Rapid and comprehensive discovery of unreported shellfish allergens using large-scale transcriptomic and proteomic resources Roni Nugraha, MSc, Sandip.

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Presentation transcript:

Rapid and comprehensive discovery of unreported shellfish allergens using large-scale transcriptomic and proteomic resources Roni Nugraha, MSc, Sandip D. Kamath, PhD, Elecia Johnston, PhD, Kyall R. Zenger, MSc(Hons), PhD, Jennifer M. Rolland, PhD, Robyn E. O'Hehir, FRACP, PhD, FRCP, FRCPath, Andreas L. Lopata, PhD Journal of Allergy and Clinical Immunology Volume 141, Issue 4, Pages 1501-1504.e8 (April 2018) DOI: 10.1016/j.jaci.2017.11.028 Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 1 A combined approach demonstrates the increased sensitivity of identifying allergens in low abundance. A.I, In silico analysis identified 22 proteins as “very likely allergenic” (aa identity ≥70%) and 73 proteins as “likely allergenic” (aa identity ≥50% and ≤70%). A.II, The expression levels of the “very likely allergenic” proteins were different across development stages and organs of the Pacific Oyster. B, Multiple spots in the raw (I) and heated extract (II) were recognized to bind serum IgE. The IgE-reactive spots in the raw and heated extract contained 332 and 26 proteins, respectively. C, Shotgun proteomics analysis of the extracts indicates higher relative abundance of IgE-binding proteins in the heated extract. D, Venn diagram displaying proteins shared by the bioinformatics approach, the allergenomic approach, and the proteomic approach. Numbers of proteins shared by the 3 methods are colored in red. E, Summary of number of potential allergens shared by different methods. Twenty-four proteins in the raw extract and 4 proteins in the heated extract were identified across all 3 methods. aa, Amino acid. Journal of Allergy and Clinical Immunology 2018 141, 1501-1504.e8DOI: (10.1016/j.jaci.2017.11.028) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E1 Workflow for identification of the potential cross-reactive allergens from Pacific Oyster (C gigas) by a combination of bioinformatics, allergenomic, and proteomic approaches. A, In silico identification based on sequence alignment was conducted to determine Pacific Oyster proteins that have amino acid sequence identity of more than 50% of the known allergens and an E value of less than 10−7. B, 2D immunoblotting against a serum pool from 6 mollusk-allergic patients was performed and the IgE-reactive proteins were identified using LC-MS/MS. C, Shotgun proteomics was used to identify total proteins in the raw and heated extracts of the Pacific Oyster. 1D, One-dimensional; 2D, two-dimensional. Journal of Allergy and Clinical Immunology 2018 141, 1501-1504.e8DOI: (10.1016/j.jaci.2017.11.028) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E2 Expression profiles of genes encoding “likely allergens” across different development stages and different tissues of the Pacific Oyster. The transcriptome expression data were obtained from GigaDB database under data set number 100030. Gene expression levels were measured by RPKM (Reads Per Kilobase per Million mapped reads). Journal of Allergy and Clinical Immunology 2018 141, 1501-1504.e8DOI: (10.1016/j.jaci.2017.11.028) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E3 Coomassie-stained 2D-PAGE of the proteins from the raw and heated extracts of the Pacific Oyster. Spot numbers indicated on the gel correspond to IgE-reactive spots that were subjected to LC/MS mass spectrometry analysis. 2D, Two-dimensional. Journal of Allergy and Clinical Immunology 2018 141, 1501-1504.e8DOI: (10.1016/j.jaci.2017.11.028) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions