1
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Howe JG, Stack G. Relationship between B-cell epitope structural properties and the immunogenicity of blood group antigens: Outlier properties of the Kell K1 antigen. Transfusion 2022; 62:2349-2362. [PMID: 36205403 DOI: 10.1111/trf.17110] [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: 05/24/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND The immunogenicities of polypeptide blood group antigens vary, despite most being created by single amino acid (AA) substitutions. To study the basis of these differences, we employed an immunoinformatics approach to determine whether AA substitution sites of blood group antigens have structural features typical of B-cell epitopes and whether the extent of B-cell epitope properties is positively related to immunogenicity. STUDY DESIGN AND METHODS Fifteen structural property prediction programs were used to determine the likelihood of β-turns, surface accessibility, flexibility, hydrophilicity, particular AA composition and AA pairs, and other B-cell epitope properties at AA substitution sites of polypeptide blood group antigens. RESULTS AA substitution sites of Lua , Jka , E, c, M, Fya , C, and S were each located in regions with at least two structural features typical of B-cell epitopes. The substitution site of K, the most immunogenic non-ABO/D antigen, scored the lowest for most B-cell epitope properties and was the only one not predicted to be part of a linear B-cell epitope. The most immunogenic antigens studied (K, Jka , Lua , E) had B-cell epitope structural properties determined by the fewest programs; the least immunogenic antigens (e.g., Fya , S, C, c) had B-cell epitope properties according to the most programs. DISCUSSION Counter to prediction, the immunogenicity of polypeptide blood group antigens was not positively related to B-cell epitope structural features present at their AA-substitution sites. Instead, it tended to be negatively related. The AA-substitution site of the most immunogenic non-ABO/D antigen, K, had the least B-cell epitope features.
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Affiliation(s)
- John G Howe
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Gary Stack
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Pathology and Laboratory Medicine Service, VA Connecticut Healthcare System, West Haven, Connecticut, USA
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2
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Caoili SEC. Comprehending B-Cell Epitope Prediction to Develop Vaccines and Immunodiagnostics. Front Immunol 2022; 13:908459. [PMID: 35874755 PMCID: PMC9300992 DOI: 10.3389/fimmu.2022.908459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
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3
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Farnudian-Habibi A, Mirjani M, Montazer V, Aliebrahimi S, Katouzian I, Abdolhosseini S, Rahmani A, Keyvani H, Ostad SN, Rad-Malekshahi M. Review on Approved and Inprogress COVID-19 Vaccines. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH 2022; 21:e124228. [PMID: 36060923 PMCID: PMC9420219 DOI: 10.5812/ijpr.124228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 11/24/2022]
Abstract
The last generation of Coronavirus named COVID-19 is responsible for the recent worldwide outbreak. Concerning the widespread and quick predominance, there is a critical requirement for designing appropriate vaccines to surmount this grave problem. Correspondingly, in this revision, COVID-19 vaccines (which are being developed until March 29th, 2021) are classified into specific and non-specific categories. Specific vaccines comprise genetic-based vaccines (mRNA, DNA), vector-based, protein/recombinant protein vaccines, inactivated viruses, live-attenuated vaccines, and novel strategies including microneedle arrays (MNAs), and nanoparticles vaccines. Moreover, specific vaccines such as BCG, MRR, and a few other vaccines are considered Non-specific. What is more, according to the significance of Bioinformatic sciences in the cutting-edge vaccine design and rapid outbreak of COVID-19, herein, Bioinformatic principles including reverse vaccinology, epitopes prediction/selection and, their further applications in the design of vaccines are discussed. Last but not least, safety, challenges, advantages, and future prospects of COVID-19 vaccines are highlighted.
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Affiliation(s)
- Amir Farnudian-Habibi
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mobina Mirjani
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahideh Montazer
- Department of Clinical Pharmacy, Virtual University of Medical Sciences, Tehran, Iran
| | - Shima Aliebrahimi
- Department of Medical Education, Virtual University of Medical Sciences, Tehran, Iran
| | - Iman Katouzian
- Australasian Nanoscience and Nanotechnology Initiative (ANNI), 8054 Monash University LPO, Clayton, 3168, Victoria, Australia
| | - Saeed Abdolhosseini
- School of Electrical and Computer Engineering, College of Engineering, University of Tehran, 14395-515 Tehran, Iran
| | - Ali Rahmani
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Nasser Ostad
- Toxicology and Poisoning Research Centre, Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Corresponding Author: Toxicology and Poisoning Research Centre, Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mazda Rad-Malekshahi
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Corresponding Author: Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
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4
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Yu PY, Zhu Y, Tan LX, Xu ZQ, Lu C, Guan XW. Immunoinformatics Construction of B Cell Epitope-Based Hypoallergenic Der f 34 Vaccine for Immunotherapy of House Dust Mite Allergy. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10337-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Mohammadzadeh R, Soleimanpour S, Pishdadian A, Farsiani H. Designing and development of epitope-based vaccines against Helicobacter pylori. Crit Rev Microbiol 2021; 48:489-512. [PMID: 34559599 DOI: 10.1080/1040841x.2021.1979934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Helicobacter pylori infection is the principal cause of serious diseases (e.g. gastric cancer and peptic ulcers). Antibiotic therapy is an inadequate strategy in H. pylori eradication because of which vaccination is an inevitable approach. Despite the presence of countless vaccine candidates, current vaccines in clinical trials have performed with poor efficacy which makes vaccination extremely challenging. Remarkable advancements in immunology and pathogenic biology have provided an appropriate opportunity to develop various epitope-based vaccines. The fusion of proper antigens involved in different aspects of H. pylori colonization and pathogenesis as well as peptide linkers and built-in adjuvants results in producing epitope-based vaccines with excellent therapeutic efficacy and negligible adverse effects. Difficulties of the in vitro culture of H. pylori, high genetic variation, and unfavourable immune responses against feeble epitopes in the complete antigen are major drawbacks of current vaccine strategies that epitope-based vaccines may overcome. Besides decreasing the biohazard risk, designing precise formulations, saving time and cost, and induction of maximum immunity with minimum adverse effects are the advantages of epitope-based vaccines. The present article is a comprehensive review of strategies for designing and developing epitope-based vaccines to provide insights into the innovative vaccination against H. pylori.
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Affiliation(s)
- Roghayeh Mohammadzadeh
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saman Soleimanpour
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Reference Tuberculosis Laboratory, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Pishdadian
- Department of Immunology, School of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Hadi Farsiani
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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6
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Rahman KS, Kaltenboeck B. Multipeptide Assays for Sensitive and Differential Detection of Anti-Chlamydia Trachomatis Antibodies. J Infect Dis 2021; 224:S86-S95. [PMID: 34396415 DOI: 10.1093/infdis/jiab016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Detection of anti-Chlamydia trachomatis (Ctr) antibodies is compromised by cross-reactivity and poor sensitivity of classic Ctr-antigens. We discovered 48 strongly reactive peptide antigens of Ctr-specific B-cell epitopes from 21 immunodominant proteins. In this study, we review the utility of peptide assays for diagnosis of Ctr infections. By combining many of these Ctr-specific B-cell epitopes from several proteins in separate or mixed multipeptide assays, they achieved vastly superior assay sensitivity and specificity over standard enzyme-linked immunosorbent assays. Such multipeptide assays eliminate cross-reactivities (false positives) and correct for stochastic gaps in antibody responses (false negatives). More importantly, we developed and validated a novel microarray platform in which hundreds of peptides from many proteins are spotted in a single reaction well. This offers the possibility of high-throughput screening of many candidate peptides for routine serological fingerprinting of Ctr infections. Discovery of optimal sets of antibody responses that associate with clinical pelvic inflammatory disease (PID) may identify diagnostically useful PID biomarker antigens.
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Affiliation(s)
- Kh Shamsur Rahman
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Bernhard Kaltenboeck
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
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7
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Collatz M, Mock F, Barth E, Hölzer M, Sachse K, Marz M. EpiDope: a deep neural network for linear B-cell epitope prediction. Bioinformatics 2021; 37:448-455. [PMID: 32915967 DOI: 10.1093/bioinformatics/btaa773] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/06/2020] [Accepted: 09/01/2020] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION By binding to specific structures on antigenic proteins, the so-called epitopes, B-cell antibodies can neutralize pathogens. The identification of B-cell epitopes is of great value for the development of specific serodiagnostic assays and the optimization of medical therapy. However, identifying diagnostically or therapeutically relevant epitopes is a challenging task that usually involves extensive laboratory work. In this study, we show that the time, cost and labor-intensive process of epitope detection in the lab can be significantly reduced using in silico prediction. RESULTS Here, we present EpiDope, a python tool which uses a deep neural network to detect linear B-cell epitope regions on individual protein sequences. With an area under the curve between 0.67 ± 0.07 in the receiver operating characteristic curve, EpiDope exceeds all other currently used linear B-cell epitope prediction tools. Our software is shown to reliably predict linear B-cell epitopes of a given protein sequence, thus contributing to a significant reduction of laboratory experiments and costs required for the conventional approach. AVAILABILITYAND IMPLEMENTATION EpiDope is available on GitHub (http://github.com/mcollatz/EpiDope). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Maximilian Collatz
- RNA Bioinformatics /High Throughput Analysis, Faculty of Mathematics and Computer Science
| | - Florian Mock
- RNA Bioinformatics /High Throughput Analysis, Faculty of Mathematics and Computer Science
| | - Emanuel Barth
- RNA Bioinformatics /High Throughput Analysis, Faculty of Mathematics and Computer Science.,Bioinformatics Core Facility Jena, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Martin Hölzer
- RNA Bioinformatics /High Throughput Analysis, Faculty of Mathematics and Computer Science.,RNA Bioinformatics/High Throughput Analysis, European Virus Bioinformatics Center (EVBC), Jena 07743, Germany
| | - Konrad Sachse
- RNA Bioinformatics /High Throughput Analysis, Faculty of Mathematics and Computer Science
| | - Manja Marz
- RNA Bioinformatics /High Throughput Analysis, Faculty of Mathematics and Computer Science.,Bioinformatics Core Facility Jena, Friedrich Schiller University Jena, Jena 07743, Germany.,RNA Bioinformatics/High Throughput Analysis, European Virus Bioinformatics Center (EVBC), Jena 07743, Germany.,RNA Bioinformatics/High Throughput Analysis, FLI Leibniz Institute for Age Research, Jena 07745, Germany
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8
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9
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Hasan MM, Khatun MS, Kurata H. iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:593-600. [PMID: 33099033 PMCID: PMC8377379 DOI: 10.1016/j.gpb.2019.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/13/2019] [Accepted: 04/19/2019] [Indexed: 12/17/2022]
Abstract
Linear B-cell epitopes are critically important for immunological applications, such as vaccine design, immunodiagnostic test, and antibody production, as well as disease diagnosis and therapy. The accurate identification of linear B-cell epitopes remains challenging despite several decades of research. In this work, we have developed a novel predictor, Identification of Linear B-cell Epitope (iLBE), by integrating evolutionary and sequence-based features. The successive feature vectors were optimized by a Wilcoxon-rank sum test. Then the random forest (RF) algorithm using the optimal consecutive feature vectors was applied to predict linear B-cell epitopes. We combined the RF scores by the logistic regression to enhance the prediction accuracy. iLBE yielded an area under curve score of 0.809 on the training dataset and outperformed other prediction models on a comprehensive independent dataset. iLBE is a powerful computational tool to identify the linear B-cell epitopes and would help to develop penetrating diagnostic tests. A web application with curated datasets for iLBE is freely accessible at http://kurata14.bio.kyutech.ac.jp/iLBE/.
