The relevance of a digestibility evaluation in the allergenicity risk assessment of novel proteins. Opinion of a joint initiative of COST action ImpARAS and COST action INFOGEST

Bioaccessibility and Antioxidant Activity of Faba Bean Peptides in Comparison to those of Pea and Soy after In Vitro Gastrointestinal Digestion and Transepithelial Transport across Caco-2 and HT29-MTX-E12 Cells

In this study, the transepithelial transport of bioactive peptides derived from faba bean flour gastrointestinal digestates was investigated, in vitro, using a Caco-2 and HT29-MTX-E12 coculture monolayer, in comparison to those of pea and soy. The profile of transported peptides was determined by mass spectrometry, and the residual antioxidant activity was assessed. The ORAC value significantly (p < 0.05) decreased after transepithelial transport (24-36% reduction) for all legumes, while the antioxidant activity in ABTS assay significantly (p < 0.05) increased, as shown by the EC50 decrease of 26-44%. Five of the nine faba bean peptides that crossed the intestinal cell monolayer exhibited antioxidant activity. Two of these peptides, TETWNPNHPEL and TETWNPNHPE, were further hydrolyzed by the cells' brush border peptidases to smaller fragments TETWNPNHP and TWNPNHPE. These metabolized peptides were synthesized, and both maintained high antioxidant activity in both ABTS (EC50 of 1.2 ± 0.2 and 0.4 ± 0.1 mM, respectively) and ORAC (2.5 ± 0.1 and 3.4 ± 0.2 mM of Trolox equivalent/mM, respectively) assays. These results demonstrated for the first time the bioaccessibility of faba bean peptides produced after in vitro gastrointestinal digestion and how their bioactive properties can be modulated during transepithelial transport.

Experimental Protocols Used to Mimic Gastrointestinal Protein Digestion: A Systematic Review

Bioactive peptides derived from native proteins modulate physiological processes in the metabolic pathways. Given that multiple protocols in the literature mimic the digestion of dietary components, gathering studies that use such models directed at protein digestion processes is critical. This systematic review aimed to gather evidence that adopted adequate experimental models to simulate human protein digestion. The databases searched were PubMed, Web of Science, ScienceDirect, Embase, Virtual Health Library, and Scopus. A total of 1985 articles were found, resulting in 20 eligible in vitro studies. The Office of Health Assessment and Translation was used to evaluate methodological quality. Seven studies used plant-based protein sources, twelve used animal protein sources, and one used both. The duration of the oral phase varied, although 60% of the studies employed a protein digestion period of 120 min. Amylase, pepsin, and pancreatin enzymes were utilized in 40% of the studies, with pH levels of 7, 3, and 7, respectively, during the oral, gastric, and intestinal phases. The INFOGEST harmonized static model was adopted by 65% of the studies; INFOGEST is the most effective model for simulating gastrointestinal protein processes in humans and can be used to answer several research questions because it describes experimental conditions close to the human physiological situation.

Role of Food Digestion and Digestive System in the Nutritional, Functional and Health Properties of Food Bioactives

The impact of food components on the human digestive system is an important area of research in the fields of nutrition and food science [...].

Dietary Intervention during Weaning and Development of Food Allergy: What Is the State of the Art?

Food allergy (FA) affects approximately 6-8% of children worldwide causing a significant impact on the quality of life of children and their families. In past years, the possible role of weaning in the development of FA has been studied. According to recent studies, this is still controversial and influenced by several factors, such as the type of food, the age at food introduction and family history. In this narrative review, we aimed to collect the most recent evidence about weaning and its role in FA development, organizing the gathered data based on both the type of study and the food. As shown in most of the studies included in this review, early food introduction did not show a potential protective role against FA development, and we conclude that further evidence is needed from future clinical trials.

Research gaps and future needs for allergen prediction in food safety

The allergenicity and protein risk assessments in food safety are facing new challenges. Demands for healthier and more sustainable food systems have led to significant advances in biotechnology, the development of more complex foods, and the search for alternative protein sources. All this has increased the pressure on the safety assessment prediction approaches anchored into requirements defined in the late 90's. In 2022, the EFSA's Panel on Genetically Modified Organisms published a scientific opinion focusing on the developments needed for allergenicity and protein safety assessments of new products derived from biotechnology. Here, we further elaborate on the main elements described in this scientific opinion and prioritize those development needs requiring critical attention. The starting point of any new recommendation would require a focus on clinical relevance and the development of a fit-for-purpose database targeted for specific risk assessment goals. Furthermore, it is imperative to review and clarify the main purpose of the allergenicity risk assessment. An internationally agreed consensus on the overall purpose of allergenicity risk assessment will accelerate the development of fit-for-purpose methodologies, where the role of exposure should be better clarified. Considering the experience gained over the last 25 years and recent scientific developments in the fields of biotechnology, allergy, and risk assessment, it is time to revise and improve the allergenicity safety assessment to ensure the reliability of allergenicity assessments for food of the future.

Improved in vitro gastrointestinal digestion protocol mimicking brush border digestion for the determination of the Digestible Indispensable Amino Acid Score (DIAAS) of different food matrices

The Digestible Indispensable Amino Acid Score (DIAAS) is the new gold standard method for the assessment of protein nutritional quality. The DIAAS is evaluated with in vivo models, that are complex, constraining and costly. There is still no established method to assess it in vitro. In this study, we proposed to add a jejunal-ileal digestion phase to the standardized in vitro gastrointestinal digestion protocol developed by the International Network of Excellence on the Fate of Food in the Gastrointestinal Tract (INFOGEST protocol) to mimic brush border digestion and to enable DIAAS assessment in vitro in a more physiologically relevant manner. This jejunal-ileal digestion phase was performed with a porcine intestinal aminopeptidase as an alternative to brush border membrane extract, which is more difficult to obtain in a standardized way. This modified INFOGEST protocol was applied to various food matrices (faba bean, pea and soy flours, whey protein isolate and caseins) and the results were compared to published in vivo data to assess the model's physiological relevance. The addition of the jejunal-ileal digestion phase lead to a significant (p < 0.05) increase of 31 and 29 % in free and total amino acid digestibility, respectively, and of 83 % on average for the in vitro DIAAS values for all food matrices. Although the in vitro DIAAS remained underestimated compared to the in vivo ones, a strong correlation between them was observed (r = 0.879, p = 0.009), stating the relevance of this last digestion phase. This improved digestion protocol is proposed as a suitable alternative to evaluate the DIAAS in vitro when in vivo assays are not applicable.

