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Mortazavi B, Molaei A, Fard NA. Multi-epitopevaccines, from design to expression; an in silico approach. Hum Immunol 2024:110804. [PMID: 38658216 DOI: 10.1016/j.humimm.2024.110804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
The development of vaccines against a wide range of infectious diseases and pathogens often relies on multi-epitope strategies that can effectively stimulate both humoral and cellular immunity. Immunoinformatics tools play a pivotal role in designing such vaccines, enhancing immune response potential, and minimizing the risk of failure. This review presents a comprehensive overview of practical tools for epitope prediction and the associated immune responses. These immunoinformatics tools facilitate the selection of epitopes based on parameters such as antigenicity, absence of toxic and allergenic sequences, secondary and tertiary structures, sequence conservation, and population coverage. The chosen epitopes can be tailored for B-cells or T-cells, both of which require further assessments covered in this study. We offer a range of suitable linkers that effectively separate cytotoxic T lymphocyte and helper T lymphocyte epitopes while preserving their functionality. Additionally, we identify various adjuvants for specific purposes. We delve into the evaluation of MHC-epitope interactions, MHC clusters, and the simulation of final constructs through molecular docking techniques. We provide diverse linkers and adjuvants optimized for epitope functions to bolster immune responses through epitope attachment. By leveraging these comprehensive tools, the development of multi-epitope vaccines holds the promise of robust immunity and a significant reduction in experimental costs.
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Affiliation(s)
- Behnam Mortazavi
- Department of systems Biotechnology, Faculty of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Molaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Najaf Allahyari Fard
- Department of systems Biotechnology, Faculty of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Martínez D, Fang L, Meza-Torres C, Garavito G, López-Lluch G, Egea E. Toward Consensus Epitopes B and T of Tropomyosin Involved in Cross-Reactivity across Diverse Allergens: An In Silico Study. Biomedicines 2024; 12:884. [PMID: 38672238 PMCID: PMC11048304 DOI: 10.3390/biomedicines12040884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 04/28/2024] Open
Abstract
Tropomyosin (TM) is a pan-allergen with cross-reactivity to arthropods, insects, and nematodes in tropical regions. While IgE epitopes of TM contribute to sensitization, T-cell (MHC-II) epitopes polarize the Th2 immune response. This study aimed to identify linear B and T consensus epitopes among house dust mites, cockroaches, Ascaris lumbricoides, shrimp, and mosquitoes, exploring the molecular basis of cross-reactivity in allergic diseases. Amino acid sequences of Der p 10, Der f 10, Blo t 10, Lit v 1, Pen a 1, Pen m 1, rAsc l 3, Per a 7, Bla g 7, and Aed a 10 were collected from Allergen Nomenclature and UniProt. B epitopes were predicted using AlgPred 2.0 and BepiPred 3.0. T epitopes were predicted with NetMHCIIpan 4.1 against 10 HLA-II alleles. Consensus epitopes were obtained through analysis and Epitope Cluster Analysis in the Immune Epitope Database. We found 7 B-cell epitopes and 28 linear T-cell epitopes binding to MHC II. A unique peptide (residues 160-174) exhibited overlap between linear B-cell and T-cell epitopes, highly conserved across tropomyosin sequences. These findings shed light on IgE cross-reactivity among the tested species. The described immuno-informatics pipeline and epitopes can inform in vitro research and guide synthetic multi-epitope proteins' design for potential allergology immunotherapies. Further in silico studies are warranted to confirm epitope accuracy and guide future experimental protocols.
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Affiliation(s)
- Dalgys Martínez
- Department of Medicine, Health Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia; (D.M.); (L.F.); (C.M.-T.); (G.G.)
- Institute for Immunological Research, University of Cartagena, Cartagena 130014, Colombia
| | - Luis Fang
- Department of Medicine, Health Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia; (D.M.); (L.F.); (C.M.-T.); (G.G.)
| | - Catherine Meza-Torres
- Department of Medicine, Health Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia; (D.M.); (L.F.); (C.M.-T.); (G.G.)
- Department of Physiology, Anatomy, and Cellular Biology, Andalusian Centre for Development Biology (CABD-CSIC-JA), Pablo de Olavide University, 41013 Seville, Spain;
| | - Gloria Garavito
- Department of Medicine, Health Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia; (D.M.); (L.F.); (C.M.-T.); (G.G.)
- Health Sciences Division, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Guillermo López-Lluch
- Department of Physiology, Anatomy, and Cellular Biology, Andalusian Centre for Development Biology (CABD-CSIC-JA), Pablo de Olavide University, 41013 Seville, Spain;
| | - Eduardo Egea
- Department of Medicine, Health Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia; (D.M.); (L.F.); (C.M.-T.); (G.G.)
