Protein allergenicity potential: What makes a protein an allergen?

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1 Protein Sequence Allergenic Potential Big Data MGVFNYETETTSVIPAARLFKAFILDGDNLF PKVAPQAISSVENIEGNGGPGTIKKISFPEG FPFKYVKDRVDEVDHTNFKYNYSVIEGGPI GDTLEKISNEIKIVATPDGGSILKISNKYHTK GDHEVKAEQVKASKEMGETLLRAVESYLL AHSDAYN HIGH LOW Smart Solutions Protein allergenicity potential: What makes a protein an allergen? BII: Vachiranee Limviphuvadh Han Hao Ma Jianmin Nguyen Ngoc Minh Vithiagaran Gunalan Sebastian Maurer-Stroh P&G: Nora Krutz Cindy Ryan, Petra Kern Frank Gerberick Universität Trier: Prof. Brunhilde Blömeke University of Manchester: Prof. Ian Kimber

2 Allergy prevalence on the rise ILSI SEA Region Symposium: Transformation Technologies and Translational Research 23 April 2018 Singapore National Academies of Sciences, Engineering, and Medicine, Health and Medicine Division, Food and Nutrition Board, Committee on Food Allergies: Global Burden, Causes, Treatment, Prevention, and Public Policy; Oria MP, Stallings VA, editors. Washington (DC): National Academies Press (US); 2016 Nov 30. Food product recalls can be costly and tarnish the reputation! Most common reasons are: Incomplete labelling Contamination Cross-contamination from other foods processed in same factory Pathogens (Listeria, Salmonella, E.coli, ) New sources/ingredients (product development) Allergy from new product, e.g. Japan soap: cases hospitalized

3 MGVFNYETETTSVIPAARLFKAFILDGDNLF PKVAPQAISSVENIEGNGGPGTIKKISFPEG FPFKYVKDRVDEVDHTNFKYNYSVIEGGPI GDTLEKISNEIKIVATPDGGSILKISNKYHTK GDHEVKAEQVKASKEMGETLLRAVESYLL AHSDAYN Allergenic protein How is a protein recognized as allergen? Immune response Figure adapted from Huby et al. Toxicological Sciences 55; (2000) Theoretically possible sequences Big data problem requiring smart solution!

4 FAO/WHO guidelines 2001 Query Protein Search Allergen sequence database Linear window similarity GVFNYETETTSVIPAARLFKAYILDGD Query: GVFNYETETTSVIPAARLFKAYILDGDAT Hit: ALFQFESDTSSVLPAVKLFKAYIIESDSA Threshold: Identical match of any 6-mer or 35% identity over 80 amino acids In 2001, an expert group from FAO/WHO defined protein sequence thresholds how similar a protein is allowed to be to any known allergen before it is also classified as potential allergen.

5 % of all non-allergenic HUMAN proteins ILSI SEA Region Symposium: Transformation Technologies and Translational Research 23 April 2018 Singapore Old guidelines produce many false positives Query Protein Search Allergen sequence database Linear window similarity GVFNYETETTSVIPAARLFKAYILDGD Using FAO/WHO mer rules, 60% of all human proteins would be classified as allergens today! Query: GVFNYETETTSVIPAARLFKAYILDGDAT Hit: ALFQFESDTSSVLPAVKLFKAYIIESDSA 2005 uniprotkb old-k6 Threshold: Identical match of any 6-mer or 35% identity over 80 amino acids k-mer based criterion for Allergen assignment of non-allergenic HUMAN proteins (False Positives) 2015 uniprotkb old-k uniprotkb new-k uniprotkb new-k6+

6 FAO/WHO guidelines 2001 Query Protein Search Allergen sequence database Linear window similarity GVFNYETETTSVIPAARLFKAYILDGD Birch pollen allergen Bet v 2 structure superimposed with human profilin: Query: GVFNYETETTSVIPAARLFKAYILDGDAT Hit: ALFQFESDTSSVLPAVKLFKAYIIESDSA Threshold: Identical match of any 6-mer or 35% identity over 80 amino acids High sequence similarity finds proteins with same protein structure fold. Allergens and non-allergens can share the same structure fold. So what makes the difference in allergenicity potential?

