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Doytchinova I, Atanasova M, Sotirov S, Dimitrov I. In Silico Identification of Peanut Peptides Suitable for Allergy Immunotherapy in HLA-DRB1*03:01-Restricted Patients. Pharmaceuticals (Basel) 2024; 17:1097. [PMID: 39204201 PMCID: PMC11357649 DOI: 10.3390/ph17081097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/24/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
Peanut allergy, a prevalent and potentially severe condition affecting millions worldwide, has been linked to specific human leukocyte antigens (HLAs), suggesting increased susceptibility. Employing an immunoinformatic strategy, we developed a "logo model" based on amino acid frequencies in the peptide binding core and used it to predict peptides originating from 28 known peanut allergens binding to HLA-DRB1*03:01, one of the susceptibility alleles. These peptides hold promise for immunotherapy in HLA-DRB1*03:01 carriers, offering reduced allergenicity compared to whole proteins. By targeting essential epitopes, immunotherapy can modulate immune responses with minimal risk of severe reactions. This precise approach could induce immune tolerance with fewer adverse effects, presenting a safer and more effective treatment for peanut allergy and other allergic conditions.
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Affiliation(s)
- Irini Doytchinova
- Drug Design and Bioinformatics Lab, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (M.A.); (S.S.); (I.D.)
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2
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Wróblewska B, Ogrodowczyk A, Wasilewska E. Immunoreactive proteins of Capsicum-based spices as a threat to human health: mass spectrometry analysis and in silico mapping. Sci Rep 2023; 13:17723. [PMID: 37853105 PMCID: PMC10584839 DOI: 10.1038/s41598-023-44775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 10/12/2023] [Indexed: 10/20/2023] Open
Abstract
Dietary patterns are changing severely, especially the consumption of highly processed foods with lots of spices is increasing, carrying an increased risk of immediate hypersensitivity (type I), in sensitised individuals, due to the possible presence of allergens, especially the hidden ones. Paprika is a fruit of the Capsicum genus, which belongs to the Solanaceae family and is commonly consumed fresh or as a spice. Despite recorded cases of anaphylaxis, its allergenicity has yet to be clearly investigated. In this study, we research to identify proteins that could trigger a severe allergic reaction in patients with an equivocal clinical picture. Two types of protein extracts extracted from 3 different paprika spices were immunoblotted with sera from patients with severe allergic symptoms, presumably to paprika. Proteins from the IgE reactive bands obtained were subjected to LC-MS/MS identification and then in silico analysis to assess their possible sensitising capacity and proinflammatory potential using online tools. The spices were shown to contain a number of incompletely investigated highly immunoreactive allergenic proteins, including proteins of foreign origin (contaminants), the presence of which can stimulate inflammatory mechanisms and cross-reactivity with other food allergens, which can threaten life and health and should be investigated in detail.
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Affiliation(s)
- Barbara Wróblewska
- Department of Food Immunology and Microbiology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, 10-748, Olsztyn, Poland
| | - Anna Ogrodowczyk
- Department of Food Immunology and Microbiology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, 10-748, Olsztyn, Poland.
| | - Ewa Wasilewska
- Department of Food Immunology and Microbiology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, 10-748, Olsztyn, Poland.