- Health Sciences Division, Universidad Simón Bolívar, Barranquilla 080002, Colombia
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Cai Y, Yin G, Huang X, Hu J, Gao Z, Guo X, Qiu Y, Sun H, Feng X. Identification of B cell epitopes located on the surface in PB2 protein of H9N2 subtype avian influenza virus. Avian Pathol 2024:1-21. [PMID: 38563198 DOI: 10.1080/03079457.2024.2338816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Avian influenza (AI) caused by H9N2 subtype avian influenza virus (AIV) poses a serious threat to poultry farming and public health due to the transmissibility and pathogenicity. The PB2 protein is a major component of the viral RNA polymerase complex (vRNP). It is of great significance for identifying the antigenic determinants of PB2 protein to explore the function of PB2 protein. In this study, PB2 sequence of H9N2 subtype AIV from 1090 to 1689 bp was cloned and expressed in the prokaryotic expression pET-28a vector. After purified, the recombinant PB2 protein with cutting gel was used to immunize BALB/c mice. After cell fusion, the Hybridoma cell lines secreting monoclonal antibodies (mAbs) targeting to PB2 protein were screened by indirect ELISA and Western blotting, and the antigenic epitopes of mAbs were identified by constructing truncated overlapping fragments in PB2 protein of H9N2 subtype AIV. The results showed that three hybridoma cell lines (4B7, 4D10, 5H1) that stably secreted mAbs special to PB2 protein were screened, and heavy chain of 4B7 was IgG2α, that of 4D10 and 5H1 were IgG1, in which three mAbs were Kappa light chain. Also, the minimum B-cell epitope recognized by 475LRGVRVSK482 and 528TITYSSPMMW537. Homology analysis showed that these two epitopes were conservative among the different subtypes of AIV strains and located on the surface of PB2 protein. The above findings provide an experimental foundation for further investigation of the function of PB2 protein and provide effective technical support for developing monoclonal antibody-based diagnostic kits.
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Affiliation(s)
- Yiqin Cai
- Key Laboratory of Animal Microbiology of China's Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Guihu Yin
- Key Laboratory of Animal Microbiology of China's Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangyu Huang
- Key Laboratory of Animal Microbiology of China's Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianing Hu
- Key Laboratory of Animal Microbiology of China's Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zichen Gao
- Key Laboratory of Animal Microbiology of China's Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Guo
- Key Laboratory of Animal Microbiology of China's Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yawei Qiu
- Key Laboratory of Animal Microbiology of China's Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Haifeng Sun
- Key Laboratory of Animal Microbiology of China's Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiuli Feng
- Key Laboratory of Animal Microbiology of China's Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
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Tian P, Sun Z, Wang M, Song J, Sun J, Zhou L, Jiang D, Zhang A, Wu Y, Zhang G. Identification of a novel linear B-cell epitope on the p30 protein of African swine fever virus using monoclonal antibodies. Virus Res 2024; 341:199328. [PMID: 38262569 PMCID: PMC10839582 DOI: 10.1016/j.virusres.2024.199328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 01/25/2024]
Abstract
The outbreak of African Swine Fever (ASF) has caused huge economic losses to the pig industry. There are no safe and effective vaccines or diagnostics available. The p30 protein serves as a key target for the detection of ASFV antibodies and is an essential antigenic protein for early serological diagnosis. Here, the p30 protein was purified after being expressed in E. coli and its immunogenicity was verified in sera from pigs naturally infected with ASFV. Furthermore, a monoclonal antibody (McAb) designated as McAb 1B4G2-4 (subtype IgG1/kappa-type) was produced and it was verified to specifically recognize the ASFV Pig/HLJ/2018/strain and eukaryotic recombinant ASFV p30 protein. The epitope identified by McAb 1B4G2-4, defining the unique B-cell epitope 164HNFIQTI170, was located using peptide scanning. Comparing amino acid (aa) sequence revealed that this epitope is conserved in all reference ASFV strains from different regions of China, including the highly pathogenic strain Georgia 2007/1 (NC_044959.2) that is widely distributed. It is also exposed to the surface of the p30 protein, suggesting that it could be an important B-cell epitope. Our study may serve as a basis for the development of serological diagnostic methods and subunit vaccines.
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Affiliation(s)
- Panpan Tian
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhuoya Sun
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Mengxiang Wang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Jinxing Song
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Junru Sun
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Lei Zhou
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Dawei Jiang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Longhu Laboratory, Zhengzhou 450046, China
| | - Angke Zhang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanan Wu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
| | - Gaiping Zhang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Longhu Laboratory, Zhengzhou 450046, China.
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Zhou L, Ren T, Liu M, Min X, Zhang L, Qin Y, Ouyang K, Chen Y, Huang W, Wei Z. Development of a monoclonal antibody specifically recognizing a linear epitope on the capsid protein of the emerging Group III Getah virus. Virology 2024; 591:109990. [PMID: 38224661 DOI: 10.1016/j.virol.2024.109990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/17/2024]
Abstract
Getah virus (GETV) is an emerging mosquito-borne alphavirus that can infect horses, pigs and other animals. Given the public health threat posed by GETV, research on its pathogenesis, diagnosis and prevention is urgently needed. In the current study, prokaryotic expression systems were used to express the capsid protein of GETV. This protein was then used to immunize BALB/c mice in order to generate monoclonal antibodies (mAbs). Subsequently, hybridoma cells secreting a mAb (2B11-4) against the capsid protein were obtained using the hybridoma technique. A B cell linear epitope, 18-PAYRPWR-24, located at the capsid protein's N-terminal region was identified using western blotting analysis with the produced mAb, 2B11-4. Sequence alignment indicated that this epitope was highly conserved in group III (GIII) strains of GETV, but varied among the other genotypes. Western blotting showed that mAb 2B11-4 could discriminate Group III GETVs from other genotypes. This study describes the preparation of a mAb against the GETV capsid protein and the identification of the specific localization of B-cell epitopes, and will contribute towards a better understanding of the biological importance of the GETV capsid protein. It will also pave the way for developing immunological detection methods and genotype diagnosis for GETVs.
