α-Gal epitope on the obtained peptides was demonstrated by an anti-α-Gal antibody and IgE from red meat allergic patients. The α-Gal digests were able to inhibit up to 86% of IgE reactivity to BTG. Importantly, basophil activation test demonstrated that the allergenic activity of BTG was retained after digestion in all four tested patients. Mass spectrometry-based peptidomics revealed that these peptides represent mostly internal and C-terminal parts of the protein, where the most potent IgE-binding α-Gal residues were identified at Asn₁₇₅₆, Asn₁₈₅₀ and Asn₂₂₃₁. Thus allergenic α-Gal epitopes are stable to pepsinolysis, reinforcing their role as clinically relevant food allergens.

Current overview of allergens of plant pathogenesis related protein families

Pathogenesis related (PR) proteins are one of the major sources of plant derived allergens. These proteins are induced by the plants as a defense response system in stress conditions like microbial and insect infections, wounding, exposure to harsh chemicals, and atmospheric conditions. However, some plant tissues that are more exposed to environmental conditions like UV irradiation and insect or fungal attacks express these proteins constitutively. These proteins are mostly resistant to proteases and most of them show considerable stability at low pH. Many of these plant pathogenesis related proteins are found to act as food allergens, latex allergens, and pollen allergens. Proteins having similar amino acid sequences among the members of PR proteins may be responsible for cross-reactivity among allergens from diverse plants. This review analyzes the different pathogenesis related protein families that have been reported as allergens. Proteins of these families have been characterized in regard to their biological functions, amino acid sequence, and cross-reactivity. The three-dimensional structures of some of these allergens have also been evaluated to elucidate the antigenic determinants of these molecules and to explain the cross-reactivity among the various allergens.

Simulated digestion for testing the stability of edible vaccine based on Cucumber mosaic virus (CMV) chimeric particle display Hepatitis C virus (HCV) peptide

Edible vaccines must survive digestive process and preserve the specific structure of the antigenic peptide to elicit effective immune response. The stability of a protein to digestive process can be predicted by subjecting it to the in vitro assay with simulated gastric fluid (SGF) and simulated intestinal fluid (SIF). Here, we describe the protocol of producing and using chimeric Cucumber mosaic virus (CMV) displaying Hepatitis C virus (HCV) derived peptide (R9) in double copy as an oral vaccine. Its stability after treatment with SGF and SIF and the preservation of the antigenic properties were verified by SDS-PAGE and immuno western blot techniques.

PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection

BACKGROUND

Assessment of potential allergenicity of protein is necessary whenever transgenic proteins are introduced into the food chain. Bioinformatics approaches in allergen prediction have evolved appreciably in recent years to increase sophistication and performance. However, what are the critical features for protein's allergenicity have been not fully investigated yet.

RESULTS

We presented a more comprehensive model in 128 features space for allergenic proteins prediction by integrating various properties of proteins, such as biochemical and physicochemical properties, sequential features and subcellular locations. The overall accuracy in the cross-validation reached 93.42% to 100% with our new method. Maximum Relevance Minimum Redundancy (mRMR) method and Incremental Feature Selection (IFS) procedure were applied to obtain which features are essential for allergenicity. Results of the performance comparisons showed the superior of our method to the existing methods used widely. More importantly, it was observed that the features of subcellular locations and amino acid composition played major roles in determining the allergenicity of proteins, particularly extracellular/cell surface and vacuole of the subcellular locations for wheat and soybean. To facilitate the allergen prediction, we implemented our computational method in a web application, which can be available at http://gmobl.sjtu.edu.cn/PREAL/index.php.

CONCLUSIONS

Our new approach could improve the accuracy of allergen prediction. And the findings may provide novel insights for the mechanism of allergies.

Characterization of Cannabis sativa allergens

BACKGROUND

Allergic sensitization to Cannabis sativa is rarely reported, but the increasing consumption of marijuana has resulted in an increase in the number of individuals who become sensitized. To date, little is known about the causal allergens associated with C sativa.

OBJECTIVE

To characterize marijuana allergens in different components of the C sativa plant using serum IgE from marijuana sensitized patients.

METHODS

Serum samples from 23 patients with a positive skin prick test result to a crude C sativa extract were evaluated. IgE reactivity was variable between patients and C sativa extracts. IgE reactivity to C sativa proteins in Western blots was heterogeneous and ranged from 10 to 70 kDa. Putative allergens derived from 2-dimensional gels were identified.