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Li Y, Sackett PW, Nielsen M, Barra C. NetAllergen, a random forest model integrating MHC-II presentation propensity for improved allergenicity prediction. BIOINFORMATICS ADVANCES 2023; 3:vbad151. [PMID: 37901344 PMCID: PMC10603389 DOI: 10.1093/bioadv/vbad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/28/2023] [Accepted: 10/13/2023] [Indexed: 10/31/2023]
Abstract
Motivation Allergy is a pathological immune reaction towards innocuous protein antigens. Although only a narrow fraction of plant or animal proteins induce allergy, atopic disorders affect millions of children and adults and cost billions in healthcare systems worldwide. In silico predictors can aid in the development of more innocuous food sources. Previous allergenicity predictors used sequence similarity, common structural domains, and amino acid physicochemical features. However, these predictors strongly rely on sequence similarity to known allergens and fail to predict protein allergenicity accurately when similarity diminishes. Results To overcome these limitations, we collected allergens from AllergenOnline, a curated database of IgE-inducing allergens, carefully removed allergen redundancy with a novel protein partitioning pipeline, and developed a new allergen prediction method, introducing MHC presentation propensity as a novel feature. NetAllergen outperformed a sequence similarity-based BLAST baseline approach, and previous allergenicity predictor AlgPred 2 when similarity to known allergens is limited. Availability and implementation The web service NetAllergen and the datasets are available at https://services.healthtech.dtu.dk/services/NetAllergen-1.0/.
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Affiliation(s)
- Yuchen Li
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Copenhagen 2800, Denmark
| | - Peter Wad Sackett
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Copenhagen 2800, Denmark
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Copenhagen 2800, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martin 1650, Argentina
| | - Carolina Barra
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Copenhagen 2800, Denmark
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Dolence JJ, Krempski JW, O’Konek JJ. Editorial: Food allergy: advances in basic and translational animal models. FRONTIERS IN ALLERGY 2023; 4:1299113. [PMID: 37885609 PMCID: PMC10598722 DOI: 10.3389/falgy.2023.1299113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Affiliation(s)
- Joseph J. Dolence
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, United States
| | - James W. Krempski
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- Mary H Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States
| | - Jessica J. O’Konek
- Mary H Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States
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Goto K, Tamehiro N, Yoshida T, Hanada H, Sakuma T, Adachi R, Kondo K, Takeuchi I. Novel Machine Learning Method AllerStat Identifies Statistically Significant Allergen-Specific Patterns in Protein Sequences. J Biol Chem 2023; 299:104733. [PMID: 37086787 DOI: 10.1016/j.jbc.2023.104733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 04/24/2023] Open
Abstract
Cutting-edge technologies such as genome editing and synthetic biology allow us to produce novel foods and functional proteins. However, their toxicity and allergenicity must be accurately evaluated. It is known that specific amino-acid sequences in proteins make some proteins allergic, but many of these sequences remain uncharacterized. In this study, we introduce a data-driven approach and a machine-learning (ML) method to find undiscovered allergen specific patterns (ASPs) among amino acid sequences. The proposed method enables an exhaustive search for amino-acid subsequences whose frequencies are statistically significantly higher in allergenic proteins. As a proof-of-concept, we created a database containing 21,154 proteins of which the presence or absence of allergic reactions are already known, and applied the proposed method to the database. The detected ASPs in this proof-of-concept study were consistent with known biological findings, and the allergenicity prediction performance using the detected ASPs was higher than extant approaches, indicating this method may be useful in evaluating the utility of synthetic foods and proteins.
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Affiliation(s)
- Kento Goto
- Department of Computer Science, Nagoya Institute of Technology. Gokiso-cho, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Norimasa Tamehiro
- Division of Biochemistry, National Institute of Health Sciences. 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takumi Yoshida
- Department of Computer Science, Nagoya Institute of Technology. Gokiso-cho, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroyuki Hanada
- Center for Advanced Intelligence Project, RIKEN. 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Takuto Sakuma
- Department of Computer Science, Nagoya Institute of Technology. Gokiso-cho, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Reiko Adachi
- Division of Biochemistry, National Institute of Health Sciences. 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Kazunari Kondo
- Division of Biochemistry, National Institute of Health Sciences. 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan.
| | - Ichiro Takeuchi
- Graduate School of Engineering, Nagoya University.Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan; Center for Advanced Intelligence Project, RIKEN. 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.