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Affiliation(s)
- Lingshan Zhou
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Tongwei Ren
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Muyang Liu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Xianglin Min
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Liping Zhang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Yifeng Qin
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530005, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, 530005, China; Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530005, China
| | - Kang Ouyang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530005, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, 530005, China; Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530005, China
| | - Ying Chen
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530005, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, 530005, China; Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530005, China
| | - Weijian Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530005, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, 530005, China; Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530005, China
| | - Zuzhang Wei
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530005, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, 530005, China; Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530005, China.
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Musundi SD, Gitaka J, Kanoi BN. Identification of conserved cross-species B-cell linear epitopes in human malaria: a subtractive proteomics and immuno-informatics approach targeting merozoite stage proteins. Front Immunol 2024; 15:1352618. [PMID: 38404581 PMCID: PMC10884153 DOI: 10.3389/fimmu.2024.1352618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/25/2024] [Indexed: 02/27/2024] Open
Abstract
Human malaria, caused by five Plasmodium species (P. falciparum, P. vivax, P. malariae, P. ovale, and P. knowlesi), remains a significant global health burden. While most interventions target P. falciparum, the species associated with high mortality rates and severe clinical symptoms, non-falciparum species exhibit different transmission dynamics, remain hugely neglected, and pose a significant challenge to malaria elimination efforts. Recent studies have reported the presence of antigens associated with cross-protective immunity, which can potentially disrupt the transmission of various Plasmodium species. With the sequencing of the Plasmodium genome and the development of immunoinformatic tools, in this study, we sought to exploit the evolutionary history of Plasmodium species to identify conserved cross-species B-cell linear epitopes in merozoite proteins. We retrieved Plasmodium proteomes associated with human malaria and applied a subtractive proteomics approach focusing on merozoite stage proteins. Bepipred 2.0 and Epidope were used to predict B-cell linear epitopes using P. falciparum as the reference species. The predictions were further compared against human and non-falciparum databases and their antigenicity, toxicity, and allergenicity assessed. Subsequently, epitope conservation was carried out using locally sequenced P. falciparum isolates from a malaria-endemic region in western Kenya (n=27) and Kenyan isolates from MalariaGEN version 6 (n=131). Finally, physiochemical characteristics and tertiary structure of the B-cell linear epitopes were determined. The analysis revealed eight epitopes that showed high similarity (70-100%) between falciparum and non-falciparum species. These epitopes were highly conserved when assessed across local isolates and those from the MalariaGEN database and showed desirable physiochemical properties. Our results show the presence of conserved cross-species B-cell linear epitopes that could aid in targeting multiple Plasmodium species. Nevertheless, validating their efficacy in-vitro and in-vivo experimentally is essential.
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Affiliation(s)
| | | | - Bernard N. Kanoi
- Centre for Malaria Elimination, Institute of Tropical Medicine, Mount Kenya University, Thika, Kenya
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Perez-Soria MME, López-Díaz DG, Jiménez-Ocampo R, Aguilar-Tipacamú G, Ueti MW, Mosqueda J. Immunization of cattle with a Rhipicephalus microplus chitinase peptide containing predicted B-cell epitopes reduces tick biological fitness. Parasitology 2024:1-10. [PMID: 38311342 DOI: 10.1017/s0031182024000143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Rhipicephalus microplus, the cattle fever tick, is the most important ectoparasite impacting the livestock industry worldwide. Overreliance on chemical treatments for tick control has led to the emergence of acaricide-resistant ticks and environmental contamination. An immunological strategy based on vaccines offers an alternative approach to tick control. To develop novel tick vaccines, it is crucial to identify and evaluate antigens capable of generating protection in cattle. Chitinases are enzymes that degrade older chitin at the time of moulting, therefore allowing interstadial metamorphosis. In this study, 1 R. microplus chitinase was identified and its capacity to reduce fitness in ticks fed on immunized cattle was evaluated. First, the predicted amino acid sequence was determined in 4 isolates and their similarity was analysed by bioinformatics. Four peptides containing predicted B-cell epitopes were designed. The immunogenicity of each peptide was assessed by inoculating 2 cattle, 4 times at 21 days intervals, and the antibody response was verified by indirect ELISA. A challenge experiment was conducted with those peptides that were immunogenic. The chitinase gene was successfully amplified and sequenced, enabling comparison with reference strains. Notably, a 99.32% identity and 99.84% similarity were ascertained among the sequences. Furthermore, native protein recognition was demonstrated through western blot assays. Chitinase peptide 3 reduced the weight and oviposition of engorged ticks, as well as larvae viability, exhibiting a 71% efficacy. Therefore, chitinase 3 emerges as a viable vaccine candidate, holding promise for its integration into a multiantigenic vaccine against R. microplus.
