Combination of two epitope identification techniques enables the rational design of soy allergen Gly m 4 mutants

Heat Treatment of Hazelnut Allergens Monitored by Polyclonal Sera and Epitope Fingerprinting

Hazelnuts are frequently involved in IgE-mediated reactions and are the main cause of nut allergies in Europe. Most food products are processed before human consumption. Food processing can modify the structure, properties, and function of proteins, and as a result, the IgE-binding capacity of allergens can be affected. In this study, we aimed to investigate epitope changes caused by the roasting of hazelnuts using epitope fingerprinting. Rabbit sera were raised against hazelnut proteins, and their epitopes were characterized. Immunoassays using specific polyclonal antibodies from rabbits targeting the main allergens in hazelnuts revealed marked reductions in the levels of Cor a 1 (PR-10), Cor a 11 (7S globulin), and Cor a 14 (2S albumin). However, rabbit antibodies can recognize different epitopes. Using antibodies that are different and characterized could help establish reliable methods for estimating the effects of treatments on the allergenicity of foods. In this work, we provide the first practical application that could lead to sets of peptide epitopes to compare and standardize immune diagnostics, even for complex protein preparations.

Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping

Precise epitope determination of therapeutic antibodies is of great value as it allows for further comprehension of mechanism of action, therapeutic responsiveness prediction, avoidance of unwanted cross reactivity, and vaccine design. The golden standard for discontinuous epitope determination is the laborious X-ray crystallography method. Here, we present a combinatorial method for rapid mapping of discontinuous epitopes by mammalian antigen display, eliminating the need for protein expression and purification. The method is facilitated by automated workflows and tailored software for antigen analysis and oligonucleotide design. These oligos are used in automated mutagenesis to generate an antigen receptor library displayed on mammalian cells for direct binding analysis by flow cytometry. Through automated analysis of 33930 primers an optimized single condition cloning reaction was defined allowing for mutation of all surface-exposed residues of the receptor binding domain of SARS-CoV-2. All variants were functionally expressed, and two reference binders validated the method. Furthermore, epitopes of three novel therapeutic antibodies were successfully determined followed by evaluation of binding also towards SARS-CoV-2 Omicron BA.2. We find the method to be highly relevant for rapid construction of antigen libraries and determination of antibody epitopes, especially for the development of therapeutic interventions against novel pathogens.

Food allergy - New risks through vegan diet? Overview of new allergen sources and current data on the potential risk of anaphylaxis

A vegan diet is increasingly en vogue, i.e., a diet based on plants, in which animal products are completely avoided, often for health and environmental reasons. The menu is supplemented with pulses (e.g., soy, lentils, peas), nuts (e.g., cashew, macadamia, almond, pecan, para, walnut) and seeds (e.g., chia, flaxseed) or pseudo-grains (quinoa, buckwheat). Indeed, the product range is expanding to include vegan foods such as milk alternatives (e.g., oat, almond, soy drinks) and cheese or meat substitutes (e.g., soy-based). Food allergies are also on the rise, with an increasing prevalence worldwide. It is worthy of note that the main allergens of anaphylactic reactions to food in adults are predominantly of plant origin, mainly pulses and nuts - the very foods that form the main source of protein in the vegan diet. In this context, allergies to storage proteins (e.g., Gly m 5 and Gly m 6 from soya beans) can lead to severe anaphylactic reactions, while highly processed substitute products containing plant protein isolates (e.g., pea flour) in concentrated form continue to be of particular concern and may therefore be allergologically problematic. In this article, we aim to provide an overview of allergens and emerging allergen sources in vegan foods and highlight the anaphylaxis risk of the vegan diet.