The role of food structure in gastric-emptying rate, absorption and metabolism

The high levels of non-communicable diseases such as CVD and type 2 diabetes mellitus are linked to obesity and poor diet. This continuing emphasis on health in relation to food is proving a powerful driver for the development of cheap but palatable and more functional foods. However, the efficacy of such foods is often hard to prove in human subjects. Thus, a suite of tools has been developed including in silico and in vitro simulations and animal models. Although animal models offer physiologically relevant platforms for research, their use for experimentation is problematic for consumers. Thus, in vitro methods such as Infogest protocols have been developed to provide digestion endpoints or even an indication of the kinetics of digestion. These protocols have been validated for a range of food systems but they still miss the final absorption step. This review discusses the use of such in vitro models and what further steps need to be included to make the bioaccessibility determination more relevant to bioavailability and human health.

Allergenicity evaluation of quinoa proteins - A study in Brown Norway rats

The popularity of quinoa seeds has increased in the last decade due to their high nutritional value and natural gluten-free composition. Consumption of new proteins may pose a risk of introducing new allergies. In the present study the immunogenicity and sensitising capacity of quinoa proteins were assessed in a dose-response experiment in Brown Norway rats in comparison to proteins from spinach and peanut. Cross-reactivity between quinoa proteins and known allergens was evaluated by in silico analyses followed by analyses with 11 selected protein extracts and their anti-sera by means of ELISAs and immunoblotting. Further, an in vitro simulated gastro-duodenal digestion was performed. Quinoa proteins were found to have an inherent medium to high immunogenicity and sensitising capacity, being able to induce specific IgG1 and IgE levels higher than spinach but lower than peanut and elicit reactions of clinical relevance similar to peanut. Quinoa proteins were generally shown to resist digestion and retain capacity to bind quinoa-specific antibodies. Quinoa proteins were shown to be cross-reactive with peanut and tree nut allergens as high sequence homology and antibody cross-binding were demonstrated. Present study suggests that quinoa pose a medium to high level of allergenicity that should be further investigated in human studies.

Protein familiarity is a fundamental but rarely operationalized concept in the safety assessment of genetically modified crops: example of phosphomannose isomerase (PMI)

Fundamental to the safety assessment of genetically modified (GM) crops is the concept of negligible risk for newly expressed proteins for which there is a history of safe use. Although this simple concept has been stated in international and regional guidance for assessing the risk of newly expressed proteins in GM crops, its full implementation by regulatory authorities has been lacking. As a result, safety studies are often repeated at a significant expenditure of resources by developers, study results are repeatedly reviewed by regulators, and animals are sacrificed needlessly to complete redundant animal toxicity studies. This situation is illustrated using the example of the selectable marker phosphomannose isomerase (PMI) for which familiarity has been established. Reviewed is the history of safe use for PMI and predictable results of newly conducted safety studies including bioinformatic comparisons, resistance to digestion, and acute toxicity that were repeated to gain regulatory reapproval of PMI expressed from constructs in recently developed GM maize. As expected, the results of these newly repeated hazard-identification and characterization studies for PMI indicate negligible risk. PMI expressed in recently developed GM crops provides an opportunity to use the concept of familiarity by regulatory authorities to reduce risk-disproportionate regulation of these new events and lessen the resulting waste of both developer and regulator resources, as well as eliminate unnecessary animal testing. This would also correctly imply that familiar proteins like PMI have negligible risk. Together, such modernization of regulations would benefit society through enabling broader and faster access to needed technologies.

A Food Matrix Triggers a Similar Allergic Immune Response in BALB/c Mice Sensitized with Native, Denatured, and Digested Ovalbumin

The search for an animal model to evaluate the allergenic potential of processed food products is still ongoing. Both the sensitization to ovalbumin (OVA) in different structural states and the allergic response triggered after intragastric or food challenges were assessed. BALB/c mice were sensitized intraperitoneally to OVA (50 µg) in different structural states (native OVA, N-OVA; denatured OVA, D-OVA; formaldehyde- and lysine-treated OVA, FK-OVA; denatured OVA-FK, OVA-DFK; peptides from pepsin digestion, Pep-OVA). Anti-OVA-specific IgE responses were evaluated using ELISA. Anaphylactic signs and mMCP-1 serum levels were evaluated after intragastric (2.0 mg/OVA) and food (0.41 mg/OVA) challenges. IgE reactivities to N-OVA and D-OVA were similar among groups (p > 0.05). After the challenges, all OVA-sensitized mice developed mild to severe anaphylactic signs (p < 0.05 vs. control). Mice sensitized to N-OVA and D-OVA had the highest mMCP-1 serum levels after challenges (p < 0.05 vs. control). Allergic responses were similar despite the different OVA doses used for the challenges. The N-OVA-sensitized murine model of egg allergy proposed in the present study holds the potential for evaluating the impact of food matrix composition and processing on the threshold of egg-allergic responses.

Food Allergens of Plant Origin

This review presents an update on the physical, chemical, and biological properties of food allergens in plant sources, focusing on the few protein families that contribute to multiple food allergens from different species and protein families recently found to contain food allergens. The structures and structural components of the food allergens in the allergen families may provide further directions for discovering new food allergens. Answers as to what makes some food proteins allergens are still elusive. Factors to be considered in mitigating food allergens include the abundance of the protein in a food, the property of short stretches of the sequence of the protein that may constitute linear IgE binding epitopes, the structural properties of the protein, its stability to heat and digestion, the food matrix the protein is in, and the antimicrobial activity to the microbial flora of the human gastrointestinal tract. Additionally, recent data suggest that widely used techniques for mapping linear IgE binding epitopes need to be improved by incorporating positive controls, and methodologies for mapping conformational IgE binding epitopes need to be developed.

Synthesis, modification and application of fish skin gelatin-based hydrogel as sustainable and versatile bioresource of antidiabetic peptide

Gelatin hydrogel is widely employed in various fields, however, commercially available gelatin hydrogels are mostly derived from mammalian which has many disadvantages due to the supply and ethical issues. In this study, the properties of hydrogels from fish-derived collagen fabricated with varying Glutaraldehyde (GA) determined. The antidiabetic properties of salmon gelatin (SG) and tilapia gelatin (TG) was also evaluated against α-glucosidase. Glutaraldehyde-crosslinked salmon gelatin and tilapia gelatin were used, and compared with different concentrations of GA by 0.05 %, 0.1 %, and 0.15 %. Water absorbency, swelling, porosity, pore size and water retention of the hydrogels were dependent on the degree of crosslinking. The synthesis of hydrogels was confirmed by FTIR study. Scanning electron microscope (SEM) observation showed that all hydrogels have a porous structure with irregular shapes and heterogeneous morphology. Performance tests showed that gelatin-GA 0.05 % mixture had the best performance. Antidiabetic bioactivity in vitro and in silico tests showed that the active peptides of SG and TG showed a high binding affinity to α-glucosidase enzyme. In conclusion, SG and TG cross-linked GA 0.05 % have the potential as an antidiabetic agent and as a useful option over mammalian-derived gelatin.