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6
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Relationship between Food Allergy and Endotoxin Concentration and the Toleration Status at 2 Years: The Japan Environment and Children's Study. Nutrients 2023; 15:nu15040968. [PMID: 36839328 PMCID: PMC9959381 DOI: 10.3390/nu15040968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Changes in household endotoxin concentration may affect the prognosis of food allergy (FA), but data on the association between household endotoxin concentration and an already-developed FA are scarce. Thus, we investigated the association between environmental endotoxin exposure and tolerance to hen's egg (HE) and cow's milk (CM) using data from children participating in the Japan Environment and Children's Study who had HE allergies (n = 204) and CM allergy (n = 72) in their first year of life. We grouped the endotoxin results into quartiles 1-4 (Q1-Q4). In children with HE allergy and with CM allergy, there was no significant difference in the prevalence of tolerance to HE and CM at 2 years old when comparing endotoxin levels of the children in Q1 with those in Q2, Q3, and Q4, respectively. However, subgroup analyses by the presence of eczema and causal foods revealed that children in Q1 had a lower prevalence of tolerance to foods in some subgroup analyses and lower causal allergen-specific immunoglobulin G4 levels. Although an individually based approach against endotoxin according to background characteristics, such as eczema and causal foods, is necessary, preventing excessive endotoxin removal might contribute to FA resolution in some children.
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Germundson DL, Nookala S, Smith NA, Warda Y, Nagamoto-Combs K. HLA-II Alleles Influence Physical and Behavioral Responses to a Whey Allergen in a Transgenic Mouse Model of Cow's Milk Allergy. FRONTIERS IN ALLERGY 2022; 3:870513. [PMID: 35769584 PMCID: PMC9234862 DOI: 10.3389/falgy.2022.870513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
The symptoms of food allergies vary significantly between individuals, likely due to genetic determinants. In humans, allergy development is initiated by antigen-presenting cells via class II human leukocyte antigen (HLA-II). The HLA-II gene is highly polymorphic, and its allelic variance is thought to influence the susceptibility of individuals to a particular allergen. However, whether antigen presentation by different HLA-II variants contributes to symptom variation is not clear. We hypothesized that HLA-II allelic variance affects symptom phenotypes, including immediate physical reactions and delayed behavioral changes, in individuals with food hypersensitivity. To test our hypothesis, male and female mice of three transgenic strains expressing an HLA-II variant, DR3, DR15, or DQ8, were used to establish a cow's milk allergy model. Mice were sensitized to a bovine whey allergen, β-lactoglobulin (BLG; Bos d 5), weekly for 5 weeks, followed by an acute oral allergen challenge. At 30 min post-challenge, BLG-sensitized DR3 mice showed moderate to severe anaphylaxis resulting in perioral redness, swelling, and death. In contrast, DQ8 and DR15 mice were generally asymptomatic. The production of allergen-specific immunoglobulins was also HLA- and sex-dependent. Both male and female DR3 and female DR15 mice significantly increased BLG-specific IgE production, while robust elevation in BLG-specific IgG1 was observed in sensitized DQ8 mice of both sexes and, to a lesser extent, in DR15 males. Furthermore, BLG-sensitized DR15 mice showed sex-specific behavior changes, with males exhibiting mobility changes and anxiety-like behavior and females showing spatial memory impairment. When splenocytes from transgenic mice were stimulated in vitro with BLG, phenotypes of immune cells were HLA- and sex-specific, further underscoring the influence of HLA-II on immune responses. Our results support that HLA-II alleles influence behavioral responses in addition to immune and physical reactions of food allergy, suggesting that certain HLA-II variants may predispose individuals to food-allergy-associated behavioral changes.