7 FoldX Free Energy ILSI SEA Region Symposium: Transformation Technologies and Translational Research 23 April 2018 Singapore Profilin family structure comparison of Allergens and non-allergens Birch Latex Stability Allergen Red negative charge Blue positive charge Birch 2.4A 1cqa Latex 3.1A 1g5u Yeast 2.35A 1k0k Human 2.2A 1awi -10 Non-Allergen Yeast Human In the Profilin family Allergens are less stable and more negatively charged.

8 Birch pollen allergen Bet v 1 in complex with Antibody Conformational epitope (5A) Red negative charges Blue positive charges

9 From Sequence to Structure Epitope Query Protein Search sequence database Old: Linear window similarity GVFNYETETTSVIPAARLFKAFILDGD Query: GVFNYETETTSVIPAARLFKAFILDGD Hit: GLFQFESDTSSVLPAVKLFKAYIIESD Query Protein (unknown structure) Search our 3D sequence database New: 3D epitope similarity GVFNYETETTSVIPAARLFKAFILDGD Query: GVFNYETETTSVIPAARLFKAFILDGD Hit: GLFQFESDTSSVLPAVKLFKAYIIESD Protein hit with known structure

10 ACCURACY ILSI SEA Region Symposium: Transformation Technologies and Translational Research 23 April 2018 Singapore From Sequence to Structure Epitope Query Protein Search sequence database Old: Linear window similarity GVFNYETETTSVIPAARLFKAFILDGD Query: GVFNYETETTSVIPAARLFKAFILDGD Hit: GLFQFESDTSSVLPAVKLFKAYIIESD Query Protein (unknown structure) Search our 3D sequence database New: 3D epitope similarity GVFNYETETTSVIPAARLFKAFILDGD Query: GVFNYETETTSVIPAARLFKAFILDGD Hit: GLFQFESDTSSVLPAVKLFKAYIIESD Performance benchmark (allergens vs nonallergens with same structure fold) Protein hit with known structure win80 3Depi

11 Database (complete list of known examples) Towards a biophysical model of protein allergenicity Structure Recognition (B cell epitopes) Structure Stability, Cleavage Sites, PTMs, Physicochem. properties Structure recognition (MHC binding) Cleavage Figure adapted from Huby et al. Toxicological Sciences 55; (2000) Allergenicity Potential = x 1 S 1 + x 2 S 2 + x 3 S 3

12 Performance benchmark (allergens vs non-allergens with same structure fold) Accuracy (FAO/WHO) PREAL AllerHunter AllergenFP AllerTOPv2 AllerCatPro

13 % strong protein hits ILSI SEA Region Symposium: Transformation Technologies and Translational Research 23 April 2018 Singapore Smart use: Mass-spec + in silico 1. Use label-free proteomics to identify abundant proteins Peptides P&G Jason Winget P&G Frank Gerberick 2. Evaluate top 50 protein hits (or above critical concentration) with our in silico tool Protein Normalize by protein length and global fragment intensity. Transform to log 2 space Sum intensities over all peptides associated with a protein Spectrum Allergens among top 50 most abundant proteins in food sources Sum fragment intensities for all spectra associated with a peptide Spinach Rice Corn Tomato Potato Wheat

14 Summary and Future Outlook Protein allergens in food are a common cause for food product recalls which are costly and tarnish the reputation! New products or new ingredients/sources could introduce protein allergens A*STAR and P&G have developed a new method to classify allergenicity potential of proteins aiming towards widespread use with industry and regulatory acceptance What can A*STAR do now for food companies? Provide protein allergen risk table for a product (based on available genome sequence of included organisms/sources or protein mass spectrometry result) using Standard FAO/WHO rules + Advanced method (to be better and more realistically informed on allergen risk for a product)

15 Protein Sequence Allergenic Potential Big Data MGVFNYETETTSVIPAARLFKAFILDGDNLF PKVAPQAISSVENIEGNGGPGTIKKISFPEG FPFKYVKDRVDEVDHTNFKYNYSVIEGGPI GDTLEKISNEIKIVATPDGGSILKISNKYHTK GDHEVKAEQVKASKEMGETLLRAVESYLL AHSDAYN HIGH LOW Smart Solutions THANK YOU! BII: Vachiranee Limviphuvadh Han Hao Ma Jianmin Nguyen Ngoc Minh Vithiagaran Gunalan Sebastian Maurer-Stroh P&G: Nora Krutz Cindy Ryan, Petra Kern Frank Gerberick Universität Trier: Prof. Brunhilde Blömeke University of Manchester: Prof. Ian Kimber