Critical features of an in vitro intestinal absorption model to study the first key aspects underlying food allergen sensitization

New types of protein sources will enter our diet in a near future, reinforcing the need for a straightforward in vitro (cell-based) screening model to test and predict the safety of these novel proteins, in particular their potential risk for de novo allergic sensitization. The Adverse Outcome Pathway (AOP) for allergen sensitization describes the current knowledge of key events underlying the complex cellular interactions that proceed allergic food sensitization. Currently, there is no consensus on the in vitro model to study the intestinal translocation of proteins as well as the epithelial activation, which comprise the first molecular initiation events (ME1-3) and the first key event of the AOP, respectively. As members of INFOGEST, we have highlighted several critical features that should be considered for any proposed in vitro model to study epithelial protein transport in the context of allergic sensitization. In addition, we defined which intestinal cell types are indispensable in a consensus model of the first steps of the AOP, and which cell types are optional or desired when there is the possibility to create a more complex cell model. A model of these first key aspects of the AOP can be used to study the gut epithelial translocation behavior of known hypo- and hyperallergens, juxtaposed to the transport behavior of novel proteins as a first screen for risk management of dietary proteins. Indeed, this disquisition forms a basis for the development of a future consensus model of the allergic sensitization cascade, comprising also the other key events (KE2-5).

Bile Acid Profile Influences Digestion Resistance and Antigenicity of Soybean 7S Protein

Soybean 7S storage protein (β-conglycinin) is the most important allergen, exhibits resistance in gastrointestinal (GI) digestion, and causes allergies in humans and animals. A previous study has demonstrated that 7S proteins contained innate amyloid aggregates, but the fate of these specific protein aggregates in intestinal digestion and correlation to allergenicity are unclear. In this study, via a modified INFOGEST static in vitro digestion and IgE binding test, we illustrate that the survived amyloid aggregates of soybean 7S protein in GI digestion might be dominant IgE epitopes of soybean protein in humans. The impact of conjugated primary bile acid salt (BS) profile on digestion resistance and immunogenicity of soybean protein is assessed, regarding the binding affinity of BS to protein aggregates with consideration of the BS composition and the physiologically relevant colloidal structure. The results show that chenodeoxycholate-containing colloidal structures exhibit high affinity and unfolding capacity to protein amyloid aggregates, promoting proteolysis by pancreatic enzymes and thus mitigating the antigenicity of soybean protein. This study presents a novel understanding of bile acid profile and colloidal structure influence on the digestibility and antigenicity of dietary proteins. It should be helpful to design in vitro digestion protocol and accurately replicate physiologically relevant digestion conditions.

Intestinal protein uptake and IgE-mediated food allergy

Food allergy is affecting 5-8% of young children and 2-4% of adults and seems to be increasing in prevalence. The cause of the increase in food allergy is largely unknown but proposed to be influenced by both environmental and lifestyle factors. Changes in intestinal barrier functions and increased uptake of dietary proteins have been suggested to have a great impact on food allergy. In this review, we aim to give an overview of the gastrointestinal digestion and intestinal barrier function and provide a more detailed description of intestinal protein uptake, including the various routes of epithelial transport, how it may be affected by both intrinsic and extrinsic factors, and the relation to food allergy. Further, we give an overview of in vitro, ex vivo and in vivo techniques available for evaluation of intestinal protein uptake and gut permeability in general. Proteins are digested by gastric, pancreatic and integral brush border enzymes in order to allow for sufficient nutritional uptake. Absorption and transport of dietary proteins across the epithelial layer is known to be dependent on the physicochemical properties of the proteins and their digestion fragments themselves, such as size, solubility and aggregation status. It is believed, that the greater an amount of intact protein or larger peptide fragments that is transported through the epithelial layer, and thus encountered by the mucosal immune system in the gut, the greater is the risk of inducing an adverse allergic response. Proteins may be absorbed across the epithelial barrier by means of various mechanisms, and studies have shown that a transcellular facilitated transport route unique for food allergic individuals are at play for transport of allergens, and that upon mediator release from mast cells an enhanced allergen transport via the paracellular route occurs. This is in contrast to healthy individuals where transcytosis through the enterocytes is the main route of protein uptake. Thus, knowledge on factors affecting intestinal barrier functions and methods for the determination of their impact on protein uptake may be useful in future allergenicity assessments and for development of future preventive and treatment strategies.

Comprehensive COMPARE database reduces allergenic risk of novel food proteins

The comprehensiveness of the allergen database used to bioinformatically compare a novel food protein with known allergens is critical to the ability to assess the allergenic risk of newly expressed proteins in genetically engineered crops. The strength of the relationship between a candidate GE protein's amino acid sequence and that of known allergens is used to predict cross-reactive risk. The number of truly novel allergen sequences added annually to the COMPARE database reflects on the comprehensiveness of our knowledge of allergen amino acid sequence diversity. Here, we investigated the most recent five years of updates to the COMPARE allergen database for truly novel entries. Results indicate that few truly novel sequences are added each year, suggesting that the database and our knowledge of allergen sequence diversity is currently quite comprehensive, and that current in silico prediction of allergenic risk for novel food proteins is robust.

Slow alignment of GMO allergenicity regulations with science on protein digestibility

The current science on food allergy supports the dual allergen exposure hypothesis where sensitization to allergenic proteins is favored by dermal and inhalation exposure, and tolerization against allergy is favored by exposure in the gut. This hypothesis is bolstered by the epidemiological evidence showing that regions where children are exposed early in life to allergenic foods have lower rates of allergy. This led medical experts to replace the previous recommendation to exclude commonly allergenic foods from the diets of young children with the current recommendation that such foods be introduced to children early in life. Past beliefs that lowering gut exposure would reduce the likelihood that a protein would be allergenic led regulators and risk assessors to consider digestively stable proteins to be of greater allergenic risk. This resulted in international guidance and government regulations for newly expressed proteins in genetically engineered crops that aligned with this belief. Despite empirical results showing that allergens are no more digestively stable than non-allergens, and that gut exposure favors tolerization over sensitization, regulations have not come into alignment with the current science prompting developers to continue to engineer proteins for increased digestibility. In some rare cases, this could potentially increase sensitization risk.

Caco-2 Cell Response Induced by Peptides Released after Digestion of Heat-Treated Egg White Proteins

The heat treatment of food proteins induces structural modifications that influence their interaction with human fluids and cells. We aimed to evaluate the Caco-2 cell response induced by peptides produced after digestion of heat-treated egg white proteins. In vitro digestion of ovalbumin (OVA), ovomucoid (OM), and lysozyme (LYS), untreated or previously heated, was performed. The digestibility of proteins and the response of Caco-2 cells exposed to peptides (<10 kDa) generated during digestion were evaluated. Intact OVA and LYS persisted after the digestion of native proteins, whereas OM was completely hydrolysed. A heat treatment at 65 °C for 30 min did not alter the digestibility of OVA, whereas at 90 °C for 3 min, protein degradation was favoured. The digestibility of OM and LYS was not affected by heat treatment. Peptides derived from OVA and OM digestion induced IL-6 and IL-8 production. OVA and LYS digestion promoted the expression of Tslp, and Il6 and Il33, respectively. A heat treatment prior to OVA digestion reduced IL-6 production and Tslp expression. It was concluded that heat treatments can reduce the release of OVA-derived peptides, but not OM and LYS, with proinflammatory activity during digestion.

