Evaluation of available IgE-binding epitope data and its utility in bioinformatics

Epitope Mapping of Lysozyme Using the Chinese Egg-Allergic Sera at Both Pooled and Individual Levels

To accurately map the B-cell linear epitopes of lysozyme (LYS) in eggs, five bioinformatics tools were first used to obtain the mimotopes. Afterward, based on the Chinese egg-allergic sera samples screened by the indirect enzyme-linked immunosorbent, the epitopes possessing the capability of binding to IgG/IgE were mapped at both pooled and individual levels by using overlapping peptides covering the complete amino acid sequence of LYS. Six B-cell linear epitopes and two dominant B-cell linear epitopes that could bind to LYS-sIgG were mapped for the first time. Seven IgE-binding epitopes and three dominant IgE-binding epitopes were also obtained. Furthermore, AA31-34 and AA88-91 were the shared dominant epitopes of LYS-sIgG and LYS-sIgE at pooled and individual levels. Overall, the mapped B-cell linear epitopes filled in the gaps in the study of LYS epitopes, and the results may provide theoretical support for the following immunotherapy of egg allergy.

Gastrointestinal digestion of hazelnut allergens on molecular level: Elucidation of degradation kinetics and resistant immunoactive peptides using mass spectrometry

SCOPE

Allergy to hazelnut seeds ranks among the most prevalent food allergies in Europe. The aim of this study was to elucidate the gastrointestinal digestion of hazelnut allergens on molecular level.

METHODS AND RESULTS

Hazelnut flour was digested in vitro following the Infogest consensus model. For six allergenic proteins, the time-dependent course of digestion was monitored by SDS-PAGE and HPLC-MS/MS, and degradation products were characterized by a bottom-up proteomics approach. Depending on the molecular structure, a specific biochemical fate was observed for each allergen, and degradation kinetics were traced back to the peptide level. 1183 peptides were characterized, including 130 peptides that carry known IgE-binding epitopes and may represent sensitizers for hazelnut allergy. The kinetics of peptide formation and degradation were determined by label-free quantification and follow a complex multi-stage mechanism.

CONCLUSION

We present a comprehensive survey on the gastrointestinal digestion of a relevant allergenic food on level of the peptidome, including the first systematic characterization and quantification of degradation products. This provides information on the differential resistance of plant food allergens and their structural elements undergoing digestion and forms the basis for a deeper understanding of the molecular principles responsible for sensitization to food allergy.

Preparation of monoclonal antibodies against gamma-type phospholipase A2 inhibitors and immunodetection of these proteins in snake blood

Background

The gamma-type phospholipase A₂ inhibitor (PLIγ) is a natural protein commonly found in snake serum, which can neutralize pathophysiological effects of snake venom phospholipases A₂. Therefore, this protein is a potential candidate to the development of a novel antivenom. To the best of our knowledge, there is no antibody currently available for PLIγ identification and characterization.

Methods

Bioinformatics prediction of epitope using DNAStar software was performed based on the sequence of Sinonatrix annularis PLIγ (SaPLIγ). The best epitope ¹⁵¹CPVLRLSNRTHEANRNDLIKVA¹⁷² was chosen and synthesized, and then conjugated to keyhole limpet hemocyanin and bovine serum albumin for use as an immunogen and plate-coating antigen, respectively.

Results

Eighteen IgG anti-PLIγ mAb hybridoma cell strains were obtained, and all the mAbs had positive interaction with recombinant His6-PLIγ and natural SaPLIγ. Moreover, the mAb from 10E9 strain was also successfully used for the immunodetection of other snake serum PLIγs. cDNA sequence alignment of those PLIγs from different snake species showed that their epitope segments were highly homologous.

Conclusions

The successful preparation of anti-PLIγmAb is significant for further investigation on the relationship between the structure and function of PLIγs, as well as the interaction between PLIγs and PLA₂s.