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Affiliation(s)
- Danielle L. Germundson
- Department of Pathology, Clinical and Translational Sciences Graduate Program, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, United States
| | - Suba Nookala
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, United States
| | - Nicholas A. Smith
- Department of Pathology, Clinical and Translational Sciences Graduate Program, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, United States
| | - Yassmine Warda
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, United States
| | - Kumi Nagamoto-Combs
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, United States
- *Correspondence: Kumi Nagamoto-Combs
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Childs CE, Munblit D, Ulfman L, Gómez-Gallego C, Lehtoranta L, Recker T, Salminen S, Tiemessen M, Collado MC. Potential Biomarkers, Risk Factors and their Associations with IgE-mediated Food Allergy in Early Life: A Narrative Review. Adv Nutr 2021; 13:S2161-8313(22)00081-3. [PMID: 34596662 PMCID: PMC8970818 DOI: 10.1093/advances/nmab122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Food allergy affects the quality of life of millions of people worldwide and presents a significant psychological and financial burden for both national and international public health. In the past few decades, the prevalence of allergic disease has been on the rise worldwide. Identified risk factors for food allergy include family history, mode of delivery, variations in infant feeding practices, prior diagnosis of other atopic diseases such as eczema, and social economic status. Identifying reliable biomarkers which predict the risk of developing food allergy in early life would be valuable in both preventing morbidity and mortality and by making current interventions available at the earliest opportunity. There is also the potential to identify new therapeutic targets. This narrative review provides details on the genetic, epigenetic, dietary and microbiome influences upon the development of food allergy and synthesizes the currently available data indicating potential biomarkers. While there is a large body of research evidence available within each field of potential risk factors, there are very limited number of studies which span multiple methodological fields, for example including immunology, microbiome, genetic/epigenetic factors and dietary assessment. We recommend that further collaborative research with detailed cohort phenotyping is required to identify biomarkers, and whether these vary between at-risk populations and the wider population. The low incidence of oral food challenge confirmed food allergy in the general population, and the complexities of designing nutritional intervention studies will provide challenges for researchers to address in generating high quality, reliable and reproducible research findings. STATEMENT OF SIGNIFICANCE Food allergy affects the quality of life of millions of people worldwide and presents a significant psychological and financial burden for both national and international public health. Identifying reliable biomarkers which predict the risk of developing food allergy would be valuable in both preventing morbidity and mortality and by making current interventions available at the earliest opportunity. This review provides details on the genetic, epigenetic, dietary and microbiome influences upon the development of food allergy. This helps in identifying reliable biomarkers to predict the risk of developing food allergy, which could be valuable in both preventing morbidity and mortality and by making interventions available at the earliest opportunity.
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Affiliation(s)
- Caroline E Childs
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Daniel Munblit
- Imperial College London, London, United Kingdom,Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child’s Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia,Inflammation, Repair and Development Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | - Carlos Gómez-Gallego
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
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Fukunaga K, Chinuki Y, Hamada Y, Fukutomi Y, Sugiyama A, Kishikawa R, Fukunaga A, Oda Y, Ugajin T, Yokozeki H, Harada N, Suehiro M, Hide M, Nakagawa Y, Noguchi E, Nakamura M, Matsunaga K, Yagami A, Morita E, Mushiroda T. Genome-wide association study reveals an association between the HLA-DPB1 ∗02:01:02 allele and wheat-dependent exercise-induced anaphylaxis. Am J Hum Genet 2021; 108:1540-1548. [PMID: 34246321 PMCID: PMC8387458 DOI: 10.1016/j.ajhg.2021.06.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022] Open
Abstract
Wheat-dependent exercise-induced anaphylaxis (WDEIA) is a life-threatening food allergy triggered by wheat in combination with the second factor such as exercise. The identification of potential genetic risk factors for this allergy might help high-risk individuals before consuming wheat-containing food. We aimed to identify genetic variants associated with WDEIA. A genome-wide association study was conducted in a discovery set of 77 individuals with WDEIA and 924 control subjects via three genetic models. The associations were confirmed in a replication set of 91 affected individuals and 435 control individuals. Summary statistics from the combined set were analyzed by meta-analysis with a random-effect model. In the discovery set, a locus on chromosome 6, rs9277630, was associated with WDEIA in the dominant model (OR = 3.95 [95% CI, 2.31-6.73], p = 7.87 × 10-8). The HLA-DPB1∗02:01:02 allele displayed the most significant association with WDEIA (OR = 4.51 [95% CI, 2.66-7.63], p = 2.28 × 10-9), as determined via HLA imputation following targeted sequencing. The association of the allele with WDEIA was confirmed in replication samples (OR = 3.82 [95% CI, 2.33-6.26], p = 3.03 × 10-8). A meta-analysis performed in the combined set revealed that the HLA-DPB1∗02:01:02 allele was significantly associated with an increased risk of WDEIA (OR = 4.13 [95% CI, 2.89-5.93], p = 1.06 × 10-14). Individuals carrying the HLA-DPB1∗02:01:02 allele have a significantly increased risk of WDEIA. Further validation of these findings in independent multiethnic cohorts is needed.