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Affiliation(s)
| | - Daniel Gustavo López-Díaz
- Immunology and Vaccines Laboratory, College of Natural Sciences, Autonomous University of Queretaro, Queretaro, QT, Mexico
- Master's Program in Sustainable Animal Health and Production, College of Natural Sciences, Autonomous University of Queretaro, QT, Mexico
| | | | - Gabriela Aguilar-Tipacamú
- CA Salud Animal y Microbiologia Ambiental, College of Natural Sciences, Autonomous University of Queretaro, QT, Mexico
| | - Massaro W Ueti
- Animal Diseases Research Unit, Agricultural Research Service, US Department of Agriculture, Pullman, Washington, 99164, USA
| | - Juan Mosqueda
- Immunology and Vaccines Laboratory, College of Natural Sciences, Autonomous University of Queretaro, Queretaro, QT, Mexico
- CA Salud Animal y Microbiologia Ambiental, College of Natural Sciences, Autonomous University of Queretaro, QT, Mexico
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Tian Y, Liang C, Zhou J, Sun F, Liu Y, Chen Y, Zhu X, Liu H, Ding P, Liu E, Zhang Y, Wu S, Wang A. Identification of a novel B-cell epitope of the African swine fever virus p34 protein and development of an indirect ELISA for the detection of serum antibodies. Front Microbiol 2024; 14:1308753. [PMID: 38282734 PMCID: PMC10814126 DOI: 10.3389/fmicb.2023.1308753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
African swine fever (ASF) is a viral disease caused by the African swine fever virus that can be highly transmitted and lethal in domestic pigs. In the absence of a vaccine, effective diagnosis is critical for minimizing the virus's spread. In recent years, with the decline of African swine fever virus (ASFV) virulence, antibody detection has become an important means of detection. ASFV nucleocapsid protein p34 is a mature hydrolytic product of pp220, which is highly conserved and has a high content in the structural protein of the virus. Prokaryotic cells were chosen to generate highly active and high-yield p34 protein, which was then used as an antigen for producing mouse monoclonal antibodies. The B-cell epitope 202QKELDKLQT210, which was highly conserved and found on the surface of the p34 protein, was first identified by an anti-p34 monoclonal antibody utilizing the peptide scanning technique and visualized in helix. This supported the viability of p34 protein detection even further. In addition, we established an indirect ELISA assay based on p34 to detect ASFV antibodies. The coincidence rate of this method with commercially available kits was shown to be 97.83%. Sensitivity analysis revealed that it could be detected in serum dilution as low as 1:6400, and there was no cross-reaction with other prevalent porcine epidemic diseases classical swine fever virus (CSFV), foot-and-mouth disease virus (FMDV), porcine reproductive and respiratory syndrome virus (PRRSV), and porcine circovirus 2 (PCV2). In summary, the established ELISA method and anti-P34 monoclonal antibody have demonstrated that the p34 protein has a promising application prospect for the detection of African swine fever antibodies.
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Affiliation(s)
- Yuanyuan Tian
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Chao Liang
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Jingming Zhou
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Fanglin Sun
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yankai Liu
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yumei Chen
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xifang Zhu
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongliang Liu
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Peiyang Ding
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Enping Liu
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying Zhang
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Sixuan Wu
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Aiping Wang
- Longhu Laboratory, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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Sharma S, Suri D, Aggarwal AN, Yadav R, Sethi S, Laal S, Verma I. Evaluation of immunodominant peptides of in vivo expressed mycobacterial antigens in an ELISA-based diagnostic assay for pulmonary tuberculosis. Braz J Microbiol 2023; 54:1751-1759. [PMID: 37198420 PMCID: PMC10485188 DOI: 10.1007/s42770-023-00998-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/27/2023] [Indexed: 05/19/2023] Open
Abstract
Non-sputum-based biomarker assay is urgently required as per WHO's target product pipeline for diagnosis of tuberculosis. Therefore, the current study was designed to evaluate the utility of previously identified proteins, encoded by in vivo expressed mycobacterial transcripts in pulmonary tuberculosis, as diagnostic targets for a serodiagnostic assay. A total of 300 subjects were recruited including smear+, smear- pulmonary tuberculosis (PTB) patients, sarcoidosis patients, lung cancer patients and healthy controls. Proteins encoded by eight in vivo expressed transcripts selected from previous study including those encoded by two topmost expressed and six RD transcripts (Rv0986, Rv0971, Rv1965, Rv1971, Rv2351c, Rv2657c, Rv2674, Rv3121) were analyzed for B-cell epitopes by peptide arrays/bioinformatics. Enzyme-linked immunosorbent assay was used to evaluate the antibody response against the selected peptides in sera from PTB and controls. Overall 12 peptides were selected for serodiagnosis. All the peptides were initially screened for their antibody response. The peptide with highest sensitivity and specificity was further assessed for its serodiagnostic ability in all the study subjects. The mean absorbance values for antibody response to selected peptide were significantly higher (p<0.001) in PTB patients as compared to healthy controls; however, the sensitivity for diagnosis of PTB was 31% for smear+ and 20% for smear- PTB patients. Thus, the peptides encoded by in vivo expressed transcripts elicited a significant antibody response, but are not suitable candidates for serodiagnosis of PTB.
