Structural bioinformatic approaches to understand cross-reactivity

Structure-based epitope prediction and assessment of cross-reactivity of Myrmecia pilosula venom-specific IgE and recombinant Sol g proteins (Solenopsis geminata)

The global distribution of tropical fire ants (Solenopsis geminata) raises concerns about anaphylaxis and serious medical issues in numerous countries. This investigation focused on the cross-reactivity of allergen-specific IgE antibodies between S. geminata and Myrmecia pilosula (Jack Jumper ant) venom proteins due to the potential emergence of cross-reactive allergies in the future. Antibody epitope analysis unveiled one predominant conformational epitope on Sol g 1.1 (PI score of 0.989), followed by Sol g 2.2, Sol g 4.1, and Sol g 3.1. Additionally, Pilosulin 1 showed high allergenic potential (PI score of 0.94), with Pilosulin 5a (PI score of 0.797) leading in B-cell epitopes. The sequence analysis indicated that Sol g 2.2 and Sol g 4.1 pose a high risk of cross-reactivity with Pilosulins 4.1a and 5a. Furthermore, the cross-reactivity of recombinant Sol g proteins with M. pilosula-specific IgE antibodies from 41 patients revealed high cross-reactivity for r-Sol g 3.1 (58.53%) and r-Sol g 4.1 (43.90%), followed by r-Sol g 2.2 (26.82%), and r-Sol g 1.1 (9.75%). Therefore, this study demonstrates cross-reactivity (85.36%) between S. geminata and M. pilosula, highlighting the allergenic risk. Understanding these reactions is vital for the prevention of severe allergic reactions, especially in individuals with pre-existing Jumper Jack ant allergy, informing future management strategies.

Immunobiological properties and structure analysis of group 13 allergen from Blomia tropicalis and its IgE-mediated cross-reactivity

Blomia tropicalis is an important species of allergenic mite. Structurally related cross-reactive allergens are involved in pathogenesis of clinical symptoms. The present study focused on recombinant allergen rBlo t 13 from B. tropicalis, including investigation of its structure, immunological properties, IgE-mediated cross-reactivity. In this work, the prokaryotic expression plasmids pET-28(a)-Blo t 13, pET-28(a)-Der f 13, and pET-28(a)-Tyr p 13 were constructed, transformed into E. coli Rosetta (DE3) pLysS, and purified by nickel affinity chromatography, respectively. By using ELISA, the IgE-binding rates were detected for rBlo t 13 and its epitope peptides, as well as the cross-reactivity among rBlo t 13, rDer f 13, and rTyr p 13. The tertiary structure of rBlo t 13 was resolved using X-ray diffraction at 2.0 Å resolution. Using IgE-ELISA, the IgE binding rate of rBlo t 13 was 60 % with Blomia tropicalis-positive sera. In the experiments of ELISA for cross-reactivity with rBlo t 13 on solid phase, the inhibition rates were 65 %, 57 % and 63 % for rBlo t 13, rDer f 13, and rTyr p 13, respectively. The structure of Blo t 13 protein contains a β-barrel structure which is composed of 10 β strands and has 2 α helices at the end of the barrel. Comparison of the tertiary structures of rBlo t 13, rDer f 13, and rTyr p 13 revealed that the β-barrel structure is highly conserved, consistent with the alignment of amino acid sequences. We obtained the recombinant protein rBlo t 13, demonstrated its cross-reactivity with Der f 13 and Tyr p 13 due to their structural similarity.

The updated Structural Database of Allergenic Proteins (SDAP 2.0) provides 3D models for allergens and incorporated bioinformatics tools

Background

Allergenic proteins can cause IgE-mediated adverse reactions in sensitized individuals. Although the sequences of many allergenic proteins have been identified, bioinformatics data analysis with advanced computational methods and modeling is needed to identify the basis for IgE binding and cross-reactivity.

Objective

We aim to present the features and use of the updated Structural Database of Allergenic Proteins 2.0 (SDAP 2.0) webserver, a unique, publicly available resource to compare allergens using specially designed computational tools and new high-quality 3-D models for most known allergens.

Methods

Previously developed and novel software tools for identifying cross-reactive allergens using sequence and structure similarity are implemented in SDAP 2.0. A comprehensive set of high-quality 3-D models of most allergens was generated with the state-of-the-art AlphaFold 2 software. A graphics tool enables the interactive visualization of IgE epitopes on experimentally determined and modeled 3-D structures.

Results

A user can search for allergens similar to a given input sequence with the FASTA algorithm or the window-based World Health Organization/International Union of Immunological Societies (WHO/IUIS) guidelines on safety concerns of novel food products. Peptides similar to known IgE epitopes can be identified with the property distance tool and conformational epitopes by the Cross-React method. The updated database contains 1657 manually curated sequences including all allergens from the IUIS database, 334 experimentally determined X-ray or NMR structures, and 1565 3-D models. Each allergen/isoallergen is classified according to its protein family.