Bioinformatic screening and detection of allergen cross-reactive IgE-binding epitopes

Protein allergens can be related by cross‐reactivity. Allergens that share relevant sequence can cross‐react, those lacking sufficient similarity in their IgE antibody‐binding epitopes do not cross‐react. Cross‐reactivity is based on shared epitopes that is based on shared sequence and higher level structure (charge and shape). Epitopes are important in predicting cross‐reactivity potential and may provide the potential to establish criteria that identify homology among allergens. Selected allergen's IgE‐binding epitope sequences were used to determine how the FASTA algorithm could be used to identify a threshold of significance. A statistical measure (expectation value, E‐value) was used to identify a threshold specific to identifying cross‐reactivity potential. Peanut Ara h 1 and Ara h 2, shrimp tropomyosin Pen a 1, and birch tree pollen allergen, Bet v 1 were sources of known epitopes. Each epitope or set of epitopes was inserted into random amino acid sequence to create hypothetical proteins used as queries to an allergen database. Alignments with allergens were noted for the ability to match the epitope's source allergen as well as any cross‐reactive or other homologous allergens. A FASTA expectation value range (1 × 10⁻⁵–1 × 10⁻⁶) was identified that could act as a threshold to help identify cross‐reactivity potential.

Application of phage peptide display technology for the study of food allergen epitopes

Phage peptide display technology has been used to identify IgE-binding mimotopes (mimics of natural epitopes) that mimic conformational epitopes. This approach is effective in the characterization of those epitopes that are important for eliciting IgE-mediated allergic responses by food allergens and those that are responsible for cross-reactivity among allergenic food proteins. Application of this technology will increase our understanding of the mechanisms whereby food allergens elicit allergic reactions, will facilitate the discovery of diagnostic reagents and may lead to mimotope-based immunotherapy.

Phage display peptide libraries in molecular allergology: from epitope mapping to mimotope-based immunotherapy

Identification of allergen epitopes is a key component in proper understanding of the pathogenesis of type I allergies, for understanding cross-reactivity and for the development of mimotope immunotherapeutics. Phage particles have garnered recognition in the field of molecular allergology due to their value not only in competitive immunoscreening of peptide libraries but also as immunogenic carriers of allergen mimotopes. They integrate epitope discovery technology and immunization functions into a single platform. This article provides an overview of allergen mimotopes identified through the phage display technique. We discuss the contribution of phage display peptide libraries in determining dominant B-cell epitopes of allergens, in developing mimotope immunotherapy, in understanding cross-reactivity, and in determining IgE epitope profiles of individual patients to improve diagnostics and individualize immunotherapy. We also discuss the advantages and pitfalls of the methodology used to identify and validate the mimotopes.

Using patient serum to epitope map soybean glycinins reveals common epitopes shared with many legumes and tree nuts

Soybean consumption is increasing in many Western diets; however, recent reviews suggest that the prevalence of soy allergy can be as high as 0.5% for the general population and up to 13% for children. The immunoglobulin-E (IgE) binding of sera from six soy-sensitive adult human subjects to soybean proteins separated by 2D gel electrophoresis was studied. Synthetic peptide sets spanning the mature glycinin subunit A2 and A3 primary sequences were used to map the IgE-binding regions. Putative epitopes identified in this study were also localized on glycinin hexamer models using bioinformatics software. We identified linear IgE-binding epitopes of the major storage protein Gly m 6 by screening individual soy-sensitive patient sera. These epitopes were then further analysed by 3D in silico model localization and compared to other plant storage protein epitopes. Web-based software applications were also used to study the ability to accurately predict epitopes with mixed results. A total of nine putative IgE-binding epitopes were identified in the glycinin A3 (A3.1-A3.3) and A2 (A2.1-A2.6) subunits. Most patients' sera IgE bound to only one or two epitopes, except for one patient's serum which bound to four different A2 epitopes. Two epitopes (A3.2 and A2.4) overlapped with a previously identified epitope hot spot of 11S globulins from other plant species. Most epitopes were predicted to be exposed on the surface of the 3D model of the glycinin hexamer. Amino acid sequence alignments of soybean acidic glycinins and other plant globulins revealed one dominant epitope hot spot among the four reported hot spots. This study may be helpful for future development of soy allergy immunotherapy and diagnosis.

