Identification of Potentially Cross-Reactive Peanut-Lupine Proteins by Computer-Assisted Search for Amino Acid Sequence Homology

Sequence-Based Prediction of Plant Allergenic Proteins: Machine Learning Classification Approach

This Article proposes a novel chemometric approach to understanding and exploring the allergenic nature of food proteins. Using machine learning methods (supervised and unsupervised), this work aims to predict the allergenicity of plant proteins. The strategy is based on scoring descriptors and testing their classification performance. Partitioning was based on support vector machines (SVM), and a k-nearest neighbor (KNN) classifier was applied. A fivefold cross-validation approach was used to validate the KNN classifier in the variable selection step as well as the final classifier. To overcome the problem of food allergies, a robust and efficient method for protein classification is needed.

Identification of a vicilin-like major allergen from Prosopis juliflora exhibiting cross- reactivity with legume food allergens

BACKGROUND

Prosopis juliflora is a clinically relevant allergic sensitizer worldwide and shares cross-reactivity with allergens from several tree pollen and food. The present study aims to purify and immunobiochemically characterize a major allergen from Prosopis pollen. The allergen was further investigated for its cross-reactivity with legume allergens.

METHODS

Prosopis extract was fractionated by Q Sepharose and Superdex 75 gel filtration column to purify the allergen. Specific IgE against purified protein was estimated via ELISA and immunoblot. The protein was subjected to mass spectrometric analysis. Glycan characterization was performed by Schiff staining and lectin binding assay followed by deglycosylation studies. The functional activity of the purified protein was evaluated by the basophil activation test. Cross-reactivity was assessed by inhibition studies with legume extracts.

RESULTS

A 35 kDa protein was purified and showed 75% IgE reactivity with the patients' sera by ELISA and immunoblot. Glycan characterization of protein demonstrated the presence of terminal glucose and mannose residues. A reduction of 40% and 27% in IgE binding was observed upon chemical and enzymatic deglycosylation of the protein, respectively. The glycoprotein allergen upregulates the expression of CD203c on basophils which was significantly reduced upon deglycosylation, signifying its biological ability to activate the effector cells. The identified protein shared significant homology with Lup an 1 from the lupine bean. Immunoblot inhibition studies of the purified allergen with legume extracts underlined high cross-reactive potential. Complete inhibition was observed with peanut and common bean, while up to 70% inhibition was demonstrated with soy, black gram, chickpea, and lima bean.

CONCLUSION

A 35 kDa vicilin-like major allergen was isolated from P. juliflora. The protein possesses glycan moieties crucial for IgE binding and basophil activation. Furthermore, the purified protein shows homology with Lup an 1 and exhibits cross-reactivity with common edible legume proteins.

A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins

Traditional food allergen identification mainly relies on in vivo and in vitro experiments, which often needs a long period and high cost. The artificial intelligence (AI)-driven rapid food allergen identification method has solved the above mentioned some drawbacks and is becoming an efficient auxiliary tool. Aiming to overcome the limitations of lower accuracy of traditional machine learning models in predicting the allergenicity of food proteins, this work proposed to introduce deep learning model-transformer with self-attention mechanism, ensemble learning models (representative as Light Gradient Boosting Machine (LightGBM) eXtreme Gradient Boosting (XGBoost)) to solve the problem. In order to highlight the superiority of the proposed novel method, the study also selected various commonly used machine learning models as the baseline classifiers. The results of 5-fold cross-validation showed that the area under the receiver operating characteristic curve (AUC) of the deep model was the highest (0.9578), which was better than the ensemble learning and baseline algorithms. But the deep model need to be pre-trained, and the training time is the longest. By comparing the characteristics of the transformer model and boosting models, it can be analyzed that, each model has its own advantage, which provides novel clues and inspiration for the rapid prediction of food allergens in the future.