Conclusions

SDAP provides access to the steadily increasing information on allergenic structures and epitopes with integrated bioinformatics tools to identify and analyze their similarities. In addition to serving the research and regulatory community, it provides clinicians with tools to identify potential coallergies in a sensitive patient and can help companies to design hypoallergenic foods and immunotherapies.

Molecular allergology approach to allergic asthma

Allergic asthma is a frequently encountered and well described asthma phenotype. However, its precise mechanisms are less known. The tools for targeted selection of patients for an optimal response to intervention (prevention or treatment) are also lacking. Here we explore the potential of the molecular allergology approach to achieve a better understanding of allergic asthma mechanisms, a precise diagnosis and an optimal management of these patients.

Identification of relevant regions on structural and nonstructural proteins of Zika virus for vaccine and diagnostic test development: an in silico approach

Zika virus (ZIKV) is an arbovirus belonging to the Flaviviridae family and the genus Flavivirus. Infection with ZIKV causes a mild, self-limiting febrile illness called Zika fever. However, ZIKV infection has been recently associated with microcephaly and Guillain-Barré syndrome. Vaccines for the disease are a high priority of World Health Organization. Several studies are currently being conducted to develop a vaccine against ZIKV, but until now there is no licensed ZIKV vaccine. This study used a novel immunoinformatics approach to identify potential T-cell immunogenic epitopes present in the structural and nonstructural proteins of ZIKV. Fourteen T-cell candidate epitopes were identified on ZIKV structural and nonstructural proteins: pr^36-50; C^61-75; C^103-117; E^374-382; E^477-491; NS2a^90-104; NS2a^174-188; NS2a^179-193; NS2a^190-204; NS2a^195-209; NS2a^200-214; NS3^175-189; and NS4a^82-96; NS4a^99-113. Among these epitopes, only E^374-382 is a human leukocyte antigen (HLA) type I restricted epitope. All identified epitopes showed a low similarity with other important flaviviruses but had a high conservation rate among the ZIKV strains and a high population coverage rate. Therefore, these predicted T-cell epitopes are potential candidates targets for development of vaccines to prevent ZIKV infection.

A robust method for the estimation and visualization of IgE cross-reactivity likelihood between allergens belonging to the same protein family

Among the vast number of identified protein families, allergens emanate from relatively few families which translates to only a small fraction of identified protein families. In allergy diagnostics and immunotherapy, interactions between immunoglobulin E and allergens are crucial because the formation of an allergen-antibody complex is necessary for triggering an allergic reaction. In allergic diseases, there is a phenomenon known as cross-reactivity. Cross-reactivity describes a situation where an individual has produced antibodies against a particular allergenic protein, but said antibodies fail to discriminate between the original sensitizer and other similar proteins that usually belong to the same family. To expound the concept of cross-reactivity, this study examines ten protein families that include allergens selected specifically for the analysis of cross-reactivity. The selected allergen families had at least 13 representative proteins, overall folds that differ significantly between families, and include relevant allergens with various potencies. The selected allergens were analyzed using information on sequence similarities and identities between members of the families as well as reports on clinically relevant cross-reactivities. Based on our analysis, we propose to introduce a new A-RISC index (Allergens’–Relative Identity, Similarity and Cross-reactivity) which describes homology between two allergens belonging to the same protein family and is used to predict the likelihood of cross-reactivity between them. Information on sequence similarities and identities, as well as on the values of the proposed A-RISC index is used to introduce four categories describing a risk of a cross-reactive reaction, namely: high, medium-high, medium-low and low. The proposed approach can facilitate analysis in component-resolved allergy diagnostics, generation of avoidance guidelines for allergic individuals, and help with the design of immunotherapy.

Genome Editing Reveals Idiosyncrasy of CNGA2 Ion Channel-Directed Antibody Immunoreactivity Toward Oxytocin

Presynaptic cGMP-gated ion (CNG) channels positively or negatively modulate neurotransmitter secretion as well as the strength of synaptic transmission. Zebrafish cGMP-gated ion channel, CNGA2a (a.k.a. CNGA5), was previously reported to be specifically enriched in synaptic terminals of zebrafish oxytocin (OXT) neurons. This conclusion was based on immunoreactivity of a monoclonal antibody (mAb) clone L55/54, which was directed against the carboxy terminal tail of the CNGA2a. To study the role of CNGA2a in oxytocin neurons function, we generated zebrafish mutants of cnga2a, cnga2b and oxt genes using clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing. We show that mAb L55/54 specifically recognizes CNGA2a protein when expressed in heterologous cell culture system. Surprisingly, anti-CNGA2a immunoreactivity was not eliminated following knockout of either cnga2a, cnga2b or both. However, knockout of oxt resulted in total loss of anti-CNGA2a mAb immunoreactivity despite the lack of sequence and structural similarities between OXT and CNGA2a proteins. Our results provide a noteworthy lesson of differences in antibody immunoreactivity, which could only be revealed using specific genetic tools.