Structure of allergens and structure based epitope predictions

The structure determination of major allergens is a prerequisite for analyzing surface exposed areas of the allergen and for mapping conformational epitopes. These may be determined by experimental methods including crystallographic and NMR-based approaches or predicted by computational methods. In this review we summarize the existing structural information on allergens and their classification in protein fold families. The currently available allergen-antibody complexes are described and the experimentally obtained epitopes compared. Furthermore we discuss established methods for linear and conformational epitope mapping, putting special emphasis on a recently developed approach, which uses the structural similarity of proteins in combination with the experimental cross-reactivity data for epitope prediction.

Analysis of the effects of polymorphism on pollen profilin structural functionality and the generation of conformational, T- and B-cell epitopes

An extensive polymorphism analysis of pollen profilin, a fundamental regulator of the actin cytoskeleton dynamics, has been performed with a major focus in 3D-folding maintenance, changes in the 2-D structural elements, surface residues involved in ligands-profilin interactions and functionality, and the generation of conformational and lineal B- and T-cell epitopes variability.

Our results revealed that while the general fold is conserved among profilins, substantial structural differences were found, particularly affecting the special distribution and length of different 2-D structural elements (i.e. cysteine residues), characteristic loops and coils, and numerous micro-heterogeneities present in fundamental residues directly involved in the interacting motifs, and to some extension these residues nearby to the ligand-interacting areas. Differential changes as result of polymorphism might contribute to generate functional variability among the plethora of profilin isoforms present in the olive pollen from different genetic background (olive cultivars), and between plant species, since biochemical interacting properties and binding affinities to natural ligands may be affected, particularly the interactions with different actin isoforms and phosphoinositides lipids species.

Furthermore, conspicuous variability in lineal and conformational epitopes was found between profilins belonging to the same olive cultivar, and among different cultivars as direct implication of sequences polymorphism. The variability of the residues taking part of IgE-binding epitopes might be the final responsible of the differences in cross-reactivity among olive pollen cultivars, among pollen and plant-derived food allergens, as well as between distantly related pollen species, leading to a variable range of allergy reactions among atopic patients. Identification and analysis of commonly shared and specific epitopes in profilin isoforms is essential to gain knowledge about the interacting surface of these epitopes, and for a better understanding of immune responses, helping design and development of rational and effective immunotherapy strategies for the treatment of allergy diseases.

Epitope mapping of the major allergen from Atlantic cod in Spanish population reveals different IgE-binding patterns

SCOPE

IgE-epitope mapping of allergens reveal important information about antigen components involved in allergic reactions. The peptide-based microarray immunoassay has been used to map epitopes of some food allergens. We developed a peptide microarray immunoassay to map allergenic epitopes in parvalbumin from Atlantic cod (Gad m 1), the most consumed cod species in Spain.

METHODS AND RESULTS

Sera from 13 fish-allergic patients with specific IgE to cod parvalbumin were used. A library of overlapping peptides was synthesized, representing the primary sequence of Gad m 1. Peptides were used to analyze allergen-specific IgE antibodies in patient sera. 100% of the patients recognized one antigenic region of 15 amino acids in length in Gad m 1. This region only partially correlated with one of the three antigenic determinants of Gad c 1 (Allergen M), parvalbumin from Baltic cod (Gadus callarias). In the 3D model of the protein, this region was located on the surface of the protein.

CONCLUSION

We have identified a relevant antigenic region in Gad m 1. This epitope could be considered as a severity marker and provides additional information to improve fish allergy diagnosis and the design of safe immunotherapeutic tools.

Analysis of conformational and sequential IgE epitopes on the major allergen Cry j 2 of Japanese cedar (Cryptomeria japonica) pollen in humans by using monoclonal antibodies for Cry j 2

PURPOSE

Japanese cedar (Cryptomeria japonica; CJ) pollinosis is a type I allergy induced by CJ pollen, and Cry j 2 is one of the major allergens in this pollen. In a previous study, we analyzed IgE epitopes on Cry j 2 in humans by using synthetic peptides. The main purpose of this study was to identify B-cell epitopes on Cry j 2 in patients with CJ pollinosis by using monoclonal antibodies (mAbs) for Cry j 2.

METHODS

We used ELISA with mAbs for the epitope analysis. Sera samples were collected from 80 patients with CJ pollinosis, and allergenic epitopes for mAbs and human IgE were identified using ELISA with synthetic peptides. The importance of the epitopes for human IgE was analyzed using an inhibition ELISA.

