Determination of the relative allergenic potency of proteins: hurdles and opportunities

Identification and semi-quantification of protein allergens in complex mixtures using proteomic and AllerCatPro 2.0 bioinformatic analyses: a proof-of-concept investigation

The demand for botanicals and natural substances in consumer products has increased in recent years. These substances usually contain proteins and these, in turn, can pose a risk for immunoglobulin E (IgE)-mediated sensitization and allergy. However, no method has yet been accepted or validated for assessment of potential allergenic hazards in such materials. In the studies here, a dual proteomic-bioinformatic approach is proposed to evaluate holistically allergenic hazards in complex mixtures of plants, insects, or animal proteins. Twelve commercial preparations of source materials (plant products, dust mite extract, and preparations of animal dander) known to contain allergenic proteins were analyzed by label-free proteomic analyses to identify and semi-quantify proteins. These were then evaluated by bioinformatics using AllerCatPro 2.0 (https://allercatpro.bii.a-star.edu.sg/) to predict no, weak, or strong evidence for allergenicity and similarity to source-specific allergens. In total, 4,586 protein sequences were identified in the 12 source materials combined. Of these, 1,665 sequences were predicted with weak or strong evidence for allergenic potential. This first-tier approach provided top-level information about the occurrence and abundance of proteins and potential allergens. With regards to source-specific allergens, 129 allergens were identified. The sum of the relative abundance of these allergens ranged from 0.8% (lamb's quarters) to 63% (olive pollen). It is proposed here that this dual proteomic-bioinformatic approach has the potential to provide detailed information on the presence and relative abundance of allergens, and can play an important role in identifying potential allergenic hazards in complex protein mixtures for the purposes of safety assessments.

Application of AllerCatPro 2.0 for protein safety assessments of consumer products

Foreign proteins are potentially immunogenic, and a proportion of these are able to induce immune responses that result in allergic sensitization. Subsequent exposure of sensitized subjects to the inducing protein can provoke a variety of allergic reactions that may be severe, or even fatal. It has therefore been recognized for some time that it is important to determine a priori whether a given protein has the potential to induce allergic responses in exposed subjects. For example, the need to assess whether transgene products expressed in genetically engineered crop plants have allergenic properties. This is not necessarily a straightforward exercise (as discussed elsewhere in this edition), but the task becomes even more challenging when there is a need to conduct an overall allergenicity safety assessment of complex mixtures of proteins in botanicals or other natural sources that are to be used in consumer products. This paper describes a new paradigm for the allergenicity safety assessment of proteins that is based on the use of AllerCatPro 2.0, a new version of a previously described web application model developed for the characterization of the allergenic potential of proteins. Operational aspects of AllerCatPro 2.0 are described with emphasis on the application of new features that provide improvements in the predictions of allergenic properties such as the identification of proteins with high allergenic concern. Furthermore, the paper provides a description of strategies of how AllerCatPro 2.0 can best be deployed as a screening tool for identifying suitable proteins as ingredients in consumer products as well as a tool, in conjunction with label-free proteomic analysis, for identifying and semiquantifying protein allergens in complex materials. Lastly, the paper discusses the steps that are recommended for formal allergenicity safety assessment of novel consumer products which contain proteins, including consideration and integration of predicted consumer exposure metrics. The article therefore provides a holistic perspective of the processes through which effective protein safety assessments can be made of potential allergenic hazards and risks associated with exposure to proteins in consumer products, with a particular focus on the use of AllerCatPro 2.0 for this purpose.

Designing healthier plant-based foods: Fortification, digestion, and bioavailability

Many consumers are incorporating more plant-based foods into their diets as a result of concerns about the environmental, ethical, and health impacts of animal sourced foods like meat, seafood, egg, and dairy products. Foods derived from animals negatively impact the environment by increasing greenhouse gas emissions, land use, water use, pollution, deforestation, and biodiversity loss. The livestock industry confines and slaughters billions of livestock animals each year. There are concerns about the negative impacts of some animal sourced foods, such as red meat and processed meat, on human health. The livestock industry is a major user of antibiotics, which is leading to a rise in the resistance of several pathogenic microorganisms to antibiotics. It is often assumed that a plant-based diet is healthier than one containing more animal sourced foods, but this is not necessarily the case. Eating more fresh fruits, vegetables, nuts, and whole grain cereals has been linked to improved health outcomes but it is unclear whether next-generation plant-based foods, such as meat, seafood, egg, and dairy analogs are healthier than the products they are designed to replace. Many of these new products are highly processed foods that contain high levels of saturated fat, sugar, starch, and salt, and low levels of micronutrients, nutraceuticals, and dietary fibers. Moreover, they are often rapidly digested in the gastrointestinal tract because processing disrupts plant tissues and releases the macronutrients. Consequently, it is important to formulate plant-based foods to reduce the levels of nutrients linked to adverse health effects and increase the levels linked to beneficial health effects. Moreover, it is important to design the food matrix so that the macronutrients are not digested and absorbed too quickly, but the micronutrients are highly bioavailable. In this article, we discuss how next-generation plant-based foods can be made healthier by controlling their nutrient profile, digestibility, and bioavailability.