Genome Editing Reveals Idiosyncrasy of CNGA2 Ion Channel-Directed Antibody Immunoreactivity Toward Oxytocin

Presynaptic cGMP-gated ion (CNG) channels positively or negatively modulate neurotransmitter secretion as well as the strength of synaptic transmission. Zebrafish cGMP-gated ion channel, CNGA2a (a.k.a. CNGA5), was previously reported to be specifically enriched in synaptic terminals of zebrafish oxytocin (OXT) neurons. This conclusion was based on immunoreactivity of a monoclonal antibody (mAb) clone L55/54, which was directed against the carboxy terminal tail of the CNGA2a. To study the role of CNGA2a in oxytocin neurons function, we generated zebrafish mutants of cnga2a, cnga2b and oxt genes using clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing. We show that mAb L55/54 specifically recognizes CNGA2a protein when expressed in heterologous cell culture system. Surprisingly, anti-CNGA2a immunoreactivity was not eliminated following knockout of either cnga2a, cnga2b or both. However, knockout of oxt resulted in total loss of anti-CNGA2a mAb immunoreactivity despite the lack of sequence and structural similarities between OXT and CNGA2a proteins. Our results provide a noteworthy lesson of differences in antibody immunoreactivity, which could only be revealed using specific genetic tools.

Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity

The phenomenon of cross-reactivity between allergenic proteins plays an important role to understand how the immune system recognizes different antigen proteins. Allergen proteins are known to cross-react if their sequence comparison shows a high sequence identity which also implies that the proteins have a similar 3D fold. In such cases, linear sequence alignment methods are frequently used to predict cross-reactivity between allergenic proteins. However, the prediction of cross-reactivity between distantly related allergens continues to be a challenging task. To overcome this problem, we developed a new structure-based computational method, Cross-React, to predict cross-reactivity between allergenic proteins available in the Structural Database of Allergens (SDAP). Our method is based on the hypothesis that we can find surface patches on 3D structures of potential allergens with amino acid compositions similar to an epitope in a known allergen. We applied the Cross-React method to a diverse set of seven allergens, and successfully identified several cross-reactive allergens with high to moderate sequence identity which have also been experimentally shown to cross-react. Based on these findings, we suggest that Cross-React can be used as a predictive tool to assess protein allergenicity and cross-reactivity.

Availability and Implementation

: Cross-React is available at: http://curie.utmb.edu/Cross-React.html.

Contact

ssnegi@utmb.edu.

The conformational IgE epitope profile of soya bean allergen Gly m 4

BACKGROUND

Birch pollen-related soya allergy is mediated by Gly m 4. Conformational IgE epitopes of Gly m 4 are unknown.

OBJECTIVE

To identify the IgE epitope profile of Gly m 4 in subjects with birch pollen-related soya allergy utilizing an epitope library presented by Gly m 4-type model proteins.

METHODS

Sera from patients with (n = 26) and without (n = 19) allergy to soya as determined by oral provocation tests were studied. Specific IgE (Bet v 1/Gly m 4) was determined by ImmunoCAP. A library of 59 non-allergenic Gly m 4-type model proteins harbouring individual and multiple putative epitopes for IgE was tested in IgE binding assays. Primary, secondary and tertiary protein structures were assessed by mass spectrometry, circular dichroism and nuclear magnetic resonance spectroscopy.

RESULTS

All subjects were sensitized to Gly m 4 and Bet v 1. Allergen-specific serum IgE levels ranged from 0.94 to > 100 kU_A /L. The avidities of serum IgE were 5.06 ng (allergic) and 1.8 ng (tolerant) as determined by EC₅₀ for IgE binding to Gly m 4. 96% (46/48) of the protein variants bound IgE. Model proteins had Gly m 4-type conformation and individual IgE binding clustered in six major surface areas. Gly m 4-specific IgE binding could be inhibited to up to 80% by model proteins harbouring individual IgE binding sites in an epitope-wise equimolar fashion. Receiver operating curve analysis revealed an area under fitted curve of up to 0.88 for model proteins and 0.66 for Gly m 4.

CONCLUSION AND CLINICAL RELEVANCE

Serum levels and avidity of Gly m 4-specific IgE do not correlate with clinical reactivity to soya. Six IgE-binding areas, represented by 23 amino acids, account for more than 80% of total IgE binding capacity of Gly m 4. Model proteins may be used for epitope-resolved diagnosis to differentiate birch-soya allergy from clinical tolerance.