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Affiliation(s)
- Koya Fukunaga
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yuko Chinuki
- Department of Dermatology, Shimane University Faculty of Medicine, Shimane 693-0021, Japan
| | - Yuto Hamada
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Kanagawa 252-0392, Japan
| | - Yuma Fukutomi
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Kanagawa 252-0392, Japan
| | - Akiko Sugiyama
- Department of Allergology, National Hospital Organization Fukuoka National Hospital, Fukuoka 810-0062, Japan
| | - Reiko Kishikawa
- Department of Allergology, National Hospital Organization Fukuoka National Hospital, Fukuoka 810-0062, Japan
| | - Atsushi Fukunaga
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Yoshiko Oda
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Tsukasa Ugajin
- Department of Dermatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroo Yokozeki
- Department of Dermatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Naoe Harada
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Masataka Suehiro
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Michihiro Hide
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Yukinobu Nakagawa
- Department of Dermatology, Course of Integrated Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Emiko Noguchi
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Masashi Nakamura
- Department of Integrative Medical Science for Allergic Disease, Fujita Health University School of Medicine, Nagoya 454-8509, Japan; General Research and Development Institute, Hoyu, Nagakute 454-8509, Japan
| | - Kayoko Matsunaga
- Department of Integrative Medical Science for Allergic Disease, Fujita Health University School of Medicine, Nagoya 454-8509, Japan
| | - Akiko Yagami
- Department of Allergology, Fujita Health University School of Medicine, Nagoya 454-8509, Japan; Fujita Health University General Allergy Center in Bantane Hospital, Nagoya 454-8509, Japan
| | - Eishin Morita
- Department of Dermatology, Shimane University Faculty of Medicine, Shimane 693-0021, Japan.
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
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Haller M, Bonczarowska JH, Rieger D, Lenz TL, Nebel A, Krause-Kyora B. Ancient DNA Study in Medieval Europeans Shows an Association Between HLA-DRB1*03 and Paratyphoid Fever. Front Immunol 2021; 12:691475. [PMID: 34335597 PMCID: PMC8320744 DOI: 10.3389/fimmu.2021.691475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/28/2021] [Indexed: 12/03/2022] Open
Abstract
Outbreaks of infectious diseases repeatedly affected medieval Europe, leaving behind a large number of dead often inhumed in mass graves. Human remains interred in two burial pits from 14th century CE Germany exhibited molecular evidence of Salmonella enterica Paratyphi C (S. Paratyphi C) infection. The pathogen is responsible for paratyphoid fever, which was likely the cause of death for the buried individuals. This finding presented the unique opportunity to conduct a paratyphoid fever association study in a European population. We focused on HLA-DRB1*03:01 that is a known risk allele for enteric fever in present-day South Asians. We generated HLA profiles for 29 medieval S. Paratyphi C cases and 24 contemporaneous controls and compared these to a modern German population. The frequency of the risk allele was higher in the medieval cases (29.6%) compared to the contemporaneous controls (13%; p = 0.189), albeit not significantly so, possibly because of small sample sizes. Indeed, in comparison with the modern controls (n = 39,689; 10.2%; p = 0.005) the frequency difference became statistically significant. This comparison also suggested a slight decrease in the allele’s prevalence between the medieval and modern controls. Up to now, this is the first study on the genetic predisposition to Salmonella infection in Europeans and the only association analysis on paratyphoid fever C. Functional investigation using computational binding prediction between HLA variants and S. Paratyphi and S. Typhi peptides supported a reduced recognition capacity of bacterial proteins by DRB1*03:01 relative to other common DRB1 variants. This pattern could potentially explain the disease association. Our results suggest a slightly reduced predisposition to paratyphoid fever in modern Europeans. The causative allele, however, is still common today, which can be explained by a trade-off, as DRB1*03:01 is protective against infectious respiratory diseases such as severe respiratory syndrome (SARS). It is thus possible that the allele also provided resistance to corona-like viruses in the past.