Lupine allergens: Clinical relevance, molecular characterization, cross-reactivity, and detection strategies

Lupine is commonly utilized as a technological food and ingredient in a great variety of processed products (snacks, bakery, meat, and dairy products) principally owing to its nutritional value and technological properties. However, its ingestion, even at trace amounts (in the range of mg protein per kg of food), can lead to severe adverse reactions in allergic individuals. Lupine belongs to the Leguminosae family, having the conglutins (α-, β-, δ-, and γ-) as allergens, among other proteins. Cross-sensitization of lupine-sensitized individuals with other legume species, mainly peanut, can occur, but the associated clinical reactivity is still unclear. The protection of the sensitized individuals should depend on an avoidance diet, which should rely on the compliance of food labeling and, as such, on their verification by analytical methods. Food processing, such as heat treatments, has an important influence on the structural properties of lupine proteins, altering their detectability and allergenicity. In this review, different aspects related with lupine allergy are described, namely, the overall prevalence, clinical relevance, diagnosis, and treatment. The characterization of lupine allergens and their potential cross-reactivity with other legumes are critically discussed. The effects of food matrix, processing, and digestibility on lupine proteins, as well as the available analytical tools for detecting lupine at trace levels in foods, are also herein emphasized.

Thyroid Autoimmunity and Lichen

Lichen planus (LP) and lichen sclerosus (LS) are cutaneous-mucous diseases with uncertain epidemiology. Current data, which are likely to be underestimated, suggest a prevalence in the general population of 0.1-4% for cutaneous LP, 1.27-2.0% for oral LP, and 0.1-3.3% for LS. While etiology of lichen is still unknown, clinical and histological evidence show an (auto)immune pathogenesis. Association of lichen with autoimmune thyroid disease (AITD) has been investigated in few studies. This association appears better defined in the case of LS, while is more controversial for LP. In both situations, the frequency of the association is higher in females. We review the available literature on the correlation between the different types of lichen and AITD, and the literature on the genetic risk factors which are shared by both conditions. Such data suggest that a common pathogenic mechanism could be the cause for co-occurrence of lichen and AITD, at least in some patients. Additionally, analyzing literature data and in continuity with our previous work on other autoimmune diseases, we suggest that molecular mimicry could trigger both diseases, and thus explain their co-occurrence.

IgE sensitization to lupine in bakers - cross-reactivity or co-sensitization to wheat flour?

BACKGROUND

Food allergy to lupine has frequently been reported in patients allergic to peanut or soy, and cross-reactivity between these legumes is known. Moreover, respiratory allergy to lupine has been described after inhalation, mostly at workplaces. Our aim was to study the frequency of lupine sensitization in European bakers with suspected bakers' allergy. Furthermore, associations between sensitizations to lupine and other plant allergens were investigated.

METHODS

One hundred and sixteen bakers with work-related allergic symptoms but without known food allergies were examined. Specific IgE (sIgE) antibodies to wheat flour, rye flour, lupine, peanut, soy and the recombinant single birch protein rBet v 1 were quantified. Selected sera were tested for cross-reactivity using ImmunoCAP inhibition and ISAC microarrays.

RESULTS

Whereas 67% of bakers were sensitized to wheat and/or rye flour, 35% showed sIgE to peanut and 33% to lupine. All lupine-positive bakers also had sIgE to either wheat flour (89%) and/or peanut (92%), and lupine sIgE correlated significantly with sIgE to peanut, soy, wheat and rye flour. Used as an inhibitor, wheat flour inhibited IgE binding to lupine in 4 out of 8 sera, indicating cross-reactivity. In microarrays, these sera showed IgE binding to lipid transfer proteins, profilins and/or cross-reactive carbohydrate determinants. Further inhibition experiments suggest that these single allergens are involved in cross-reactivity.

CONCLUSION

One third of 116 symptomatic bakers showed sIgE to lupine. At least some of these sensitizations were based on cross-reactivity between lupine and wheat flour. However, the considerable sensitization rate could also be a sign that the use of lupine flour in bakeries may be of occupational relevance.

