Dataset Information

1:1 FASTA update: Using the power of E-values in FASTA to detect potential allergen cross-reactivity.

ABSTRACT: In the context of regulatory assessment of transgenic proteins for potential allergenicity, a previous investigation demonstrated that a 1:1 FASTA comparison using an E-value of 1.0E-09 as a criterion is superior to the conventional FASTA search (using the whole sequence as a query) for >35% identity over 80 amino acids, but with improved specificity. A further study, using groups of known cross-reactive peanut allergens, indicates the sensitivity of this approach is superior to the conventional FASTA search and equivalent to 80-mer sliding window FASTA search recommended by WHO/FAO. Specifically, the 1:1 FASTA approach eliminated the technical issues resulting from lack of identification of short query sequences with high identity to known allergens, or high identity over short amino acid stretches, and different E-value settings when searching for >35% identity over 80aa. Based on the performance of this simple application of existing bioinformatics tools, and its ease of implementation and interpretation in the context of a regulatory assessment, we advocate that adoption of this 1:1 FASTA approach as a supplement to the FAO/WHO/ CODEX criterion (>35% identity over 80aa) formulated 13 years ago. Adoption of this approach eliminates many biologically irrelevant homology hits generated by the FAO/WHO/CODEX criterion and improves the safety assessment of GM crops.

SUBMITTER: Song P

PROVIDER: S-EPMC5598423 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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1:1 FASTA update: Using the power of <i>E</i>-values in FASTA to detect potential allergen cross-reactivity.

Song Ping P Herman Rod R Kumpatla Siva S

Toxicology reports 20150820

In the context of regulatory assessment of transgenic proteins for potential allergenicity, a previous investigation demonstrated that a 1:1 FASTA comparison using an <i>E</i>-value of 1.0E-09 as a criterion is superior to the conventional FASTA search (using the whole sequence as a query) for >35% identity over 80 amino acids, but with improved specificity. A further study, using groups of known cross-reactive peanut allergens, indicates the sensitivity of this approach is superior to the conve ...[more]

PMID: 28962455

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Project description:BackgroundDiscovered and described 40 years ago, non-specific lipid transfer proteins (nsLTP) are present in many plant species and play an important role protecting plants from stressors such as heat or drought. In the last 20 years, sensitization to nsLTP and consequent reactions to plant foods has become an increasing concern.AimThe aim of this paper is to review the evidence for the structure and function of nsLTP allergens, and cross-reactivity, sensitization, and epidemiology of nsLTP allergy.Materials and methodsA Task Force, supported by the European Academy of Allergy & Clinical Immunology (EAACI), reviewed current evidence and provide a signpost for future research. The search terms for this paper were "Non-specific Lipid Transfer Proteins", "LTP syndrome", "Pru p 3", "plant food allergy", "pollen-food syndrome".ResultsMost nsLTP allergens have a highly conserved structure stabilised by 4-disulphide bridges. Studies on the peach nsLTP, Pru p 3, demonstrate that nsLTPs are very cross-reactive, with the four major IgE epitopes of Pru p 3 being shared by nsLTP from other botanically related fruits. These nsLTP allergens are to varying degrees resistant to heat and digestion, and sensitization may occur through the oral, inhaled or cutaneous routes. In some populations, Pru p 3 is the primary and sole sensitizing allergen, but many are poly-sensitised both to botanically un-related nsLTP in foods, and non-food sources of nsLTP such as Cannabis sativa, Platanus acerifolia, (plane tree), Ambrosia artemisiifolia (ragweed) and Artemisia vulgaris (mugwort). Initially, nsLTP sensitization appeared to be limited to Mediterranean countries, however more recent studies suggest clinically relevant sensitization occurs in North Atlantic regions and also countries in Northern Europe, with nsLTP sensitisation profiles being broadly similar.DiscussionThese robust allergens have the potential to sensitize and provoke symptoms to a large number of plant foods, including those which are raw, cooked or processed. It is unknown why some sensitized individuals develop clinical symptoms to foods whereas others do not, or indeed what other allergens besides Pru p 3 may be primary sensitising allergens. It is clear that these allergens are also relevant in non-Mediterranean populations and there needs to be more recognition of this.ConclusionNon-specific LTP allergens, present in a wide variety of plant foods and pollens, are structurally robust and so may be present in both raw and cooked foods. More studies are needed to understand routes of sensitization and the world-wide prevalence of clinical symptoms associated with sensitization to these complex allergens.

Project description:PurposePet-derived allergens are the common indoor inhalant allergens. Among them, cat and dog allergens constitute more than 80% of animal allergic patients, which greatly affect the quality-of-life of patients and increase the burden of social health care. The aim of this study was to identify Cat-Niemann pick type C2 (NPC2) protein, a homologue of Can f 7, as a new allergen.MethodsCat-NPC2 complementary DNA (cDNA) was cloned and optimized for amplification and expression in Escherichia coli. Then, recombinant Cat-NPC2 (rCat-NPC2) was purified by Ni2+ affinity chromatography. The allergenicity was assessed by enzyme-linked immunosorbent assay (ELISA), western blot and basophil activation test (BAT). Based on the sequence similarity, the cross-reactivity between Cat-NPC2 and Can f 7 was investigated by inhibition ELISA. Circular dichroism spectroscopy and homology modeling were used to characterize the structure of Cat-NPC2.ResultsThe cDNA sequence of Cat-NPC2 was cloned with a 450-bp open reading frame coding for 149 amino acids (GenBank MN_737596). The condon-optimized NPC2 gene was subcloned and expressed in E. coli with a molecular weight of 18.9 kDa. The native Cat-NPC2 was detected in cat dander extracts. The allergenicity determined by ELISA, western blot and BAT suggested at least 14.5% cat-allergic patients displayed high specific immunoglobulin E (IgE) recognition of Cat-NPC2. The predicted structure of Cat-NPC2 was found to consist of 7 β-strands arranged in 2 β-sheets. An ELISA based assay showed that rCat-NPC2 bound to cholesterol in a dose dependent manner. Based on the structure and sequence similarities, IgE cross-reactivity was demonstrated between Cat-NPC2 and Can f 7/Der f 2.ConclusionsIn the study, a novel cat allergen, belonging to the NPC2 protein family, was identified and characterized at both molecular and immunological levels. The study will offer a deeper understanding of cat allergens and improve a component-resolved diagnosis in pet allergy.

Dataset Information

1:1 FASTA update: Using the power of E-values in FASTA to detect potential allergen cross-reactivity.

Publications

1:1 FASTA update: Using the power of <i>E</i>-values in FASTA to detect potential allergen cross-reactivity.

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