Position paper of the EAACI: food allergy due to immunological cross-reactions with common inhalant allergens

In older children, adolescents, and adults, a substantial part of all IgE-mediated food allergies is caused by cross-reacting allergenic structures shared by inhalants and foods. IgE stimulated by a cross-reactive inhalant allergen can result in diverse patterns of allergic reactions to various foods. Local, mild, or severe systemic reactions may occur already after the first consumption of a food containing a cross-reactive allergen. In clinical practice, clinically relevant sensitizations are elucidated by skin prick testing or by the determination of specific IgE in vitro. Component-resolved diagnosis may help to reach a diagnosis and may predict the risk of a systemic reaction. Allergy needs to be confirmed in cases of unclear history by oral challenge tests. The therapeutic potential of allergen immunotherapy with inhalant allergens in pollen-related food allergy is not clear, and more placebo-controlled studies are needed. As we are facing an increasing incidence of pollen allergies, a shift in sensitization patterns and changes in nutritional habits, and the occurrence of new, so far unknown allergies due to cross-reactions are expected.

Food allergies resulting from immunological cross-reactivity with inhalant allergens: Guidelines from the German Society for Allergology and Clinical Immunology (DGAKI), the German Dermatology Society (DDG), the Association of German Allergologists (AeDA) and the Society for Pediatric Allergology and Environmental Medicine (GPA)

A large proportion of immunoglobulin E (IgE)-mediated food allergies in older children, adolescents and adults are caused by cross-reactive allergenic structures. Primary sensitization is most commonly to inhalant allergens (e.g. Bet v 1, the major birch pollen allergen). IgE can be activated by various cross-reactive allergens and lead to a variety of clinical manifestations. In general, local and mild — in rare cases also severe and systemic — reactions occur directly after consumption of the food containing the cross-reactive allergen (e. g. plant-derived foods containing proteins of the Bet v 1 family). In clinical practice, sensitization to the primary responsible inhalant and/or food allergen can be detected by skin prick tests and/or in vitro detection of specific IgE. Component-based diagnostic methods can support clinical diagnosis. For individual allergens, these methods may be helpful to estimate the risk of systemic reactions. Confirmation of sensitization by oral provocation testing is important particulary in the case of unclear case history. New, as yet unrecognized allergens can also cause cross-reactions.

The therapeutic potential of specific immunotherapy (SIT) with inhalant allergens and their effect on pollen-associated food allergies is currently unclear: results vary and placebo-controlled trials will be necessary in the future. Pollen allergies are very common. Altogether allergic sensitization to pollen and cross-reactive food allergens are very common in our latitudes. The actual relevance has to be assessed on an individual basis using the clinical information.

Cite this as Worm M, Jappe U, Kleine-Tebbe J, Schäfer C, Reese I, Saloga J, Treudler R, Zuberbier T, Wassmann A, Fuchs T, Dölle S, Raithel M, Ballmer-Weber B, Niggemann B, Werfel T. Food allergies resulting from immunological cross-reactivity with inhalant allergens. Allergo J Int 2014; 23: 1–16 DOI 10.1007/s40629-014-0004-6

Occupational airborne exposure, specific sensitization and the atopic status: evidence of a complex interrelationship

Background

We have investigated the relationship between atopic status and long-term occupational exposure to latex proteins or methyl diethyl diisocyanate (MDI) as high and low molecular weight asthma-inducing agents, respectively.

Methods

This study is based on retrospective analyses of two groups of symptomatic outpatients: 184 healthcare workers with latex exposure and 156 workers with isocyanate (MDI) exposure. We analysed atopic and non-atopic subgroups according to exposure duration and the frequencies of specific sensitization.

Results

45% of the healthcare subgroup specifically sensitized to latex were atopic, whereas in the non-sensitized healthcare subgroup only 26% were atopic. On the other hand, subjects specifically sensitized to MDI were rarely atopic (only 15%), whereas in the subgroup non-sensitized to MDI atopy was present in 38%. After prolonged durations of exposure, the proportion of atopics was further elevated in most healthcare subgroups but it decreased in the MDI-exposed subjects.

Conclusions

We hypothesize that latex proteins as sensitizing agents might promote the development of atopy, whereas exposure to the low molecular weight MDI might inhibit the atopic status.