Nahrungsmittelallergie - Neue Risiken durch vegane Ernährung? Überblick zu neuen Allergenquellen und aktuelle Daten zum Anaphylaxierisiko: Food allergy - New risks through vegan diet? Overview of new allergen sources and current data on the potential risk of anaphylaxis

Zunehmend mehr Menschen ernähren sich aus gesundheitlichen und Umweltaspekten ausschließlich von pflanzlichen Nahrungsmitteln (vegan). Dabei werden vielfach Hülsenfrüchte (wie Soja, Linsen, Erbsen), Schalenfrüchte (Cashew, Macadamia, Mandel, Pekan‐, Para‐ und Walnuss), Samen und Saaten (wie Chia, Leinsamen) oder (Pseudo‐)Getreide (wie Quinoa, Buchweizen) verzehrt. Vegane Milchalternativen sind Hafer‐, Mandel‐ und Sojadrinks, auch Käse‐ sowie Fleischersatzprodukte basieren oft auf einer Sojagrundlage. Gleichzeitig nimmt die Prävalenz von Nahrungsmittelallergien weltweit zu. Pflanzenallergene aus Hülsen‐ und Schalenfrüchten, die in der veganen Ernährung die Hauptproteinquelle ausmachen, zählen zu den häufigsten Auslösern von Nahrungsmittelallergien bei Erwachsenen. Dabei kommt es bei Allergien auf Speicherproteine (wie Gly m 5 und Gly m 6 aus der Sojabohne) zu teils schweren anaphylaktischen Reaktionen. Besonderes Augenmerk liegt weiter auf hochverarbeiteten Ersatzprodukten, die Pflanzenproteinisolate (zum Beispiel Erbsenmehl) in konzentrierter Form enthalten und damit allergologisch problematisch werden können. In diesem Artikel geben wir einen Überblick über wichtige Allergene und neue Allergenquellen in ausgesuchten veganen Nahrungsmitteln und betrachten die vegane Ernährung unter allergologischen Aspekten.

Peptide epitopes as biomarkers of soya sensitization in rBet v 1 immunotherapy of birch-related soya allergy

BACKGROUND

There are no diagnostic and/or prognostic markers of the treatment outcome in patients receiving allergen immunotherapy (AIT). Although numerous allergen epitopes are known, their value in this context has not been investigated. This paper deals with re-evaluation of sera from patients who underwent AIT against rBet v 1 for treatment of their soya allergy (BASALIT trial).

OBJECTIVE

To evaluate the diagnostic and/or prognostic potential of allergen epitopes recognition by antibodies from patients with birch-related soya allergy before and after rBet v 1-immunotherapy.

METHODS

PR-10 epitope-binding profiles from 34 patients were identified in silico using a statistical peptide phage display at start and at end of AIT. IgE- and IgG-binding to these peptide epitopes was measured in peptide microarrays. Clinical relevance of epitopes was evaluated by comparing these measurements to a number of treatment outcome measures recorded during double-blind placebo-controlled food challenge at start and end of AIT.

RESULTS

We showed that IgG- and IgE-recognition of peptide epitopes after AIT were surrogate markers of 5 out of 12 analysed treatment outcome measures using this patient cohort. Seven epitopes were identified from multiple PR-10 allergen sequences. Twenty-six peptide epitopes were used for IgG and IgE measurements. IgE-binding to one of the epitopes was associated with stronger intensity of oral tingling/itching after ingesting soya at start of AIT. IgG recognizing two other epitopes at start of AIT could predict decreased Cor a 1-specific IgE concentration (p = .043) and decreased lip swelling intensity (p = .016) after AIT. Tolerance to increasing amounts of soy at food challenge correlated with IgG-binding to another epitope at start of AIT (p = .046).

CONCLUSION

IgG- and IgE-binding to peptide epitopes in PR-10 is a potential indicator of the outcome and clinical course of AIT of soya-sensitized patients with rBet v 1.

Investigation of the differences in the effect of (-)-epigallocatechin gallate and proanthocyanidins on the functionality and allergenicity of soybean protein isolate

In this study, the differences in effects of (-)-epigallocatechin gallate (EGCG) and proanthocyanidins (PC) on the functionality and allergenicity of soybean protein isolate (SPI) were studied. SDS-PAGE demonstrated that SPI-PC conjugates exhibited more high-molecular-weight polymers (>180 kDa) than SPI-EGCG conjugates. Structural analysis showed that SPI-PC conjugates exhibited more disordered structures and protein-unfolding, improving the accessibility of PC to modify SPI, compared to SPI-EGCG conjugates. LC/MS-MS demonstrated that PC caused more modification of SPI and major soybean allergens than EGCG, resulting in a lower abundance of epitopes. The successful attachment of EGCG and PC to SPI significantly increased antioxidant capacity in conjugates. Furthermore, SPI-PC conjugates exhibited greater emulsifying activity and lower immunoglobulin E (IgE) binding capacity than SPI-EGCG conjugates, which was attributed to more disordered structure and protein-unfolding in SPI-PC conjugates. It is implied that proanthocyanidins may be promising compounds to interact with soybean proteins to produce functional and hypoallergenic foods.