IgE-Binding and Immunostimulating Properties of Enzymatic Crosslinked Milk Proteins as Influenced by Food Matrix and Digestibility

Dairy foods are essential in the diet, although in some susceptible individuals they may cause allergy to cow's milk proteins. Therefore, alternative methods are sought to reduce their allergenicity. Transglutaminase (TG) is widely used in dairy products mainly to improve texture. Although it has been claimed that TG can be used to modify the digestibility and allergenicity of foods, its impact within a real matrix has been rarely studied. The aim of this work was to assess the allergenic potential of crosslinked skim milk (SM), milk casein fraction (CN), and whey protein (WP). To this purpose, inhibition ELISA with sera from milk allergic patients, in vitro activation tests of mouse mast cells and splenocytes, and simulated gastrointestinal digestion assays were performed. The results showed that cross-linking increased the binding of IgE to WP, but decreased IgE-binding to SM and CN. However, no differences were observed in the ability of cross-linked proteins to induce mast cell degranulation compared to native proteins. The cross-linking of SM and CN reduced Th2 cytokine release from the splenocytes of sensitized mice. All TG-treated samples exhibited more resistance to in vitro digestion than the untreated proteins and the human IgE binding capacity after digestion was higher. In conclusion, TG treatment of milk proteins does not reduce the risk of eliciting allergic symptoms in cow's milk allergic patients.

pH-dependent structural diversity of profilin allergens determines thermal stability

The family of profilin allergens is a common class of proteins found in plants, viruses and various eukaryotes including mammals. Profilins are characterized by an evolutionary conserved structural fold, which is responsible for their cross-reactive nature of Immunoglobulin E (IgE) antibodies. Despite their high overall structural similarity, they exhibit substantial differences in their biophysical properties, such as thermal and pH stability. To understand the origin of these functional differences of Amb a 8, Art v 4 and Bet v 2, we performed constant pH molecular dynamics simulation in combination with Gaussian accelerated MD simulations. Depending on the respective protonation at different pH levels, we find distinct differences in conformational flexibility, which are consistent with experimentally determined melting temperatures. These variations in flexibility are accompanied by ensemble shifts in the conformational landscape and quantified and localized by residue-wise B-factors and dihedral entropies. These findings strengthen the link between flexibility of profilin allergens and their thermal stability. Thus, our results clearly show the importance of considering protonation dependent conformational ensembles in solution to elucidate biophysical differences between these structurally similar allergens.

Simulated gastric fluid assay for estimating the digestibility of newly expressed proteins in GE crops: Missteps in development and interpretation

Digestive stability of a food protein in simulated gastric fluid (SGF) continues to be considered a risk factor for allergy, even though the current science does not support this belief. Methodological shortcomings of the adaption of the SGF assay for use with purified proteins has been cited as a reason to discount results that do not conform to this belief. Missteps in conducting and interpreting the results of SGF assays are reviewed here. However, these methodological shortcomings do not invalidate the conclusion that allergenic proteins are not systematically more stable to digestion than non-allergens. The growing evidence for the dual allergen exposure hypothesis, whereby sensitization to food allergens is primarily caused by dermal and inhalation exposure to food dust, and tolerization against food allergy is primarily induced by gut exposure in food, likely explains why the digestive stability of a protein is not a risk factor for allergenicity.

Cottonseed Meal Protein Isolate as a New Source of Alternative Proteins: A Proteomics Perspective

Cottonseed meal (CSM) is a good source of dietary proteins but is unsuitable for human consumption due to its gossypol content. To unlock its potential, we developed a protein extraction process with a gossypol removal treatment to generate CSM protein isolate (CSMPI) with ultra-low gossypol content. This process successfully reduced the free and total gossypol content to 4.8 ppm and 147.2 ppm, respectively, far below the US FDA limit. In addition, the functional characterisation of CSMPI revealed a better oil absorption capacity and water solubility than pea protein isolate. Proteome profiling showed that the treatment improved protein identification, while SDS-PAGE analysis indicated that the treatment did not induce protein degradation. Amino acid analysis revealed that post-treated CSMPI was rich in branched-chain amino acids (BCAAs). Mass spectrometry analysis of various protein fractions obtained from an in vitro digestibility assay helped to establish the digestibility profile of CSM proteins. Several potential allergens in CSMPI were also found using allergenic prediction software, but further evaluation based on their digestibility profiles and literature reviews suggests that the likelihood of CSMPI allergenicity remains low. Overall, our results help to navigate and direct the application of CSMPIs as alternative proteins toward nutritive human food application.

Assessing protein digestibility in allergenicity risk assessment: A comparison of in silico and high throughput in vitro gastric digestion assays

The susceptibility of a novel food protein to digestion in the pepsin resistance test is widely used to inform the allergenicity risk assessment process. However, it does not model the variation in the intragastric environment found in vivo. Consequently a 96-well plate format in vitro gastric digestion protocol has been developed with a high and low pepsin activity test executed at pH 1.2, 2.5, 5.5 and 6.5. It was used to analyse seven allergens (from milk, egg, peach and peanut) and two non-allergens (cytochrome c and zein). Digestion was monitored using SDS-PAGE and densitometry. In silico predictions were not confirmed experimentally for most of the proteins studied. Proteins were ranked according to half-life and showed susceptibility to digestion was related to the stability of protein structure and protein solubility rather than allergenicity per se. Highly digestible proteins, such as β-casein and Ara h 1, generated abundant resistant fragments Mr > 3.5 kDa in the low pepsin activity test which could be immunologically significant within the context of allergenicity risk assessment for susceptible groups such as infants. The high- and low pepsin activity tests used in this study provided complementary data to support allergenicity risk assessment and used only 10 mg protein.

Is There Evidence of Health Risks From Exposure to Micro- and Nanoplastics in Foods?

The human health impact of exposure to micro (MP) and nanoplastics (NP) from food remains unknown. There are several gaps in knowledge that prevent a complete risk assessment of them. First, the fact that some plastics may be chemically harmful, either directly toxic themselves or because they absorb and carry other components, which makes these particles may possess 3 types of hazards, physical, chemical and biological. In addition, the levels at which toxic effects may occur are unknown and there is a lack of studies to estimate the levels to which we are exposed. Plastic particles can induce physical stress and damage, apoptosis, necrosis, inflammation, oxidative stress and immune responses, which could contribute to the development of diseases such as cancer, metabolic disorders, and neurodevelopmental conditions, among others. In addition, they may have effects on other pathologies that have not yet been studied, such as food allergy, where they could act modifying the digestibility of food allergens, increasing intestinal permeability, promoting an intestinal inflammatory environment or causing intestinal dysbiosis, which could promote food allergen sensitization. However, given the limited information on the presence of MP and especially NP in food, further research is needed to estimate whether they could amplify the risk of allergic sensitization to food proteins and to elucidate the risk to human health.

