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Pomés A, Smith SA, Chruszcz M, Mueller GA, Brackett NF, Chapman MD. Precision engineering for localization, validation, and modification of allergenic epitopes. J Allergy Clin Immunol 2024; 153:560-571. [PMID: 38181840 PMCID: PMC10939758 DOI: 10.1016/j.jaci.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/20/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
The allergen-IgE interaction is essential for the genesis of allergic responses, yet investigation of the molecular basis of these interactions is in its infancy. Precision engineering has unveiled the molecular features of allergen-antibody interactions at the atomic level. High-resolution technologies, including x-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy, determine allergen-antibody structures. X-ray crystallography of an allergen-antibody complex localizes in detail amino acid residues and interactions that define the epitope-paratope interface. Multiple structures involving murine IgG mAbs have recently been resolved. The number of amino acids forming the epitope broadly correlates with the epitope area. The production of human IgE mAbs from B cells of allergic subjects is an exciting recent development that has for the first time enabled an actual IgE epitope to be defined. The biologic activity of defined IgE epitopes can be validated in vivo in animal models or by measuring mediator release from engineered basophilic cell lines. Finally, gene-editing approaches using the Clustered Regularly Interspaced Short Palindromic Repeats technology to either remove allergen genes or make targeted epitope engineering at the source are on the horizon. This review presents an overview of the identification and validation of allergenic epitopes by precision engineering.
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Affiliation(s)
| | - Scott A Smith
- Vanderbilt University Medical Center, Nashville, Tenn
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Smith BRE, Reid Black K, Bermingham M, Agah S, Glesner J, Versteeg SA, van Ree R, Pena-Amelunxen G, Aglas L, Smith SA, Pomés A, Chapman MD. Unique allergen-specific human IgE monoclonal antibodies derived from patients with allergic disease. FRONTIERS IN ALLERGY 2023; 4:1270326. [PMID: 37901762 PMCID: PMC10602672 DOI: 10.3389/falgy.2023.1270326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Allergic reactions are mediated by human IgE antibodies that bind to and cross-link allergen molecules. The sites on allergens that are recognized by IgE antibodies have been difficult to investigate because of the paucity of IgE antibodies in a human serum. Here, we report the production of unique human IgE monoclonal antibodies to major inhaled allergens and food allergens that can be produced at scale in perpetuity. Materials and methods The IgE antibodies were derived from peripheral blood mononuclear cells of symptomatic allergic patients, mostly children aged 3-18 years, using hybridoma fusion technology. Total IgE and allergen-specific IgE was measured by ImmunoCAP. Their specificity was confirmed through ELISA and immunoblotting. Allergenic potency measurements were determined by ImmunoCAP inhibition. Biological activity was determined in vitro by comparing β-hexosaminidase release from a humanized rat basophilic cell line. Results Human IgE monoclonal antibodies (n = 33) were derived from 17 allergic patients with symptoms of allergic rhinitis, asthma, atopic dermatitis, food allergy, eosinophilic esophagitis, or red meat allergy. The antibodies were specific for five inhaled allergens, nine food allergens, and alpha-gal and had high levels of IgE (53,450-1,702,500 kU/L) with ratios of specific IgE to total IgE ranging from <0.01 to 1.39. Sigmoidal allergen binding curves were obtained through ELISA, with low limits of detection (<1 kU/L). Allergen specificity was confirmed through immunoblotting. Pairs of IgE monoclonal antibodies to Ara h 6 were identified that cross-linked after allergen stimulation and induced release of significant levels of β-hexosaminidase (35%-80%) from a humanized rat basophilic cell line. Conclusions Human IgE monoclonal antibodies are unique antibody molecules with potential applications in allergy diagnosis, allergen standardization, and identification of allergenic epitopes for the development of allergy therapeutics. The IgE antibody probes will enable the unequivocal localization and validation of allergenic epitopes.
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Affiliation(s)
| | | | | | - Sayeh Agah
- InBio, Charlottesville, VA, United States
| | | | - Serge A. Versteeg
- Department of Experimental Immunology, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Ronald van Ree
- Department of Experimental Immunology, Amsterdam University Medical Center, Amsterdam, Netherlands
| | | | - Lorenz Aglas
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Scott A. Smith
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Anna Pomés
- InBio, Charlottesville, VA, United States
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Grant TL, Wood RA, Chapman MD. Indoor Environmental Exposures and Their Relationship to Allergic Diseases. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:2963-2970. [PMID: 37652348 PMCID: PMC10927277 DOI: 10.1016/j.jaip.2023.08.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
Cockroach, dust mite, cat, dog, mouse, and molds are major indoor allergens that have been associated with the development of allergic diseases and disease morbidity in allergen-sensitized individuals. Physical characteristics, such as allergen particle size, hydrophobicity, and charge, can determine an allergen's propensity to become airborne, location of respiratory tract penetration, and ability to elicit IgE responses in genetically predisposed individuals. Standardization and recent advancements in indoor allergen assessment serve to identify sources and distribution of allergens in a patient's home and public environment, inform public policy, and monitor the efficacy of allergen avoidance and therapeutics. Allergen exposure interventions have yielded mixed results with current US and international asthma guidelines differing on recommendations. A pragmatic, patient-centered approach to allergen avoidance includes: (1) tailoring intervention to the patient's sensitization and exposure status, (2) using a rigorous multifaceted intervention strategy to reduce allergen exposure as much as possible, and (3) beginning the intervention as soon as the patient is diagnosed. Further research into the risks/benefits of early allergen exposure, rapid and affordable in-home allergen assessment, and best practices for environmental control measures for asthma is needed.
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Affiliation(s)
- Torie L Grant
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Md.
| | - Robert A Wood
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Md
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Hu D, Irving AT. Massively-multiplexed epitope mapping techniques for viral antigen discovery. Front Immunol 2023; 14:1192385. [PMID: 37818363 PMCID: PMC10561112 DOI: 10.3389/fimmu.2023.1192385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Following viral infection, viral antigens bind specifically to receptors on the surface of lymphocytes thereby activating adaptive immunity in the host. An epitope, the smallest structural and functional unit of an antigen, binds specifically to an antibody or antigen receptor, to serve as key sites for the activation of adaptive immunity. The complexity and diverse range of epitopes are essential to study and map for the diagnosis of disease, the design of vaccines and for immunotherapy. Mapping the location of these specific epitopes has become a hot topic in immunology and immune therapy. Recently, epitope mapping techniques have evolved to become multiplexed, with the advent of high-throughput sequencing and techniques such as bacteriophage-display libraries and deep mutational scanning. Here, we briefly introduce the principles, advantages, and disadvantages of the latest epitope mapping techniques with examples for viral antigen discovery.