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Affiliation(s)
- Sumedha Sharma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Deepti Suri
- Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Ashutosh N. Aggarwal
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Rakesh Yadav
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Sunil Sethi
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Suman Laal
- Department of Pathology, New York University School of Medicine, New York, NY 10010 USA
| | - Indu Verma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
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10
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Kamble PR, Kulkarni B, Malaviya A, Bajaj M, Breed AA, Jagtap D, Mahale S, Pathak BR. Comparison of Anti-Trop2 Extracellular Domain Antibodies Generated Against Peptide and Protein Immunogens for Targeting Trop2-Positive Tumour Cells. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04706-4. [PMID: 37656352 DOI: 10.1007/s12010-023-04706-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
Trophoblast antigen 2 (Trop2) is a transmembrane glycoprotein upregulated in multiple solid tumours. Trop2-based passive immunotherapies are in clinical trials, while Trop2 targeting CAR-T cell-based therapies are also reported. Information about its T- and B-cell epitopes is needed for it to be pursued as an active immunotherapeutic target. This study focused on identification of immunodominant epitopes in the Trop2 extracellular domain (ECD) that can mount an efficient anti-Trop2 antibody response. In silico analysis using various B-cell epitope prediction tools was carried out to identify linear and conformational B-cell epitopes in the ECD of Trop2. Three linear peptide immunogens were shortlisted and synthesized. Along with linear peptides, truncated Trop2 ECD that possesses combination of linear and conformational epitopes was also selected. Recombinant protein immunogen was produced in 293-F suspension culture system and affinity purified. Antisera against different immunogens were characterized by ELISA and Western blotting. Two anti-peptide antisera detected recombinant and ectopically expressed Trop2 protein; however, they were unable to recognize the endogenous Trop2 protein expressed by cancer cells. Antibodies against truncated Trop2 ECD could bind to the endogenous Trop2 expressed on the surface of cancer cells. In addition to their high avidity, these polyclonal anti-sera against truncated Trop2 protein also mediated antibody-dependent cell-mediated cytotoxicity (ADCC). In summary, our comparative analysis demonstrated the utility of truncated Trop2 ECD as a promising candidate to be pursued as an active immunotherapeutic molecule against Trop2-positive cancer cells.
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Affiliation(s)
- Pradnya R Kamble
- Cellular and Structural Biology Division, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, 400012, India
| | - Bhalchandra Kulkarni
- Cellular and Structural Biology Division, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, 400012, India
| | | | - Madhulika Bajaj
- Cellular and Structural Biology Division, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, 400012, India
| | - Ananya A Breed
- Cellular and Structural Biology Division, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, 400012, India
| | - Dhanashree Jagtap
- Cellular and Structural Biology Division, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, 400012, India
| | - Smita Mahale
- Cellular and Structural Biology Division, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, 400012, India
| | - Bhakti R Pathak
- Cellular and Structural Biology Division, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, 400012, India.
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11
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Batsuli G, Ito J, York ES, Cox C, Baldwin W, Gill S, Lollar P, Meeks SL. Factor VIII antibody immune complexes modulate the humoral response to factor VIII in an epitope-dependent manner. Front Immunol 2023; 14:1233356. [PMID: 37720212 PMCID: PMC10501482 DOI: 10.3389/fimmu.2023.1233356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/11/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction Soluble antigens complexed with immunoglobulin G (IgG) antibodies can induce robust adaptive immune responses in vitro and in animal models of disease. Factor VIII immune complexes (FVIII-ICs) have been detected in individuals with hemophilia A and severe von Willebrand disease following FVIII infusions. Yet, it is unclear if and how FVIII-ICs affect antibody development over time. Methods In this study, we analyzed internalization of FVIII complexed with epitope-mapped FVIII-specific IgG monoclonal antibodies (MAbs) by murine bone marrow-derived dendritic cells (BMDCs) in vitro and antibody development in hemophilia A (FVIII-/-) mice injected with FVIII-IC over time. Results FVIII complexed with 2-116 (A1 domain MAb), 2-113 (A3 domain MAb), and I55 (C2 domain MAb) significantly increased FVIII uptake by BMDC but only FVIII/2-116 enhanced antibody titers in FVIII-/- mice compared to FVIII alone. FVIII/4A4 (A2 domain MAb) showed similar FVIII uptake by BMDC to that of isolated FVIII yet significantly increased antibody titers when injected in FVIII-/- mice. Enhanced antibody responses observed with FVIII/2-116 and FVIII/4A4 complexes in vivo were abrogated in the absence of the FVIII carrier protein von Willebrand factor. Conclusion These findings suggest that a subset of FVIII-IC modulates the humoral response to FVIII in an epitope-dependent manner, which may provide insight into the antibody response observed in some patients with hemophilia A.
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Affiliation(s)
- Glaivy Batsuli
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Jasmine Ito
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Elizabeth S. York
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Courtney Cox
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Wallace Baldwin
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Surinder Gill
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Pete Lollar
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Shannon L. Meeks
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA, United States
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12
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Howe JG, Stack G. Search of a genomic sequence database for potential novel blood group antigens: Investigation into why some amino acid substitutions are not immunogenic. Transfusion 2023. [PMID: 37386886 DOI: 10.1111/trf.17459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND Polypeptide blood group antigens are typically identified through investigation of the antibodies they induce. Human genome sequence databases are a new tool to identify AA substitutions that potentially create blood group antigens. STUDY DESIGN AND METHODS The Erythrogene genomic sequence database was searched for missense mutations not known to be blood group antigens in the extracellular domains of selected RBC proteins in European populations. Any mutations found with prevalence of 1%-90% and not known to have induced antibodies in transfusion practice were analyzed using protein structural analysis and epitope prediction programs to determine why they apparently lack immunogenicity. RESULTS Thirteen missense mutations not known to create blood group antigens were identified in the extracellular domains of Kell, BCAM, and RhD proteins, but not in RhCE, Urea Transporter 1 (Kidd), Atypical Chemokine Receptor 1 (Duffy), glycophorin A or glycophorin B. While 11 of the 13 mutations had low prevalence (<1%), a Kell Ser726Pro substitution and a BCAM Val196Ile substitution had predicted phenotype prevalences of 43.2% and 5.7%, respectively. Ser726Pro had multiple properties of a linear B-cell epitope, but possible suboptimal protein location for B-cell receptor binding and limited T-cell epitope possibilities. Val196Ile was not predicted to be in a linear B-cell epitope. CONCLUSION Multiple potential new blood group antigens of low prevalence were identified. Whether they are antigenic remains to be determined. Two higher prevalence variants in Kell and BCAM are unlikely antigens, otherwise their antibodies presumably would already have been identified. Possible reasons for their poor immunogenicity were identified.
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Affiliation(s)
- John G Howe
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Gary Stack
- Pathology and Laboratory Medicine Service, VA Connecticut Healthcare System, West Haven, Connecticut, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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13
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Li J, Yan J, Gao Y, Liu X, Sun H, Bai J, Jiang P. Identification of new conserved linear B-cell epitopes in the 3AB and 3C protein of Senecavirus A. Vet Microbiol 2023; 283:109780. [PMID: 37263042 DOI: 10.1016/j.vetmic.2023.109780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/03/2023]
Abstract
Senecavirus A (SVA) is a member of the Picornaviridae family, Senecavirus genus. The outbreak of swine vesicular disease caused by SVA has presented a significant threat to pig husbandry and public health, resulting in substantial economic losses. In this study, recombinant SVA 3AB and 3C proteins were expressed in the prokaryotic system, purified, and utilized to generate eight monoclonal antibodies (mAbs) specific to SVA 3AB or 3C proteins. Three B-cell epitopes recognized by these mAbs were subsequently identified by Western blotting. The mAbs 3G3, 3D6, and 3B7 against 3AB recognize the epitope 90NAYDGPKKNS100; the mAbs 2C10, 2C8, and 2D12 against 3C recognize the epitope 75FTHHGLPTDL85, and the mAbs 3C4 and 4A11 against 3C recognize the epitope 95DQMPARNSRV105. Moreover, all three epitopes are highly conserved in different SVA strains and are exposed on the surface of 3AB or 3C proteins, potentially representing important B-cell epitopes. This study constitutes the first report of SVA nonstructural protein epitopes, which may be beneficial for developing innovative detection methods and vaccines and for investigating the roles of 3AB and 3C in viral replication.
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Affiliation(s)
- Jian Li
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Junfang Yan
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanni Gao
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing Liu
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Haifeng Sun
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Bai
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
| | - Ping Jiang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
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14
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Abstract
Coronaviruses are widespread in nature and can infect mammals and poultry, making them a public health concern. Globally, prevention and control of emerging and re-emerging animal coronaviruses is a great challenge. The mechanisms of virus-mediated immune responses have important implications for research on virus prevention and control. The antigenic epitope is a chemical group capable of stimulating the production of antibodies or sensitized lymphocytes, playing an important role in antiviral immune responses. Thus, it can shed light on the development of diagnostic methods and novel vaccines. Here, we have reviewed advances in animal coronavirus antigenic epitope research, aiming to provide a reference for the prevention and control of animal and human coronaviruses. Supplementary Information The online version contains supplementary material available at 10.1186/s44149-023-00080-0.
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Affiliation(s)
- Mingjun Su
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Guanghui Zheng
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Xiangwen Xu
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Houhui Song
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
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15
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Lundin SB, Kann H, Fulurija A, Andersson B, Nakka SS, Andersson LM, Gisslén M, Harandi AM. A novel precision-serology assay for SARS-CoV-2 infection based on linear B-cell epitopes of Spike protein. Front Immunol 2023; 14:1166924. [PMID: 37251407 PMCID: PMC10213285 DOI: 10.3389/fimmu.2023.1166924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction The COVID-19 pandemic illustrates the need for serology diagnostics with improved accuracy. While conventional serology based on recognition of entire proteins or subunits thereof has made significant contribution to the antibody assessment space, it often suffers from sub-optimal specificity. Epitope-based, high-precision, serology assays hold potential to capture the high specificity and diversity of the immune system, hence circumventing the cross-reactivity with closely related microbial antigens. Methods We herein report mapping of linear IgG and IgA antibody epitopes of the SARS-CoV-2 Spike (S) protein in samples from SARS-CoV-2 exposed individuals along with certified SARS-CoV-2 verification plasma samples using peptide arrays. Results We identified 21 distinct linear epitopes. Importantly, we showed that pre-pandemic serum samples contain IgG antibodies reacting to the majority of protein S epitopes, most likely as a result of prior infection with seasonal coronaviruses. Only 4 of the identified SARS-CoV-2 protein S linear epitopes were specific for SARS-CoV-2 infection. These epitopes are located at positions 278-298 and 550-586, just proximal and distal to the RBD, as well as at position 1134-1156 in the HR2 subdomain and at 1248-1271 in the C-terminal subdomain of protein S. To substantiate the applicability of our findings, we tested three of the high-accuracy protein S epitopes in a Luminex assay, using a certified validation plasma sample set from SARS-CoV-2 infected individuals. The Luminex results were well aligned with the peptide array results, and correlated very well with in-house and commercial immune assays for RBD, S1 and S1/S2 domains of protein S. Conclusion We present a comprehensive mapping of linear B-cell epitopes of SARS-CoV-2 protein S, that identifies peptides suitable for a precision serology assay devoid of cross-reactivity. These results have implications for development of highly specific serology test for exposure to SARS-CoV-2 and other members of the coronaviridae family, as well as for rapid development of serology tests for future emerging pandemic threats.
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Affiliation(s)
- Samuel B. Lundin
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Biotome Pty Ltd, Perth, WA, Australia
- Biotome AB, Kullavik, Sweden
| | - Hanna Kann
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Alma Fulurija
- Biotome Pty Ltd, Perth, WA, Australia
- Biotome AB, Kullavik, Sweden
- School of Biomedical Sciences, Marshall Centre, University of Western Australia, Perth, WA, Australia
| | - Björn Andersson
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sravya S. Nakka
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Lars-Magnus Andersson
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Infectious Diseases, Gothenburg, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Infectious Diseases, Gothenburg, Sweden
| | - Ali M. Harandi
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
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16
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Affonso de Oliveira JF, Zhao Z, Xiang Y, Shin MD, Villaseñor KE, Deng X, Shukla S, Chen S, Steinmetz NF. COVID-19 vaccines based on viral nanoparticles displaying a conserved B-cell epitope show potent immunogenicity and a long-lasting antibody response. Front Microbiol 2023; 14:1117494. [PMID: 37152732 PMCID: PMC10157238 DOI: 10.3389/fmicb.2023.1117494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/13/2023] [Indexed: 05/09/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 sparked intensive research into the development of effective vaccines, 50 of which have been approved thus far, including the novel mRNA-based vaccines developed by Pfizer and Moderna. Although limiting the severity of the disease, the mRNA-based vaccines presented drawbacks, such as the cold chain requirement. Moreover, antibody levels generated by these vaccines decline significantly after 6 months. These vaccines deliver mRNA encoding the full-length spike (S) glycoprotein of SARS-CoV-2, but must be updated as new strains and variants of concern emerge, creating a demand for adjusted formulations and booster campaigns. To overcome these challenges, we have developed COVID-19 vaccine candidates based on the highly conserved SARS CoV-2, 809-826 B-cell peptide epitope (denoted 826) conjugated to cowpea mosaic virus (CPMV) nanoparticles and bacteriophage Qβ virus-like particles, both platforms have exceptional thermal stability and facilitate epitope delivery with inbuilt adjuvant activity. We evaluated two administration methods: subcutaneous injection and an implantable polymeric scaffold. Mice received a prime-boost regimen of 100 μg per dose (2 weeks apart) or a single dose of 200 μg administered as a liquid formulation, or a polymer implant. Antibody titers were evaluated longitudinally over 50 weeks. The vaccine candidates generally elicited an early Th2-biased immune response, which stimulates the production of SARS-CoV-2 neutralizing antibodies, followed by a switch to a Th1-biased response for most formulations. Exceptionally, vaccine candidate 826-CPMV (administered as prime-boost, soluble injection) elicited a balanced Th1/Th2 immune response, which is necessary to prevent pulmonary immunopathology associated with Th2 bias extremes. While the Qβ-based vaccine elicited overall higher antibody titers, the CPMV-induced antibodies had higher avidity. Regardless of the administration route and formulation, our vaccine candidates maintained high antibody titers for more than 50 weeks, confirming a potent and durable immune response against SARS-CoV-2 even after a single dose.
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Affiliation(s)
| | - Zhongchao Zhao
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, United States
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
| | - Yi Xiang
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, United States
| | - Matthew D. Shin
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, United States
| | | | - Xinyi Deng
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, United States
| | - Sourabh Shukla
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, United States
| | - Shaochen Chen
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, United States
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, CA, United States
| | - Nicole F. Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, United States
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, CA, United States
- Department of Radiology, University of California, San Diego, La Jolla, CA, United States
- Center for Engineering in Cancer, University of California, San Diego, La Jolla, CA, United States
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17
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Zhang SJ, Liu J, Niu B, Zhu YM, Zhao DM, Chen WY, Liu RQ, Bu ZG, Hua RH. Comprehensive mapping of antigenic linear B-cell epitopes on K205R protein of African swine fever virus with monoclonal antibodies. Virus Res 2023; 328:199085. [PMID: 36889544 DOI: 10.1016/j.virusres.2023.199085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023]
Abstract
African swine fever virus causes an acute, highly contagious swine disease with high mortality, leading to enormous losses in the pig industry. The K205R, a nonstructural protein of African swine fever virus, is abundantly expressed in the cytoplasm of infected cells at the early stage of infection and induces a strong immune response. However, to date, the antigenic epitopes of this immunodeterminant have not been characterized. In the present study, the K205R protein was expressed in a mammalian cell line and purified using Ni-affinity chromatography. Furthermore, three monoclonal antibodies (mAbs; 5D6, 7A8, and 7H10) against K205R were generated. Indirect immunofluorescence assay and western blot results showed that all three mAbs recognized native and denatured K205R in African swine fever virus (ASFV)-infected cells. To identify the epitopes of the mAbs, a series of overlapping short peptides were designed and expressed as fusion proteins with maltose-binding protein. Subsequently, the peptide fusion proteins were probed with monoclonal antibodies using western blot and enzyme-linked immunosorbent assay. The three target epitopes were fine-mapped; the core sequences of recognized by the mAbs 5D6, 7A8, and 7H10 were identified as 157FLTPEIQAILDE168, 154REKFLTP160, and 136PTNAMFFTRSEWA148, respectively. Probing with sera from ASFV-infected pigs in a dot blot assay demonstrated that epitope 7H10 was the immunodominant epitope of K205R. Sequence alignment showed that all epitopes were conserved across ASFV strains and genotypes. To our knowledge, this is the first study to characterize the epitopes of the antigenic K205R protein of ASFV. These findings may serve as a basis for the development of serological diagnostic methods and subunit vaccines.
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Affiliation(s)
- Shu-Jian Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jing Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Bei Niu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yuan-Mao Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Dong-Ming Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Wei-Ye Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Ren-Qiang Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhi-Gao Bu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Rong-Hong Hua
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China.