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Affiliation(s)
- Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Mst Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Biomedical Informatics R&D Center, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.
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10
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Parvizpour S, Pourseif MM, Razmara J, Rafi MA, Omidi Y. Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches. Drug Discov Today 2020; 25:1034-1042. [DOI: 10.1016/j.drudis.2020.03.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/12/2020] [Accepted: 03/06/2020] [Indexed: 12/26/2022]
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11
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Rahman KS, Kaltenboeck B. Multi-peptide ELISAs overcome cross-reactivity and inadequate sensitivity of conventional Chlamydia pneumoniae serology. Sci Rep 2019; 9:15078. [PMID: 31636331 PMCID: PMC6803651 DOI: 10.1038/s41598-019-51501-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022] Open
Abstract
Cross-reactivity of classical chlamydial antigens compromises Chlamydia (C.) pneumoniae serology. By testing with 185 human antisera, we expanded 18 previously discovered C. pneumoniae-specific B-cell epitopes to 48 peptide antigens from 12 C. pneumoniae immunodominant proteins. For specific detection of antibodies against C. pneumoniae, we developed novel ELISAs with strongly reactive individual peptide antigens and mixtures of these peptides. By comparison to a composite reference standard (CRS) for anti-C. pneumoniae antibody status of human sera, the top-performing CpnMixF12 peptide assay showed 91% sensitivity at 95% specificity, significantly higher than 4 commercial anti-C. pneumoniae IgG ELISAs (36-12% sensitivity at 95% specificity). Human C. pneumoniae (Cpn) and C. trachomatis (Ctr) seroreactivity was 54% biased towards co-positivity in commercial Cpn and Ctr ELISAs, but unbiased in Cpn and Ctr peptide antibody assays, suggesting severe cross-reactivity of commercial ELISAs. Using hyperimmune mouse sera against each of 11 Chlamydia spp., we confirm that commercial Cpn and Ctr ELISA antigens are cross-reactive among all Chlamydia spp., but Cpn and Ctr peptide antigens react only with antisera against the cognate chlamydial species. With simultaneously high specificity and sensitivity, and convenient use for non-specialized laboratories, these ELISAs have the potential to improve serodiagnosis of C. pneumoniae infection.
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Affiliation(s)
- Kh Shamsur Rahman
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.
| | - Bernhard Kaltenboeck
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
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12
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Khatun S, Hasan M, Kurata H. Efficient computational model for identification of antitubercular peptides by integrating amino acid patterns and properties. FEBS Lett 2019; 593:3029-3039. [PMID: 31297788 DOI: 10.1002/1873-3468.13536] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/25/2019] [Accepted: 07/05/2019] [Indexed: 12/30/2022]
Abstract
Tuberculosis (TB) is a leading killer caused by Mycobacterium tuberculosis. Recently, anti-TB peptides have provided an alternative approach to combat antibiotic tolerance. We have developed an effective computational predictor, identification of antitubercular peptides (iAntiTB), by the integration of multiple feature vectors deriving from the amino acid sequences via random forest (RF) and support vector machine (SVM) classifiers. The iAntiTB combines the RF and SVM scores via linear regression to enhance the prediction accuracy. To make a robust and accurate predictor, we prepared the two datasets with different types of negative samples. The iAntiTB achieved area under the ROC curve values of 0.896 and 0.946 on the training datasets of the first and second datasets, respectively. The iAntiTB outperformed the other existing predictors.