Group 10 allergens (tropomyosins) from house-dust mites may cause covariation of sensitization to allergens from other invertebrates

Group 10 allergens (tropomyosins) have been assumed to be a major cause of cross-reactivity between house-dust mites (HDMs) and other invertebrates. Despite all of the published data regarding the epidemiology, percent IgE binding and level of sensitization in the population, the role of tropomyosin as a cross-reactive allergen in patients with multiple allergy syndrome still remains to be elucidated. Homology between amino acid sequences reported in allergen databases of selected invertebrate tropomyosins was determined with Der f 10 as the reference allergen. The 66.9 and 54.4% identities were found with selected crustacean and insect species, respectively, whereas only 20.4% identity was seen with mollusks. A similar analysis was performed using reported B-cell IgE-binding epitopes from Met e1 (shrimp allergen) and Bla g7 (cockroach allergen) with other invertebrate tropomyosins. The percent identity in linear sequences was higher than 35% in mites, crustaceans, and cockroaches. The polar and hydrophobic regions in these groups were highly conserved. These findings suggest that tropomyosin may be a major cause of covariation of sensitization between HDMs, crustaceans, and some species of insects and mollusks.

Colonoscopic allergen provocation test with rBet v 1 in patients with pollen-associated food allergy

BACKGROUND

After consumption of fruits, nuts, and vegetables, several patients with pollen allergy experience gastrointestinal (GI) tract symptoms that are possibly caused by pollen-associated food allergy. The aim of this study was to evaluate the colonoscopic allergen provocation (COLAP) test using the recombinant birch pollen allergen Bet v 1 (rBet v 1) for in vivo diagnosis of pollen-associated food allergy manifesting in the GI tract.

METHODS

Thirty-four patients with a history of adverse reactions to food, GI tract symptoms, and birch pollen pollinosis and five healthy controls underwent COLAP test. Twenty minutes after endoscopic challenge of the cecal mucosa with rBet v 1, the mucosal wheal and flare reaction was registered semiquantitatively, and tissue biopsy specimens were examined for eosinophil mucosal activation.

RESULTS

The mucosal reaction to rBet v 1 was correlated with the presence of pollinosis (P = 0.004), history of adverse reaction to Bet v 1-associated food allergens (P = 0.001), and tissue eosinophils' activation (P < 0.001). A wheal and flare reaction in the COLAP test was observed in 13 of 16 patients (81%) with a history of GI tract symptoms associated with the ingestion of Bet v 1-related foods and in four of 18 (22%) patients with a negative history (P < 0.001). The control group did not develop visible mucosal reactions to rBet v 1. Systemic anaphylactic reactions did not occur.

CONCLUSIONS

The mucosal administration of rBet v 1 by COLAP test provides a new diagnostic tool that might support the diagnosis of Bet v 1-associated food allergy manifesting in the GI tract.

Suggested improvements for the allergenicity assessment of genetically modified plants used in foods

Genetically modified (GM) plants are increasingly used for food production and industrial applications. As the global population has surpassed 7 billion and per capita consumption rises, food production is challenged by loss of arable land, changing weather patterns, and evolving plant pests and disease. Previous gains in quantity and quality relied on natural or artificial breeding, random mutagenesis, increased pesticide and fertilizer use, and improved farming techniques, all without a formal safety evaluation. However, the direct introduction of novel genes raised questions regarding safety that are being addressed by an evaluation process that considers potential increases in the allergenicity, toxicity, and nutrient availability of foods derived from the GM plants. Opinions vary regarding the adequacy of the assessment, but there is no documented proof of an adverse effect resulting from foods produced from GM plants. This review and opinion discusses current practices and new regulatory demands related to food safety.

An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces

Recent progress in the biochemical classification and structural determination of allergens and allergen-antibody complexes has enhanced our understanding of the molecular determinants of allergenicity. Databases of allergens and their epitopes have facilitated the clustering of allergens according to their sequences and, more recently, their structures. Groups of similar sequences are identified for allergenic proteins from diverse sources, and all allergens are classified into a limited number of protein structural families. A gallery of experimental structures selected from the protein classes with the largest number of allergens demonstrate the structural diversity of the allergen universe. Further comparison of these structures and identification of areas that are different from innocuous proteins within the same protein family can be used to identify features specific to known allergens. Experimental and computational results related to the determination of IgE binding surfaces and methods to define allergen-specific motifs are highlighted.

Factors influencing the incidence and prevalence of food allergy

Food allergy is an increasing problem in Europe and elsewhere and severe reactions to food are also becoming more common. As food allergy is usually associated with other forms of allergic sensitisation it is likely that many risk factors are common to all forms of allergy. However the potential severity of the disease and the specific public heath measures required for food allergy make it important to identify the specific risk factors for this condition. Food allergy is unusual in that it often manifests itself very early in life and commonly remits with the development of tolerance. Hypotheses that explain the distribution of food allergy include specific genetic polymorphisms, the nature of the allergens involved and the unique exposure to large quantities of allergen through the gut. Progress has been made in developing more specific and testable hypotheses but the evidence for any of these is still only preliminary. Further collaborative research is required to develop an appropriate public health response to this growing problem.