RESULTS

Four independent epitopes (epitope #1, #2, #3, and #4) were identified on Cry j 2 with the use of mAbs. Epitope #3 and #4, corresponding to peptides No. 25 and No. 33, respectively, were newly determined as epitopes for mAbs and human IgE. Inhibition ELISA showed that not only epitope #2 (sequential) but epitope #1 (conformational) may play an important role in the CJ pollinosis.

CONCLUSIONS

Our results revealed 4 epitopes, including two new ones, on Cry j 2. We also found that inhibition ELISA with appropriate mAbs could be a viable method of evaluating the importance of the conformational and sequential epitopes for human IgE. These results are beneficial for the development of safer and more efficient therapeutic strategies for treating CJ pollinosis.

Interpreting the biological relevance of bioinformatic analyses with T-DNA sequence for protein allergenicity

Global regulatory agencies require bioinformatic sequence analysis as part of their safety evaluation for transgenic crops. Analysis typically focuses on encoded proteins and adjacent endogenous flanking sequences. Recently, regulatory expectations have expanded to include all reading frames of the inserted DNA. The intent is to provide biologically relevant results that can be used in the overall assessment of safety. This paper evaluates the relevance of assessing the allergenic potential of all DNA reading frames found in common food genes using methods considered for the analysis of T-DNA sequences used in transgenic crops. FASTA and BLASTX algorithms were used to compare genes from maize, rice, soybean, cucumber, melon, watermelon, and tomato using international regulatory guidance. Results show that BLASTX for maize yielded 7254 alignments that exceeded allergen similarity thresholds and 210,772 alignments that matched eight or more consecutive amino acids with an allergen; other crops produced similar results. This analysis suggests that each nontransgenic crop has a much greater potential for allergenic risk than what has been observed clinically. We demonstrate that a meaningful safety assessment is unlikely to be provided by using methods with inherently high frequencies of false positive alignments when broadly applied to all reading frames of DNA sequence.

IgE epitopes of intact and digested Ara h 1: a comparative study in humans and rats

BACKGROUND

Allergen epitope characterization provides valuable information useful for the understanding of proteins as food allergens. It is believed that IgE epitopes in general are conformational, nevertheless, for food allergens known to sensitize through the gastrointestinal tract linear epitopes have been suggested to be of great importance.

OBJECTIVE

The aim of this study was to identify IgE specific epitopes of intact and digested Ara h 1, and to compare epitope patterns between humans and rats.

METHODS

Sera from five peanut allergic patients and five Brown Norway rats were used to identify intact and digested Ara h 1-specific IgE epitopes by competitive immunoscreening of a phage-displayed random hepta-mer peptide library using polyclonal IgE from the individual sera. The resulting peptide sequences were mapped on the surface of a three-dimensional structure of the Ara h 1 molecule to mimic epitopes using a computer-based algorithm.

RESULTS

Patients as well as rats were shown to have individual IgE epitope patterns. All epitope mimics were conformational and found to cluster into three different areas of the Ara h 1 molecule. Five epitope motifs were identified by patient IgE, which by far accounted for most of the eluted peptide sequences. Epitope patterns were rather similar for both intact and digested Ara h 1 as well as for humans and rats.

CONCLUSIONS

Individual patient specific epitope patterns have been identified for the major allergen Ara h 1. IgE binding epitopes have been suggested as biomarkers for persistency and severity of food allergy, wherefore recognition of particular epitope patterns or motifs could be a valuable tool for prevention, diagnosis, and treatment of food allergy.

Digested Ara h 1 loses sensitizing capacity when separated into fractions

The major peanut allergen Ara h 1 is an easily digestible protein under physiological conditions. The present study revealed that pepsin digestion products of Ara h 1 retained the sensitizing potential in a Brown Norway rat model, while this sensitizing capacity was lost by separating the digest into fractions by gel permeation chromatography. Protein chemical analysis showed that the peptide composition as well as the aggregation profiles of the fractions of Ara h 1 digest differed from that of the whole pool. These results indicate that the sensitizing capacity of digested Ara h 1 is a consequence of the peptides being in an aggregated state resembling the intact molecule or that most peptides of the digests need to be present in the same solution, having a synergistic or adjuvant effect and thereby augmenting the immune response against other peptides.