Three Parts of the Plant Genome: On the Way to Success in the Production of Recombinant Proteins

Recombinant proteins are the most important product of current industrial biotechnology. They are indispensable in medicine (for diagnostics and treatment), food and chemical industries, and research. Plant cells combine advantages of the eukaryotic protein production system with simplicity and efficacy of the bacterial one. The use of plants for the production of recombinant proteins is an economically important and promising area that has emerged as an alternative to traditional approaches. This review discusses advantages of plant systems for the expression of recombinant proteins using nuclear, plastid, and mitochondrial genomes. Possibilities, problems, and prospects of modifications of the three parts of the genome in light of obtaining producer plants are examined. Examples of successful use of the nuclear expression platform for production of various biopharmaceuticals, veterinary drugs, and technologically important proteins are described, as are examples of a high yield of recombinant proteins upon modification of the chloroplast genome. Potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated. Although these opportunities have not yet been exploited, potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated.

Structural and Immunologic Properties of the Major Soybean Allergen Gly m 4 Causing Anaphylaxis

Gly m 4 is the major soybean allergen, causing birch pollen cross allergic reactions. In some cases, Gly m 4-mediated anaphylaxis takes place, but the causative factors are still unknown. Here, we studied the structural and immunologic properties of Gly m 4 to shed light on this phenomenon. We showed that Gly m 4 retained its structure and IgE-binding capacity after heating. Gly m 4 was cleaved slowly under nonoptimal gastric conditions mimicking duodenal digestion, and IgE from the sera of allergic patients interacted with the intact allergen rather than with its proteolytic fragments. Similar peptide clusters of Bet v 1 and Gly m 4 were formed during allergen endolysosomal degradation in vitro, but their sequence identity was insignificant. Animal polyclonal anti-Gly m 4 and anti-Bet v 1 IgG weakly cross-reacted with Bet v 1 and Gly m 4, respectively. Thus, we supposed that not only conserved epitopes elicited cross-reactivity with Bet v 1, but also variable epitopes were present in the Gly m 4 structure. Our data suggests that consumption of moderately processed soybean-based drinks may lead to the neutralizing of gastric pH as a result of which intact Gly m 4 can reach the human intestine and cause IgE-mediated system allergic reactions.

Recent Progress on Vaccines Produced in Transgenic Plants

The development of vaccines from plants has been going on for over two decades now. Vaccine production in plants requires time and a lot of effort. Despite global efforts in plant-made vaccine development, there are still challenges that hinder the realization of the final objective of manufacturing approved and safe products. Despite delays in the commercialization of plant-made vaccines, there are some human vaccines that are in clinical trials. The novel coronavirus (SARS-CoV-2) and its resultant disease, coronavirus disease 2019 (COVID-19), have reminded the global scientific community of the importance of vaccines. Plant-made vaccines could not be more important in tackling such unexpected pandemics as COVID-19. In this review, we explore current progress in the development of vaccines manufactured in transgenic plants for different human diseases over the past 5 years. However, we first explore the different host species and plant expression systems during recombinant protein production, including their shortcomings and benefits. Lastly, we address the optimization of existing plant-dependent vaccine production protocols that are aimed at improving the recovery and purification of these recombinant proteins.

Investigation of differences in allergenicity of protein from different soybean cultivars through LC/MS-MS

Soybean allergy is a health-threatening issue and identifying raw soybeans with low allergenicity is important for producing hypoallergenic soybean products. Soybean allergy is mainly triggered by soybean proteins. In this study, the protein profiles, allergen compositions, and epitopes in protein from different soybean cultivars (R1, R2 and R3) were evaluated by SDS-PAGE and LC/MS-MS, and their allergenicity was assessed by indirect ELISA and Western blot analysis using the serum IgE of patients allergic to soybeans. The lowest allergenicity was observed in R3, probably resulting from the low concentration of Gly m 4-Gly m 6. The allergenicity of soybeans is affected by multiple allergens rather than a single allergen. Venn diagram, PCA, heatmap, and peptide map analyses have shown the differences in protein and peptide profiles among soybean proteins from different soybean cultivars. Epitope analysis further demonstrated that low contents of dominant epitopes in Gly m 4 and Gly m 5 contributed to low allergenicity in R3, although R3 contained high contents of no-dominant epitopes.