Prick by prick induced anaphylaxis in a patient with peanuts and lupine allergy: awareness of risks and role of component resolved diagnosis

A case of anaphylaxis is reported in the course of a prick by prick with Lupinus albus and roasted peanut in a 20-year-old woman. We focused on some main topics. First of all it seems important to underscore the potential risks connected to the practice of the prick-by-prick with fresh foods in allergic patients, especially when testing cross-reactive substances, such as White Lupine, peanuts, or soy. It is important that clinicians who perform prick tests be aware of the risk related with in vivo tests in allergic patients. Second, we discuss the problem of the hidden allergens, such as White Lupine flour, or soy flour which are utilized to improve wheat flour because of their lower cost. Patients with a demonstrated allergy to peanuts should be assessed for lupine allergy and informed about the “hidden allergens” issue. Finally, we believe that component resolved diagnosis, the serum specific IgE against molecular components, that is normally considered a second-level diagnostic step has an important role even as a first line approach at least in some selected cases.

Skin prick test reactivity to lupin in comparison to peanut, pea, and soybean in atopic and non-atopic German subjects: A preliminary cross-sectional study

The increasing use of lupin in food processing poses a problem of potential (cross-)allergic reactions. To evaluate the prevalence of sensitization to lupin in comparison to that of other legumes skin prick tests were performed with lupin, pea, peanut, and soybean in atopic (n = 81) and non-atopic (n = 102) German adults. Of these 183 subjects, 20 subjects had to be excluded due to invalid skin prick tests (reaction to histamine <3 mm or to sodium chloride >2 mm). Thus, skin prick tests of 163 subjects were included in final analyses. Of 163 subjects, 18 had a positive reaction to at least one legume tested. Overall skin prick test reactivity was different among non-atopic and atopic subjects (P = 0.005). Altogether, six subjects (4%) were sensitized to lupin, 12 (7%) to pea, 5 (3%) to peanut, and 8 (5%) to soybean. Two (2%) of the 92 non-atopic subjects and 4 (6%) of the 71 atopic subjects had a positive skin prick test to lupin. Of the 6 subjects sensitized to lupin, 3 (50%) were also sensitized to pea, 3 (50%) to peanut, and 5 (83%) to soybean. In conclusion, the prevalence rates of lupin sensitization were comparable to or even lower than those of pea, peanut, and soybean. To date, lupin allergy is suspected to be relatively uncommon in the overall German population since lupin sensitization occurred in only 2% of non-atopic subjects. However, there is a clear risk of a lupin allergy in predisposed subjects, since the frequency of lupin sensitization was 6% in atopic subjects. In particular, subjects with existing sensitization or allergy to other legumes are at higher risk for a sensitization or allergy to lupin due to cross-reactivity.

Cross-reactivity of peanut allergens

Peanut seeds are currently widely used as source of human food ingredients in the United States of America and in European countries due to their high quality protein and oil content. This article describes the classification and molecular biology of peanut seed allergens with particular reference to their cross-reactivities. Currently, the IUIS allergen nomenclature subcommittee accepts 12 peanut allergens. Two allergens belong to the cupin and four to the prolamin superfamily, and six are distributed among profilins, Bet v 1-like proteins, oleosins, and defensins. Clinical observations frequently report an association of peanut allergy with allergies to legumes, tree nuts, seeds, fruits and pollen. Molecular cross-reactivity has been described between members of the Bet v 1-like proteins, the non-specific lipid transfer proteins, and the profilins. This review also addresses the less well-studied cross-reactivity between cupin and prolamin allergens of peanuts and of other plant food sources and the recently discovered cross-reactivity between peanut allergens of unrelated protein families.

Lupine, a source of new as well as hidden food allergens

The present review summarizes current knowledge about lupine allergy, potential sensitization routes, cross-reactions between lupine and other legumes, and the respective IgE-binding proteins. Since the 1990 s, lupine flour is used as a substitute for or additive to other flours, mostly wheat flour, in several countries of the EU. In 1994, the first case of an immediate-type allergy after ingestion of lupine flour-containing pasta was reported. Since then, the number of published incidents following ingestion or inhalation of lupine flour is rising. So far, the Lupinus angustifolius beta-conglutin has been designated as the allergen Lup an 1 by the International Union of Immunological Societies Allergen Nomenclature Subcommittee. Initially, publications focussed on the fact that peanut-allergic patients were at risk to develop anaphylaxis to lupine due to cross-reactivity between peanut and lupine. At present, however, the ratio between cases of pre-existing legume allergy (mostly peanut allergy) to de novo sensitization to lupine seed is nearly 1:1. Although in December 2006, lupine and products thereof were included in the EU foodstuff allergen list according to the Commission Directive 2006/142/EC amending Annex IIIA of Directive 2000/13/EC in order to prevent severe reactions caused by "hidden food allergens", the majority of patients and medical personnel are still not aware of raw lupine seed as potentially dangerous food allergen.