Risk–benefit assessment of seaweed Allergenicity risk assessment of novel protein

As the world population rapidly grows, there is a clear need for alternative food sources, particularly for the provision of protein. Seaweed is one such alternative source of protein that requires greater investigation. In this context, a working programme within the European Food Risk Assessment (EU‐FORA) Fellowship Programme framework was developed at National Food Institute – Technical University of Denmark. This Programme is an initiative of the EFSA with the aim to build a European risk assessment community. The purpose of this technical report is to describe the activities in which the fellow was involved. As part of the Research Group for Risk–Benefit, the fellow performed a risk–benefit assessment of seaweed Palmaria palmata gaining an in‐depth expertise in all the steps. The health impact of Palmaria palmata consumption was estimated, considering its high nutritional value but also highlighting concerns towards some components. Simultaneous to the work on the risk–benefit, the fellow also worked within the Research Group for Food Allergy, specifically on the allergenicity risk assessment of a plant‐based novel protein (seaweed protein) using different laboratory assays. Seaweed protein digestibility was assessed, and its digestion products were characterised and assessed for immunogenicity. Finally, the fellow collaborated with the Research Group for Microbial Biotechnology and Biorefining in the development of a novel food (alfalfa protein) application dossier to be submitted to EFSA, gaining expertise in the risk assessment of a novel food. In conclusion, the present working programme, together with additional activities and training provided by different institutions, enabled the fellow to gain a broader perspective in food safety, particularly concerning seaweed, novel foods and the safety assessment of novel proteins.

Erroneous Belief that Digestive Stability Predicts Allergenicity May Lead to Greater Risk for Novel Food Proteins

There continues to be an erroneous belief that allergens (especially food allergens) are more resistant to gastrointestinal digestion than non-allergens. Government regulations based on this erroneous belief may result in technology developers altering the amino acid sequences of digestively stable native proteins to create digestively unstable modified versions for expression in genetically engineered crops. However, an investigation where a known stable allergen was modified to make it more digestible eliminated the protein’s ability to tolerize against allergy in a mouse model, which is consistent with the dual allergen exposure hypothesis. Thus, the false belief that digestive stability increases the allergenic risk of novel food proteins (e.g., such as expressed in genetically engineered crops) could, in some cases, lead to introduction of digestively unstable modified protein versions with greater sensitization risk. However, it is noteworthy that developers have historically been very effective at preventing allergens from being introduced into crops based on the other components of the weight-of-evidence assessment of allergenic risk such that no newly expressed protein in any commercialized genetically engineered crop has ever been documented to cause allergy in anyone.

Advances in static in vitro digestion models after the COST action Infogest consensus protocol

In vitro digestion models are essential to predictively evaluate the bioaccessibility and bioactivity of food molecules or natural products. Dynamic models better simulate the gastrointestinal conditions as they reproduce similar physiological environments. Despite this, static methods, also known as biochemical methods, represent a simple and useful approach for the study of different types of molecules, with a broad applicability in the nutritional, pharmaceutical, and toxicological fields. In addition, static models can be validated, avoiding the disadvantage of a difficult reproducibility of dynamic in vitro systems and inter-individual variations of in vivo experiments. A crucial point in the standardization of static models was the COST Action Infogest in 2014, which elaborated an international consensus static digestion method to harmonize experimental conditions and has general guidelines, thus allowing the comparison of studies and data. The aim of our review is to underline the impact of the Infogest consensus method and the development and evolution of in vitro static methods in the following years, with a focus on food applications.

No Glycation Required: Interference of Casein in AGE Receptor Binding Tests

For the determination of the binding of heated cow’s milk whey proteins such as β-lactoglobulin to the receptors expressed on immune cells, inhibition ELISA with the soluble form of the receptor for advanced glycation end products (sRAGE) and scavenger receptor class B (CD36) has been successfully used in the past. However, binding to heated and glycated caseins in this read-out system has not been tested. In this study, inhibition ELISA was applied to measure the binding of cow’s milk casein alone, as well as all milk proteins together, which underwent differential heat treatment, to sRAGE and CD36, and we compared those results to a dot blot read out. Moreover, binding to sRAGE and CD36 of differentially heated milk protein was measured before and after in vitro digestion. Casein showed binding to sRAGE and CD36, independent from the heat treatment, in ELISA, while the dot blot showed only binding to high-temperature-heated milk protein, indicating that the binding is not related to processing but to the physicochemical characteristics of the casein. This binding decreased after passage of casein through the intestinal phase.

The pattern of peptides released from dairy and egg proteins is highly dependent on the simulated digestion scenario

Evaluating the gastrointestinal (GI) fate of proteins is part of the assessment to determine whether proteins are safe to consume. In vitro digestion tests are often used for screening purposes in the evaluation of potential allergenicity. However, the current pepsin resistant test used by the European Food Safety Authority, only corresponds to fasted gastric conditions representative of a late phase adult stomach. In addition, these tests are performed on isolated proteins and the effect of the food matrix and processing are not systematically considered. The aim of this research is to compare three different static in vitro GI scenarios that are physiologically relevant. Namely, an infant, early phase (fed state) adult and late phase (fasted state) adult model. These protocols are applied to well-characterised isolated dairy (β-lactoglobulin and β-casein) and egg (lysozyme and ovalbumin) proteins and the impact of food matrix/processing on their proteolysis is also investigated. A combination of SDS-PAGE, LC-MS/MS and spectrophotometric assay was used for the evaluation of the proteolysis. Results highlight differences across the three GI scenarios whether on isolated proteins or within food matrices. The infant model led to incomplete digestion, leaving intact egg proteins, either isolated or in the food matrix, and intact β-lactoglobulin in the milk. In addition, peptides greater than 9 amino acids were found throughout the intestinal phase for all proteins studied, regardless of the scenario. This reinforces the difficulty of linking protein digestibility to potential allergenicity because many other factors are involved that need further investigation.