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Affiliation(s)
- Diya Hu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Aaron T. Irving
- Department of Clinical Laboratory Studies, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Infection, Immunity & Cancer, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
- Biomedical and Health Translational Research Centre of Zhejiang Province (BIMET), Haining, China
- College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
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5
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Zhang Y, Che H, Li C, Jin T. Food Allergens of Plant Origin. Foods 2023; 12:foods12112232. [PMID: 37297475 DOI: 10.3390/foods12112232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
This review presents an update on the physical, chemical, and biological properties of food allergens in plant sources, focusing on the few protein families that contribute to multiple food allergens from different species and protein families recently found to contain food allergens. The structures and structural components of the food allergens in the allergen families may provide further directions for discovering new food allergens. Answers as to what makes some food proteins allergens are still elusive. Factors to be considered in mitigating food allergens include the abundance of the protein in a food, the property of short stretches of the sequence of the protein that may constitute linear IgE binding epitopes, the structural properties of the protein, its stability to heat and digestion, the food matrix the protein is in, and the antimicrobial activity to the microbial flora of the human gastrointestinal tract. Additionally, recent data suggest that widely used techniques for mapping linear IgE binding epitopes need to be improved by incorporating positive controls, and methodologies for mapping conformational IgE binding epitopes need to be developed.
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Affiliation(s)
- Yuzhu Zhang
- US Department of Agriculture, Agricultural Research Service, Pacific West Area, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
| | - Huilian Che
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Caiming Li
- US Department of Agriculture, Agricultural Research Service, Pacific West Area, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
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6
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Gul M, Ayan E, Destan E, Johnson JA, Shafiei A, Kepceoğlu A, Yilmaz M, Ertem FB, Yapici İ, Tosun B, Baldir N, Tokay N, Nergiz Z, Karakadioğlu G, Paydos SS, Kulakman C, Ferah CK, Güven Ö, Atalay N, Akcan EK, Cetinok H, Arslan NE, Şabanoğlu K, Aşci B, Tavli S, Gümüsboğa H, Altuntaş S, Otsuka M, Fujita M, Teki N Ş, Çi Ftçi H, Durdaği S, Karaca E, Kaplan Türköz B, Kabasakal BV, Kati A, DeMi Rci H. Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source. Sci Rep 2023; 13:8123. [PMID: 37208392 DOI: 10.1038/s41598-023-33989-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.
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Affiliation(s)
- Mehmet Gul
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Esra Ayan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Ebru Destan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - J Austin Johnson
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Alaleh Shafiei
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Abdullah Kepceoğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Koç University Surface Science and Technology Center (KUYTAM), Koç University, Istanbul, Türkiye
| | - Merve Yilmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Fatma Betül Ertem
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - İlkin Yapici
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Bilge Tosun
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nilüfer Baldir
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nurettin Tokay
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Zeliş Nergiz
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Koç University Isbank Center for Infectious Diseases (KUISCID), Koç University, Istanbul, Türkiye
| | - Gözde Karakadioğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Seyide Seda Paydos
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Cahine Kulakman
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Cengiz Kaan Ferah
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Ömür Güven
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Necati Atalay
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science, Gebze Technical University, Kocaeli, Türkiye
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Enver Kamil Akcan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Türkiye
| | - Haluk Cetinok
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nazlı Eylül Arslan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Arel University, Istanbul, Türkiye
| | - Kardelen Şabanoğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yıldız Technical University, Istanbul, Türkiye
| | - Bengisu Aşci
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Serra Tavli
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Helin Gümüsboğa
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Sevde Altuntaş
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- Department of Tissue Engineering, Hamidiye Institute of Health Sciences, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Drug Discovery, Science Farm Ltd., Kumamoto, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Şaban Teki N
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- The Scientific and Technological Research Council of Türkiye (TÜBİTAK) Marmara Research Center (MAM), Life Sciences, Kocaeli, Türkiye
- Department of Basic Medical Sciences, Division of Medical Biology, Faculty of Medicine, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Halilibrahim Çi Ftçi
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Drug Discovery, Science Farm Ltd., Kumamoto, Japan
| | - Serdar Durdaği
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Türkiye
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
| | - Burcu Kaplan Türköz
- Department of Food Engineering, Faculty of Engineering, Ege University, Izmir, Türkiye
| | - Burak Veli Kabasakal
- Turkish Accelerator and Radiation Laboratory (TARLA), Ankara University, Ankara, Türkiye
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Ahmet Kati
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- Department of Biotechnology, Hamidiye Institute of Health Sciences, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Hasan DeMi Rci
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye.
- Koç University Isbank Center for Infectious Diseases (KUISCID), Koç University, Istanbul, Türkiye.
- SLAC National Laboratory, Stanford PULSE Institute, Menlo Park, CA, USA.
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Chen Y, Jin T, Li M, Yun X, Huan F, Liu Q, Hu M, Wei X, Zheng P, Liu G. Crystal Structure Analysis of Sarcoplasmic-Calcium-Binding Protein: An Allergen in Scylla paramamosain. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1214-1223. [PMID: 36602420 DOI: 10.1021/acs.jafc.2c07267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The structure of allergenic proteins provides important information about the binding of allergens to antibodies. In this study, the crystal structure of Scy p 4 with a resolution of 1.60 Å was obtained by X-ray diffraction. Epitope mapping of Scy p 4 revealed that linear epitopes are located on the surface of Scy p 4. Also, conformational epitopes are mostly located in the structural conservative region. Further structural comparison, surface electrostatic potential, and hydrogen bond force analysis showed that mutation of Asp70 and Asp18/20/70 would lead to calcium-binding capacity being lost and destruction of allergenicity. Furthermore, a comparative analysis of structure showed that sarcoplasmic-calcium-binding protein (SCP) had high sequence, secondary, and spatial structural identity in crustaceans, which may be an important factor leading to cross-reactivity among crustaceans. The structure of Scy p 4 provides a template for epitope evaluation and localization of SCPs, which will help to reveal cross-reactivity among species.