Bioinformatics and the allergy assessment of agricultural biotechnology products: industry practices and recommendations

Bioinformatic tools are being increasingly utilized to evaluate the degree of similarity between a novel protein and known allergens within the context of a larger allergy safety assessment process. Importantly, bioinformatics is not a predictive analysis that can determine if a novel protein will ''become" an allergen, but rather a tool to assess whether the protein is a known allergen or is potentially cross-reactive with an existing allergen. Bioinformatic tools are key components of the 2009 CodexAlimentarius Commission's weight-of-evidence approach, which encompasses a variety of experimental approaches for an overall assessment of the allergenic potential of a novel protein. Bioinformatic search comparisons between novel protein sequences, as well as potential novel fusion sequences derived from the genome and transgene, and known allergens are required by all regulatory agencies that assess the safety of genetically modified (GM) products. The objective of this paper is to identify opportunities for consensus in the methods of applying bioinformatics and to outline differences that impact a consistent and reliable allergy safety assessment. The bioinformatic comparison process has some critical features, which are outlined in this paper. One of them is a curated, publicly available and well-managed database with known allergenic sequences. In this paper, the best practices, scientific value, and food safety implications of bioinformatic analyses, as they are applied to GM food crops are discussed. Recommendations for conducting bioinformatic analysis on novel food proteins for potential cross-reactivity to known allergens are also put forth.

Early recovery from cow's milk allergy is associated with decreasing IgE and increasing IgG4 binding to cow's milk epitopes

BACKGROUND

The dynamics and balance of allergen-specific IgE, IgG4, and IgA binding might contribute to the development of tolerance in patients with cow's milk allergy (CMA). Profiling of antibody binding to cow's milk (CM) protein epitopes might help in predicting the natural history of allergy.

OBJECTIVE

We sought to investigate differences in IgE, IgG4, and IgA binding to CM epitopes over time between patients with early recovery or with persisting CMA.

METHODS

We studied serum samples at the time of diagnosis (mean age, 7 months), 1 year later, and at follow-up (mean age, 8.6 years) from 11 patients with persisting IgE-mediated CMA at age 8 to 9 years and 12 patients who recovered by age 3 years. We measured the binding of IgE, IgG4, and IgA antibodies to sequential epitopes derived from 5 major CM proteins with a peptide microarray-based immunoassay. We analyzed the data with a novel image-processing method together with machine learning prediction.

RESULTS

IgE epitope-binding patterns were stable over time in patients with persisting CMA, whereas binding decreased in patients who recovered early. Binding patterns of IgE and IgG4 overlapped. Among patients who recovered early, the signal of IgG4 binding increased and that of IgE decreased over time. IgE and IgG4 binding to a panel of alpha(s1)-, alpha(s2)-, beta-, and kappa-casein regions predicted outcome with significant accuracy.

CONCLUSIONS

Attaining tolerance to CM is associated with decreased epitope binding by IgE and a concurrent increase in corresponding epitope binding by IgG4.

The role of immunoglobulin E-binding epitopes in the characterization of food allergy

PURPOSE OF REVIEW

Allergen-specific immunoglobulin E (IgE) antibodies play a central role in food allergic reactions. IgE epitope mapping of food allergens may provide information regarding patient's clinical history and contribute to food allergy diagnosis/prognosis. The goal of this article is to review recent developments in the methods for IgE epitope mapping and the role of IgE-binding epitopes in the characterization of food allergy.

RECENT FINDINGS

Recent studies have suggested a potential role for sequential IgE-binding epitopes as biomarkers for characterizing various phenotypes of food allergy. Studies of allergens in milk, peanut, egg and wheat have shown a correlation between IgE sequential epitope diversity and patients' allergy severity or persistence. Several informative epitopes in milk allergens have been identified as candidate biomarkers to predict the development of tolerance to milk. However, limitations with current methods of IgE-binding epitope identification need to be addressed before they can be applied in the diagnosis/prognosis of food allergy.

SUMMARY

IgE epitope mapping has the potential to become an additional tool for the diagnosis/prognosis of food allergy and lead to a better understanding of the pathogenesis and tolerance induction of food allergy.