Mass spectrometric analysis of digesta does not improve the allergenicity assessment of GM crops

An investigation of the potential allergenicity of newly expressed proteins in genetically modified (GM) crops comprises part of the assessment of GM crop safety. However, allergenicity is not completely predictable from a definitive assay result or set of protein characteristics, and scientific opinions regarding the data that should be used to assess allergenicity are continuously evolving. Early studies supported a correlation between the stability of a protein exposed to digestive enzymes such as pepsin and the protein’s status as a potential allergen, but over time the conclusions of these earlier studies were not confirmed. Nonetheless, many regulatory authorities, including the European Food Safety Authority (EFSA), continue to require digestibility analyses as a component of GM crop risk assessments. Moreover, EFSA has recently investigated the use of mass spectrometry (MS), to make digestion assays more predictive of allergy risk, because it can detect and identify small undigested peptides. However, the utility of MS is questionable in this context, since known allergenic peptides are unlikely to exist in protein candidates intended for commercial development. These protein candidates are pre-screened by the same bioinformatics processes that are normally used to identify MS targets. Therefore, MS is not a standalone allergen identification method and also cannot be used to predict previously unknown allergenic epitopes. Thus, the suggested application of MS for analysis of digesta does not improve the poor predictive power of digestion assays in identifying allergenic risk.

Gastric Enzyme Supplementation Inhibits Food Allergy in a BALB/c Mouse Model

Impaired gastric digestion due to suppressed gastric acidity enhances the risk for food allergy development. In the current study, we aimed to evaluate the impact of a supported gastric digestion via application of a pharmaceutical gastric enzyme solution (GES) on food allergy development and allergic reactions in a BALB/c mouse model. The ability of the GES to restore hypoacidic conditions was tested in mice treated with gastric acid suppression medication. To evaluate the impact on allergic symptoms, mice were orally sensitized with ovalbumin (OVA) under gastric acid suppression and subjected to oral challenges with or without GES. The immune response was evaluated by measurement of antibody titers, cytokine levels, mucosal allergy effector cell influx and regulatory T-cell counts. Clinical response was objectified by core body temperature measurements after oral OVA challenge. Supplementation of GES transiently restored physiological pH levels in the stomach after pharmaceutical gastric acid suppression. During oral sensitization, supplementation of gastric enzymes significantly reduced systemic IgE, IgG1 and IgG2a levels and allergic symptoms. In food allergic mice, clinical symptoms were reduced by co-administration of the gastric enzyme solution. Support of gastric digestion efficiently prevents food allergy induction and alleviates clinical symptoms in our food allergy model.

Two Faces of Milk Proteins Peptides with Both Allergenic and Multidimensional Health Beneficial Impact- Integrated In Vitro/In Silico Approach

The main food-origin antigens that the infant's body is in contact with are cow's milk proteins (CMP). Still, CMP are one of the main sources of beneficial biologically active peptides that play a role in treatment of non-communicable diseases. Safe methods to quickly predict the sensitizing potential of food proteins among their range of health-promoting properties are essential. The aim of study was to adapt an integrated approach combining several in silico (IS) studies and in vitro (IV) assays to screen the multifunctionality of CMP-derived peptides. Major histocompatability complex type II MHC II-binders, interleukin-4 and -10 inducers, interferon γ -inducers and immunobioactivity tools were used to predict the peptide-power of inducing allergies or tolerance. A comparison of the peptide profiless revealed the presence of one identical and one overlapping sequence in IS and IV hydrolysate. By IS analysis, four of 24 peptides were found to have high affinity and stimulate IL-4 expression, and by IV, one of seven peptides had this potential (Bos d9 peptide DIPNPIGSENSEK (195-208)). Three IV peptides may induce IL-10 expression. The IV/IS assessment seems promising agents for peptides' potential determination dedicated only to preliminary screening of peptides. The IV verification is still crucial in further steps of studies.

Digestion and Transport across the Intestinal Epithelium Affects the Allergenicity of Ara h 1 and 3 but Not of Ara h 2 and 6

Scope

No accepted and validated methods are currently available which can accurately predict protein allergenicity. In this study, the role of digestion and transport on protein allergenicity is investigated.

Methods and results

Peanut allergens (Ara h 1, 2, 3, and 6) and a milk allergen (β‐lactoglobulin) are transported across pig intestinal epithelium using the InTESTine model and afterward basophil activation is measured to assess the (remaining) functional properties. Additionally, allergens are digested by pepsin prior to epithelial transport and their allergenicity is assessed in a human mast cell activation assay. Remarkably, transported Ara h 1 and 3 are not able to activate basophils, in contrast to Ara h 2 and 6. Digestion prior to transport results in a significant increase in mast cell activation of Ara h 1 and 3 dependent on the length of digestion time. Activation of mast cells by Ara h 2 and 6 is unaffected by digestion prior to transport.

Conclusions

Digestion and transport influences the allergenicity of Ara h 1 and 3, but not of Ara h 2 and 6. The influence of digestion and transport on protein allergenicity may explain why current in vitro assays are not predictive for allergenicity.

pH-Induced Local Unfolding of the Phl p 6 Pollen Allergen From cpH-MD

Susceptibility to endosomal degradation is a decisive contribution to a protein's immunogenicity. It is assumed that the processing kinetics of structured proteins are inherently linked to their probability of local unfolding. In this study, we quantify the impact of endosomal acidification on the conformational stability of the major timothy grass pollen allergen Phl p 6. We use state of the art sampling approaches in combination with constant pH MD techniques to profile pH-dependent local unfolding events in atomistic detail. Integrating our findings into the current view on type 1 allergic sensitization, we characterize local protein dynamics in the context of proteolytic degradation at neutral and acidic pH for the wild type protein and point mutants with varying proteolytic stability. We analyze extensive simulation data using Markov state models and retrieve highly reliable thermodynamic and kinetic information at varying pH levels. Thereby we capture the impact of endolysosomal acidification on the structure and dynamics of the Phl p 6 mutants. We find that upon protonation at lower pH values, the conformational flexibilities in key areas of the wild type protein, i.e., T-cell epitopes and early proteolytic cleavage sites, increase significantly. A decrease of the pH even leads to local unfolding in otherwise stable secondary structure elements, which is a prerequisite for proteolytic cleavage. This effect is even more pronounced in the destabilized mutant, while no unfolding was observed for the stabilized mutant. In summary, we report detailed structural models which rationalize the experimentally observed cleavage pattern during endosomal acidification.

Statement on in vitro protein digestibility tests in allergenicity and protein safety assessment of genetically modified plants

This statement supplements and updates the GMO Panel guidance document on allergenicity of genetically modified (GM) plants published in 2017. In that guidance document, the GMO Panel considered that additional investigations on in vitro protein digestibility were needed before providing any additional recommendations in the form of guidance to applicants. Thus, an interim phase was proposed to assess the utility of an enhanced in vitro digestion test, as compared to the classical pepsin resistance test. Historically, resistance to degradation by pepsin using the classical pepsin resistance test has been considered as additional information, in a weight-of-evidence approach, for the assessment of allergenicity and toxicity of newly expressed proteins in GM plants. However, more recent evidence does not support this test as a good predictor of allergenic potential for hazard. Furthermore, there is a need for more reliable systems to predict the fate of the proteins in the gastrointestinal tract and how they interact with the relevant human cells. Nevertheless, the classical pepsin resistance test can still provide some information on the physicochemical properties of novel proteins relating to their stability under acidic conditions. But other methods can be used to obtain data on protein's structural and/or functional integrity. It is acknowledged that the classical pepsin resistance test is embedded into international guidelines, e.g. Codex Alimentarius and Regulation (EU) No 503/2013. For future development, a deeper understanding of protein digestion in the gastrointestinal tract could enable the framing of more robust strategies for the safety assessment of proteins. Given the high complexity of the digestion and absorption process of dietary proteins, it is needed to clarify and identify the aspects that could be relevant to assess potential risks of allergenicity and toxicity of proteins. To this end, a series of research questions to be addressed are also formulated in this statement.