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Affiliation(s)
- Yiyu Chen
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian 361021, China
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Tengchuan Jin
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Mengsi Li
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian 361021, China
| | - Xiao Yun
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian 361021, China
| | - Fei Huan
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian 361021, China
| | - Qingmei Liu
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian 361021, China
| | - Mengjun Hu
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian 361021, China
| | - Xiaofeng Wei
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Peiyi Zheng
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Guangming Liu
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian 361021, China
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Childers MC, Daggett V. Molecular Dynamics Methods for Antibody Design. Methods Mol Biol 2023; 2552:109-124. [PMID: 36346588 DOI: 10.1007/978-1-0716-2609-2_5] [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] [Indexed: 06/16/2023]
Abstract
Complex and coordinated dynamics are closely connected with protein functions, including the binding of antibodies to antigens. Knowledge of such dynamics could improve the design of antibodies. Molecular dynamics (MD) simulations provide a "computational microscope" that can resolve atomic motions and inform antibody design efforts.
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Affiliation(s)
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
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9
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Abstract
Serial crystallography (SX) is an emerging technique to determine macromolecules at room temperature. SX with a pump–probe experiment provides the time-resolved dynamics of target molecules. SX has developed rapidly over the past decade as a technique that not only provides room-temperature structures with biomolecules, but also has the ability to time-resolve their molecular dynamics. The serial femtosecond crystallography (SFX) technique using an X-ray free electron laser (XFEL) has now been extended to serial synchrotron crystallography (SSX) using synchrotron X-rays. The development of a variety of sample delivery techniques and data processing programs is currently accelerating SX research, thereby increasing the research scope. In this editorial, I briefly review some of the experimental techniques that have contributed to advances in the field of SX research and recent major research achievements. This Special Issue will contribute to the field of SX research.
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Czyzewski A, Krawiec F, Brzezinski D, Porebski PJ, Minor W. Detecting anomalies in X-ray diffraction images using convolutional neural networks. EXPERT SYSTEMS WITH APPLICATIONS 2021; 174:114740. [PMID: 34366575 PMCID: PMC8341115 DOI: 10.1016/j.eswa.2021.114740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Our understanding of life is based upon the interpretation of macromolecular structures and their dynamics. Almost 90% of currently known macromolecular models originated from electron density maps constructed using X-ray diffraction images. Even though diffraction images are critical for structure determination, due to their vast amounts and noisy, non-intuitive nature, their quality is rarely inspected. In this paper, we use recent advances in machine learning to automatically detect seven types of anomalies in X-ray diffraction images. For this purpose, we utilize a novel X-ray beam center detection algorithm, propose three different image representations, and compare the predictive performance of general-purpose classifiers and deep convolutional neural networks (CNNs). In benchmark tests on a set of 6,311 X-ray diffraction images, the proposed CNN achieved between 87% and 99% accuracy depending on the type of anomaly. Experimental results show that the proposed anomaly detection system can be considered suitable for early detection of sub-optimal data collection conditions and malfunctions at X-ray experimental stations.
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Affiliation(s)
- Adam Czyzewski
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
| | - Faustyna Krawiec
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
| | - Dariusz Brzezinski
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
- Center for Biocrystallographic Research, Institute of
Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-714, Poland
- Center for Artificial Intelligence and Machine Learning,
Poznan University of Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
| | - Przemyslaw Jerzy Porebski
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
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11
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Goodman RE, Chapman MD, Slater JE. The Allergen: Sources, Extracts, and Molecules for Diagnosis of Allergic Disease. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2021; 8:2506-2514. [PMID: 32888526 DOI: 10.1016/j.jaip.2020.06.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/10/2020] [Accepted: 06/24/2020] [Indexed: 01/30/2023]
Abstract
Allergenic source materials include pollen, molds, animal dander, and insects; food allergens from nuts, grains, and animals; venoms; and salivary proteins from insects and ticks. Clinical diagnostic tests have used heterogeneous extracts from allergen source materials for skin prick tests (SPTs). In vitro laboratory methods using immunoassays or microarrays can detect serum IgE directed against allergenic proteins where clinical testing may not be suitable. Clinicians rely primarily on licensed commercial extracts of allergens for SPTs. Manufacturers and regulatory agencies have standardized selected extracts for identity, composition, and potency. Allergen sources contain multiple proteins. The IgE antibody responses to these proteins vary between allergic subjects as does the quantity of specific IgE. Component-resolved molecular diagnostics can be used to improve the specificity of allergy testing and resolve clinical cross-reactivities that may affect treatment outcomes. This clinical commentary will review methods for the production, evaluation, and standardization of allergen extracts from the perspective of diagnostic testing that may be useful for allergists in practice.
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Affiliation(s)
- Richard E Goodman
- Food Allergy Research and Resource Program, University of Nebraska, Lincoln, Neb.
| | | | - Jay E Slater
- Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Md
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Di Muzio M, Wildner S, Huber S, Hauser M, Vejvar E, Auzinger W, Regl C, Laimer J, Zennaro D, Wopfer N, Huber CG, van Ree R, Mari A, Lackner P, Ferreira F, Schubert M, Gadermaier G. Hydrogen/deuterium exchange memory NMR reveals structural epitopes involved in IgE cross-reactivity of allergenic lipid transfer proteins. J Biol Chem 2021; 295:17398-17410. [PMID: 33453986 DOI: 10.1074/jbc.ra120.014243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Indexed: 01/30/2023] Open
Abstract
Identification of antibody-binding epitopes is crucial to understand immunological mechanisms. It is of particular interest for allergenic proteins with high cross-reactivity as observed in the lipid transfer protein (LTP) syndrome, which is characterized by severe allergic reactions. Art v 3, a pollen LTP from mugwort, is frequently involved in this cross-reactivity, but no antibody-binding epitopes have been determined so far. To reveal human IgE-binding regions of Art v 3, we produced three murine high-affinity mAbs, which showed 70-90% coverage of the allergenic epitopes from mugwort pollen-allergic patients. As reliable methods to determine structural epitopes with tightly interacting intact antibodies under native conditions are lacking, we developed a straightforward NMR approach termed hydrogen/deuterium exchange memory (HDXMEM). It relies on the slow exchange between the invisible antigen-mAb complex and the free 15N-labeled antigen whose 1H-15N correlations are detected. Due to a memory effect, changes of NH protection during antibody binding are measured. Differences in H/D exchange rates and analyses of mAb reactivity to homologous LTPs revealed three structural epitopes: two partially cross-reactive regions around α-helices 2 and 4 as well as a novel Art v 3-specific epitope at the C terminus. Protein variants with exchanged epitope residues confirmed the antibody-binding sites and revealed strongly reduced IgE reactivity. Using the novel HDXMEM for NMR epitope mapping allowed identification of the first structural epitopes of an allergenic pollen LTP. This knowledge enables improved cross-reactivity prediction for patients suffering from LTP allergy and facilitates design of therapeutics.
