Protein Allergens, Toxins, and Bioinformatics (PATB) Committee

Mission Statement

The PATB is committed to advancing the scientific understanding of the relevant parameters defining allergenic proteins and protein toxins, and encouraging the development of reliable and accurate methodologies for characterizing the allergenic potential of novel proteins in order to leverage the potential of bioinformatics approaches in accomplishing these efforts.

Renaming the Committee: PATC to PATB

Formerly the Protein Allergenicity Technical Committee (PATC), the committee has adopted a new designation, the Protein Allergens, Toxins and Bioinformatics (PATB) Committee, to embrace a broader scope, expertise, interests, and collaborators in the fields of bioinformatics and protein toxins, while strengthening its core focus in allergenicity.

Working Groups

  • Celiac Disease

    Project initiated in October 2023. A call for participants was released by the committee during Summer 2023 and a team 10 participants from 9 organizations has been assembled. This pilot study will test the potential of microbial derived peptides to mimic gluten peptides in activating early events in the cascade triggering Celiac Disease, using organoid models derived from Celiac patients and healthy individuals. The committee is aiming to evaluate the clinical relevance of non-gluten peptides that share similarity with the disease-causing gluten peptides, in triggering Celiac disease. Experimental work will be conducted thanks to a collaboration with leading Celiac Disease experts at Massachusetts General Hospital.

  • Digestibility Working Group: Food Matrix Project

    This research project aims to study the impact of food matrices on the digestibility of proteins and complements the work completed on digestibility in vitro models, by testing whether protocols that take matrices into account would provide a better discrimination of allergens and nonallergens than protocols focusing on purified proteins in solution. In 2020, the experimental work was concluded. The data are being analyzed and a publication is planned in 2021.

  • Immunogenicity

    This working group aims to examine application of an in vitro protocol for identifying specific T-cells and antibodies from nonallergic and allergic patients to pairs of proteins from the same protein family but with different allergenicity. After some delays in the anticipated start date due to the COVID-19 pandemic, the project officially received the green light from the leading institution, Copenhagen University Hospital at Gentofte (Copenhagen, Denmark) in late 2020.

  • Protein Toxins Task Force

    The goals of the task force are to (1) investigate approaches for identifying protein toxins and (2) suggest specific guidelines to identify new protein toxins. In 2019, the task force undertook a literature review to identify current approaches being used and leading experts in the topic to design the workshop held in 2020. The workshop covered recent advances in protein toxins biology, described the use of computational biology for protein toxins identification and characterization with in silico approaches, and discussed the applicability of existing tools and resources for safety assessment of novel food biotechnology products.

  • COMPARE Allergen Database

    Development and annual update of a database of protein allergen sequences is ongoing. The eighth version of the database was released in January 2024. Throughout the year, the team re-initiates and conducts the 10-month-long process leading to the next annual update of the COMPARE Database. Visit COMPARE at https://comparedatabase.org for more details.

HESI Staff

Leadership Team

  • Ronald van Ree, PhD

    Academic Medical Center, University of Amsterdam

  • Andre Silvanovich, PhD

    Retired from Bayer CropScience

Committee Events

Filter

PATC Non-IgE Mediated Immune Reactions to Foods Workshop

October 12, 2016 – October 13, 2016

Rome, Italy

  • HESI - Health and Environmental Sciences Institute

This workshop provided an opportunity to discuss the current state of the science in immunologic mechanisms of non-IgE mediated food allergy with a specific emphasis on use of these data to assess food safety.

Read more

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				PATB Webinar Header
			
						REGISTER HERE
					
	
 


The Health and Environmental Sciences Institute (HESI) Protein Allergens, Toxins, and Bioinformatics (PATB) committee will be hosting a webinar to discuss emerging opportunities and innovations in the biotechnology and food safety assessment arenas. See details below!


Details


    

  • Date: Wednesday, May 22, 2019
    • 

  • Time: 11 AM - 12:30 PM EST
    • 

  • Registration: Click here to register.
    • 


				dna
	
 


Speakers:


    

  • Scott McClain, Regulatory Product Safety Scientist, Syngenta Crop Protection (USA), PATB Committee Co-Chair
    • 

  • Lars Poulsen, Head of Research, Allergy Clinic, Copenhagen University Hospital at Gentofte (Denmark), Member of the COMPARE Database Peer-Review Expert Panel
    • 


	
Advances in agricultural and food biotechnology bring the opportunity to improve the way we grow food and feed crops. As part of the requirements to ensure food safety, it is vital to mitigate potential risks of introducing new allergens or unintended components in the food chain that could induce adverse reactions in humans.