Characteristic amino acid distribution around segments unique to allergens

Epitopes are located at the surface of allergens with which antibodies specifically bind. On the assumption that fragments unique to allergens have common, characteristic amino acid sequences, we compared the amino acid sequences of allergens with those of non-allergens. Segments around fragments unique to allergens showed wavelet-like distributions for several amino acids. Charged residues, alanine and glycine had positive peaks at the centre of the unique segments with small valleys on both sides, while aromatic residues, proline and cysteine showed the inverse distribution. Furthermore, the wavelet-like distribution of amino acids could be represented by a universal distribution function together with an index characterizing the intensity of the wavelet. Using the universal distribution function and the novel index of amino acids, we developed a simple method for extracting segments and fragments that are unique to allergens. The significance of the universal distribution function and the novel index is also discussed, by comparing the plot of the allergen-unique fragments index and dynamic fluctuation in the three dimensional structure of birch pollen allergen as both a single molecule and a complex with the corresponding antibody.

Scientific advancement of novel protein allergenicity evaluation: an overview of work from the HESI Protein Allergenicity Technical Committee (2000-2008)

The safety assessment of genetically modified crops includes the evaluation for potential allergenicity. The current 'state-of-the-science' utilizes a weight of evidence approach, as outlined by the Codex Alimentarius commission (Alinorm 03/34 A), recognizing no single endpoint is predictive of the allergenic potential of a novel protein. This approach evaluates: whether the gene source is allergenic, sequence similarity to known allergens, and protein resistance to pepsin in vitro. If concerns are identified, serological studies may be necessary to determine if a protein has IgE binding similar to known allergens. Since there was a lack of standardized/validated methods to conduct the allergenicity assessment, a committee was assembled under the International Life Sciences Institute Health and Environmental Sciences Institute to address this issue. Over the last eight years, the Protein Allergenicity Technical Committee has convened workshops and symposia with allergy experts and government authorities to refine methods that underpin the assessment for potential protein allergenicity. This publication outlines this ongoing effort, summarizing workshops and formal meetings, referencing publications, and highlighting outreach activities. The purpose is to (1) outline 'the state-of-the-science' in predicting protein allergenicity in the context of current international recommendations for novel protein safety assessment, and (2) identify approaches that can be improved and future research needs.

Relevance of IgE binding to short peptides for the allergenic activity of food allergens

BACKGROUND

Analysis of IgE antibody binding to epitopes provides information for food allergy diagnosis and management and construction of hypoallergenic candidate vaccines, but the contribution of sequential epitopes to functionally relevant IgE binding is not fully understood.

OBJECTIVES

We sought to study the impact of IgE-binding peptides described as major sequence epitopes in the literature on IgE-binding capacity of 2 selected food allergens.

METHODS

IgE-binding peptides of the food allergens Ara h 2 (peanut) and Pen a 1 (shrimp) were identified. Synthetic soluble peptides representing the identified sequences were assessed for their capacity to inhibit IgE binding to the parent allergens by means of ELISA and in mediator release assay. The IgE-binding capacity of unfolded recombinant (r) Ara h 2 was analyzed. A hybrid tropomyosin carrying the IgE-binding regions of Pen a 1 grafted into the structural context of the nonallergenic mouse tropomyosin was applied in ELISA inhibition experiments and ImmunoCAP analysis.

RESULTS

Although IgE-binding peptides representing sections of the allergen sequences were detected, no relevant capacity to inhibit the IgE binding to the parent allergen in ELISA or basophil activation test was observed. Unfolded rAra h 2 showed reduced IgE-binding capacity compared with folded rAra h 2 and failed to elicit mediator release. Hybrid tropomyosin bound less IgE than rPen a 1 in ImmunoCAP analysis and revealed marginal inhibitory capacity.

CONCLUSION

Peptides identified as major sequence epitopes on Pen a 1 and Ara h 2 show little contribution to the IgE binding of the allergens studied.