Are Physicochemical Properties Shaping the Allergenic Potency of Plant Allergens?

This review searched for published evidence that could explain how different physicochemical properties impact on the allergenicity of food proteins and if their effects would follow specific patterns among distinct protein families. Owing to the amount and complexity of the collected information, this literature overview was divided in two articles, the current one dedicated to protein families of plant allergens and a second one focused on animal allergens. Our extensive analysis of the available literature revealed that physicochemical characteristics had consistent effects on protein allergenicity for allergens belonging to the same protein family. For example, protein aggregation contributes to increased allergenicity of 2S albumins, while for legumins and cereal prolamins, the same phenomenon leads to a reduction. Molecular stability, related to structural resistance to heat and proteolysis, was identified as the most common feature promoting plant protein allergenicity, although it fails to explain the potency of some unstable allergens (e.g. pollen-related food allergens). Furthermore, data on physicochemical characteristics translating into clinical effects are limited, mainly because most studies are focused on in vitro IgE binding. Clinical data assessing how these parameters affect the development and clinical manifestation of allergies is minimal, with only few reports evaluating the sensitising capacity of modified proteins (addressing different physicochemical properties) in murine allergy models. In vivo testing of modified pure proteins by SPT or DBPCFC is scarce. At this stage, a systematic approach to link the physicochemical properties with clinical plant allergenicity in real-life scenarios is still missing.

Bringing the digestibility of prebiotics into focus: update of carbohydrate digestion models

Oro-gastrointestinal digestion of dietary carbohydrates involves up to six different carbohydrases in a multistage process. Enzymes from the small intestinal brush border membrane play a major role in the digestibility of these substrates. However, to date, the inclusion of these small intestinal enzymes has been dismissed in most in vitro studies carried out, despite their importance in the degradation of carbohydrates. Several in vitro and in vivo studies have demonstrated the capability of brush border enzymes to degrade certain "non-digestible" carbohydrates to a different extent depending on their structural composition (monomeric composition, glycosidic linkage, etc.). In this sense, considering the available evidence, mucosal disaccharidases embedded in the small intestinal brush border membrane vesicles must be considered in addition to α-amylases; therefore, new approaches for the evaluation of the digestibility of carbohydrates have been recently reported. These new methods based on the utilization of the small intestinal enzymes present in the brush border membrane aim to fulfill the final and key step of the digestion of carbohydrates in the small intestine. Here, rat small intestinal extract enzymes as well as brush border membrane vesicles from pig have emerged as very reliable and useful tools to evaluate carbohydrate digestion. Thus, this review aims to go briefly through the most relevant digestion methods for carbohydrates that are currently available and to highlight the new improved methods, which include mammalian intestinal enzymes, and their current use in the evaluation of the digestibility of prebiotics.

Immunogenic Potential of Beer Types Brewed With Hordeum and Triticum spp. Malt Disclosed by Proteomics

The protein/peptide composition of five beer kinds, including two experimental beer-like products brewed with einkorn (Triticum monococcum), a beer labeled as “gluten-free,” a traditional all-barley malt and a wheat (T. aestivum) containing beer, was characterized with HPLC-ESI MS/MS-based proteomics. To enlarge the characterization of the components, the polypeptides were fractionated according to their molecular size (cut-off 6 kDa). All the beer types contained a variety of polypeptides arising from all the gliadin subfamilies (α-/β-, γ-, and ω-gliadins) able to induce an immune response in celiac disease (CD) patients in addition to a panel of IgE-reactive food allergens. Wheat storage proteins were heavily hydrolyzed in the beer samples brewed with einkorn. The presence of gluten-like fragments, also including the 25-mer and 33-mer-like of α-gliadin, was confirmed in beer brewed with barley and wheat malt as well as in the gluten-free beer. Both CD-toxic and allergenic peptides of all beer samples were drastically degraded when subjected to a simulated gastroduodenal (GD) digestion. After in vitro digestion, the level of gluten-like peptides assayed with the G12 competitive ELISA, was below the threshold (20 ppm) for a food to be considered as “gluten-free.” A few gliadin-derived epitopes occurred in the digests of beers crafted with wheat or Norberto-ID331 line of einkorn. In contrast, digests of all barley malt and gluten-free beers did not contain detectable gluten-like epitopes, but only minor fragments of hordeins and IgE-reactive food allergens. All beer samples evoked a weak immune response on gliadin-reactive celiac T cells isolated from intestinal biopsies of celiac patients. Compared to undigested polypeptides, the response was markedly reduced by GD digestion. Although the consumption of a moderate amount of beer brewed with barley or einkorn could deliver a relatively low amount of CD-toxic epitopes, the findings of this study emphasize the urgent need of a reliable and accurate quantification of gluten epitopes in all types of beer, also including the gluten-free one, to compute realistically the contribution of beer to the overall gluten intake, which can be responsible of intestinal tissue damages in celiacs.

In vitro gastroduodenal and jejunal brush border membrane digestion of raw and roasted tree nuts

Heat treatments induce chemical/physical modifications, which may affect the stability to enzymatic digestion and consequently the allergenicity of food proteins to a varying extent, depending on the time/temperature regimen. Herein, we evaluated the stability to digestion of whole tree nut (walnuts, hazelnuts and almonds) allergens in a food digestion model reflecting the real one by, taking into consideration the allergen-containing processed (roasted) food. To this aim, whole raw and roasted tree nuts were subjected to in vitro digestion combining the harmonized oral-gastric-duodenal digestion models with brush border membrane enzymes (BBM) to simulate the jejunal degradation of peptides. The degradation of allergens was monitored by integrated proteomic/peptidomic and bio-informatic tools. Roasting increased digestibility of tree nuts, since very few peptides were detected in digested samples (<6.5 kDa fraction). After BBM digestion step, the degradation of peptides was enhanced in roasted walnuts and hazelnuts compared to the raw counterpart. Conversely, almond allergens showed a different behaviour, since the presence of resistant peptides was more evident for roasted almonds, probably because of the hydrolysis of high molecular weight aggregates generated during roasting. Our results provide new insight into the relationship between thermal processing and metabolic fate of tree nut allergens, highlighting the importance of investigating the digestion stability of whole allergenic food, rather than purified proteins.