Linear IgE-epitope mapping and comparative structural homology modeling of hazelnut and English walnut 11S globulins

Allergic reactions to walnuts and hazelnuts can be serious. The 11S globulins (legumins) have been identified as important allergens in these and other nuts and seeds. Here we identify the linear IgE-binding epitopes of walnut and hazelnut 11S globulins, and generate 3D 11S globulin models to map the locations of the epitopes for comparison to other allergenic homologues. Linear IgE-epitope mapping was performed by solid-phase overlapping 15-amino acid peptides probed with IgE from pooled allergic human sera. Several walnut (Jug r 4) and hazelnut (Cor a 9) 11S globulin peptides with reactivity to patient IgE were identified. Comparative alignment with cashew (Ana o 2), peanut (Ara h 3), and soybean G1 (Gly m 6.0101) and G2 (Gly m 6.0201) allergenic homologues revealed several shared allergenic 'hot spots'. Homology modeling was performed based on the atomic structure of the soybean glycinin. Surface map comparisons between the tree nut and peanut homologues revealed structural motifs that could be important for IgE elicitation and binding and show that, contrary to predictions, the reactive epitopes are widely distributed throughout the monomeric subunits, both internally and externally, including regions occluded by quaternary subunit association. These findings reveal structural features that may be important to allergenicity and cross-reactivity of this protein class.

Genomic characterization of putative allergen genes in peach/almond and their synteny with apple

Background

Fruits from several species of the Rosaceae family are reported to cause allergic reactions in certain populations. The allergens identified belong to mainly four protein families: pathogenesis related 10 proteins, thaumatin-like proteins, lipid transfer proteins and profilins. These families of putative allergen genes in apple (Mal d 1 to 4) have been mapped on linkage maps and subsequent genetic study on allelic diversity and hypoallergenic traits has been carried out recently. In peach (Prunus persica), these allergen gene families are denoted as Pru p 1 to 4 and for almond (Prunus dulcis)Pru du 1 to 4. Genetic analysis using current molecular tools may be helpful to establish the cause of allergenicity differences observed among different peach cultivars. This study was to characterize putative peach allergen genes for their genomic sequences and linkage map positions, and to compare them with previously characterized homologous genes in apple (Malus domestica).

Results

Eight Pru p/du 1 genes were identified, four of which were new. All the Pru p/du 1 genes were mapped in a single bin on the top of linkage group 1 (G1). Five Pru p/du 2 genes were mapped on four different linkage groups, two very similar Pru p/du 2.01 genes (A and B) were on G3, Pru p/du 2.02 on G7,Pru p/du 2.03 on G8 and Pru p/du 2.04 on G1. There were differences in the intron and exon structure in these Pru p/du 2 genes and in their amino acid composition. Three Pru p/du 3 genes (3.01–3.03) containing an intron and a mini exon of 10 nt were mapped in a cluster on G6. Two Pru p/du 4 genes (Pru p/du 4.01 and 4.02) were located on G1 and G7, respectively. The Pru p/du 1 cluster on G1 aligned to the Mal d 1 clusters on LG16; Pru p/du 2.01A and B on G3 to Mal d 2.01A and B on LG9; the Pru p/du 3 cluster on G6 to Mal d 3.01 on LG12; Pru p/du 4.01 on G1 to Mal d 4.03 on LG2; and Pru p/du 4.02 on G7 to Mal d 4.02 on LG2.

Conclusion

A total of 18 putative peach/almond allergen genes have been mapped on five linkage groups. Their positions confirm the high macro-synteny between peach/almond and apple. The insight gained will help to identify key genes causing differences in allergenicity among different cultivars of peach and other Prunus species.

Characteristic motifs for families of allergenic proteins

The identification of potential allergenic proteins is usually done by scanning a database of allergenic proteins and locating known allergens with a high sequence similarity. However, there is no universally accepted cut-off value for sequence similarity to indicate potential IgE cross-reactivity. Further, overall sequence similarity may be less important than discrete areas of similarity in proteins with homologous structure. To identify such areas, we first classified all allergens and their subdomains in the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/) to their closest protein families as defined in Pfam, and identified conserved physicochemical property motifs characteristic of each group of sequences. Allergens populate only a small subset of all known Pfam families, as all allergenic proteins in SDAP could be grouped to only 130 (of 9318 total) Pfams, and 31 families contain more than four allergens. Conserved physicochemical property motifs for the aligned sequences of the most populated Pfam families were identified with the PCPMer program suite and catalogued in the webserver MotifMate (http://born.utmb.edu/motifmate/summary.php). We also determined specific motifs for allergenic members of a family that could distinguish them from non-allergenic ones. These allergen specific motifs should be most useful in database searches for potential allergens. We found that sequence motifs unique to the allergens in three families (seed storage proteins, Bet v 1, and tropomyosin) overlap with known IgE epitopes, thus providing evidence that our motif based approach can be used to assess the potential allergenicity of novel proteins.