Safety assessment of biotechnology products for potential risk of food allergy: implications of new research

Food allergy is a potential risk associated with use of transgenic proteins in crops. Currently, safety assessment involves consideration of the source of the introduced protein, in silico amino acid sequence homology comparisons to known allergens, physicochemical properties, protein abundance in the crop, and, when appropriate, specific immunoglobulin E binding studies. Recently conducted research presented at an International Life Sciences Institute/Health and Environmental Sciences Institute-hosted workshop adds to the scientific foundation for safety assessment of transgenic proteins in five areas: structure/activity, serum screening, animal models, quantitative proteomics, and basic mechanisms. A web-based tool is now available that integrates a database of allergenic proteins with a variety of computational tools which could be used to improve our ability to predict allergenicity based on structural analysis. A comprehensive strategy and model protocols have been developed for conducting meaningful serum screening, an extremely challenging process. Several animal models using oral sensitization with adjuvant and one dermal sensitization model have been developed and appear to distinguish allergenic from non-allergenic food extracts. Data presented using a mouse model suggest that pepsin resistance is indicative of allergenicity. Certain questions remain to be addressed before considering animal model validation. Gel-free mass spectrometry is a viable alternative to more labor-intensive approaches to quantitative proteomics. Proteomic data presented on four nontransgenic varieties of soy suggested that if known allergen expression in genetically modified crops falls within the range of natural variability among commercial varieties, there appears to be no need to test further. Finally, basic research continues to elucidate the etiology of food allergy.

Resolution and identification of major peanut allergens using a combination of fluorescence two-dimensional differential gel electrophoresis, Western blotting and Q-TOF mass spectrometry

Peanut allergy is triggered by several proteins known as allergens. In this study, the complexity the peanut allergome is investigated with proteomic tools. The strength of this investigation resides in combining the high-resolving power and reproducibility of fluorescence two-dimensional differential gel electrophoresis with specific immunological detection as well as polypeptide sequencing by high-resolution mass spectrometry. Matching of the peanut proteins in 2D gels was achieved by differential labelling whereby peanut proteins and purified allergens (Ara h 1, Ara h 2 or Ara h 3/4) were run on the same gel. Ten protein spots on a mass line of ca. 63-68 kDa were likely to correspond to Ara h 1. Two doublets on two different mass lines at ca. 16 and 18 kDa matched with purified allergen Ara h 2. The basic and acidic sub-units of Ara h 3/4 were observed at masses of ca. 25 kDa and 40-45 kDa, respectively. Subsequently the antibody-binding capacity of spots corresponding to peanut allergens was investigated by Western blotting of 2D gels using antibodies (IgY) raised against Ara h 1, Ara h 2 and the recombinant 40 kDa sub-unit of Ara h 3/4. Final confirmation of the identity of the protein spots matched after 2D electrophoresis and identified by Western blotting was obtained by in-gel digestion of protein spots and analysis by quadrupole time-of-flight mass spectrometry. By using the method developed in our work, the location and identification of two different isoforms of the allergen Ara h 1, the allergen Ara h 2 and six isoforms of the allergen Ara h 3/4 in 2D peanut protein maps was established.

Potential, pitfalls, and prospects of food allergy diagnostics with recombinant allergens or synthetic sequential epitopes

This article aims to critically review developments in food allergy diagnostics with regard to the verification of specific IgE antibodies and the identification of the responsible allergens. Results of IgE-binding tests with food extracts are hampered by cross-reactive proteins, low-quality test agents, or both. Specificity can be increased by defining adequate cutoff values, whereas sensitivity can be improved by using high-quality test agents. IgE-binding tests with purified allergens enabled reliable quantification of allergen-specific IgE titers, with higher levels found in individuals with food allergy compared with individuals without food allergy. However, the overlap in individual test reactivity between allergic and nonallergic subjects complicates interpretation. Recombinant allergens and synthetic sequential epitopes enabled detection of sensitization profiles, with IgE specific to several allergens and substructures now being suggested as markers of severity, persistence, or both. However, high-power quantitative studies with larger numbers of patients are required to confirm these markers. IgE-binding tests merely indicate sensitization, whereas the final proof of clinical relevance still relies on family/case history, physical examinations, and provocation tests. Novel technologies promise superior diagnostics. Microarray technology permits simultaneous measurement of multiple IgE reactivities regarding specificity, abundance, reactivity, or interaction. Improved functional tests might enable reliable estimation of the clinical relevance of IgE sensitizations at justifiable expenses.