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Affiliation(s)
- Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan.,Biomedical Informatics R&D Center, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
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13
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Demolombe V, de Brevern AG, Felicori L, NGuyen C, Machado de Avila RA, Valera L, Jardin-Watelet B, Lavigne G, Lebreton A, Molina F, Moreau V. PEPOP 2.0: new approaches to mimic non-continuous epitopes. BMC Bioinformatics 2019; 20:387. [PMID: 31296178 PMCID: PMC6625012 DOI: 10.1186/s12859-019-2867-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/30/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits in replacing a protein which is difficult to produce, or toxic. Using peptides is less expensive. Peptides are easier to manipulate, and can be used as drugs. Continuous epitopes predicted by bioinformatics tools are commonly used and these sequential epitopes are used as is in further experiments. Numerous discontinuous epitope predictors have been developed but only two bioinformatics tools have been proposed so far to predict peptide sequences: Superficial and PEPOP 2.0. PEPOP 2.0 can generate series of peptide sequences that can replace continuous or discontinuous epitopes in their interaction with their cognate antibody. RESULTS We have developed an improved version of PEPOP (PEPOP 2.0) dedicated to answer to experimentalists' need for a tool able to handle proteins and to turn them into peptides. The PEPOP 2.0 web site has been reorganized by peptide prediction category and is therefore better formulated to experimental designs. Since the first version of PEPOP, 32 new methods of peptide design were developed. In total, PEPOP 2.0 proposes 35 methods in which 34 deal specifically with discontinuous epitopes, the most represented epitope type in nature. CONCLUSION Through the presentation of its user-friendly, well-structured new web site conceived in close proximity to experimentalists, we report original methods that show how PEPOP 2.0 can assist biologists in dealing with discontinuous epitopes.
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Affiliation(s)
- Vincent Demolombe
- BPMP, CNRS, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Alexandre G de Brevern
- INSERM UMR-S 1134, DSIMB, F-75739, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, Univ de la Réunion, Univ des Antilles, UMR 1134, F-75739, Paris, France.,INTS, F-75739, Paris, France.,Laboratoire d'Excellence GR-Ex, F75737, Paris, France
| | - Liza Felicori
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Christophe NGuyen
- Sys2Diag UMR 9005 CNRS/ALCEDIAG, Complex System Modeling and Engineering for Diagnosis, Cap delta/Parc Euromédecine, 1682 rue de la Valsière CS 61003, 34184, Montpellier Cedex 4, France
| | - Ricardo Andrez Machado de Avila
- Programa de Pós-Graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma, Santa Catarina, 88806-000, Brazil
| | - Lionel Valera
- Bio-Rad Laboratories, 1682 Rue de la Valsière CS 61003, 34184, Montpellier CEDEX 04, France
| | | | | | - Aurélien Lebreton
- Service d'hématologie biologique, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Franck Molina
- Sys2Diag UMR 9005 CNRS/ALCEDIAG, Complex System Modeling and Engineering for Diagnosis, Cap delta/Parc Euromédecine, 1682 rue de la Valsière CS 61003, 34184, Montpellier Cedex 4, France
| | - Violaine Moreau
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Univ Montpellier, 29, route de Navacelles, 34090, Montpellier, France.
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14
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Mixed Chlamydia trachomatis Peptide Antigens Provide a Specific and Sensitive Single-Well Colorimetric Enzyme-Linked Immunosorbent Assay for Detection of Human Anti -C. trachomatis Antibodies. mSphere 2018; 3:3/6/e00484-18. [PMID: 30404936 PMCID: PMC6222056 DOI: 10.1128/msphere.00484-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
For detection of anti-C. trachomatis antibodies by serological assays, use of classical chlamydial antigens results in high cross-reactivity and poor sensitivity. Previously, we discovered 48 strongly reactive peptide antigens of C. trachomatis-specific B-cell epitopes from 21 immunodominant proteins, and individual testing and combined scoring of 5 to 11 peptide antigens provided highly sensitive and specific detection of anti-C. trachomatis antibodies in chemiluminescent ELISAs. To simplify this method, this study established a single-well labor-saving colorimetric ELISA using a mixture of 12 strongly reactive C. trachomatis peptide antigens (Ctr Mix1) for detection of anti-C. trachomatis antibodies. This Ctr Mix1 ELISA (94% sensitivity and 98% specificity) outperformed 4 commercial ELISAs (49% to 79% sensitivity and 98% specificity). This ELISA can be easily implemented and commercialized, with convenient setup for use in nonspecialized laboratories. Thus, this mixed peptide assay with superior specificity and sensitivity will improve serodiagnosis of C. trachomatis infections. Sensitive and specific detection of anti-Chlamydia trachomatis antibodies in standard enzyme-linked immunosorbent assays (ELISAs) is compromised by cross-reactivity and poor sensitivity of classical C. trachomatis antigens. Previously, we discovered 48 strongly reactive peptide antigens of C. trachomatis-specific B-cell epitopes from 21 immunodominant proteins. By comprehensive individual testing of 11 top-ranked peptide antigens, we found very high sensitivity and specificity for detection of anti-C. trachomatis antibodies in chemiluminescent ELISAs. The current study established a labor-saving colorimetric ELISA by using a mixture of 12 strongly reactive C. trachomatis peptide antigens (Ctr Mix1) in a single well/serum rather than assaying reactivity to each individual peptide. For performance evaluation, we used a simulated population of 212 anti-C. trachomatis antibody-positive and -negative sera from 125 women with NAAT-confirmed active C. trachomatis infection and from 87 healthy women at low risk for C. trachomatis infection. In comparison to a composite reference standard (CRS) for anti-C. trachomatis antibody status, the Ctr Mix1 IgG ELISA achieved 93.9% sensitivity, significantly superior to the 49% to 79% sensitivities of four commercial anti-C. trachomatis IgG ELISAs, and 98% specificity of all tested assays. Compared to the labor-intensive individual peptide testing, this mixed peptide ELISA retained high specificity with only marginal, ∼5% sensitivity loss. By ROC-AUC, likelihood ratio, and predictive value analyses, the Ctr Mix1 ELISA performed satisfactorily at 10% to 75% prevalence range of anti-C. trachomatis antibodies but significantly better than commercial ELISAs. Thus, the labor-saving mixed peptide colorimetric ELISA format provides simultaneously high specificity and sensitivity for detection of anti-C. trachomatis antibodies. IMPORTANCE For detection of anti-C. trachomatis antibodies by serological assays, use of classical chlamydial antigens results in high cross-reactivity and poor sensitivity. Previously, we discovered 48 strongly reactive peptide antigens of C. trachomatis-specific B-cell epitopes from 21 immunodominant proteins, and individual testing and combined scoring of 5 to 11 peptide antigens provided highly sensitive and specific detection of anti-C. trachomatis antibodies in chemiluminescent ELISAs. To simplify this method, this study established a single-well labor-saving colorimetric ELISA using a mixture of 12 strongly reactive C. trachomatis peptide antigens (Ctr Mix1) for detection of anti-C. trachomatis antibodies. This Ctr Mix1 ELISA (94% sensitivity and 98% specificity) outperformed 4 commercial ELISAs (49% to 79% sensitivity and 98% specificity). This ELISA can be easily implemented and commercialized, with convenient setup for use in nonspecialized laboratories. Thus, this mixed peptide assay with superior specificity and sensitivity will improve serodiagnosis of C. trachomatis infections.