The Health and Environmental Sciences Institute (HESI) Protein Allergens, Toxins, and Bioinformatics (PATB) committee engages international collaborative teams of academics, clinicians, regulators, and industry scientists who conduct research, design and populate public database resources, and convene trainings on the use and evaluation of biotechnology products.  The PATB oversees the creation, maintenance, and distribution of the Comprehensive Protein Allergen Resource (COMPARE) Database whose use in conjunction bioinformatic tools, offers an effective means for assessing allergenic potential of novel food proteins. 


Webinar attendees will:


    

  • Learn directly from experts in the committee about the nuts and bolts of food safety assessment of biotechnology products, the committee contributions to the field and new emerging issues
    • 

  • Engage in an interactive discussion about emerging opportunities, challenges, and innovations in the biotechnology and food safety assessment arenas
    • 



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				FAAM Workshop Logo_revised large 4
			
						REGISTRATION HERE
					
			
						MEETING AGENDA
					
	Details

Location: Tivoli Hotel and Congress Center - Copenhagen, Denmark

Dates: October 17 - 18, 2018

There will also be another meeting at the Tivoli Hotel and Congress Center in Copenhagen, Denmark, called FAAM 2018, a EAACI Focused Meeting. FAAM 2018 will take place from 18 -20 October 2018. Please consider attending both events! Find more information on the event here.


 

About

In the growing field of allergy research, scientists can approach protein characterization and allergy hazard assessment in diverse ways. The Health and Environmental Sciences Institute (HESI) Protein Allergens, Toxins, and Bioinformatics (PATB) committee supports original basic research that seeks to uncover the interplay between protein allergenicity and the physicochemical properties of allergenic proteins. The PATB also oversees the creation, maintenance and distribution of the Comprehensive Protein Allergen Resource (COMPARE) Database whose use in conjunction bioinformatic tools, offers an effective means for assessing allergenic potential of novel food proteins.  PATB’s focus on basic allergy research, coupled with bioinformatic methods for allergenic hazard assessment is unique within the scientific community as it supports an ever-increasing awareness of allergenicity among consumers and regulators. Topics to be covered in this workshop will include historic aspects of food allergy assessment, the evolution of bioinformatics as it relates to allergy assessment, and recent changes in regulations regarding novel food proteins.

This educational workshop will cover advances in protein allergy research and inform the use of novel approaches for the identification of potential food allergens. This event will be of interest to government regulators, those involved in food allergy and celiac disease research, and scientists involved in food safety and risk assessment.

				dreamstime_xl_71979237
	
 


Objectives


Evaluate bioinformatics approaches to characterize the allergenicity potential of novel proteins and inform allergy safety assessment.


Discuss real-world examples of: 1) a product development case-study describing the utility of bioinformatics in protein characterization, and 2) a practical application of the EFSA 2017 Guidance.


Provide insights from new research, ranging from modifications of allergen epitopes at the single amino-acid level, to using protein structural modeling for allergenicity prediction, to the relation between enzymes and allergenic activity.

	
Introduction

Overview of contributions and research of the HESI PATB to Bioinformatics Analysis of the Potential Allergenicity of Novel Proteins 

Greg Ladics, Dupont (Download Presentation)

 

Session I: Bioinformatics Approaches to Protein Characterization and Allergy Safety Assessment


A history of bioinformatics: development of in silico approaches to evaluate food proteins 

Andre Silvanovich, Bayer Crop Science (Download Presentation)
Protein sequence analysis tools and resources to detect potential allergens 

Rob Finn, European Bioinformatics Institute (EBI) (Download Presentation)
Case Study: Allergenic risk of insect proteins

Kitty Verhoeckx, TNO (Download Presentation)
The COMPARE Allergen Database: a public, comprehensive protein allergen resource for allergenicity safety assessment

Lars Poulsen, University of Copenhagen (Download Presentation)
Novel methods to identify allergenicity potential of proteins 

Sebastian Maurer-Stroh, A*STAR Bioinformatics Institute (BII), Singapore (Download Presentation)

 


Session II: Other Considerations for Allergen Safety Assessment

The PATB “Allergen Rebuild Project”: can the conservative replacement of amino acids in an allergen epitope affect IgE binding and cross-reactivity? 

Ronald van Ree, Academic Medical Center, University of Amsterdam
Development of a Random Forest model for predicting allergenicity of new and modified proteins

Tanja Krone, TNO
Cross-reactive carbohydrate determinants and allergenicity  

Edzard Spillner, Aarhus University (Download Presentation)

 


Session III: Non-IgE Mediated Allergy 

Overview of known non-IgE mediated diseases and progress in immunology of non-IgE diseases 

Antonella Cianferoni, Children’s Hospital of Philadelphia (Download Presentation)
In silico tools to predict potential celiac disease toxicity 

Frits Koning, Leiden University (Download Presentation)
Application of EFSA 2017 bioinformatic guidance for non-IgE mediated immune disease 

Andre Silvanovich, Bayer Crop Science (Download Presentation)
Considerations for small peptide analyses in SGF 

Scott McClain, Syngenta (Download Presentation)

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				PATB Webinar Header
			
						REGISTER HERE
					
	
 


The Health and Environmental Sciences Institute (HESI) Protein Allergens, Toxins, and Bioinformatics (PATB) committee will be hosting a webinar to discuss emerging opportunities and innovations in the biotechnology and food safety assessment arenas. See details below!