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Affiliation(s)
- Martina Di Muzio
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Sabrina Wildner
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Sara Huber
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Michael Hauser
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Eva Vejvar
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Werner Auzinger
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Christof Regl
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Josef Laimer
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Danila Zennaro
- Centri Associati di Allergologica Molecolare (CAAM), Latina, Italy
| | - Nicole Wopfer
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Christian G Huber
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Ronald van Ree
- Department of Experimental Immunology and of Otorhinolaryngology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Adriano Mari
- Centri Associati di Allergologica Molecolare (CAAM), Latina, Italy
| | - Peter Lackner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Fatima Ferreira
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Mario Schubert
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria.
| | - Gabriele Gadermaier
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria.
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13
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Hindley JP, Oliver MA, Thorpe C, Cullinane A, Wuenschmann S, Chapman MD. Bos d 11 in baked milk poses a risk for adverse reactions in milk-allergic patients. Clin Exp Allergy 2020; 51:132-140. [PMID: 33141480 DOI: 10.1111/cea.13774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/06/2020] [Accepted: 10/28/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Patients are commonly challenged with foods containing baked milk, for example muffins, yet little is known about the specific allergen content of muffins used in milk challenges or of the effect that baking has on allergenicity. OBJECTIVE Our objective was to compare the levels of major milk allergens in uncooked and baked muffins using monoclonal immunoassays and IgE antibody binding before and after baking. METHODS Uncooked and baked muffins were prepared using recipes from Mount Sinai and Imperial College. Allergen levels were compared by ELISA for Bos d 5 (β-lactoglobulin) and Bos d 11 (β-casein). IgE reactivity was assessed using sera from milk-sensitized donors in direct binding and inhibition ELISA. RESULTS Bos d 5 was reduced from 680 µg/g in uncooked muffin mix to 0.17 µg/g in baked muffins, representing a >99% decrease after baking. Conversely, Bos d 11 levels in baked muffin remained high and only decreased by 30% from a mean of 4249 µg/g in uncooked muffin mix to 2961 µg/g when baked (~181 mg Bos d 11 per muffin). Baked muffins retained ~70% of the IgE binding to uncooked muffin mix. Baked muffin extract inhibited IgE binding to uncooked muffin mix by up to 80%, demonstrating retention of in vitro IgE reactivity. CONCLUSIONS AND CLINICAL RELEVANCE High levels of Bos d 11 in baked muffins pose a risk for adverse reactions, especially in patients who have high anti-casein IgE antibodies.
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Affiliation(s)
| | | | - Cathy Thorpe
- Indoor Biotechnologies Inc, Charlottesville, VA, USA
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14
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Pomés A, Mueller GA, Chruszcz M. Structural Aspects of the Allergen-Antibody Interaction. Front Immunol 2020; 11:2067. [PMID: 32983155 PMCID: PMC7492603 DOI: 10.3389/fimmu.2020.02067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/29/2020] [Indexed: 12/23/2022] Open
Abstract
The development of allergic disease involves the production of IgE antibodies upon allergen exposure in a process called sensitization. IgE binds to receptors on the surface of mast cells and basophils, and subsequent allergen exposure leads to cross-linking of IgE antibodies and release of cell mediators that cause allergy symptoms. Although this process is quite well-understood, very little is known about the epitopes on the allergen recognized by IgE, despite the importance of the allergen-antibody interaction for the allergic response to occur. This review discusses efforts to analyze allergen-antibody interactions, from the original epitope mapping studies using linear peptides or recombinant allergen fragments, to more sophisticated technologies, such as X-ray crystallography and nuclear magnetic resonance. These state-of-the-art approaches, combined with site-directed mutagenesis, have led to the identification of conformational IgE epitopes. The first structures of an allergen (egg lysozyme) in complex with Fab fragments from IgG antibodies were determined in the 1980s. Since then, IgG has been used as surrogate for IgE, due to the difficulty of obtaining monoclonal IgE antibodies. Technical developments including phage display libraries have contributed to progress in epitope mapping thanks to the isolation of IgE antibody constructs from combinatorial libraries made from peripheral blood mononuclear cells of allergic donors. Most recently, single B cell antibody sequencing and human hybridomas are new breakthrough technologies for finally obtaining human IgE monoclonal antibodies, ideal for epitope mapping. The information on antigenic determinants will facilitate the design of hypoallergens for immunotherapy and the investigation of the fundamental mechanisms of the IgE response.
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Affiliation(s)
- Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA, United States
| | - Geoffrey A Mueller
- National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, United States
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15
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Brzezinski D, Dauter Z, Minor W, Jaskolski M. On the evolution of the quality of macromolecular models in the PDB. FEBS J 2020; 287:2685-2698. [PMID: 32311227 PMCID: PMC7340579 DOI: 10.1111/febs.15314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 03/02/2020] [Accepted: 03/26/2020] [Indexed: 01/06/2023]
Abstract
Crystallographic models of biological macromolecules have been ranked using the quality criteria associated with them in the Protein Data Bank (PDB). The outcomes of this quality analysis have been correlated with time and with the journals that published papers based on those models. The results show that the overall quality of PDB structures has substantially improved over the last ten years, but this period of progress was preceded by several years of stagnation or even depression. Moreover, the study shows that the historically observed negative correlation between journal impact and the quality of structural models presented therein seems to disappear as time progresses.