RESULTS

Prominent IgE reactive bands included a 23-kDa oxygen-evolving enhancer protein 2 and a 50-kDa protein identified to be the photosynthetic enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase. Additional proteins were identified in the proteomic analysis, including those from adenosine triphosphate synthase, glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, and luminal binding protein (heat shock protein 70), suggesting these proteins are potential allergens. Deglycosylation studies helped refine protein allergen identification and demonstrated significant IgE antibodies against plant oligosaccharides that could help explain cross-reactivity.

CONCLUSION

Identification and characterization of allergens from C sativa may be helpful in further understanding allergic sensitization to this plant species.

Evaluation and integration of existing methods for computational prediction of allergens

Background

Allergy involves a series of complex reactions and factors that contribute to the development of the disease and triggering of the symptoms, including rhinitis, asthma, atopic eczema, skin sensitivity, even acute and fatal anaphylactic shock. Prediction and evaluation of the potential allergenicity is of importance for safety evaluation of foods and other environment factors. Although several computational approaches for assessing the potential allergenicity of proteins have been developed, their performance and relative merits and shortcomings have not been compared systematically.

Results

To evaluate and improve the existing methods for allergen prediction, we collected an up-to-date definitive dataset consisting of 989 known allergens and massive putative non-allergens. The three most widely used allergen computational prediction approaches including sequence-, motif- and SVM-based (Support Vector Machine) methods were systematically compared using the defined parameters and we found that SVM-based method outperformed the other two methods with higher accuracy and specificity. The sequence-based method with the criteria defined by FAO/WHO (FAO: Food and Agriculture Organization of the United Nations; WHO: World Health Organization) has higher sensitivity of over 98%, but having a low specificity. The advantage of motif-based method is the ability to visualize the key motif within the allergen. Notably, the performances of the sequence-based method defined by FAO/WHO and motif eliciting strategy could be improved by the optimization of parameters. To facilitate the allergen prediction, we integrated these three methods in a web-based application proAP, which provides the global search of the known allergens and a powerful tool for allergen predication. Flexible parameter setting and batch prediction were also implemented. The proAP can be accessed at http://gmobl.sjtu.edu.cn/proAP/main.html.

Conclusions

This study comprehensively evaluated sequence-, motif- and SVM-based computational prediction approaches for allergens and optimized their parameters to obtain better performance. These findings may provide helpful guidance for the researchers in allergen-prediction. Furthermore, we integrated these methods into a web application proAP, greatly facilitating users to do customizable allergen search and prediction.

Allergenicity assessment of the papaya ringspot virus coat protein expressed in transgenic rainbow papaya

The virus-resistant, transgenic commercial papaya Rainbow and SunUp (Carica papaya L.) have been consumed locally in Hawaii and elsewhere in the mainland United States and Canada since their release to planters in Hawaii in 1998. These papaya are derived from transgenic papaya line 55-1 and carry the coat protein (CP) gene of papaya ringspot virus (PRSV). The PRSV CP was evaluated for potential allergenicity, an important component in assessing the safety of food derived from transgenic plants. The transgene PRSV CP sequence of Rainbow papaya did not exhibit greater than 35% amino acid sequence homology to known allergens, nor did it have a stretch of eight amino acids found in known allergens which are known common bioinformatic methods used for assessing similarity to allergen proteins. PRSV CP was also tested for stability in simulated gastric fluid and simulated intestinal fluid and under various heat treatments. The results showed that PRSV CP was degraded under conditions for which allergenic proteins relative to nonallergens are purported to be stable. The potential human intake of transgene-derived PRSV CP was assessed by measuring CP levels in Rainbow and SunUp along with estimating the fruit consumption rates and was compared to potential intake estimates of PRSV CP from naturally infected nontransgenic papaya. Following accepted allergenicity assessment criteria, our results show that the transgene-derived PRSV CP does not pose a risk of food allergy.

Mechanisms underlying differential food allergy response to heated egg

BACKGROUND

Egg white proteins are usually subjected to heating, making them edible for the majority of children with egg allergy.

OBJECTIVE

We sought to investigate the underlying mechanisms responsible for the reduced allergenicity displayed by heat-treated egg white allergens.

METHODS

C3H/HeJ mice were orally sensitized with ovalbumin (OVA) or ovomucoid and challenged with native or heated proteins to evaluate their allergenicity. Immunoreactivity was assessed by immunoblotting using sera from children with egg allergy. In vitro gastrointestinal digestion of native and heated OVA and ovomucoid was studied by SDS-PAGE and liquid chromatography. Intestinal uptake of intact native and heated OVA and ovomucoid by human intestinal epithelial (Caco-2) cells was investigated. Rat basophil leukemia cells passively sensitized with mouse serum and human basophils passively sensitized with serum from children with egg allergy were used to assess the effector cell activation by heated, digested, and transported OVA and ovomucoid.