Allergenicity of Fermented Foods: Emphasis on Seeds Protein-Based Products

Food allergy is an IgE-mediated abnormal response to otherwise harmless food proteins, affecting between 5% and 10% of the world preschool children population and 1% to 5% adults. Several physical, chemical, and biotechnological approaches have been used to reduce the allergenicity of food allergens. Fermentation processes that contribute to technological and desirable changes in taste, flavor, digestibility, and texture of food products constitute one of these approaches. Lactic acid bacteria (LAB), used as starter cultures in dairy products, are a subject of increasing interest in fermentation of plant proteins. However, the studies designed to assess the impact of LAB on reduction of allergenicity of seed proteins are at an early stage. This review presents the current knowledge on food fermentation, with a focus on seed proteins that are increasingly used as ingredients, and its impacts on food potential allergenicity.

Presence of small resistant peptides from new in vitro digestion assays detected by liquid chromatography tandem mass spectrometry: An implication of allergenicity prediction of novel proteins?

The susceptibility of newly expressed proteins to digestion by gastrointestinal proteases (e.g., pepsin) has long been regarded as one of the important endpoints in the weight-of-evidence (WOE) approach to assess the allergenic risk of genetically modified (GM) crops. The European Food Safety Authority (EFSA) has suggested that current digestion study protocols used for this assessment should be modified to more accurately reflect the diverse physiological conditions encountered in human populations and that the post-digestion analysis should include analytical methods to detect small peptide digestion products.The susceptibility of two allergens (beta-lactoglobin (β-Lg) and alpha-lactalbumin (α-La)) and two non-allergens (hemoglobin (Hb) and phosphofructokinase (PFK)) to proteolytic degradation was investigated under two pepsin digestion conditions (optimal pepsin digestion condition: pH 1.2, 10 U pepsin/μg test protein; sub-optimal pepsin digestion condition: pH 5.0, 1 U pepsin/10 mg test protein), followed by 34.5 U trypsin/mg test protein and 0.4 U chymotrypsin/mg test protein digestion in the absence or presence of bile salts. All samples were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in conjunction with Coomassie Blue staining and, in parallel, liquid chromatography tandem mass spectrometry (LC-MS) detection. The results provide following insights: 1) LC-MS methodology does provide the detection of small peptides; 2) Peptides are detected in both allergens and non-allergens from all digestion conditions; 3) No clear differences among the peptides detected from allergen and non-allergens; 4) The differences observed in SDS-PAGE between the optimal and sub-optimal pepsin digestion conditions are expected and align with kinetics and properties of the specific enzymes; 5) The new methodology with new digestion conditions and LC-MS detection does not provide any differentiating information for prediction whether a protein is an allergen. The classic pepsin resistance assay remains the most useful assessment of the potential exposure of an intact newly expressed protein as part of product safety assessment within a WOE approach.

Dynamics Rationalize Proteolytic Susceptibility of the Major Birch Pollen Allergen Bet v 1

Proteolytic susceptibility during endolysosomal degradation is decisive for allergic sensitization. In the major birch pollen allergen Bet v 1 most protease cleavage sites are located within its secondary structure elements, which are inherently inaccessible to proteases. The allergen thus must unfold locally, exposing the cleavage sites to become susceptible to proteolysis. Hence, allergen cleavage rates are presumed to be linked to their fold stability, i.e., unfolding probability. Yet, these locally unfolded structures have neither been captured in experiment nor simulation due to limitations in resolution and sampling time, respectively. Here, we perform classic and enhanced molecular dynamics (MD) simulations to quantify fold dynamics on extended timescales of Bet v 1a and two variants with higher and lower cleavage rates. Already at the nanosecond-timescale we observe a significantly higher flexibility for the destabilized variant compared to Bet v 1a and the proteolytically stabilized mutant. Estimating the thermodynamics and kinetics of local unfolding around an initial cleavage site, we find that the Bet v 1 variant with the highest cleavage rate also shows the highest probability for local unfolding. For the stabilized mutant on the other hand we only find minimal unfolding probability. These results strengthen the link between the conformational dynamics of allergen proteins and their stability during endolysosomal degradation. The presented approach further allows atomistic insights in the conformational ensemble of allergen proteins and provides probability estimates below experimental detection limits.

Evidence runs contrary to digestive stability predicting protein allergenicity

A dogma has persisted for over two decades that food allergens are more stable to digestion compared with non-allergenic proteins. This belief has become enshrined in regulations designed to assess the allergenic risk of novel food proteins. While the empirical evidence accumulated over the last 20+ years has largely failed to confirm a correlation between digestive stability and the allergenic status of proteins, even those who accept this finding often assert that this shortfall is the result of faulty assay design rather than lack of causality. Here, we outline why digestive stability may not in fact correlate with allergenic potential.

Protein digestion of different protein sources using the INFOGEST static digestion model

In vitro digestion systems are valuable tools for understanding and monitoring the complex behavior of food degradation during digestion, thus proving to be good candidates for replacing in vivo assays. The aim of the present work was to study protein hydrolysis in a selection of different protein sources using the harmonized INFOGEST static protocol: three isolated proteins (collagen, zein, and whey protein) and five foods (sorghum flour, wheat bran cereals, peanuts, black beans, and pigeon peas). The proteins of all the substrates were analyzed by SDS-PAGE and HPLC-MS/MS. Individual amino acid composition was analyzed by high-performance liquid chromatography (HPLC). EAA/NEAA (essential amino acids/ nonessential amino acids) ratios in the substrates from low to high were as follows: wheat bran cereals, peanuts, collagen, zein, whey protein, sorghum, pigeon peas, and black beans. The results revealed sorghum, whey protein, and zein as good sources of BCAA. In all substrates, no intact protein from the substrates was visually detected by SDS-PAGE after the intestinal phase of in vitro digestion with the INFOGEST protocol. However, digestion-resistant peptides were detected in all substrates after the intestinal digestion phase. Protein hydrolysis was high in whey protein isolate and pigeon pea and low for wheat bran cereals and bovine collagen.

Allergen false-detection using official bioinformatic algorithms

Bioinformatic amino acid sequence searches are used, in part, to assess the potential allergenic risk of newly expressed proteins in genetically engineered crops. Previous work has demonstrated that the searches required by government regulatory agencies falsely implicate many proteins from rarely allergenic crops as an allergenic risk. However, many proteins are found in crops at concentrations that may be insufficient to cause allergy. Here we used a recently developed set of high-abundance non-allergenic proteins to determine the false-positive rates for several algorithms required by regulatory bodies, and also for an alternative 1:1 FASTA approach previously found to be equally sensitive to the official sliding-window method, but far more selective. The current investigation confirms these earlier findings while addressing dietary exposure.