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Abstract
Current serological assays for species-specific detection of anti-Chlamydia species antibodies suffer from well-known shortcomings in specificity and ease of use. Due to the high prevalences of both anti-C. trachomatis and anti-C. pneumoniae antibodies in human populations, species-specific serology is unreliable. Therefore, novel specific and simple assays for chlamydial serology are urgently needed. Conventional antigens are problematic due to extensive cross-reactivity within Chlamydia spp. Using accurate B cell epitope prediction and a robust peptide ELISA methodology developed in our laboratory, we identified immunodominant C. trachomatis B cell epitopes by screening performed with sera from C. trachomatis-infected women. We discovered 38 novel human host-dependent antigens from 20 immunodominant C. trachomatis proteins, in addition to confirming 10 host-independent mouse serum peptide antigens that had been identified previously. This extended set of highly specific C. trachomatis peptide antigens can be used in simple ELISA or multiplexed microarray formats and will provide high specificity and sensitivity to human C. trachomatis serodiagnosis. Chlamydia species-specific serology is compromised by cross-reactivity of the gold standard microimmunofluorescence (MIF) or commercial enzyme-linked immunosorbent assays (ELISAs). This study was conducted to discover novel C. trachomatis-specific peptide antigens that were recognized only by the antibody response of the natural human host. We evaluated a library of 271 peptide antigens from immunodominant C. trachomatis proteins by reactivity with 125 C. trachomatis antibody-positive sera from women with PCR-confirmed C. trachomatis infection and 17 C. trachomatis antibody-negative sera from low-risk women never diagnosed with C. trachomatis infection. These C. trachomatis peptide antigens had been predicted in silico to contain B cell epitopes but had been nonreactive with mouse hyperimmune sera against C. trachomatis. We discovered 38 novel human host-dependent antigens from 20 immunodominant C. trachomatis proteins (PmpD, IncE, IncG, CT529, CT618, CT442, TarP, CT143, CT813, CT795, CT223, PmpC, CT875, CT579, LcrE, IncA, CT226, CT694, Hsp60, and pGP3). Using these human sera, we also confirmed 10 C. trachomatis B cell epitopes from 6 immunodominant C. trachomatis proteins (OmpA, PmpD, IncE, IncG, CT529, and CT618) as host species-independent epitopes that had been previously identified by their reactivity with mouse hyperimmune sera against C. trachomatis. ELISA reactivities against these peptides correlated strongly with the C. trachomatis microimmunofluorescence (MIF) text results (Pearson’s correlation coefficient [R] = 0.80; P < 10−6). These C. trachomatis peptide antigens do not cross-react with antibodies against other Chlamydia species and are therefore suitable for species-specific detection of antibodies against C. trachomatis. This study identified an extended set of peptide antigens for simple C. trachomatis-specific ELISA serology. IMPORTANCE Current serological assays for species-specific detection of anti-Chlamydia species antibodies suffer from well-known shortcomings in specificity and ease of use. Due to the high prevalences of both anti-C. trachomatis and anti-C. pneumoniae antibodies in human populations, species-specific serology is unreliable. Therefore, novel specific and simple assays for chlamydial serology are urgently needed. Conventional antigens are problematic due to extensive cross-reactivity within Chlamydia spp. Using accurate B cell epitope prediction and a robust peptide ELISA methodology developed in our laboratory, we identified immunodominant C. trachomatis B cell epitopes by screening performed with sera from C. trachomatis-infected women. We discovered 38 novel human host-dependent antigens from 20 immunodominant C. trachomatis proteins, in addition to confirming 10 host-independent mouse serum peptide antigens that had been identified previously. This extended set of highly specific C. trachomatis peptide antigens can be used in simple ELISA or multiplexed microarray formats and will provide high specificity and sensitivity to human C. trachomatis serodiagnosis.