RESULTS

Heated OVA and ovomucoid did not induce symptoms of anaphylaxis in sensitized mice when administered orally. Heating did not completely destroy IgE-binding capacity of OVA or ovomucoid but enhanced in vitro digestibility of OVA. Digestion of both OVA and ovomucoid diminished mediator release in rat basophil leukemia assay and basophil activation. Heating of allergens prevented transport across human intestinal epithelial cells in a form capable of triggering basophil activation or T-cell activation.

CONCLUSION

Heat treatment reduces allergenicity of OVA and ovomucoid. This is partially a result of the enhanced gastrointestinal digestibility of heated OVA and the inability of heated OVA or ovomucoid to be absorbed in a form capable of triggering basophils.

Comparative study of in vitro digestibility of major allergen tropomyosin and other food proteins of Chinese mitten crab (Eriocheir sinensis)

BACKGROUND

China is the largest producer and consumer of aquatic products in the world; however, many people in China suffer from allergies upon consuming crab. Stability in simulated gastric fluid is regarded as an important parameter for the estimation of food allergenicity.

RESULTS

The digestive stability of allergenic protein tropomyosin (TM) and other food proteins from Chinese mitten crab in simulated gastric fluid (SGF) and simulated intestinal fluid (SIF) digestion assay systems was investigated and compared by SDS-PAGE, western blot and inhibition ELISA. In the SGF system, proteins such as the original band of myosin heavy chain (MHC) and actin were rapidly degraded within a short period of time, while TM was relatively resistant to pepsin digestion. In the SIF system, MHC was easily decomposed, while TM and actin were similarly resistant to digestion. Further study by IgE immunoblotting and inhibition ELISA using sera from crab-allergic patients indicated that allergenicity of TM was partially decreased.

CONCLUSION

Chinese mitten crab major allergen TM was resistant to pepsin while relatively susceptible to trypsin and chymotrypsin digestion. Both SDS-PAGE using purified TM and western blot using myofibrillar proteins indicated that the degradation pattern of TM by SGF and SIF was not affected by the presence of other myofibrillar proteins. Inhibition ELISA results revealed that proteinase digestion is effective in reducing the allergenicity of crab TM.

Allergenicity assessment of genetically modified cucumber mosaic virus (CMV) resistant tomato (Solanum lycopersicon)

Cucumber mosaic virus (CMV) has been identified as the causal agent of several disease epidemics in most countries of the world. Insect-mediated virus diseases, such as those caused by CMV, caused remarkable loss of tomato (Solanum lycopersicon) production in Taiwan. With expression of the CMV coat protein gene (Cmvcp) in a local popular tomato cultivar L4783, transgenic tomato line R8 has showed consistent CMV resistance through T(0) to T(8). In this report, the allergenicity of the CMV coat protein (CMV cp) expressed in transgenic tomato R8 was assessed by investigation of the expression of the transgene source of protein, sequence similarity with known allergens, and resistance to pepsin hydrolysis. There is no known account for either the CMV or its coat protein being an allergen. The result of a bioinformatic search also showed no significant homology between CMV cp and any known allergen. The pepsin-susceptible property of recombinant CMV cp was revealed by a simulated gastric fluid (SGF) assay. Following the most recent FAO/WHO decision tree, all results have indicated that CMV cp was a protein with low possibility to be an allergen and the transgenic tomato R8 should be considered as safe as its host.

Safety assessment and detection method of genetically modified Chinese Kale (Brassica oleracea cv. alboglabra )

Sporamins are tuberous storage proteins and account for 80% of soluble protein in sweet potato tubers with trypsin-inhibitory activity. The expression of sporamin protein in transgenic Chinese kale (line BoA 3-1) conferred insecticidal activity toward corn earworm [ Helicoverpa armigera (Hubner)] in a previous report. In this study, we present a preliminary safety assessment of transgenic Chinese kale BoA 3-1. Bioinformatic and simulated gastric fluid (SGF) analyses were performed to evaluate the allergenicity of sporamin protein. The substantial equivalence between transgenic Chinese kale and its wild-type host has been demonstrated by the comparison of important constituents. A reliable real-time polymerase chain reaction (PCR) detection method was also developed to control sample quality. Despite the results of most evaluations in this study being negative, the safety of sporamin in transgenic Chinese kale BoA 3-1 was uncluded because of the allergenic risk revealed by bioinformatic analysis.