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Affiliation(s)
- Magdalena Haller
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | | | - Dirk Rieger
- Department of Archaeology, Hanseatic City of Lübeck Historic Monuments Protection Authority, Lübeck, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, Hamburg, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
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11
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Ogrodowczyk AM, Dimitrov I, Wróblewska B. Two Faces of Milk Proteins Peptides with Both Allergenic and Multidimensional Health Beneficial Impact- Integrated In Vitro/ In Silico Approach. Foods 2021; 10:163. [PMID: 33466712 PMCID: PMC7828788 DOI: 10.3390/foods10010163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/28/2020] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
The main food-origin antigens that the infant's body is in contact with are cow's milk proteins (CMP). Still, CMP are one of the main sources of beneficial biologically active peptides that play a role in treatment of non-communicable diseases. Safe methods to quickly predict the sensitizing potential of food proteins among their range of health-promoting properties are essential. The aim of study was to adapt an integrated approach combining several in silico (IS) studies and in vitro (IV) assays to screen the multifunctionality of CMP-derived peptides. Major histocompatability complex type II MHC II-binders, interleukin-4 and -10 inducers, interferon γ -inducers and immunobioactivity tools were used to predict the peptide-power of inducing allergies or tolerance. A comparison of the peptide profiless revealed the presence of one identical and one overlapping sequence in IS and IV hydrolysate. By IS analysis, four of 24 peptides were found to have high affinity and stimulate IL-4 expression, and by IV, one of seven peptides had this potential (Bos d9 peptide DIPNPIGSENSEK (195-208)). Three IV peptides may induce IL-10 expression. The IV/IS assessment seems promising agents for peptides' potential determination dedicated only to preliminary screening of peptides. The IV verification is still crucial in further steps of studies.
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Affiliation(s)
- Anna Maria Ogrodowczyk
- Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Department of Immunology and Food Microbiology, Tuwima 10, 10-748 Olsztyn, Poland;
| | - Ivan Dimitrov
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
| | - Barbara Wróblewska
- Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Department of Immunology and Food Microbiology, Tuwima 10, 10-748 Olsztyn, Poland;
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Laha A, Ghosh A, Moitra S, Biswas H, Saha NC, Bhattacharya S, Saha GK, Podder S. Association of HLA-DQ and IL13 gene variants with challenge-proven shrimp allergy in West Bengal, India. Immunogenetics 2020; 72:489-498. [PMID: 33175217 DOI: 10.1007/s00251-020-01185-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022]
Abstract
Little is known about genetic factors and mechanisms underlying shrimp allergy. Genome-wide association studies identified HLA class-II and IL13 genes as highly plausible candidates for shrimp allergy. The present study was designed to investigate potential associations of HLA-DQ rs9275596, IL13 rs20541, and IL13 rs1800925 polymorphisms with challenge-proven shrimp allergy using the data from 532 people of West Bengal, India; selected on basis of positive skin prick test, elevated specific IgE and medical history. Risk genotypes, i.e., HLA-DQ rs9275596 CC, IL13 rs20541 AA, and IL13 rs1800925 TT, were found to be significantly associated with challenge positive shrimp allergy (P = 0.04, 0.01, and 0.03, respectively). Distribution of genotypes for HLA-DQ and IL13 polymorphisms in allergic and control subjects showed significant difference between younger (20-40 years) and older (> 40 years) age group (P = 0.006). Risk genotypes significantly associated with elevated shrimp-specific IgE. IL13 TA haplotype significantly associated with shrimp allergy and elevated specific IgE (P = 0.02). Synergistic effect of IL13 TA haplotype-HLA-DQ rs9275596 CC genotype interaction significantly elevated specific IgE (P = 0.03). The present study suggests that HLA-DQ and IL13 polymorphisms pose major risk for shrimp allergic patients in West Bengal, India and thus could be helpful for early target-specific therapeutic intervention in near future.