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Affiliation(s)
- Dariusz Brzezinski
- Center for Biocrystallographic ResearchInstitute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
- Institute of Computing SciencePoznan University of TechnologyPoland
- Center for Artificial Intelligence and Machine LearningPoznan University of TechnologyPoland
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVAUSA
| | - Zbigniew Dauter
- Synchrotron Radiation Research SectionMacromolecular Crystallography LaboratoryNational Cancer InstituteArgonne National LaboratoryArgonneILUSA
| | - Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVAUSA
| | - Mariusz Jaskolski
- Center for Biocrystallographic ResearchInstitute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
- Department of CrystallographyFaculty of ChemistryA. Mickiewicz UniversityPoznanPoland
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16
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Polysaccharide-Based Injection Matrix for Serial Crystallography. Int J Mol Sci 2020; 21:ijms21093332. [PMID: 32397185 PMCID: PMC7247560 DOI: 10.3390/ijms21093332] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 12/21/2022] Open
Abstract
Serial crystallography (SX) provides an opportunity to observe the molecular dynamics of macromolecular structures at room temperature via pump-probe studies. The delivery of crystals embedded in a viscous medium via an injector or syringe is widely performed in synchrotrons or X-ray free-electron laser facilities with low repetition rates. Various viscous media have been developed; however, there are cases in which the delivery material undesirably interacts chemically or biologically with specific protein samples, or changes the stability of the injection stream, depending on the crystallization solution. Therefore, continued discovery and characterization of new delivery media is necessary for expanding future SX applications. Here, the preparation and characterization of new polysaccharide (wheat starch (WS) and alginate)-based sample delivery media are introduced for SX. Crystals embedded in a WS or alginate injection medium showed a stable injection stream at a flow rate of < 200 nL/min and low-level X-ray background scattering similar to other hydrogels. Using these media, serial millisecond crystallography (SMX) was performed, and the room temperature crystal structures of glucose isomerase and lysozyme were determined at 1.9–2.0 Å resolutions. WS and alginate will allow an expanded application of sample delivery media in SX experiments.
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17
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Fernández-Quintero ML, Loeffler JR, Waibl F, Kamenik AS, Hofer F, Liedl KR. Conformational selection of allergen-antibody complexes-surface plasticity of paratopes and epitopes. Protein Eng Des Sel 2019; 32:513-523. [PMID: 32719844 PMCID: PMC7451023 DOI: 10.1093/protein/gzaa014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022] Open
Abstract
Antibodies have the ability to bind various types of antigens and to recognize different antibody-binding sites (epitopes) of the same antigen with different binding affinities. Due to the conserved structural framework of antibodies, their specificity to antigens is mainly determined by their antigen-binding site (paratope). Therefore, characterization of epitopes in combination with describing the involved conformational changes of the paratope upon binding is crucial in understanding and predicting antibody-antigen binding. Using molecular dynamics simulations complemented with strong experimental structural information, we investigated the underlying binding mechanism and the resulting local and global surface plasticity in the binding interfaces of distinct antibody-antigen complexes. In all studied allergen-antibody complexes, we clearly observe that experimentally suggested epitopes reveal less plasticity, while non-epitope regions show high surface plasticity. Surprisingly, the paratope shows higher conformational diversity reflected in substantially higher surface plasticity, compared to the epitope. This work allows a visualization and characterization of antibody-antigen interfaces and might have strong implications for antibody-antigen docking and in the area of epitope prediction.
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Affiliation(s)
- Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020 Innsbruck, Austria
| | - Johannes R Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020 Innsbruck, Austria
| | - Anna S Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020 Innsbruck, Austria
| | - Florian Hofer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020 Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020 Innsbruck, Austria,To whom correspondence should be addressed. E-Mail:
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18
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Dall'Antonia F, Keller W. SPADE web service for prediction of allergen IgE epitopes. Nucleic Acids Res 2019; 47:W496-W501. [PMID: 31066444 PMCID: PMC6602491 DOI: 10.1093/nar/gkz331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 04/30/2019] [Indexed: 11/12/2022] Open
Abstract
The specific interaction of allergens with IgE antibodies and the allergen mediated cross-linking of receptor-bound IgE are key events of allergic diseases. The elucidation of the IgE binding sites (the epitopes) on the allergen surface is an important goal of allergy research. Only few allergen-specific IgE epitopes have been determined experimentally to date. Epitope prediction methods represent a viable alternative to experimental methods and have worked well with linear epitopes. However, as most IgE epitopes are of conformational and/or discontinuous nature sequence based prediction methods have had limited success in these cases. Here, we present the web server of the program SPADE (https://spade.uni-graz.at), which is the server implementation of a previously published program (1). In this approach we utilize the structural homology of cross-reactive allergens combined with the immunological cross-reactivity data for the discrimination of putative IgE-binding sites from non-cross-reactive surface patches. The method, although predictive, does not rely on machine-learning algorithms and does not require training data. The SPADE server features an easy-to-use interface, an automated pipeline consisting of third-party, as well as own, newly developed routines and a comprehensive output page.
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Affiliation(s)
- Fabio Dall'Antonia
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Walter Keller
- Institute of Molecular Biosciences, BioTechMed, University of Graz, Humboldtstraße 50, 8010 Graz, Austria
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19
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Nam KH. Sample Delivery Media for Serial Crystallography. Int J Mol Sci 2019; 20:E1094. [PMID: 30836596 PMCID: PMC6429298 DOI: 10.3390/ijms20051094] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 01/19/2023] Open
Abstract
X-ray crystallographic methods can be used to visualize macromolecules at high resolution. This provides an understanding of molecular mechanisms and an insight into drug development and rational engineering of enzymes used in the industry. Although conventional synchrotron-based X-ray crystallography remains a powerful tool for understanding molecular function, it has experimental limitations, including radiation damage, cryogenic temperature, and static structural information. Serial femtosecond crystallography (SFX) using X-ray free electron laser (XFEL) and serial millisecond crystallography (SMX) using synchrotron X-ray have recently gained attention as research methods for visualizing macromolecules at room temperature without causing or reducing radiation damage, respectively. These techniques provide more biologically relevant structures than traditional X-ray crystallography at cryogenic temperatures using a single crystal. Serial femtosecond crystallography techniques visualize the dynamics of macromolecules through time-resolved experiments. In serial crystallography (SX), one of the most important aspects is the delivery of crystal samples efficiently, reliably, and continuously to an X-ray interaction point. A viscous delivery medium, such as a carrier matrix, dramatically reduces sample consumption, contributing to the success of SX experiments. This review discusses the preparation and criteria for the selection and development of a sample delivery medium and its application for SX.
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Affiliation(s)
- Ki Hyun Nam
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea.
- Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Korea.
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20
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Mueller GA, Min J, Foo ACY, Pomés A, Pedersen LC. Structural Analysis of Recent Allergen-Antibody Complexes and Future Directions. Curr Allergy Asthma Rep 2019; 19:17. [PMID: 30815753 DOI: 10.1007/s11882-019-0848-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
PURPOSE OF REVIEW Allergen-antibody complexes are extremely valuable in describing the detailed molecular features of epitopes. This review summarizes insights gained from recently published co-structures and what obstacles impede the acquisition of further data. RECENT FINDINGS Structural epitope data helped define the epitopes of two anti-Fel d 1 antibodies undergoing phase I clinical trials, providing a greater level of detail than was possible through hydrogen-deuterium exchange protection studies. Separately, a human camelid-like antibody structure with lysozyme described several unique features in a long variable loop that interacted with the active site cleft of Gal d 4. Finally, a co-structure conclusively demonstrated that Phl p 7 could function as a superantigen and that an antibody could simultaneously recognize two epitopes. These remarkable assertions would not have been possible without visualization of the complex. Only three new complexes have appeared in the last few years, suggesting that there are major impediments to traditional production and crystallization. The structural data was extremely valuable in describing epitopes. New techniques like cryo-EM may provide an alternative to crystallography.
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Affiliation(s)
- Geoffrey A Mueller
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA.
| | - Jungki Min
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA
| | - Alexander C Y Foo
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA
| | - Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA, USA
| | - Lars C Pedersen
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA
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21
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Chruszcz M, Kapingidza AB, Dolamore C, Kowal K. A robust method for the estimation and visualization of IgE cross-reactivity likelihood between allergens belonging to the same protein family. PLoS One 2018; 13:e0208276. [PMID: 30496313 PMCID: PMC6264518 DOI: 10.1371/journal.pone.0208276] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/14/2018] [Indexed: 12/11/2022] Open
Abstract
Among the vast number of identified protein families, allergens emanate from relatively few families which translates to only a small fraction of identified protein families. In allergy diagnostics and immunotherapy, interactions between immunoglobulin E and allergens are crucial because the formation of an allergen-antibody complex is necessary for triggering an allergic reaction. In allergic diseases, there is a phenomenon known as cross-reactivity. Cross-reactivity describes a situation where an individual has produced antibodies against a particular allergenic protein, but said antibodies fail to discriminate between the original sensitizer and other similar proteins that usually belong to the same family. To expound the concept of cross-reactivity, this study examines ten protein families that include allergens selected specifically for the analysis of cross-reactivity. The selected allergen families had at least 13 representative proteins, overall folds that differ significantly between families, and include relevant allergens with various potencies. The selected allergens were analyzed using information on sequence similarities and identities between members of the families as well as reports on clinically relevant cross-reactivities. Based on our analysis, we propose to introduce a new A-RISC index (Allergens’–Relative Identity, Similarity and Cross-reactivity) which describes homology between two allergens belonging to the same protein family and is used to predict the likelihood of cross-reactivity between them. Information on sequence similarities and identities, as well as on the values of the proposed A-RISC index is used to introduce four categories describing a risk of a cross-reactive reaction, namely: high, medium-high, medium-low and low. The proposed approach can facilitate analysis in component-resolved allergy diagnostics, generation of avoidance guidelines for allergic individuals, and help with the design of immunotherapy.
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Affiliation(s)
- Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
- * E-mail:
| | - A. Brenda Kapingidza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Coleman Dolamore
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Krzysztof Kowal
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Department of Experimental Allergology and Immunology, Medical University of Bialystok, Bialystok, Poland
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WHO/IUIS Allergen Nomenclature: Providing a common language. Mol Immunol 2018; 100:3-13. [PMID: 29625844 DOI: 10.1016/j.molimm.2018.03.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 03/06/2018] [Indexed: 11/23/2022]
Abstract
A systematic nomenclature for allergens originated in the early 1980s, when few protein allergens had been described. A group of scientists led by Dr. David G. Marsh developed a nomenclature based on the Linnaean taxonomy, and further established the World Health Organization/International Union of Immunological Societies (WHO/IUIS) Allergen Nomenclature Sub-Committee in 1986. Its stated aim was to standardize the names given to the antigens (allergens) that caused IgE-mediated allergies in humans. The Sub-Committee first published a revised list of allergen names in 1986, which continued to grow with rare publications until 1994. Between 1994 and 2007 the database was a text table online, then converted to a more readily updated website. The allergen list became the Allergen Nomenclature database (www.allergen.org), which currently includes approximately 880 proteins from a wide variety of sources. The Sub-Committee includes experts on clinical and molecular allergology. They review submissions of allergen candidates, using evidence-based criteria developed by the Sub-Committee. The review process assesses the biochemical analysis and the proof of allergenicity submitted, and aims to assign allergen names prior to publication. The Sub-Committee maintains and revises the database, and addresses continuous challenges as new "omics" technologies provide increasing data about potential new allergens. Most journals publishing information on new allergens require an official allergen name, which involves submission of confidential data to the WHO/IUIS Allergen Nomenclature Sub-Committee, sufficient to demonstrate binding of IgE from allergic subjects to the purified protein.
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Mazzucchelli G, Holzhauser T, Cirkovic Velickovic T, Diaz‐Perales A, Molina E, Roncada P, Rodrigues P, Verhoeckx K, Hoffmann‐Sommergruber K. Current (Food) Allergenic Risk Assessment: Is It Fit for Novel Foods? Status Quo and Identification of Gaps. Mol Nutr Food Res 2018; 62:1700278. [PMID: 28925060 PMCID: PMC5814866 DOI: 10.1002/mnfr.201700278] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/28/2017] [Indexed: 01/08/2023]
Abstract
Food allergies are recognized as a global health concern. In order to protect allergic consumers from severe symptoms, allergenic risk assessment for well-known foods and foods containing genetically modified ingredients is installed. However, population is steadily growing and there is a rising need to provide adequate protein-based foods, including novel sources, not yet used for human consumption. In this context safety issues such as a potential increased allergenic risk need to be assessed before marketing novel food sources. Therefore, the established allergenic risk assessment for genetically modified organisms needs to be re-evaluated for its applicability for risk assessment of novel food proteins. Two different scenarios of allergic sensitization have to be assessed. The first scenario is the presence of already known allergenic structures in novel foods. For this, a comparative assessment can be performed and the range of cross-reactivity can be explored, while in the second scenario allergic reactions are observed toward so far novel allergenic structures and no reference material is available. This review summarizes the current analytical methods for allergenic risk assessment, highlighting the strengths and limitations of each method and discussing the gaps in this assessment that need to be addressed in the near future.