AllerCatPro 2.0: a web server for predicting protein allergenicity potential

Proteins in food and personal care products can pose a risk for an immediate immunoglobulin E (IgE)-mediated allergic response. Bioinformatic tools can assist to predict and investigate the allergenic potential of proteins. Here we present AllerCatPro 2.0, a web server that can be used to predict protein allergenicity potential with better accuracy than other computational methods and new features that help assessors making informed decisions. AllerCatPro 2.0 predicts the similarity between input proteins using both their amino acid sequences and predicted 3D structures towards the most comprehensive datasets of reliable proteins associated with allergenicity. These datasets currently include 4979 protein allergens, 162 low allergenic proteins, and 165 autoimmune allergens with manual expert curation from the databases of WHO/International Union of Immunological Societies (IUIS), Comprehensive Protein Allergen Resource (COMPARE), Food Allergy Research and Resource Program (FARRP), UniProtKB and Allergome. Various examples of profilins, autoimmune allergens, low allergenic proteins, very large proteins, and nucleotide input sequences showcase the utility of AllerCatPro 2.0 for predicting protein allergenicity potential. The AllerCatPro 2.0 web server is freely accessible at https://allercatpro.bii.a-star.edu.sg.

Identifying a reference list of respiratory sensitizers for the evaluation of novel approaches to study respiratory sensitization

The induction of immunological responses that trigger bio-physiological symptoms in the respiratory tract following repeated exposure to a substance, is known as respiratory sensitization. The inducing compound is known as a respiratory sensitizer. While respiratory sensitization by high molecular weight (HMW) materials is recognized and extensively studied, much less information is available regarding low molecular weight (LMW) materials as respiratory sensitizers. Variability of symptoms presented in humans from such exposures, limited availability of (and access to) documented reports, and the absence of standardized and validated test models, hinders the identification of true respiratory sensitizers. This review aims to sort suspected LMW respiratory sensitizers based on available compelling, reasonable, inadequate, or questionable evidence in humans from occupational exposures and use this information to compose a reference list of reported chemical respiratory sensitizers for scientific research purposes. A list of 97 reported respiratory sensitizers was generated from six sources, and 52 LMW organic chemicals were identified, reviewed, and assigned to the four evidence categories. Less than 10 chemicals were confirmed with compelling evidence for induction of respiratory sensitization in humans from occupational exposures. Here, we propose the reference list for developing novel research on respiratory sensitization.

Enzymes and sensitization via skin exposure: A critical analysis

Some proteins, including enzymes, can induce allergic sensitization of various types, including allergic sensitization of the respiratory tract. There is now an increased understanding of the role that the skin plays in the development of IgE-mediated allergy and this prompts the question whether topical exposure to enzymes used widely in consumer cleaning products could result in allergic sensitization. Here, the evidence that proteins can interact with the skin immune system and the way they do so is reviewed, together with a consideration of the experience gained over decades of the use of enzymes in laundry and cleaning products. The conclusion drawn is that although transcutaneous sensitization to proteins can occur (typically through compromised skin) resulting in IgE antibody-mediated allergy, in practice such skin contact with enzymes used in laundry and cleaning products does not appear to pose a significant risk of allergic disease. Further, the evidence summarized in this publication support the view that proteins do not pose a risk of allergic contact dermatitis.

A rapid test for the environmental detection of pigeon antigen

INTRODUCTION

Avoidance of inhaled bird antigens is essential to prevent hypersensitivity pneumonitis disease progression. The aim of the present study was to develop a sandwich enzyme link immunoassay (ELISA) and an immunochromatographic test (ICT) and compare their ability to detect pigeon antigens in environmental samples.

METHODS

An amplified sandwich ELISA using pigeon serum as a calibration standard and a ICT using gold-labeled anti-pigeon serum antibodies for the rapid detection of pigeon antigens in environmental samples were developed. Twenty-two different airborne samples were collected and analysed using both methods. Strip density values obtained with ICT were calculated and compared with the concentrations determined by the ELISA method for pigeon antigens. Strips results were also visually analysed by five independent evaluators.

RESULTS

The ELISA method to quantify pigeon antigen had a broader range (58.4 and 10,112.2 ng/ml), compared to the ICT assay (420 to 3360 ng/ml). A kappa index of 0.736 (p < 0.0001) was obtained between the observers evaluating the ICT strips. The results of the ELISA and the relative density of the ICT showed a highly significant correlation (rs:0.935; p < 0.0001). Bland-Altman plot also confirmed excellent agreement between the two methods (mean difference: -1.626; p < 0.0001).

CONCLUSIONS

Since there was a good correlation between both assays, we can conclude that the rapid and simple ICT assay is a good and valid alternative, which does not require expensive equipment, for the validated ELISA technique.

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.