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Comprehensive Molecular Serology of Human Chlamydia trachomatis Infections by Peptide Enzyme-Linked Immunosorbent Assays. mSphere 2018; 3:3/4/e00253-18. [PMID: 30068559 PMCID: PMC6070734 DOI: 10.1128/msphere.00253-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
For detection of anti-Chlamydia trachomatis antibodies by serological assays, use of classical whole-organism chlamydial antigens results in high cross-reactivity. These antigens bind mainly antibodies against the major outer membrane protein (OmpA) and bind antibodies against other immunodominant non-OmpA proteins to a lesser extent, resulting in poor assay sensitivity. The specificity of C. trachomatis serology is also compromised by the high prevalence of cross-reactive anti-C. pneumoniae antibodies in human populations. We previously identified 48 highly specific C. trachomatis B cell epitope peptide antigens of 21 immunodominant proteins. This study validated peptide antigen-based novel ELISAs that provide highly specific and sensitive detection of anti-C. trachomatis antibodies. Compared to four commercial ELISAs that achieved only poor sensitivities (51.5% to 64.8%), the combined signals of 5 to 11 peptides provided high sensitivity (86.5% to 91.8%) at the same 98% specificity. Thus, by using multiple peptide antigens of immunodominant proteins, we created simple ELISAs with specificity and sensitivity superior to standard C. trachomatis serodiagnosis. Sensitive species-specific detection of anti-Chlamydia trachomatis antibodies is compromised by cross-reactivity of the C. trachomatis antigens used in standard microimmunofluorescence (MIF) testing and enzyme-linked immunosorbent assays (ELISAs). Previously, we discovered 48 strongly reactive C. trachomatis-specific B cell epitope peptides from 21 immunodominant proteins. Here we comprehensively evaluated the 11 top-ranked C. trachomatis-specific peptide antigens from 8 proteins for use in C. trachomatis serology. Sera from 125 women with nucleic acid amplification test (NAAT)-confirmed active C. trachomatis infection and from 49 healthy women with a low risk of C. trachomatis infection were used as anti-C. trachomatis antibody-positive and -negative sera. Results obtained for detection of IgG1, IgG3, and IgA1 antibodies against the 11 C. trachomatis peptide antigens were compared to results from 4 commercial anti-C. trachomatis IgG ELISAs. Using composite reference standards (CRS) of all assays for anti-C. trachomatis antibody status, commercial ELISAs detected antibodies in antibody-positive women with sensitivities of 51.5% to 64.8%. In contrast, a combination of the results of all 11 peptides detected IgG (IgG1 and IgG3) antibodies with 91.8% sensitivity, and a labor-saving combination of the 5 optimal peptides still detected antibodies in antibody-positive women with 86.5% sensitivity (all at 98% specificity). The superior performance of the combined peptide ELISAs was confirmed by area under the receiver operating characteristic curve (ROC-AUC), likelihood ratio, and predictive value analyses. The higher sensitivity of the peptide assays results from using multiple B cell epitopes of several C. trachomatis immunodominant proteins, including OmpA, compared to exclusively using the OmpA antigens used in commercial ELISAs. Thus, ELISAs with combined use of synthetic peptide antigens for C. trachomatis antibody detection have the advantage of simultaneous high sensitivity and high specificity. IMPORTANCE For detection of anti-Chlamydia trachomatis antibodies by serological assays, use of classical whole-organism chlamydial antigens results in high cross-reactivity. These antigens bind mainly antibodies against the major outer membrane protein (OmpA) and bind antibodies against other immunodominant non-OmpA proteins to a lesser extent, resulting in poor assay sensitivity. The specificity of C. trachomatis serology is also compromised by the high prevalence of cross-reactive anti-C. pneumoniae antibodies in human populations. We previously identified 48 highly specific C. trachomatis B cell epitope peptide antigens of 21 immunodominant proteins. This study validated peptide antigen-based novel ELISAs that provide highly specific and sensitive detection of anti-C. trachomatis antibodies. Compared to four commercial ELISAs that achieved only poor sensitivities (51.5% to 64.8%), the combined signals of 5 to 11 peptides provided high sensitivity (86.5% to 91.8%) at the same 98% specificity. Thus, by using multiple peptide antigens of immunodominant proteins, we created simple ELISAs with specificity and sensitivity superior to standard C. trachomatis serodiagnosis.