EVALLER: a web server for in silico assessment of potential protein allergenicity

Bioinformatics testing approaches for protein allergenicity, involving amino acid sequence comparisons, have evolved appreciably over the last several years to increased sophistication and performance. EVALLER, the web server presented in this article is based on our recently published 'Detection based on Filtered Length-adjusted Allergen Peptides' (DFLAP) algorithm, which affords in silico determination of potential protein allergenicity of high sensitivity and excellent specificity. To strengthen bioinformatics risk assessment in allergology EVALLER provides a comprehensive outline of its judgment on a query protein's potential allergenicity. Each such textual output incorporates a scoring figure, a confidence numeral of the assignment and information on high- or low-scoring matches to identified allergen-related motifs, including their respective location in accordingly derived allergens. The interface, built on a modified Perl Open Source package, enables dynamic and color-coded graphic representation of key parts of the output. Moreover, pertinent details can be examined in great detail through zoomed views. The server can be accessed at http://bioinformatics.bmc.uu.se/evaller.html.

Proteomics-based approach to detect and identify major allergens in processed peanuts by capillary LC-Q-TOF (MS/MS)

An MS-based method, combining reversed-phase capillary liquid chromatography (capillary LC) with quadrupole time-of-flight tandem mass spectrometry (nano-ESI Q-TOF MS/MS), was developed with the aim of identifying a set of peptides that can function as markers for peanut allergens. Emphasis was given to the identification of the three major peanut allergens Ara h 1, Ara h 2, and Ara h 3, because these proteins are considered to represent >30% of the total protein content of peanut and are directly relevant for the allergenic potential of this food. The analytical data obtained were used to perform databank searching in combination with de novo sequencing and led to the identification of a multitude of sequence tags for all three peanut allergens. Food processing such as roasting of peanuts is known to affect the stability of proteins and was shown to influence the detection of allergen sequence tags. The analysis of raw and roasted peanuts allowed the identification of five peanut-specific sequence tags that can function as markers of the specific allergenic proteins. For Ara h 1, two peptide markers were proposed, namely, VLEENAGGEQEER (m/z 786.88, charge 2+) and DLAFPGSGEQVEK (m/z 688.85, charge 2+), whereas for Ara h 2 only one peptide, RQQWELQGDR (m/z 439.23, charge 3+), was found to satisfy the required conditions. For Ara h 3, the two specific peptides, SPDIYNPQAGSLK (m/z 695.35, charge 2+) and SQSENFEYVAFK (m/z 724.84, charge 2+), were selected. Other peptides have been proposed as indicative for food processing.

Practical and predictive bioinformatics methods for the identification of potentially cross-reactive protein matches

A bioinformatics comparison of proteins introduced into food crops through genetic engineering provides a mechanism to identify those proteins that may present an increased risk of allergic reactions for individuals with existing allergies. The goal is to identify proteins that are known to be allergens or are so similar to an allergen that they may induce allergic cross-reactions. Three comparative approaches have traditionally been used, or considered for safety evaluations. One identifies any short (6-8) amino acid segment of the protein that exactly matches a known allergen sequence. The second is an overall primary sequence comparison using Basic Local Alignment Search Tool (BLAST) or FASTA to find matches of greater than 35% identity over 80 amino acids. The third is based on 3-D prediction programs to identify 3-D similarities that might predict potential cross-reactivity. The utility of each of these approaches was debated in the bioinformatics workshop. The consensus agreement from the expert workshop participants was that the short-segment match (e. g., 6-8 amino acids) provides an unacceptably high rate of false positive matches and an uncertain rate of true positive matches, and was not particularly useful for an allergenicity evaluation performed in the context of comprehensive safety evaluation. There was no consensus regarding the most appropriate bioinformatics method, an acceptable scoring criteria for triggering closer examination subsequent to a positive match, or an acceptable scoring mechanism for ranking the utility of the various 3-D approaches that were discussed during the workshop. However, the general consensus was that the most practical approach at this time is to evaluate primary sequence identities to known allergens using either FASTA or BLAST. While there was good agreement that identities of greater than 35% over 80 or more amino acids (recommended by Codex in 2003) is quite conservative, the conclusion was that additional data or studies would be needed to justify changing this criterion as there is some evidence that some individuals sensitized to proteins in evolutionarily conserved protein families may experience cross-reactions to proteins sharing approximately 40% identity.