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Affiliation(s)
- Gabriel Mazzucchelli
- Laboratory of Mass Spectrometry – MolSysDepartment of ChemistryUniversity of LiegeLiegeBelgium
| | | | - Tanja Cirkovic Velickovic
- Center of Excellence for Molecular Food SciencesUniversity of Belgrade – Faculty of ChemistryBelgradeSerbia
- Ghent University Global CampusYeonsu‐guIncheonSouth Korea
| | | | | | - Paola Roncada
- Istituto Sperimentale Italiano Lazzaro SpallanzaniMilanoItaly
| | - Pedro Rodrigues
- CCMARCenter of Marine ScienceUniversity of AlgarveFaroPortugal
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24
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Mueller GA. Contributions and Future Directions for Structural Biology in the Study of Allergens. Int Arch Allergy Immunol 2017; 174:57-66. [PMID: 28992615 DOI: 10.1159/000481078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Allergy is defined as an inappropriate immune response to something normally considered harmless. The symptomatic immune response is driven by IgE antibodies directed against allergens. The study of allergens has contributed significantly to our understanding of allergic disease in 3 main areas. First, identifying allergens as the cause of symptoms and developing allergen standards has led to many advances in exposure assessment and patient diagnostics. Second, a biochemical understanding of allergens has suggested a number of hypotheses related to the mechanisms of allergic sensitization. And finally, studies of allergen-antibody interactions have contributed to understanding the cross-reactivity of allergens, mapping patient epitopes, and the development of hypoallergens. In this review, a few select cases are highlighted where structural biology, in particular, has contributed significantly to allergen research and provided new avenues for investigation.
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Affiliation(s)
- Geoffrey A Mueller
- Department of Health and Human Services, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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Alessandri C, Ferrara R, Bernardi ML, Zennaro D, Tuppo L, Giangrieco I, Tamburrini M, Mari A, Ciardiello MA. Diagnosing allergic sensitizations in the third millennium: why clinicians should know allergen molecule structures. Clin Transl Allergy 2017; 7:21. [PMID: 28725346 PMCID: PMC5513363 DOI: 10.1186/s13601-017-0158-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/05/2017] [Indexed: 01/06/2023] Open
Abstract
Diagnostic tests to detect allergic sensitization were introduced at the end of the nineteenth century but only in the late 1990s did the advent of molecular allergology revolutionize the approach to the allergic patient. Personalized Medicine, a medical procedure that separates patients into different groups with different medical decisions, practices and interventions has sanctioned this change. In fact, in the last few years molecular allergology and the observation that not every patient has the same allergic profile, even when allergic to the same allergenic source, has originated the concept "one size does not fit all". This new approach requires the identification of still unknown allergens, but also the more detailed investigation of those already known. In depth studies of the structure-function relationships in allergenic molecules can reveal the structural determinants involved in the IgE-binding. Then, the knowledge of the epitope profile of each allergen and of the environmental/experimental conditions affecting the exposure of IgE-binding epitopes can provide important contributions to the understanding of cross-reaction processes and to the improvement of diagnosis, immunotherapy and the overall patient treatment. The evolution of diagnostic systems cannot ignore these new needs in this field.
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Affiliation(s)
- C Alessandri
- CAAM - Centri Associati di Allergologia Molecolare, Rome, Italy
| | - R Ferrara
- CAAM - Centri Associati di Allergologia Molecolare, Rome, Italy
| | - M L Bernardi
- CAAM - Centri Associati di Allergologia Molecolare, Rome, Italy
| | - D Zennaro
- CAAM - Centri Associati di Allergologia Molecolare, Rome, Italy
| | - L Tuppo
- Istituto di Bioscienze e Biorisorse - IBBR-CNR, Naples, Italy
| | - I Giangrieco
- Istituto di Bioscienze e Biorisorse - IBBR-CNR, Naples, Italy
| | - M Tamburrini
- Istituto di Bioscienze e Biorisorse - IBBR-CNR, Naples, Italy
| | - A Mari
- CAAM - Centri Associati di Allergologia Molecolare, Rome, Italy.,Allergy Data Laboratories s.c., Latina, Italy
| | - M A Ciardiello
- Istituto di Bioscienze e Biorisorse - IBBR-CNR, Naples, Italy
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Hu T, Sprague ER, Fodor M, Stams T, Clark KL, Cowan-Jacob SW. The impact of structural biology in medicine illustrated with four case studies. J Mol Med (Berl) 2017; 96:9-19. [PMID: 28669027 DOI: 10.1007/s00109-017-1565-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/12/2017] [Accepted: 06/15/2017] [Indexed: 12/18/2022]
Abstract
The contributions of structural biology to drug discovery have expanded over the last 20 years from structure-based ligand optimization to a broad range of clinically relevant topics including the understanding of disease, target discovery, screening for new types of ligands, discovery of new modes of action, addressing clinical challenges such as side effects or resistance, and providing data to support drug registration. This expansion of scope is due to breakthroughs in the technology, which allow structural information to be obtained rapidly and for more complex molecular systems, but also due to the combination of different technologies such as X-ray, NMR, and other biophysical methods, which allows one to get a more complete molecular understanding of disease and ways to treat it. In this review, we provide examples of the types of impact molecular structure information can have in the clinic for both low molecular weight and biologic drug discovery and describe several case studies from our own work to illustrate some of these contributions.
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Affiliation(s)
- Tiancen Hu
- Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA
| | | | - Michelle Fodor
- Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA
| | - Travis Stams
- Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA
| | - Kirk L Clark
- Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA
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Abstract
PURPOSE OF REVIEW The purpose of this review is to evaluate the most recent findings on indoor allergens and their impact on allergic diseases. RECENT FINDINGS Indoor allergens are present inside buildings (home, work environment, school), and given the chronic nature of the exposures, indoor allergies tend to be associated with the development of asthma. The most common indoor allergens are derived from dust mites, cockroaches, mammals (including wild rodents and pets), and fungi. The advent of molecular biology and proteomics has led to the identification, cloning, and expression of new indoor allergens, which have facilitated research to elucidate their role in allergic diseases. This review is an update on new allergens and their molecular features, together with the most recent reports on their avoidance for allergy prevention and their use for diagnosis and treatment. Research progress on indoor allergens will result in the development of new diagnostic tools and design of coherent strategies for immunotherapy.
