Rapid and comprehensive discovery of unreported shellfish allergens using large-scale transcriptomic and proteomic resources

The second data set contained 2117 allergen sequences compiled from 2 main allergen databases: the World Health Organization and International Union of Immunological Societies Allergen Nomenclature (http://www.allergen.org/)E2 and the Food Allergy Research and Resource Program (Version 16, http://ww...

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Published in:Journal of allergy and clinical immunology 2018-04, Vol.141 (4), p.1501-1504.e8
Main Authors: Nugraha, Roni, Kamath, Sandip D., Johnston, Elecia, Zenger, Kyall R., Rolland, Jennifer M., O'Hehir, Robyn E., Lopata, Andreas L.
Format: Article
Language:English
Subjects:
Allergens
Allergens - immunology
Allergies
Amino acids
Animals
Bioinformatics
Cockroaches
Crangon crangon
Crustaceans
Dehydrogenases
Fruit trees
Fungi
Genomes
Humans
Immunology
Immunotherapy
Kinases
Proteins
Proteomics
Proteomics - methods
Seafood - analysis
Shellfish
Shellfish - analysis
Shellfish Hypersensitivity - genetics
Shellfish Hypersensitivity - immunology
Shellfish Hypersensitivity - metabolism
Transcriptome - immunology
α-Amylase
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Summary:The second data set contained 2117 allergen sequences compiled from 2 main allergen databases: the World Health Organization and International Union of Immunological Societies Allergen Nomenclature (http://www.allergen.org/)E2 and the Food Allergy Research and Resource Program (Version 16, http://www.allergenonline.org/).E3 Genbank accession IDs of all allergenic proteins were collected from these databases and the IDs uploaded in the Batch Entrez menu on the National Center for Biotechnology Information Web site to obtain the sequence of the protein and remove duplicate proteins. The latest distribution of protein families from the allergen data set was defined by running the hmmscan programE4 against the Pfam database (version 29.0).E5 The BLASTP program was used to align the Pacific Oyster proteins and the repertoire of known allergens using a cutoff E value of 10−7 and sequence identity of more than 50%.Gene expression analysis of potential allergens in the Pacific Oyster The expression levels of potential allergen genes were analyzed from the available RNA sequencing data from the oyster genome project.E1 The expression profiles were analyzed from 2 developmental stages (spat and juvenile) and from 10 adult organs: the adductor muscle, the digestive gland, the female gonad, the male gonad, the gill, the hemocyte, the labial palp, the outer mantle, the inner mantle, and the remaining tissue. Dried gel pieces were rehydrated with 20 ng/μL of trypsin dissolved in 40 mM ammonium bicarbonate and 10% acetonitrile for 1 hour at room temperature and subsequently incubated overnight at 37°C. The digested proteins were acidified using 0.1% formic acid and the peptides were concentrated on a SpeedVac and subjected to Liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis.Patient selection Five subjects with a convincing clinical history of allergic reactivity to shellfish and 1 nonatopic subject were recruited from the Alfred Hospital Allergy Clinic, Melbourne, Victoria, Australia. Entry Protein name Homologous allergen in the IUIS database∗ Amino acid (aa) identity (%) Overlap (aa) E value Organism Route of sensitization Source 1 B7XC66 Tropomyosin† Hel as 1 75.7 284 4.00 × 10−133 Helix aspersa (Brown garden snail) Ingestion Animal 2 K1PCV6 Triosephosphate isomerase Cra c 8 74.03 77 2.00 × 10−41 Crangon crangon (North sea shrimp) Ingestion Animal 3 K1PJ59 Triosephosphate isomerase Der f 25 73.37 169 6.00 × 10−92 Dermatophagoides farinae (HDM) Inhala
ISSN:0091-6749
1097-6825
DOI:10.1016/j.jaci.2017.11.028