Plant-Based Cell-Free Transcription and Translation of Recombinant Proteins

Plant cell-free lysates contain all the cellular components of the protein biosynthesis machinery, providing an alternative to intact plant cells, tissues, and whole plants for the production of recombinant proteins. Cell-free lysates achieve rapid protein production (within hours or days) and allow the synthesis of proteins that are cytotoxic or unstable in living cells. The open nature of cell-free lysates and their homogeneous and reproducible performance is ideal for protein production, especially for screening applications, allowing the direct addition of nucleic acid templates encoding proteins of interest, as well as other components such as enzyme substrates, chaperones, artificial amino acids, or labeling molecules. Here we describe procedures for the production of recombinant proteins in the ALiCE (Almost Living Cell-free Expression) system, a lysate derived from tobacco cell suspension cultures that can be used to manufacture protein products for molecular and biochemical analysis as well as applications in the pharmaceutical industry.

Plant molecular farming for the production of valuable proteins - Critical evaluation of achievements and future challenges

Recombinant proteins play an important role in many areas of our lives. For example, recombinant enzymes are used in the food and chemical industries and as high-quality proteins for research, diagnostic and therapeutic applications. The production of recombinant proteins is still dominated by expression systems based on microbes and mammalian cells, although the manufacturing of recombinant proteins in plants - known as molecular farming - has been promoted as an alternative, cost-efficient strategy for three decades. Several molecular farming products have reached the market, but the number of success stories has been limited by industrial inertia driven by perceptions of low productivity, the high cost of downstream processing, and regulatory hurdles that create barriers to translation. Here, we discuss the technical and economic factors required for the successful commercialization of molecular farming, and consider potential future directions to enable the broader application of production platforms based on plants.

Plant-Derived Cell-Free Biofactories for the Production of Secondary Metabolites

Cell-free expression systems enable the production of proteins and metabolites within a few hours or days. Removing the cellular context while maintaining the protein biosynthesis apparatus provides an open system that allows metabolic pathways to be installed and optimized by expressing different numbers and combinations of enzymes. This facilitates the synthesis of secondary metabolites that are difficult to produce in cell-based systems because they are toxic to the host cell or immediately converted into downstream products. Recently, we developed a cell-free lysate derived from tobacco BY-2 cell suspension cultures for the production of recombinant proteins. This system is remarkably productive, achieving yields of up to 3 mg/mL in a one-pot in vitro transcription-translation reaction and contains highly active energy and cofactor regeneration pathways. Here, we demonstrate for the first time that the BY-2 cell-free lysate also allows the efficient production of several classes of secondary metabolites. As case studies, we synthesized lycopene, indigoidine, betanin, and betaxanthins, which are useful in the food, cosmetic, textile, and pharmaceutical industries. Production was achieved by the co-expression of up to three metabolic enzymes. For all four products, we achieved medium to high yields. However, the yield of betanin (555 μg/mL) was outstanding, exceeding the level reported in yeast cells by a factor of more than 30. Our results show that the BY-2 cell-free lysate is suitable not only for the verification and optimization of metabolic pathways, but also for the efficient production of small to medium quantities of secondary metabolites.

Identification of Seasonal Variations of Antibodies against PR-10-Specific Epitopes Can Be Improved Using Peptide-Phage Display

BACKGROUND

In pollinosis patients, allergen-specific antibody titers show seasonal variations. Little is known about these variations at the epitope level.

OBJECTIVES

We aimed at investigating seasonal variations on the level of allergen epitope recognition in patients with Bet v 1-related food allergy using a peptide phage display approach.

METHODS

Serum samples collected over 1 year from 4 patients of the placebo arm of the birch-associated soya allergy immunotherapy trial were included. To identify epitopes from Bet v 1-related food allergens, patient sera were used in peptide phage display experiments. In silico analysis of enriched allergen-related motifs was performed.

RESULTS

We identified epitope motifs related to Bet v 1 and its homologs in soya and hazelnut (Gly m 4 and Cor a 1, respectively) that were enriched in accordance with birch and hazel pollen exposure. Within several weeks after the birch pollen season peak, the pattern of identified epitope motifs differed considerably among patients. Data for amino acid preferences in homologous Bet v 1 and Cor a 1 epitope motifs identified for one of the investigated patients suggest changes in concentration or specificity of serum antibodies for the Cor a 1 epitope motif.

CONCLUSIONS

Peptide phage display data suggest an impact of birch and hazel pollen exposure on the recognition pattern of Bet v 1-like allergen epitopes. Epitope-oriented analyses could provide deeper, personalized details regarding the allergen epitope recognition influenced by pollen exposure beyond the capability of current methods.

Food allergomics based on high-throughput and bioinformatics technologies

Food allergy is a serious food safety problem worldwide, and the investigation of food allergens is the foundation of preventing and treating them, but relevant knowledge is far from sufficient. With the advent of the "big data era", it has been possible to investigate food allergens by high-throughput methods, proposing the concept of allergomics. Allergomics is the discipline studying the repertoire of allergens, which has relatively higher throughput and is faster and more sensitive than conventional methods. This review introduces the basis of allergomics and summarizes its major strategies and applications. Particularly, strategies based on immunoblotting, phage display, allergen microarray, and bioinformatics are reviewed in detail, and the advantages and limitations of each strategy are discussed. Finally, further development of allergomics is predicted. This provides basic theories and recent advances in food allergomics research, which could be insightful for both food allergy research and practical applications.

Identification of antigenic sites destructed by high hydrostatic pressure (HHP) of the β subunit of β-conglycinin

β-conglycinin is one of the most allergenic proteins, and its constituent subunits α', α, and β are all potential allergens to humans. In the present study, we concentrated on the destructed antigenic sites of β subunit of β-conglycinin after high hydrostatic pressure (HHP) treatment. In this paper, the overlapping gene fragments of the β subunit of β-conglycinin were amplified by polymerase chain reaction (PCR) and cloned into T7 phage vectors. After being packaged in vitro, the recombinant T7 phage was constructed, and the overlapping fragments of the β subunit were displayed on the phage surface. The recombinant phages that expressed the overlapping fragments of the β subunit were used to react with specific antiserum by indirect ELISA to identify the HHP destructed antigenic sites. After three rounds of expression and identification, we used synthetic peptide technology to identify that the obtained fragment was a conformational epitope. We further confirmed that HHP treatment changed the conformational structure of β-conglycinin, which reduced the antigenicity of the protein.

Simplified Tracking of a Soy Allergen in Processed Food Using a Monoclonal Antibody-Based Sandwich ELISA Targeting the Soybean 2S Albumin Gly m 8

Soybean allergens in food samples are currently detected in most cases using enzyme-linked immunosorbent assays (ELISAs) based on antibodies raised against bulk soybean proteins or specifically targeting soybean trypsin inhibitor, conglycinin, or glycinin. The various commercial ELISAs lack standardized reference material, and the results are often inaccurate because the antibodies cross-react with proteins from other legumes. Furthermore, the isolation of allergenic proteins involves laborious denaturing extraction conditions. To tackle these challenges, we have developed a novel sandwich ELISA based on monoclonal antibodies raised against the soybean 2S albumin Gly m 8 and a recombinant Gly m 8 reference protein with native-analogous characteristics. The antibodies do not cross-react with other legume proteins, and the extraordinary stability and solubility of Gly m 8 allows it to be extracted even from complex matrices after processing. The Gly m 8 ELISA therefore achieves greater specificity and reproducibility than current ELISA tests.

Antibody response after hepatitis B vaccine boost mapped with peptide-phage display

Recombinant hepatitis B virus vaccines confer protection by eliciting specific antibodies against the hepatitis B surface antigen (HBsAg), known as anti-HBs. However, the performance of rapid anti-HBs diagnostic tests generates concerns regarding consistency. Novel indicators of protection might be developed by monitoring changes in targeted HBsAg-epitope profile after vaccination. In this work, we test the feasibility of our peptide-phage display platform in identifying B-cell epitopes targeted at different time-points after hepatitis B vaccination. We combined this platform with a unique approach for in silico analysis of enriched sequences. Serum samples collected from one single patient who had two boosting immunizations against hepatitis B virus were used in two-rounds of selection experiments. Five epitope candidates from HBsAg were identified in silico; most of them were previously reported in the literature. Our results suggest that the number of recognized HBsAg epitopes is related to the decrease of anti-HBs over time.