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Affiliation(s)
- Anna Pomés
- Indoor Biotechnologies, Inc., 700 Harris Street, Charlottesville, VA, 22903, USA.
| | - Martin D Chapman
- Indoor Biotechnologies, Inc., 700 Harris Street, Charlottesville, VA, 22903, USA
| | - Sabina Wünschmann
- Indoor Biotechnologies, Inc., 700 Harris Street, Charlottesville, VA, 22903, USA
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28
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Sánchez-Borges M, Fernandez-Caldas E, Thomas WR, Chapman MD, Lee BW, Caraballo L, Acevedo N, Chew FT, Ansotegui IJ, Behrooz L, Phipatanakul W, Gerth van Wijk R, Pascal D, Rosario N, Ebisawa M, Geller M, Quirce S, Vrtala S, Valenta R, Ollert M, Canonica GW, Calderón MA, Barnes CS, Custovic A, Benjaponpitak S, Capriles-Hulett A. International consensus (ICON) on: clinical consequences of mite hypersensitivity, a global problem. World Allergy Organ J 2017; 10:14. [PMID: 28451053 PMCID: PMC5394630 DOI: 10.1186/s40413-017-0145-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/27/2017] [Indexed: 01/09/2023] Open
Abstract
Since mite allergens are the most relevant inducers of allergic diseases worldwide, resulting in significant morbidity and increased burden on health services, the International Collaboration in Asthma, Allergy and Immunology (iCAALL), formed by the American Academy of Allergy, Asthma and Immunology (AAAAI), the American College of Allergy, Asthma and Immunology (ACAAI), the European Academy of Allergy and Clinical Immunology (EAACI), and the World Allergy Organization (WAO), has proposed to issue an International Consensus (ICON) on the clinical consequences of mite hypersensitivity. The objectives of this document are to highlight aspects of mite biology that are clinically relevant, to update the current knowledge on mite allergens, routes of sensitization, the genetics of IgE responses to mites, the epidemiologic aspects of mite hypersensitivity, the clinical pictures induced by mites, the diagnosis, specific immunotherapeutic approaches, and prevention.
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Affiliation(s)
- Mario Sánchez-Borges
- Allergy and Clinical Immunology Department, Centro Médico Docente La Trinidad, Caracas, Venezuela
- Clínica El Avila, 6ª transversal Urb. Altamira, Piso 8, Consultoria 803, Caracas, 1060 Venezuela
| | - Enrique Fernandez-Caldas
- Inmunotek S.L., Madrid, Spain and Division of Allergy and Immunology, University of South Florida College of Medicine, Tampa, FL USA
| | - Wayne R. Thomas
- Telethon Kids Institute, University of Western Australia, Crawley, WA Australia
| | | | - Bee Wah Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Luis Caraballo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | | | - Fook Tim Chew
- Department of Biological Sciences, Allergy and Molecular Immunology Laboratory, Functional Genomics Laboratories, National University of Singapore, Singapore, Singapore
| | | | - Leili Behrooz
- Division of Immunology and Allergy, Boston Cshildren’s Hospital, Harvard Medical School, Boston, MA USA
| | - Wanda Phipatanakul
- Division of Immunology and Allergy, Boston Cshildren’s Hospital, Harvard Medical School, Boston, MA USA
| | - Roy Gerth van Wijk
- Department of Internal Medicine, Allergology, Erasmus MC, Rotterdam, the Netherlands
| | - Demoly Pascal
- Division of Allergy, Department of Pulmonology, University Hospital of Montpellier, Paris, France
- Montpellier and Pierre Louis Institute of Epidemiology and Public Health, Sorbonne Universités, Paris, France
| | - Nelson Rosario
- Federal University of Parana, Rua General Carneiro, Curitiba, Brazil
| | - Motohiro Ebisawa
- Department of Allergy, Clinical Research Center for Allergology and Rheumatology, Sagamihara National Hospital, Sagamihara, Kanagawa Japan
| | - Mario Geller
- Division of Medicine, Academy of Medicine of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Santiago Quirce
- Department of Allergy, Hospital La Paz Institute for Health Research and CIBER of Respiratory Diseases (CIBERES), Madrid, Spain
| | - Susanne Vrtala
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Rudolf Valenta
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Markus Ollert
- Department of Infection & Immunity, Laboratory of Immunogenetics and Allergology, Luxembourg Institute of Health, Luxembourg, UK
| | - Giorgio Walter Canonica
- Allergy & Respiratory Diseases Clinic, University of Genoa, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Moises A. Calderón
- Section of Allergy and Clinical Immunology, Imperial College London – NHLI, London, United Kingdom
| | - Charles S. Barnes
- Division of Allergy/Immunology, Children’s Mercy Hospital, Kansas City, MO USA
| | - Adnan Custovic
- Department of Paediatrics, Imperial College London, London, United Kingdom
| | - Suwat Benjaponpitak
- Division of Pediatric Allergy/Immunology/Rheumatology, Department of Pediatrics, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Arnaldo Capriles-Hulett
- Allergy and Clinical Immunology Department, Centro Médico Docente La Trinidad, Caracas, Venezuela
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29
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Pomés A, Chapman MD, Wünschmann S. Indoor Allergens and Allergic Respiratory Disease. Curr Allergy Asthma Rep 2016. [PMID: 27184001 DOI: 10.1007/s11882-016-0622-9.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PURPOSE OF REVIEW The purpose of this review is to evaluate the most recent findings on indoor allergens and their impact on allergic diseases. RECENT FINDINGS Indoor allergens are present inside buildings (home, work environment, school), and given the chronic nature of the exposures, indoor allergies tend to be associated with the development of asthma. The most common indoor allergens are derived from dust mites, cockroaches, mammals (including wild rodents and pets), and fungi. The advent of molecular biology and proteomics has led to the identification, cloning, and expression of new indoor allergens, which have facilitated research to elucidate their role in allergic diseases. This review is an update on new allergens and their molecular features, together with the most recent reports on their avoidance for allergy prevention and their use for diagnosis and treatment. Research progress on indoor allergens will result in the development of new diagnostic tools and design of coherent strategies for immunotherapy.
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Affiliation(s)
- Anna Pomés
- Indoor Biotechnologies, Inc., 700 Harris Street, Charlottesville, VA, 22903, USA.
| | - Martin D Chapman
- Indoor Biotechnologies, Inc., 700 Harris Street, Charlottesville, VA, 22903, USA
| | - Sabina Wünschmann
- Indoor Biotechnologies, Inc., 700 Harris Street, Charlottesville, VA, 22903, USA
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