Details


    

  • Date: Wednesday, May 22, 2019
    • 

  • Time: 11 AM - 12:30 PM EST
    • 

  • Registration: Click here to register.
    • 


				dna
	
 


Speakers:


    

  • Scott McClain, Regulatory Product Safety Scientist, Syngenta Crop Protection (USA), PATB Committee Co-Chair
    • 

  • Lars Poulsen, Head of Research, Allergy Clinic, Copenhagen University Hospital at Gentofte (Denmark), Member of the COMPARE Database Peer-Review Expert Panel
    • 


	
Advances in agricultural and food biotechnology bring the opportunity to improve the way we grow food and feed crops. As part of the requirements to ensure food safety, it is vital to mitigate potential risks of introducing new allergens or unintended components in the food chain that could induce adverse reactions in humans.


The Health and Environmental Sciences Institute (HESI) Protein Allergens, Toxins, and Bioinformatics (PATB) committee engages international collaborative teams of academics, clinicians, regulators, and industry scientists who conduct research, design and populate public database resources, and convene trainings on the use and evaluation of biotechnology products.  The PATB oversees the creation, maintenance, and distribution of the Comprehensive Protein Allergen Resource (COMPARE) Database whose use in conjunction bioinformatic tools, offers an effective means for assessing allergenic potential of novel food proteins. 


Webinar attendees will:


    

  • Learn directly from experts in the committee about the nuts and bolts of food safety assessment of biotechnology products, the committee contributions to the field and new emerging issues
    • 

  • Engage in an interactive discussion about emerging opportunities, challenges, and innovations in the biotechnology and food safety assessment arenas
    • 



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Committee Publications

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A Multi-Laboratory Evaluation of a Common In Vitro Pepsin Digestion Assay Protocol Used in Assessing the Safety of Novel Proteins

Regulatory Toxicology and Pharmacology, 2004

Thomas K, Aalbers M, Bannon GA, Bartels M, Dearman RJ, Esdaile DJ, ...
  • HESI - Health and Environmental Sciences Institute

Evaluation of the potential allergenicity of proteins derived from genetically modified foods has involved a weight of evidence approach that incorporates an evaluation of protein digestibility in pepsin.

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Agricultural Biotechnology Safety Assessment

Chinese Journal of Preventative Medicine, 2015

McClain S, Jones W, He X, Ladics G, Bartholomaeus A, Raybould A, ...
  • HESI - Health and Environmental Sciences Institute

Genetically modified (GM) crops were first introduced to farmers in 1995 with the intent to provide better crop yield and meet the increasing demand for food and feed.

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Allergic Sensitization: Food- and Protein-Related Factors

Clinical and Translational Allergy, 2014

McClain S, Bowman C, Fernández-Rivas M, Ladics GS, Ree Rv
  • HESI - Health and Environmental Sciences Institute

Presented here are emerging capabilities to precisely measure endogenous allergens in soybean and maize, consideration of food matrices on allergens, and proteolytic activity of allergens.

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Allergic Sensitization: Host-Immune Factors

Clinical and Translational Allergy, 2014

van Ree R, Hummelshoj L, Plantinga M, Poulsen L, Swindle E
  • HESI - Health and Environmental Sciences Institute

Allergic sensitization is the outcome of a complex interplay between the allergen and the host in a given environmental context.

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Allergic Sensitization: Screening Methods

Clinical and Translational Allergy, 2014

Ladics GS, Fry J, Goodman R, Herouet-Guicheney C, ...
  • HESI - Health and Environmental Sciences Institute

Experimental in silico, in vitro, and rodent models for screening and predicting protein sensitizing potential are discussed, including whether there is evidence of new sensitizations and allergies since the introduction of genetically modified crops in 1996, the importance of linear versus conformational epitopes, and ...

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Assessment of Potential Adjuvanticity of Cry Proteins

Regulatory Toxicology and Pharmacology, 2016

Joshi SS, Barnett B, Doerrer NG, Glenn K, Herman RA, ...

Genetically modified (GM) crops have achieved success in the marketplace and their benefits extend beyond the overall increase in harvest yields to include lowered use of insecticides and decreased carbon dioxide emissions. The most widely grown GM crops contain gene/s for targeted insect protection, herbicide tolerance, or ...

Read more

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