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Manavalan B, Govindaraj RG, Shin TH, Kim MO, Lee G. iBCE-EL: A New Ensemble Learning Framework for Improved Linear B-Cell Epitope Prediction. Front Immunol 2018; 9:1695. [PMID: 30100904 PMCID: PMC6072840 DOI: 10.3389/fimmu.2018.01695] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/10/2018] [Indexed: 11/13/2022] Open
Abstract
Identification of B-cell epitopes (BCEs) is a fundamental step for epitope-based vaccine development, antibody production, and disease prevention and diagnosis. Due to the avalanche of protein sequence data discovered in postgenomic age, it is essential to develop an automated computational method to enable fast and accurate identification of novel BCEs within vast number of candidate proteins and peptides. Although several computational methods have been developed, their accuracy is unreliable. Thus, developing a reliable model with significant prediction improvements is highly desirable. In this study, we first constructed a non-redundant data set of 5,550 experimentally validated BCEs and 6,893 non-BCEs from the Immune Epitope Database. We then developed a novel ensemble learning framework for improved linear BCE predictor called iBCE-EL, a fusion of two independent predictors, namely, extremely randomized tree (ERT) and gradient boosting (GB) classifiers, which, respectively, uses a combination of physicochemical properties (PCP) and amino acid composition and a combination of dipeptide and PCP as input features. Cross-validation analysis on a benchmarking data set showed that iBCE-EL performed better than individual classifiers (ERT and GB), with a Matthews correlation coefficient (MCC) of 0.454. Furthermore, we evaluated the performance of iBCE-EL on the independent data set. Results show that iBCE-EL significantly outperformed the state-of-the-art method with an MCC of 0.463. To the best of our knowledge, iBCE-EL is the first ensemble method for linear BCEs prediction. iBCE-EL was implemented in a web-based platform, which is available at http://thegleelab.org/iBCE-EL. iBCE-EL contains two prediction modes. The first one identifying peptide sequences as BCEs or non-BCEs, while later one is aimed at providing users with the option of mining potential BCEs from protein sequences.
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Affiliation(s)
| | - Rajiv Gandhi Govindaraj
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea.,Institute of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Myeong Ok Kim
- Division of Life Science and Applied Life Science (BK21 Plus), College of Natural Sciences, Gyeongsang National University, Jinju, South Korea
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea.,Institute of Molecular Science and Technology, Ajou University, Suwon, South Korea
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18
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Zhang M, Zheng J, Nussinov R, Ma B. Molecular Recognition between Aβ-Specific Single-Domain Antibody and Aβ Misfolded Aggregates. Antibodies (Basel) 2018; 7:E25. [PMID: 31544877 PMCID: PMC6640678 DOI: 10.3390/antib7030025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
Aβ is the toxic amyloid polypeptide responsible for Alzheimer's disease (AD). Prevention and elimination of the Aβ misfolded aggregates are the promising therapeutic strategies for the AD treatments. Gammabody, the Aβ-Specific Single-domain (VH) antibody, recognizes Aβ aggregates with high affinity and specificity and reduces their toxicities. Employing the molecular dynamics simulations, we studied diverse gammabody-Aβ recognition complexes to get insights into their structural and dynamic properties and gammabody-Aβ recognitions. Among many heterogeneous binding modes, we focused on two gammabody-Aβ recognition scenarios: recognition through Aβ β-sheet backbone and on sidechain surface. We found that the gammabody primarily uses the complementarity-determining region 3 (CDR3) loop with the grafted Aβ sequence to interact with the Aβ fibril, while CDR1/CDR2 loops have very little contact. The gammabody-Aβ complexes with backbone binding mode are more stable, explaining the gammabody's specificity towards the C-terminal Aβ sequence.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical & Biomolecular Engineering, the University of Akron, Akron, OH 44325, USA.
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, the University of Akron, Akron, OH 44325, USA.
| | - Ruth Nussinov
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Buyong Ma
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
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19
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MacRaild CA, Seow J, Das SC, Norton RS. Disordered epitopes as peptide vaccines. Pept Sci (Hoboken) 2018; 110:e24067. [PMID: 32328540 PMCID: PMC7167742 DOI: 10.1002/pep2.24067] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/08/2018] [Accepted: 03/09/2018] [Indexed: 01/23/2023]
Abstract
The development of clinically useful peptide-based vaccines remains a long-standing goal. This review highlights that intrinsically disordered protein antigens, which lack an ordered three-dimensional structure, represent excellent starting points for the development of such vaccines. Disordered proteins represent an important class of antigen in a wide range of human pathogens, and, contrary to widespread belief, they are frequently targets of protective antibody responses. Importantly, disordered epitopes appear invariably to be linear epitopes, rendering them ideally suited to incorporation into a peptide vaccine. Nonetheless, the conformational properties of disordered antigens, and hence their recognition by antibodies, frequently depend on the interactions they make and the context in which they are presented to the immune system. These effects must be considered in the design of an effective vaccine. Here we discuss these issues and propose design principles that may facilitate the development of peptide vaccines targeting disordered antigens.
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Affiliation(s)
- Christopher A. MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal ParadeParkville3052Australia
| | - Jeffrey Seow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal ParadeParkville3052Australia
| | - Sreedam C. Das
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal ParadeParkville3052Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal ParadeParkville3052Australia
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20
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A novel synthetic peptide microarray assay detects Chlamydia species-specific antibodies in animal and human sera. Sci Rep 2018; 8:4701. [PMID: 29549361 PMCID: PMC5856796 DOI: 10.1038/s41598-018-23118-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/05/2018] [Indexed: 12/22/2022] Open
Abstract
Serological analysis of Chlamydia (C.) spp. infections is still mainly based on micro-immunofluorescence and ELISA. To overcome the limitations of conventional serology, we have designed a novel microarray carrying 52 synthetic peptides representing B-cell epitopes from immunodominant proteins of all 11 chlamydial species. The new assay has been validated using monospecific mouse hyperimmune sera. Subsequently, serum samples from cattle, sheep and humans with a known history of chlamydial infection were examined. For instance, the specific humoral response of sheep to treatment with a C. abortus vaccine has been visualized against a background of C. pecorum carriership. In samples from humans, dual infection with C. trachomatis and C. pneumoniae could be demonstrated. The experiments revealed that the peptide microarray assay was capable of simultaneously identifying specific antibodies to each Chlamydia spp. The actual assay represents an open platform test that can be complemented through future advances in Chlamydia proteome research. The concept of the highly parallel multi-antigen microarray proven in this study has the potential to enhance our understanding of antibody responses by defining not only a single quantitative response, but also the pattern of this response. The added value of using peptide antigens will consist in unprecedented serodiagnostic specificity.