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Affiliation(s)
- Arghya Laha
- Allergology and Applied Entomology Research Laboratory, Department of Zoology, University of Burdwan, Bardhaman, 713104, West Bengal, India
| | - Amlan Ghosh
- Department of Life Sciences, Presidency University, Kolkata, 700073, West Bengal, India
| | - Saibal Moitra
- Allergy and Asthma Research Centre, Kolkata- 700029, West Bengal, India
| | - Himani Biswas
- Post Graduate Department of Zoology, Krishnagar Government College, Krishnagar, 741101, West Bengal, India
| | - Nimai Chandra Saha
- Vice-Chancellor, University of Burdwan, Bardhaman, 713104, West Bengal, India
| | - Srijit Bhattacharya
- Post Graduate Department of Physics, Barasat Government College, Kolkata, 700124, West Bengal, India
| | - Goutam Kumar Saha
- Department of Zoology, University of Calcutta, Kolkata, 700019, West Bengal, India
| | - Sanjoy Podder
- Allergology and Applied Entomology Research Laboratory, Department of Zoology, University of Burdwan, Bardhaman, 713104, West Bengal, India.
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Kostara M, Chondrou V, Sgourou A, Douros K, Tsabouri S. HLA Polymorphisms and Food Allergy Predisposition. J Pediatr Genet 2020; 9:77-86. [PMID: 32341809 DOI: 10.1055/s-0040-1708521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/31/2019] [Indexed: 12/16/2022]
Abstract
Food allergy (FA) is a growing health problem that affects ∼8% of the children worldwide. Although the prevalence of FA is increasing, the underlying genetic mechanisms responsible for the onset of this immune disorder are not yet clarified. Genetic factors seem to play a leading role in the development of FA, though interaction with environmental factors cannot be excluded. The broader network of genetic loci mediating the risk of this complex disorder remains to be identified. The human leucocyte antigen (HLA) has been associated with various immune disorders, including FA. This review aims to unravel the potential associations between HLA gene functions and the manifestation and outcome of FA disorders. Exploring new aspects of FA development with the perspective to improve our understanding of the multifaceted etiology and the complex biological mechanisms involved in FA is essential.