The property distance index PD predicts peptides that cross-react with IgE antibodies

Similarities in the sequence and structure of allergens can explain clinically observed cross-reactivities. Distinguishing sequences that bind IgE in patient sera can be used to identify potentially allergenic protein sequences and aid in the design of hypo-allergenic proteins. The property distance index PD, incorporated in our Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/), may identify potentially cross-reactive segments of proteins, based on their similarity to known IgE epitopes. We sought to obtain experimental validation of the PD index as a quantitative predictor of IgE cross-reactivity, by designing peptide variants with predetermined PD scores relative to three linear IgE epitopes of Jun a 1, the dominant allergen from mountain cedar pollen. For each of the three epitopes, 60 peptides were designed with increasing PD values (decreasing physicochemical similarity) to the starting sequence. The peptides synthesized on a derivatized cellulose membrane were probed with sera from patients who were allergic to Jun a 1, and the experimental data were interpreted with a PD classification method. Peptides with low PD values relative to a given epitope were more likely to bind IgE from the sera than were those with PD values larger than 6. Control sequences, with PD values between 18 and 20 to all the three epitopes, did not bind patient IgE, thus validating our procedure for identifying negative control peptides. The PD index is a statistically validated method to detect discrete regions of proteins that have a high probability of cross-reacting with IgE from allergic patients.

Recent advances in the understanding of egg allergens: basic, industrial, and clinical perspectives

The emergence of egg allergy has had both industrial and clinical implications. In industrialized countries, egg allergy accounts for one of the most prevalent food hypersensitivities, especially in children. Atopic dermatitis represents the most common clinical manifestation in infancy; however, the range of clinical signs is broad and encompasses life-threatening anaphylaxis. The dominant egg allergens are proteins and are mainly present in the egg white, for example, ovalbumin, ovomucoid, ovotransferrin, and lysozyme. However, egg yolk also displays low-level allergenicity, for example, alpha-livetin. Strict avoidance of the offending food remains the most common recommendation for egg-allergic individuals. Nevertheless, the omnipresence of egg-derived components in prepackaged or prepared foods makes it difficult. Therefore, more efficient preventive approaches are investigated to protect consumers from inadvertent exposure and ensuing adverse reactions. On the one hand, commercial kits have become readily available that allow for the detection of egg contaminants at trace levels. On the other hand, attempts to produce hypoallergenic egg-containing products through food-processing techniques have met with promising results, but the approach is limited due to its potentially undesirable effects on the unique functional and sensory attributes of egg proteins. Therefore, the development of preventive or curative strategies for egg allergy remains strongly warranted. Pilot studies have suggested that oral immunotherapy (IT) with raw or cooked preparations of egg may represent a safe alternative, immediately available to allergic subjects, but remains applicable to only nonanaphylactic patients. Due to the limitations of conventional IT, novel forms of immunotherapy are sought based on information obtained from the molecular characterization of major egg allergens. In the past decade, promising approaches to the treatment and prevention of egg allergy have been explored and include, among others, the production of hypoallergenic recombinant egg proteins, the development of customized peptides, and bacterial-mediated immunotherapy. Nonspecific approaches have also been evaluated, and preliminary trials with the use of probiotic bacteria have yielded encouraging results. The current understanding of egg allergens offers novel approaches toward the making of food products safe for human consumption and the development of efficient immunotherapeutic strategies.

Multivariate statistical analysis of large-scale IgE antibody measurements reveals allergen extract relationships in sensitized individuals

BACKGROUND

Many allergenic sources are reportedly cross-reactive because of protein structural similarities. Although several aggregations are well characterized, no holistic mapping of IgE reactivity has hitherto been reported.

OBJECTIVE

The aim of this study was to disclose relevant associations within a large set of allergen preparations, as revealed by specific IgE antibody levels in blood sera of multireactive human donors.

METHODS

A dataset of recorded IgE antibody serum concentrations of 1011 nonidentifiable multireactive individuals (devoid of clinical records) to 89 allergen extracts was compiled for in silico analysis. Various algorithms were used to identify specific multivariate dependencies between the IgE antibody levels.

RESULTS

Exhaustive cluster analysis demonstrates that IgE antibody responses to the 89 extracts can be aggregated into 12 stable formations. These clusters hold both well-known relationships, unexpected patterns, and unknown patterns, the latter categories being exemplified by the coclustering of wasp and certain seafood and a clear differentiation among pollen allergens.

CONCLUSION

Identified relationships within several well-known groups of cross-reactive allergen extracts confirm the applicability of dedicated multivariate data analysis within the allergology field. Moreover, some of the unexpected IgE reactivity associations in sensitized human subjects might help in identifying new relationships with potential importance to allergy.