Lupin allergy and lupin sensitization among patients with suspected food allergy

BACKGROUND

Lupin, a legume with good nutritional value, is used in food production today, most often in bakery products. Lupin sensitization is often seen among patients with reactions to legumes, but the number of reports describing lupin anaphylaxis is also increasing.

OBJECTIVE

To investigate the occurrence of lupin sensitization, cross-reactivity, and lupin allergy among patients with suspected food allergy in Finland, where lupin is a labeled ingredient in few products.

METHODS

The occurrence of positive skin prick test (SPT) reactions to lupin seed flour was studied among 1522 patients with suspected food allergy from November 1, 2005, through December 31, 2007. Clinical histories and diagnostic SPT results were analyzed among patients with positive SPT results to lupin. For 1 patient, ImmunoSpot and lupin radioallergosorbent test inhibition methods were used.

RESULTS

Lupin sensitization was shown in 25 of 1522 patients (1.6%), and probable lupin allergy was diagnosed in 7 of 25 patients, in whom the clinical symptoms varied from anaphylaxis and respiratory symptoms to contact urticaria and itchy mouth. Cross-reactions or concurrent reactions to other legumes were seen in 18 of 25 patients.

CONCLUSIONS

Clinically relevant lupin allergy often occurs in patients without atopic background or other food allergies, although lupin sensitization most commonly seems to represent cross-reactivity to other legumes. The occurrence of lupin allergy in a country where lupin has not been traditionally used is surprisingly common, suggesting that short-term use of modest amounts of lupin can cause serious allergic reactions.

Cross-reactivity of pollen and food allergens: soybean Gly m 4 is a member of the Bet v 1 superfamily and closely resembles yellow lupine proteins

In many cases, patients allergic to birch pollen also show allergic reactions after ingestion of certain fruits or vegetables. This observation is explained at the molecular level by cross-reactivity of IgE antibodies induced by sensitization to the major birch pollen allergen Bet v 1 with homologous food allergens. As IgE antibodies recognize conformational epitopes, a precise structural characterization of the allergens involved is necessary to understand cross-reactivity and thus to develop new methods of allergen-specific immunotherapy for allergic patients. Here, we report the three-dimensional solution structure of the soybean allergen Gly m 4, a member of the superfamily of Bet v 1 homologous proteins and a cross-reactant with IgE antibodies originally raised against Bet v 1 as shown by immunoblot inhibition and histamine release assays. Although the overall fold of Gly m 4 is very similar to that of Bet v 1, the three-dimensional structures of these proteins differ in detail. The Gly m 4 local structures that display those differences are also found in proteins from yellow lupine with known physiological function. The three-dimensional structure of Gly m 4 may thus shed some light on the physiological function of this subgroup of PR10 proteins (class 10 of pathogenesis-related proteins) and, in combination with immunological data, allow us to propose surface patches that might represent cross-reactive epitopes.