Safety assessment of bacterial choline oxidase protein introduced in transgenic crops for tolerance against abiotic stress

Genetically modified crops have resistance to abiotic stress by introduction of choline oxidase protein. In the present study, the safety of choline oxidase protein derived from Arthrobacter globiformis was assessed for toxicity and allergenicity. The protein was stable at 90 degrees C for 1 h. Toxicity studies of choline oxidase in mice showed no significant difference (p > 0.05) from control in terms of growth, body weight, food consumption, and blood biochemical indices. Histology of gut tissue of mice fed protein showed normal gastric mucosal lining and villi in jejunum and ileum sections. Specific IgE in serum and IL-4 release in splenic culture supernatant were low in choline oxidase treated mice, comparable to control. Intravenous challenge with choline oxidase did not induce any adverse reaction, unlike ovalbumin group mice. Histology of lung tissues from choline oxidase sensitized mice showed normal airways, whereas ovalbumin-sensitized mice showed inflamed airways with eosinophilic infiltration and bronchoconstriction. ELISA carried out with food allergic patients' sera revealed no significant IgE affinity with choline oxidase. Also, choline oxidase did not show any symptoms of toxicity and allergenicity in mice.

Molluscan shellfish allergy

Food allergies affect approximately 3.5-4.0% of the worldwide population. Immediate-type food allergies are mediated by the production of IgE antibodies to specific proteins that occur naturally in allergenic foods. Symptoms are individually variable ranging from mild rashes and hives to life-threatening anaphylactic shock. Seafood allergies are among the most common types of food allergies on a worldwide basis. Allergies to fish and crustacean shellfish are very common. Molluscan shellfish allergies are well known but do not appear to occur as frequently. Molluscan shellfish allergies have been documented to all classes of mollusks including gastropods (e.g., limpet, abalone), bivalves (e.g., clams, oysters, mussels), and cephalopods (e.g., squid, octopus). Tropomyosin, a major muscle protein, is the only well-recognized allergen in molluscan shellfish. The allergens in oyster (Cra g 1), abalone (Hal m 1), and squid (Tod p 1) have been identified as tropomyosin. Cross-reactivity to tropomyosin from other molluscan shellfish species has been observed with sera from patients allergic to oysters, suggesting that individuals with allergies to molluscan shellfish should avoid eating all species of molluscan shellfish. Cross-reactions with the related tropomyosin allergens in crustacean shellfish may also occur but this is less clearly defined. Occupational allergies have also been described in workers exposed to molluscan shellfish products by the respiratory and/or cutaneous routes. With food allergies, one man's food may truly be another man's poison. Individuals with food allergies react adversely to the ingestion of foods and food ingredients that most consumers can safely ingest (Taylor and Hefle, 2001). The allergens that provoke adverse reactions in susceptible individuals are naturally occurring proteins in the specific foods (Bush and Hefle, 1996). Molluscan shellfish, like virtually all foods that contain protein, can provoke allergic reactions in some individuals.

Gastrointestinal digestion of food allergens: effect on their allergenicity

This paper reviews the in vitro digestion models developed to assess the stability digestion of food allergens, as well as the factors derived from the methodology and food structure that may affect the assay results. The adequacy of using the digestion stability of food allergens as a criterion for assessing potential allergenicity is also discussed. Data based on the traditional pepsin digestibility test in simulated gastric fluid are discussed in detail, with special attention to the influence of the pH and pepsin: allergen ratio in the pepsinolysis rate. This review points out the importance of using physiologically relevant in vitro digestion systems for evaluating digestibility of allergens. This would imply the sequential use of digestive enzymes in physiological concentrations, simulation of the stomach/small intestine environment (multi-phase models) with addition of surfactants such as phospholipids or bile salts, as well as the consideration of the gastrointestinal transit and the effect of the food matrices on the allergen digestion and subsequent absorption through the intestinal mucosa. In vitro gastrointestinal digestion protocols should be preferably combined with immunological assays in order to elucidate the role of large digestion-resistant fragments and the influence of the food matrix on the stimulation of the immune system.

Cys155 of 27 kDa maize γ-zein is a key amino acid to improve its in vitro digestibility

Twenty-seven kilodalton gamma-zein is a subclass of the maize zein storage proteins and, due to its localization at the protein body periphery, is critical to digestibility characteristics of all zeins. This protein had low in vitro digestibility, presumably due to its high Cys content (7.35 mol%) that is similar to the hard-to-digest analogous sorghum protein, gamma-kafirin. Therefore, each of the conserved disulfide-bonded Cys' was mutated to create C144A, C148A, C155A, and C156A maize gamma-zein mutants. The C155A showed a remarkable increase in digestibility to proteases - pepsin, chymotrypsin, and trypsin. A high conservation of this Cys among cereal gamma-prolamins indicates the utility of this finding.

Review of the development of methodology for evaluating the human allergenic potential of novel proteins

Safety assessment of novel proteins in genetic-engineered foods is a key component of the overall safety evaluation for these products. Since allergens are typically proteins, assessment of the potential allergenicity of the novel proteins in genetically engineered foods is critical. This article reviews methods available to assess the potential allergenicity of novel proteins, as well as problems and deficiencies in the existing methods. The role of bioinformatics and knowledge of allergenic epitopes in developing new approaches to this problem is discussed.