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21
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Bommana S, Walker E, Desclozeaux M, Timms P, Polkinghorne A. Humoral immune response against two surface antigens of Chlamydia pecorum in vaccinated and naturally infected sheep. PLoS One 2017; 12:e0188370. [PMID: 29190736 PMCID: PMC5708773 DOI: 10.1371/journal.pone.0188370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 10/24/2017] [Indexed: 01/29/2023] Open
Abstract
Chlamydia pecorum is a globally recognised livestock pathogen due to the significant clinical and economic impact it poses to livestock producers. Routine serological diagnosis is through a complement fixation test (CFT), which is often criticised for cross-reactivity, poor sensitivity and specificity. Although serology remains the preferred method in veterinary diagnostic laboratories, serological assays based on surface antigens of C. pecorum have not been established until now. In this study, we evaluated the use of two chlamydial recombinant protein antigens (PmpG and MOMP-G) by a direct IgG ELISA method for detection of ovine anti-chlamydial antibodies. Using the Pepscan method we then identified B cell epitopes across PmpG and MOMP-G proteins, in lambs with (a) naturally occurring asymptomatic C. pecorum infections (b) C. pecorum-associated polyarthritis and (c) recombinant PmpG and MOMP-G vaccine. Plasma IgG antibodies to PmpG in natural infection of lambs were detected earlier in infection than CFT and served as an acute phase marker. Antibodies to MOMP-G IgG were significantly heightened in lambs with C. pecorum-associated polyarthritis. PmpG and MOMP-G specific B-cell epitope mapping revealed epitope responses in immunised lambs cluster with some of the epitope responses in naturally infected lambs. B-cell epitope mapping further revealed that lambs with polyarthritis recognised several unique PmpG (50% frequency, peptide 8, 25, 40, 41 and 50) and MOMP (50% frequency, peptide 50) epitopes in comparison to asymptomatic infections. The findings of this study will have implications towards improved serodiagnosis of C. pecorum infections in livestock and inform the downstream development of alternative peptide-based antigens for future C. pecorum vaccine studies.
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Affiliation(s)
- Sankhya Bommana
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Evelyn Walker
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
- Central West Local Land Services, Dubbo, Australia
| | - Marion Desclozeaux
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Peter Timms
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
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Tang VH, Stewart GA, Chang BJ. Dermatophagoides pteronyssinus lytFM encoding an NlpC/P60 endopeptidase is also present in mite-associated bacteria that express LytFM variants. FEBS Open Bio 2017; 7:1267-1280. [PMID: 28904857 PMCID: PMC5586350 DOI: 10.1002/2211-5463.12263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 06/05/2017] [Accepted: 06/19/2017] [Indexed: 12/25/2022] Open
Abstract
The bodies and faecal pellets of the house dust mite (HDM), Dermatophagoides pteronyssinus, are the source of many allergenic and nonallergenic proteins. One of these, the 14-kDa bacteriolytic enzyme LytFM, originally isolated from the spent HDM growth medium, may contribute to bacteriolytic activity previously detected by zymography at 14 kDa in the culture supernatants of some bacterial species isolated from surface-sterilised HDM. Based on previously reported findings of lateral gene transfer between microbes and their eukaryotic hosts, we investigated the presence of lytFM in the genomes of nine Gram-positive bacteria from surface-sterilised HDM, and the expression by these isolates of LytFM and its variants LytFM1/LytFM2. The lytFM gene was detected by PCR in the genomes of three of the isolates: Bacillus licheniformis strain 1, B. licheniformis strain 2 and Staphylococcus aureus. Expression of the variant LytFM1 was detected in culture supernatants of these bacteria by mass spectrometry (MS) and ELISA, and the bacterial LytFM proteins were shown by zymography to be able to hydrolyse peptidoglycan. Our previous reports of LytFM homologues in other mite species and their phylogenetic analysis had suggested that they originated from a common mite ancestor. The phylogenetic analysis reported herein and the detection of other D. pteronyssinus proteins by MS in the culture supernatants of the three isolates that secreted LytFM1 further support the hypothesis of lateral gene transfer to the bacterial endosymbionts from their HDM host. The complete sequence homology observed between the genes amplified from the microbes and those in their eukaryotic host indicated that the lateral gene transfer was an event that occurred recently.
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Affiliation(s)
- Vivian H Tang
- Marshall Centre for Infectious Diseases Research and Training School of Biomedical Sciences The University of Western Australia Crawley WA Australia
| | - Geoffrey A Stewart
- Marshall Centre for Infectious Diseases Research and Training School of Biomedical Sciences The University of Western Australia Crawley WA Australia
| | - Barbara J Chang
- Marshall Centre for Infectious Diseases Research and Training School of Biomedical Sciences The University of Western Australia Crawley WA Australia
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