The immunome of soy bean allergy: Comprehensive identification and characterization of epitopes

BACKGROUND

The precise mapping of multiple antibody epitopes recognized by patients' sera allows a more detailed and differentiated understanding of immunological diseases. It may lead to the development of novel therapies and diagnostic tools.

OBJECTIVE

Mapping soy bean specific epitopes relevant for soy bean allergy patients and persons sensitized to soy bean, and analysis of their IgE/IgG binding spectrum.

METHODS

Identification of epitopes using sera, applying an optimized peptide phage display library followed by next-generation sequencing, specially designed in silico data analysis and subsequent peptide microarray analysis.

RESULTS

We were able to identify more than 400 potential epitope motifs in soy bean proteins. More than 60% of them have not yet been described as potential epitopes. Eighty-three peptides, representing the 42 most frequently found epitope candidates, were validated by microarray analysis using 50 sera from people who have been tested positive in skin prick test (SPT). Of these peptides, 56 were bound by antibodies, 55 by serum IgE, 43 by serum IgG and 30 by both. Person-specific epitope patterns were found for each individual and protein.

CONCLUSIONS

For individuals with clinical symptoms, epitope resolved analyses reveal a high prevalence of IgE binding to a few soy bean specific epitopes. Evaluation of individual immune profiles of patients with soy bean sensitization allows the identification of peptides that do facilitate studying individual IgE/IgG epitope binding patterns. This enables discrimination of sensitization from disease, such assay test has the potential to replace SPT assays.

Critical Analysis of the Commercial Potential of Plants for the Production of Recombinant Proteins

Over the last three decades, the expression of recombinant proteins in plants and plant cells has been promoted as an alternative cost-effective production platform. However, the market is still dominated by prokaryotic and mammalian expression systems, the former offering high production capacity at a low cost, and the latter favored for the production of complex biopharmaceutical products. Although plant systems are now gaining widespread acceptance as a platform for the larger-scale production of recombinant proteins, there is still resistance to commercial uptake. This partly reflects the relatively low yields achieved in plants, as well as inconsistent product quality and difficulties with larger-scale downstream processing. Furthermore, there are only a few cases in which plants have demonstrated economic advantages compared to established and approved commercial processes, so industry is reluctant to switch to plant-based production. Nevertheless, some plant-derived proteins for research or cosmetic/pharmaceutical applications have reached the market, showing that plants can excel as a competitive production platform in some niche areas. Here, we discuss the strengths of plant expression systems for specific applications, but mainly address the bottlenecks that must be overcome before plants can compete with conventional systems, enabling the future commercial utilization of plants for the production of valuable proteins.

Anti-Drug Antibodies: Emerging Approaches to Predict, Reduce or Reverse Biotherapeutic Immunogenicity

The development of anti-drug antibodies (ADAs) following administration of biotherapeutics to patients is a vexing problem that is attracting increasing attention from pharmaceutical and biotechnology companies. This serious clinical problem is also spawning creative research into novel approaches to predict, avoid, and in some cases even reverse such deleterious immune responses. CD4⁺ T cells are essential players in the development of most ADAs, while memory B-cell and long-lived plasma cells amplify and maintain these responses. This review summarizes methods to predict and experimentally identify T-cell and B-cell epitopes in therapeutic proteins, with a particular focus on blood coagulation factor VIII (FVIII), whose immunogenicity is clinically significant and is the subject of intensive current research. Methods to phenotype ADA responses in humans are described, including T-cell stimulation assays, and both established and novel approaches to determine the titers, epitopes and isotypes of the ADAs themselves. Although rational protein engineering can reduce the immunogenicity of many biotherapeutics, complementary, novel approaches to induce specific tolerance, especially during initial exposures, are expected to play significant roles in future efforts to reduce or reverse these unwanted immune responses.