CLINICAL IMPLICATIONS

Although clinical implications from this study should be validated in subsequent investigations with documentation on symptoms included, we believe this seminal approach is a key step toward the development of new analysis tools for interpretation of allergy data generated by using high-throughput recording systems.

Comparison of conventional FASTA identity searches with the 80 amino acid sliding window FASTA search for the elucidation of potential identities to known allergens

Food and Agriculture Organization/World Health Organization (FAO/WHO) recommended that IgE cross-reactivity between a transgenic protein and allergen be considered when there is >or= 35% identity over a sliding "window" of 80 amino acids. Our objective was to evaluate the false positive and negative rates observed using the FAO/WHO versus conventional FASTA analyses. Data used as queries against allergen databases and analyzed to assess false positive rates included: 1,102 hypothetical corn ORFs; 907 randomly selected proteins; 89 randomly selected corn proteins; and 97 corn seed proteins. To evaluate false negative rates of both methods: Bet v 1a along with several crossreacting fruit/vegetable allergens and a bean alpha-amylase inhibitor were used as queries. Both methods were also evaluated for their ability to detect a putative nonallergenic test protein containing a sequence derived from Ara h 1. FASTA versions 3.3t0 and 3.4t25 were utilized. Data indicate a conventional FASTA analysis produced fewer false positives and equivalent false negative rates. Conventional FASTA versus sliding window derived E scores were generally more significant. Results suggest a conventional FASTA search provides more relevant identity to the query protein and better reflects the functional similarities between proteins. It is recommended that the conventional FASTA analysis be conducted to compare identities of proteins to allergens.

Structural insight into protein T1, the non-allergenic member of the Bet v 1 allergen family-An in silico analysis

BACKGROUND

Bet v 1 family is a large group of allergens present in pollen and plant-derived foods. They show similarity in sequence and 3D structure, properties often correlated to their cross-reactivity. protein T1 is a naturally occurring non-allergenic member of this group, which, in spite of having 35-85% sequence similarity, does not exhibit antibody-mediated cross-reactivity with other members of the Bet v 1 allergen family. This protein has been suggested to be a good model to study structural features critically needed for allergenicity and cross-reactivity.

OBJECTIVE

Structural bioinformatic approach to analyze the properties of protein T1 in relation to allergenicity and cross-reactivity.

METHODS

A 3D model of protein T1 was constructed by the homology modeling procedure and was compared to the structure of Bet v 1 with special reference to conservation, solvent accessibility and electrostatic properties of the residues across the antigenic surface.

RESULTS

The over-all fold of the homology model of T1 resembles that of the Bet v 1 group. The change in the solvent-accessible surface of the IgG (BV16)-binding residues has been quantified to be 75%. Comparing the allergenically potent dimer structure of Bet v 1 (predicted structure available in MSD of European Bioinformatics Institute), with the non-allergenic monomer, the BV16-binding surface and the p-loop seem to be of less importance for Bet v 1-mediated in vivo cross-linking of IgE. Instead, we think that other surface-exposed conserved patches are more significant. Absence of cross-reactivity between T1 and Bet v 1 comes from the lack of surface conservation leading to changes in the conformational as well as electrostatic properties. On the other hand, certain changes in the sequence, that might hinder dimerization of this protein, may result in the loss of allergenicity. Lastly, our structural docking experiment shows that protein T1 can bind two molecules of Brassinolide ligands like the other members of the Bet v 1 family.

CONCLUSION

Lack of dimerization and surface conservation might explain the reason why T1 is neither allergenic, nor cross-reactive to Bet v 1 group, although this protein can be a potential carrier for brassinosteroids.

Lipid transfer protein allergy: primary food allergy or pollen/food syndrome in some cases

PURPOSE OF REVIEW

To summarize recent findings on non-specific lipid transfer proteins in food allergy, with a specific focus on the localization, stability and route of sensitization.

RECENT FINDINGS

Plant non-specific lipid transfer proteins are major food allergens, especially in the Mediterranean area. They have been identified as allergens in a number of foods and the list grows ever longer. As non-specific lipid transfer proteins are considered to be "true" food allergens that sensitize directly via the gastrointestinal tract their stability during food processing and gastric digestion has been studied in more detail. In addition, several groups have tried to determine the sensitization patterns of lipid transfer protein-reactive patients, to determine and possibly clarify the observed geographical differences in sensitization. Different sensitization routes (via the respiratory tract or even transdermally) have been suggested.

SUMMARY

As the structure and molecular properties of non-specific lipid transfer proteins are resolved and more purified non-specific lipid transfer proteins become available for diagnostic purposes, detailed studies on the sensitization pattern and route are becoming feasible. Continuing studies on the pattern of lipid transfer protein sensitization will give more insight into the development and possible treatment of lipid transfer protein-related food allergy.

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.