AlgPred: prediction of allergenic proteins and mapping of IgE epitopes

In this study a systematic attempt has been made to integrate various approaches in order to predict allergenic proteins with high accuracy. The dataset used for testing and training consists of 578 allergens and 700 non-allergens obtained from A. K. Bjorklund, D. Soeria-Atmadja, A. Zorzet, U. Hammerling and M. G. Gustafsson (2005) Bioinformatics, 21, 39-50. First, we developed methods based on support vector machine using amino acid and dipeptide composition and achieved an accuracy of 85.02 and 84.00%, respectively. Second, a motif-based method has been developed using MEME/MAST software that achieved sensitivity of 93.94 with 33.34% specificity. Third, a database of known IgE epitopes was searched and this predicted allergenic proteins with 17.47% sensitivity at specificity of 98.14%. Fourth, we predicted allergenic proteins by performing BLAST search against allergen representative peptides. Finally hybrid approaches have been developed, which combine two or more than two approaches. The performance of all these algorithms has been evaluated on an independent dataset of 323 allergens and on 101 725 non-allergens obtained from Swiss-Prot. A web server AlgPred has been developed for the predicting allergenic proteins and for mapping IgE epitopes on allergenic proteins (http://www.imtech.res.in/raghava/algpred/). AlgPred is available at www.imtech.res.in/raghava/algpred/.

Evaluation of the sensitization rates and identification of IgE-binding components in wild and genetically modified potatoes in patients with allergic disorders

Background

The potato is one of the most common types of genetically modified (GM) food. However, there are no published data evaluating the impact of genetic manipulations on the allergenicity of GM potatoes. To compare the allergenicity of GM potatoes with that of wild-type potatoes using in vivo and in vitro methods in adult allergy patients sensitized to potatoes.

Methods

A total of 1886 patients with various allergic diseases and 38 healthy controls participated in the study. Skin-prick testing and IgE-ELISA were carried out with extracts prepared from wild-type and GM potatoes. An ELISA inhibition test was used to confirm the binding specificity. IgE-binding components in extracts from the two types of potato were identified by SDS-PAGE and IgE-immunoblotting. The effects of digestive enzymes and heat on the allergenicity of the extracts was evaluated by preincubating the potatoes with or without simulated gastric and intestinal fluids in the absence or presence of heat.

Results

Positive responses (ratio of the wheal size induced by the allergen to that induced by histamine (A/H) ≥ 2+) to wild-type or GM potato extracts, as demonstrated by the skin-prick test, were observed in 108 patients (5.7%). Serum-specific IgE was detected in 0–88% of subjects who tested positively. ELISA inhibition tests indicated significant inhibition when extract from each type of potato was added. IgE-immunoblot analysis demonstrated the presence of 14 IgE-binding components within the wild-type potato and 9 within the GM potato. Furthermore, a common 45-kDa binding component that yielded similar IgE-binding patterns was noted in more than 80% of the reactions using sera from patients sensitized to wild-type or GM potato. Exposure to simulated gastric fluid and heat treatment similarly inhibited IgE binding by extracts from wild-type and GM potatoes, whereas minimal changes were obtained following exposure of the extracts to simulated intestinal fluid.

Conclusion

Our results strongly suggest that genetic manipulation of potatoes does not increase their allergenic risk. The sensitization rate of adult allergy patients to both types of extract was 5.7%, and a common major allergen (45 kDa) was identified.

Genetically modified plants and food hypersensitivity diseases: usage and implications of experimental models for risk assessment

The recent advances in biotechnology in the plant industry have led to increasing crop production and yield that in turn has increased the usage of genetically modified (GM) food in the human food chain. The usage of GM foods for human consumption has raised a number of fundamental questions including the ability of GM foods to elicit potentially harmful immunological responses, including allergic hypersensitivity. To assess the safety of foods derived from GM plants including allergenic potential, the US FDA, Food and Agriculture Organization of the United Nations (FAO)/World Health Organization (WHO), and the EU have developed approaches for evaluation assessment. One assessment approach that has been a very active area of research and debate is the development and usage of animal models to assess the potential allergenicity of GM foods. A number of specific animal models employing rodents, pigs, and dogs have been developed for allergenicity assessment. However, validation of these models is needed and consideration of the criteria for an appropriate animal model for the assessment of allergenicity in GM plants is required. We have recently employed a BALB/c mouse model to assess the potential allergenicity of GM plants. We have been able to demonstrate that this model is able to detect differences in antigenicity and identify aspects of protein post-translational modifications that can alter antigenicity. Furthermore, this model has also enabled us to examine the usage of GM plants as a therapeutic approach for the treatment of allergic diseases. This review discusses the current approaches to assess the allergenic potential of GM food and particularly focusing on the usage of animal models to determine the potential allergenicity of GM foods and gives an overview of our recent findings and implications of these studies.