Purification and characterization of natural Ara h 8, the Bet v 1 homologous allergen from peanut, provides a novel isoform

The peanut allergen Ara h 8 is an important allergen for birch pollen allergic patients because of the cross-reactivity to the homologous Bet v 1. As the existence of Ara h 8 has been shown at the cDNA level so far (AY328088) and the allergen has indirectly been detected as natural protein, it was the aim of our study to identify natural Ara h 8 in peanut extract and to develop a purification strategy. This was achieved using a unique combination of purification steps, including optimized extraction conditions, size exclusion and ion exchange chromatography and treatment of the interfering contaminants with iodoacetic acid. A characterization of the protein by microsequencing showed discrepancies to the deduced amino acid sequence of AY328088. For this reason, we cloned and expressed a new Ara h 8 isoform from cDNA (EU046325). This IgE-reactive protein corresponds to the results of microsequencing, ESI-FTICR-MS and trypsin fingerprinting analysis of the authentic and purified nAra h 8. Apart from the ultimate use of recombinant allergens for diagnostic procedures, there is also a scientific need for the natural counterpart, as it represents an excellent reference point by which to compare protein characteristics and to standardize diagnostic and therapeutic allergens.

Proteomic analysis of lupin seed proteins to identify conglutin Beta as an allergen, Lup an 1

Lupin products may be valuable as human foods because of their high protein content and potential anticholesterolemic properties. However, a small percentage of the population is allergic to lupin. In this study, we use in vitro IgE binding and mass spectrometry to identify conglutin beta, a major storage protein, as an allergen in seeds of Lupinus angustifolius and Lupinus albus. Purification of conglutin beta from L. angustifolius flour confirmed that serum IgE binds to this protein. Where IgE in sera recognized lupin proteins on Western blots, it recognized conglutin beta, suggesting this protein is a major allergen for lupin. The L. angustifolius conglutin beta allergen has been designated Lup an 1 by the International Union of Immunological Societies (IUIS) allergen nomenclature subcommittee.

Anaphylactic reaction to lupine flour

Roasted lupine seeds have been used as snack food in Mediterranean countries for years. Since the 1990s, lupine flour has been used as a substitute for or additive to other flours in countries of the European Union; usually the amount is so low that no declaration is required. Since 1994, a number of cases of immediate-type allergy to lupine flour-containing products have been published. A 52-year-old woman developed facial and mucosal edema, followed by dizziness and shortness of breath a few minutes after ingestion of a nut croissant containing lupine flour; she required emergency care. Allergy diagnostic tests revealed a total IgE of 116 kU/l, a highly elevated concentration of IgE specific for lupine seed (42.9 kU/l) and birch pollen IgE of 2.57 kU/l. Skin prick test with native lupine flour was strongly positive. Allergy against lupine seeds may develop de novo or via cross-reactivity to legumes, particularly peanuts, the latter being detectable in up to 88% of cases, founded on a strong sequence similarity between lupine and peanut allergens. In our patient, no cross-reactivity could be detected via immunoblotting, indicating a rare monovalent sensitization to lupine flour. Treatment consists of avoidance of lupine flour-containing products. Patients with proven peanut allergy should also avoid lupine flour because of the major risk of cross-reaction.

Peanut allergy: Emerging concepts and approaches for an apparent epidemic

Peanut allergy is typically lifelong, often severe, and potentially fatal. Because reactions can occur from small amounts, the allergy presents patients with significant obstacles to avoid allergic reactions. In North America and the United Kingdom, prevalence rates among schoolchildren are now in excess of 1%, framing an increasing public health concern and raising research questions about environmental, immunologic, and genetic factors that may influence outcomes of peanut allergy. This review focuses on recent observations that continue to question the influences of maternal and infant diet on outcomes of peanut allergy, and explore how peanut may be uniquely suited to induce an allergic response. We highlight studies that affect current diagnosis, management, and the nature of advice that can be provided to patients, including the utility of diagnostic tests, doses that elicit reactions, characteristics of reactions from exposure, issues of cross-reactivity, concerns about peanut contamination of manufactured goods, and the natural course of the allergy. Clinical, molecular, and immunologic advances are reviewed, highlighting research discoveries that influence strategies for improved diagnosis, prevention, and treatment. Among the therapeutic strategies reviewed are sublingual and oral immunotherapy, anti-IgE, Chinese herbal medicine, and vaccine strategies.