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Affiliation(s)
- Maria Kostara
- Department of Paediatrics, Ioannina University Hospital, Ioannina, Greece
| | - Vasiliki Chondrou
- Laboratory of Biology, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Argyro Sgourou
- Laboratory of Biology, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Konstantinos Douros
- Allergology and Pulmonology Unit, 3rd Pediatric Department, Attikon Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Sophia Tsabouri
- Department of Paediatrics, Child Health Department, School of Medicine, University of Ioannina, Ioannina, Greece
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Simon D. Recent Advances in Clinical Allergy and Immunology. Int Arch Allergy Immunol 2018; 177:324-333. [PMID: 30399611 DOI: 10.1159/000494931] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 01/19/2023] Open
Abstract
Allergic diseases are of great concern because of their high prevalence, which is still rising in several regions, their impact on patients' physical and psychological health, the huge burden they place on patients' quality of life, as well as the socioeconomic consequences that they cause. Recent research has provided new data on both genetic and environmental risk factors of atopic/allergic diseases. The application of new technologies such as "omics" has allowed a better understanding of the pathogenesis and has helped with the identification of therapeutic targets. Immense progress has been made in developing and applying novel, targeted therapies, for example for asthma and urticaria. Intensive efforts are being made to find biomarkers that help to classify patients, to identify their potential responsiveness to specific therapies, and to monitor the disease severity. Based on recent insights in the pathogenesis of food allergy and drug hypersensitivity, novel strategies for diagnostics, allergen avoidance, and induction of tolerance have been developed. Here, we summarize important findings in the field of clinical allergy and immunology with a special focus on asthma, allergic rhinitis, atopic dermatitis, food allergy, urticaria, angioedema, and drug hypersensitivity.
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Affiliation(s)
- Dagmar Simon
- Department of Dermatology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,
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Retinoic acid prevents immunogenicity of milk lipocalin Bos d 5 through binding to its immunodominant T-cell epitope. Sci Rep 2018; 8:1598. [PMID: 29371615 PMCID: PMC5785490 DOI: 10.1038/s41598-018-19883-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 01/04/2018] [Indexed: 02/08/2023] Open
Abstract
The major cow’s milk allergen Bos d 5 belongs to the lipocalin protein family, with an intramolecular pocket for hydrophobic ligands. We investigated whether Bos d 5 when loaded with the active vitamin A metabolite retinoic acid (RA), would elicit differential immune responses compared to the unloaded state. By in silico docking an affinity energy of −7.8 kcal/mol was calculated for RA into Bos d 5. Loading of RA to Bos d 5 could be achieved in vitro, as demonstrated by ANS displacement assay, but had no effect on serum IgE binding in tolerant or challenge-positive milk allergic children. Bioinformatic analysis revealed that RA binds to the immunodominant T-cell epitope region of Bos d 5. In accordance, Bos d 5 significantly suppressed the CD3+ CD4+ cell numbers, proliferative response and IL-10, IL-13 and IFN-γ secretion from stimulated human PBMCs only when complexed with RA. This phenomenon was neither associated with apoptosis of T-cells nor with the activation of Foxp3+ T-cells, but correlated likely with enhanced stability to lysosomal digestion due to a predicted overlap of Cathepsin S cleavage sites with the RA binding site. Taken together, proper loading of Bos d 5 with RA may suppress its immunogenicity and prevent its allergenicity.
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Radauer C. Navigating through the Jungle of Allergens: Features and Applications of Allergen Databases. Int Arch Allergy Immunol 2017; 173:1-11. [PMID: 28456806 DOI: 10.1159/000471806] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The increasing number of available data on allergenic proteins demanded the establishment of structured, freely accessible allergen databases. In this review article, features and applications of 6 of the most widely used allergen databases are discussed. The WHO/IUIS Allergen Nomenclature Database is the official resource of allergen designations. Allergome is the most comprehensive collection of data on allergens and allergen sources. AllergenOnline is aimed at providing a peer-reviewed database of allergen sequences for prediction of allergenicity of proteins, such as those planned to be inserted into genetically modified crops. The Structural Database of Allergenic Proteins (SDAP) provides a database of allergen sequences, structures, and epitopes linked to bioinformatics tools for sequence analysis and comparison. The Immune Epitope Database (IEDB) is the largest repository of T-cell, B-cell, and major histocompatibility complex protein epitopes including epitopes of allergens. AllFam classifies allergens into families of evolutionarily related proteins using definitions from the Pfam protein family database. These databases contain mostly overlapping data, but also show differences in terms of their targeted users, the criteria for including allergens, data shown for each allergen, and the availability of bioinformatics tools.
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Affiliation(s)
- Christian Radauer
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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