Chestnut as a food allergen: identification of major allergens

To evaluate the clinical significance of chestnut as a food allergen in Korea, skin prick test and ELISA were done in 1,738 patients with respiratory allergies. To identify the IgE binding components, IgE-immunoblotting, 2D IgE-immunoblotting and MALDITOF were performed. To observe the effects of digestive enzymes and a boiling treatment, simulated gastric fluid (SGF) and simulated intestinal fluids (SIF) were incubated with chestnut extracts, and IgE-immunoblotting were then repeated. Skin prick test revealed that 56 (3.2%) patients showed more than 2+ of allergen to histamine ratio to chestnut. Among the 21 IgE binding components, 9 bands were found in more than 50% of the sera tested and the 24 kDa protein had the highest binding intensity. The amino acid sequence of the 24 kDa protein (pI 6.3) had homology with legume protein of oak tree. SGF, SIF and boiling treatment were able to suppress the IgE binding components. In conclusion, chestnut ingestion was shown to induce IgE mediated responses with a 3.2% sensitization rate. Twenty one IgE binding components and one new allergen (the 24 kDa protein) were identified. Digestive enzymes and boiling treatment were able to decrease the allergenic potency.

WebAllergen: a web server for predicting allergenic proteins

WebAllergen is a web server that predicts the potential allergenicity of proteins. The query protein will be compared against a set of prebuilt allergenic motifs that have been obtained from 664 known allergen proteins. The query will also be compared with known allergens that do not have detectable allergenic motifs. Moreover, users are allowed to upload their own allergens as alternative training sequences on which a new set of allergenic motifs will be built. The query sequences can also be compared with these motifs.

AVAILABILITY

http://weballergen.bii.a-star.edu.sg/

Stability of the major allergen Brazil nut 2S albumin (Ber e 1) to physiologically relevant in vitro gastrointestinal digestion

The major 2S albumin allergen from Brazil nuts, Ber e 1, was subjected to gastrointestinal digestion using a physiologically relevant in vitro model system either before or after heating (100 degrees C for 20 min). Whilst the albumin was cleaved into peptides, these were held together in a much larger structure even when digested by using a simulated phase 1 (gastric) followed by a phase 2 (duodenal) digestion system. Neither prior heating of Ber e 1 nor the presence of the physiological surfactant phosphatidylcholine affected the pattern of proteolysis. After 2 h of gastric digestion, approximately 25% of the allergen remained intact, approximately 50% corresponded to a large fragment of M(r) 6400, and the remainder comprised smaller peptides. During duodenal digestion, residual intact 2S albumin disappeared quickly, but a modified form of the 'large fragment' remained, even after 2 h of digestion, with a mass of approximately 5000 Da. The 'large fragment' comprised several smaller peptides that were identified, by using different MS techniques, as deriving from the large subunit. In particular, sequences corresponding to the hypervariable region (Q37-M47) and to another peptide (P42-P69), spanning the main immunoglobulin E epitope region of 2S albumin allergens, were found to be largely intact following phase 1 (gastric) digestion. They also contained previously identified putative T-cell epitopes. These findings indicate that the characteristic conserved skeleton of cysteine residues of 2S albumin family and, particularly, the intrachain disulphide bond pattern of the large subunit, play a critical role in holding the core protein structure together even after extensive proteolysis, and the resulting structures still contain potentially active B- and T-cell epitopes.

1,3-beta-glucanases as candidates in latex-pollen-vegetable food cross-reactivity

BACKGROUND

1,3-beta-glucanases (group 2 of pathogenesis-related proteins) are enzymes widely distributed among higher plants and have been recently proven to be significant allergens.

OBJECTIVE

The aim of this work was to study the potential implication of 1,3-beta-glucanases in cross-reactivities among latex, pollen and vegetable foods.

METHODS

The cDNA encoding the N-terminal domain (NtD) of Ole e 9, a major allergenic 1,3-beta-glucanase from olive pollen, was amplified by polymerase chain reaction and produced as a recombinant protein in Pichia pastoris (recombinant N-terminal domain, rNtD). Circular dichroism, ELISA, immunoblotting and immunoblotting inhibition experiments were carried out. Sera from olive pollen allergic patients and a rNtD-specific polyclonal antiserum were used.