Novel polyclonal-monoclonal-based ELISA utilized to examine lupine (Lupinus species) content in food products

Sweet lupines are increasingly used in food production. Cause for concern has been expressed due to the increase in reported lupine-induced allergic incidents and the association between lupine and peanut allergies. In the current study, a polyclonal-monoclonal antibody-based sandwich ELISA for the detection of lupine proteins in foods was developed. The assay was sensitive to both native and processed proteins from Lupinus angustifolius and Lupinus albus and had a detection limit of 1 mug/g. Intra- and interassay coefficients of variation were <5 and <17%, respectively. A selection of 112 food samples, both with and without lupine declaration, was evaluated for their content of lupine. The data showed that the majority were in agreement with the respective labeling. However, some inconsistency was seen, typically in bread/rolls and soy flours.

Bioinformatics approaches to classifying allergens and predicting cross-reactivity

Allergenic proteins from very different environmental sources have similar sequences and structures. This fact may account for multiple allergen syndromes, whereby a myriad of diverse plants and foods may induce a similar IgE-based reaction in certain patients. Identifying the common triggering protein in these sources, in silico, can aid designing individualized therapy for allergen sufferers. This article provides an overview of databases on allergenic proteins, and ways to identify common proteins that may be the cause of multiple allergy syndromes. The major emphasis is on the relational Structural Database of Allergenic Proteins (SDAP []), which includes cross-referenced data on the sequence, structure, and IgE epitopes of over 800 allergenic proteins, coupled with specially developed bioinformatics tools to group all allergens and identify discrete areas that may account for cross-reactivity. SDAP is freely available on the Web to clinicians and patients.

Monoclonal Antibodies against the Candidate Lupin Allergens α-Conglutin and β-Conglutin

BACKGROUND

The ingestion of dietary products containing sweet lupin (such as Lupinus albus or Lupinus angustifolius) has been reported to cause IgE-mediated allergic reactions. Recent studies have indicated lupin globulins as important IgE binding proteins. The aim of the present study was to generate and characterize monoclonal antibodies (mAbs) against lupin seed proteins.

METHODS

Mice were immunized with a protein isolate from L. albus and mAbs were obtained by hybridoma techniques. Albumins and globulins were extracted, and the globulin fraction was separated further into conglutins by anion exchange chromatography. Specificities, binding patterns and applications of the mAbs were investigated by immunochemical methods.

RESULTS

Five mAbs were produced: Lu11 (an IgG2b antibody), Lu8, Lu18, Lu34 and Lu35 (all IgM antibodies). The mAbs reacted strongly with protein isolates from both L. albus and L. angustifolius. All mAbs are directed towards the lupin globulin fraction; Lu11 and Lu18 recognize alpha-conglutin, while Lu8, Lu34 and Lu35 recognize beta-conglutin. In addition, Lu11 inhibited the binding of IgE from patients with positive skin prick tests to lupin proteins in a competitive ELISA by approximately 30%. Furthermore, preliminary results show that Lu11 can be used to develop a sensitive method for the detection of alpha-conglutin in foods.

CONCLUSIONS

Lupin globulins are immunogenic and alpha-conglutin is a potential allergen. This is the first study describing mAbs against the candidate lupin allergens, emphasizing the importance of additional studies on conglutins in lupin allergy.

Unsuspected Lupin Allergens Hidden in Food

BACKGROUND

Lupin is a herbaceous plant from the legume family whose seed allergens usually have cross-reaction with peanut. Lupin flour is used in human nutrition because of its high nutritional and functional qualities.

AIMS

The aim of this work was to detect non-specified lupin proteins contained in several manufactured foods.

METHODS

Serum from a patient suffering anaphylactic episodes after ingestion of a certain brand of cookies and with oral allergy syndrome after eating chicken bouillon was used as a tracer. Lupin seeds and commercial food extracts were analyzed by SDS-PAGE, immunoblotting and immunoblotting inhibition. Lupin extract allergenicity after thermal processing was also analyzed.

RESULTS

A lupin allergen with a molecular weight close to 14 kDa was detected in extracts from cookies, a chicken bouillon cube and a chicken dehydrated soup.

CONCLUSIONS

The presence of unsuspected, hidden non-specified lupin sources in food labeling was demonstrated. According to the results of this study, it is important for food-allergic patients that food labels should declare all the components irrespective of their quantity.