RESULTS

The NtD of Ole e 9 has been produced at high yield in the yeast P. pastoris and possesses 1,3-beta-glucanase activity. The expressed polypeptide conserves IgE and IgG immunodominant epitopes of the whole Ole e 9. A rNtD-specific polyclonal antiserum and sera from olive pollen allergic patients allowed detection of IgG and IgE reactive peptidic epitopes common to 1,3-beta-glucanase Ole e 9 in extracts from ash and birch pollen, tomato, potato, bell-pepper, banana and latex.

CONCLUSION

rNtD and homologous glucanases are new molecules to be used in diagnostic protocols as they could help to identify allergic pollen patients who are at risk for developing allergic symptoms to fruits, vegetables and latex.

Safety assessment by in vitro digestibility and allergenicity of genetically modified maize with an amaranth 11S globulin

Prospective testing for allergenicity of proteins obtained from sources with no prior history of causing allergy has been difficult to perform. Thus, the objective of this work was to assess the food safety of genetically modified maize with an amaranth globulin protein termed amarantin. Transgenic maize lines evaluated showed, in relation to nontransgenic, 4-35% more protein and 0-44% higher contents of specific essential amino acids. Individual sequence analysis with known amino acid sequences, reported as allergens, showed that none of these IgE elicitors were identified in amarantin. Amarantin was digested within the first 15 min by Simulated Gastric Fluid treatment as observed by Western blot. Expressed amarantin did not induce important levels of specific IgE antibodies in BALB/c mice, as analyzed by ELISA. We conclude that the transgenic maize with amarantin is not an important allergenicity inducer, just as nontransgenic maize.

Public health issues related with the consumption of food obtained from genetically modified organisms

Genetically Modified Organisms (GMOs) are a fact of modern agriculture and a major field of discussion in biotechnology. As science incessantly achieves innovative and unexpected breakthroughs, new medical, political, ethical and religious debates arise over the production and consumption of transgenic organisms. Despite no described medical condition being directly associated with a diet including approved GM crops in large exposed populations such as 300,000,000 Americans and a billion Chinese, public opinion seems to look at this new technology with either growing concern or even disapproval. It is generally recognized that a high level of vigilance is necessary and highly desirable, but it should also be considered that GMOs are a promising new challenge for the III Millennium societies, with remarkable impact on many disciplines and fields related to biotechnology. To acquire a basic knowledge on GMO production, GM-food consumption, GMO interaction with humans and environment is of primary importance for risk assessment. It requires availability of clear data and results from rigorous experiments. This review will focus on public health risks related with a GMO-containing diet. The objective is to summarize state of the art research, provide fundamental technical information, point out problems and perspectives, and make available essential tools for further research. Are GMO based industries and GMO-derived foods safe to human health? Can we consider both social, ethical and public health issues by means of a constant and effective monitoring of the food chain and by a clear, informative labeling of the products? Which are the so far characterized or alleged hazards of GMOs? And, most importantly, are these hazards actual, potential or merely contrived? Several questions remain open; answers and solutions belong to science, to politics and to the personal opinion of each social subject.

Analysis of avocado allergen (Prs a 1) IgE-binding peptides generated by simulated gastric fluid digestion

BACKGROUND

Resistance to pepsin digestion has been claimed to be a characteristic of food allergens that can induce severe adverse reactions. Moreover, pepsin treatment is included in protocols to evaluate the potential allergenicity of transgenic foods. Allergenic plant class I chitinases, such as avocado Prs a 1, are the panallergens involved in the latex-fruit syndrome. Previous reports indicated their susceptibility to simulated gastric fluid (SGF) digestion.

OBJECTIVE

We sought to evaluate the IgE-binding capacity and the in vivo reactivity of the SGF products of the avocado allergen Prs a 1.

METHODS

Patients with a clinical history of latex-fruit allergy syndrome, a positive skin prick test (SPT) response to Prs a 1, and specific IgE to avocado were selected. Untreated and SGF-digested Prs a 1 samples were analyzed by means of IgE and IgG immunoblotting, IgE immunoblotting and ELISA-inhibition assays, and SPTs. Peptides from SGF-digested samples were fractionated by means of HPLC, characterized by N-terminal amino acid sequencing and matrix-assisted laser desorption/ionization analysis, and tested for in vivo reactivity with SPTs.

RESULTS

Neither protein staining nor IgE immunoblotting with a pool of sera from allergic patients resulted in the detection of any band after SDS-PAGE separation of an SGF-digested sample of Prs a 1. However, this sample showed a similar inhibitory potency to that of untreated Prs a 1 in both immunoblot- and ELISA-inhibition assays (up to 70% inhibition of the IgE binding to crude avocado extract) and induced positive SPT responses in 5 of 8 allergic patients. Peptides from SGF-digested Prs a 1 were separated by means of HPLC, and 4 of them reached more than 50% inhibition values when using avocado extract as the solid phase in ELISA-inhibition assays. Reactive peptides were located both in the N-terminal hevein-like domain and in the catalytic domain of Prs a 1. Those corresponding to the hevein-like domain (approximately 5100 d) produced positive SPT responses in 5 of 8 allergic patients, whereas 2 peptides located in the catalytic domain (approximately 1400 and 2500 d) were reactive in 2 or 3 of the 8 patients.

CONCLUSION

Prs a 1 was extensively degradated when subjected to SGF digestion. However, the resulting peptides, particularly those corresponding to the hevein-like domain, were clearly reactive both in vitro and in vivo.

One foot in the furrow: linkages between agriculture, plant pathology, and public health

Plant pathology is a field of biology that focuses on understanding the nature of disease in plants as well as on more practical aspects of preventing and controlling plant diseases in crop plants that are important to agriculture. Throughout history, plant diseases have had significant effects on human health and welfare. Several examples, in both historical and contemporary contexts, are presented in this review to show how plant pathogens, biotechnology, and farming practices have affected public health. Specific topics illustrating clear linkages between agriculture and human health include allergens in the environment, food-safety and agricultural practices, mycotoxigenic fungi, agrobioterrorism, and the biological control of plant diseases. The further argument is made that in order to monitor and ensure that good health and safety practices are maintained from "farm to fork," public health specialists may benefit from the resources and expertise of agricultural scientists.

Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE - binding linear epitopes of allergens

BACKGROUND

Transgenic proteins expressed by genetically modified food crops are evaluated for their potential allergenic properties prior to marketing, among others by identification of short identical amino acid sequences that occur both in the transgenic protein and allergenic proteins. A strategy is proposed, in which the positive outcomes of the sequence comparison with a minimal length of six amino acids are further screened for the presence of potential linear IgE-epitopes. This double track approach involves the use of literature data on IgE-epitopes and an antigenicity prediction algorithm.

RESULTS

Thirty-three transgenic proteins have been screened for identities of at least six contiguous amino acids shared with allergenic proteins. Twenty-two transgenic proteins showed positive results of six- or seven-contiguous amino acids length. Only a limited number of identical stretches shared by transgenic proteins (papaya ringspot virus coat protein, acetolactate synthase GH50, and glyphosate oxidoreductase) and allergenic proteins could be identified as (part of) potential linear epitopes.

CONCLUSION

Many transgenic proteins have identical stretches of six or seven amino acids in common with allergenic proteins. Most identical stretches are likely to be false positives. As shown in this study, identical stretches can be further screened for relevance by comparison with linear IgE-binding epitopes described in literature. In the absence of literature data on epitopes, antigenicity prediction by computer aids to select potential antibody binding sites that will need verification of IgE binding by sera binding tests. Finally, the positive outcomes of this approach warrant further clinical testing for potential allergenicity.

Children and genetically engineered food: potentials and problems

Changes in food production and dietary practices are occurring faster than our understanding of their potential impact on children's health. Traditionally, pediatric gastroenterologists have studied food with respect to its nutritive value and digestibility, its influence on metabolism, its growth-promoting characteristics, and its relationship to risk and severity of disease. Biotechnology is now expanding the science of food to include disease prevention and treatment, as well as the feeding of children on a global scale. Bioengineered ("genetically modified", or "transgenic") plants were initially developed to enhance the food supply by increasing crop yields. Such previously developed transgenic plants are now prevalent worldwide and appear in many processed food products. The implementation of the technology of genetic modulation of food plants has led to considerable fear, controversy, and confusion as the understanding of the technology is poor in the general population. This review presents an overview of genetically modified food crops and their potential unique benefits and risks to children's health. Political, economical, and ecological issues related to transgenic crops are not discussed.

Genetically engineered foods: implications for food allergy

The products of agricultural biotechnology, including such common foods as corn and soybeans, are already reaching the consumer marketplace. Consumer exposure to such foods is already fairly significant, particularly in the USA. Thus far, no reports exist regarding allergic reactions to the crops that have been approved for introduction into the food supply. These crops have been modified to only a minor extent by comparison with their traditional counterparts, and the level of expression of new and novel proteins is quite low. Thus, consumer exposure to these novel proteins is very low and unlikely to result in allergic sensitization. Nevertheless, foods produced through agricultural biotechnology must be assessed for safety, including their potential allergenicity, before they may be approved by worldwide regulatory agencies for entry into the food supply. However, the adequacy of the current approach to the assessment of the potential allergenicity of foods produced through agricultural biotechnology has been the subject of considerable scientific and regulatory debate.