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Ataides LS, de Moraes Maia F, Conte FP, Isaac L, Barbosa AS, da Costa Lima-Junior J, Avelar KES, Rodrigues-da-Silva RN. Sph2 (176-191) and Sph2 (446-459): Identification of B-Cell Linear Epitopes in Sphingomyelinase 2 (Sph2), Naturally Recognized by Patients Infected by Pathogenic Leptospires. Vaccines (Basel) 2023; 11:vaccines11020359. [PMID: 36851237 PMCID: PMC9959207 DOI: 10.3390/vaccines11020359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Sphingomyelin is a major constituent of eukaryotic cell membranes, and if degraded by bacteria sphingomyelinases may contribute to the pathogenesis of infection. Among Leptospira spp., there are five sphingomyelinases exclusively expressed by pathogenic leptospires, in which Sph2 is expressed during natural infections, cytotoxic, and implicated in the leptospirosis hemorrhagic complications. Considering this and the lack of information about associations between Sph2 and leptospirosis severity, we use a combination of immunoinformatics approaches to identify its B-cell epitopes, evaluate their reactivity against samples from leptospirosis patients, and investigate the role of antibodies anti-Sph2 in protection against severe leptospirosis. Two B-cell epitopes, Sph2(176-191) and Sph2(446-459), were predicted in Sph2 from L. interrogans serovar Lai, presenting different levels of identity when compared with other pathogenic leptospires. These epitopes were recognized by about 40% of studied patients with a prevalence of IgG antibodies against both Sph2(176-191) and Sph2(446-459). Remarkably, just individuals with low reactivity to Sph2(176-191) presented clinical complications, while high responders had only mild symptoms. Therefore, we identified two B-cell linear epitopes, recognized by antibodies of patients with leptospirosis, that could be further explored in the development of multi-epitope vaccines against leptospirosis.
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Affiliation(s)
- Laura Sant’Anna Ataides
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil
| | - Fernanda de Moraes Maia
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil
| | - Fernando Paiva Conte
- Laboratório Piloto Eucariotos, Instituto de Tecnologia em Imunobiológicos, FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil
| | - Lourdes Isaac
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | - Angela Silva Barbosa
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo 05503-900, SP, Brazil
| | - Josué da Costa Lima-Junior
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil
| | - Kátia Eliane Santos Avelar
- Laboratório de Referência Nacional para Leptospirose, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil
| | - Rodrigo Nunes Rodrigues-da-Silva
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil
- Correspondence: or ; Tel.: +55-21982054291
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He W, Shi X, Guan H, Zou Y, Zhang S, Jiang Z, Su S. Identification of a novel linear B-cell epitope in porcine deltacoronavirus nucleocapsid protein. Appl Microbiol Biotechnol 2023; 107:651-61. [PMID: 36602561 DOI: 10.1007/s00253-022-12348-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/29/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023]
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus that caused diarrhea and/or vomiting in neonatal piglets worldwide. Coronaviruses nucleocapsid (N) protein is the most conserved structural protein for viral replication and possesses good antigenicity. In this study, three monoclonal antibodies (mAbs), 3B4, 4D3, and 4E3 identified as subclass IgG2aκ were prepared using the lymphocytic hybridoma technology against PDCoV N protein. Furthermore, the B-cell epitope recognized by mAb 4D3 was mapped by dozens of overlapping truncated recombinant proteins based on the western blotting. The polypeptide 28QFRGNGVPLNSAIKPVE44 (EP-4D3) in the N-terminal of PDCoV N protein was identified as the minimal linear epitope for binding mAb 4D3. And the EP-4D3 epitope's amino acid sequence homology study revealed that PDCoV strains are substantially conserved, with the exception of the Alanine43 substitution Valine43 in the China lineage, the Early China lineage, and the Thailand, Vietnam, and Laos lineage. The epitope sequences shared high similarity (94.1%) with porcine coronavirus HKU15-155 (PorCoV HKU15), Asian leopard cats coronavirus (ALCCoV), sparrow coronavirus HKU17 (SpCoV HKU17), and sparrow deltacoronavirus. In contrast, the epitope sequences shared a very low homology (11.8 to 29.4%) with other porcine CoVs (PEDV, TGEV, PRCV, SADS-CoV, PHEV). Overall, the study will enrich the biological function of PDCoV N protein and provide foundational data for further development of diagnostic applications. KEY POINTS: • Three monoclonal antibodies against PDCoV N protein were prepared. • Discovery of a novel B-cell liner epitope (28QFRGNGVPLNSAIKPVE44) of PDCoV N protein. • The epitope EP-4D3 was conserved among PDCoV strains.
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20
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De-Simone SG, Napoleão-Pêgo P, Gonçalves PS, Lechuga GC, Cardoso SV, Provance DW, Morel CM, da Silva FR. B-Cell Epitope Mapping of the Vibrio cholera Toxins A, B, and P and an ELISA Assay. Int J Mol Sci 2022; 24:531. [PMID: 36613974 PMCID: PMC9820764 DOI: 10.3390/ijms24010531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Oral immunization with the choleric toxin (CT) elicits a high level of protection against its enterotoxin activities and can control cholera in endemic settings. However, the complete B-cell epitope map of the CT that is responsible for protection remains to be clarified. A library of one-hundred, twenty-two 15-mer peptides covering the entire sequence of the three chains of the CT protein (CTP) was prepared by SPOT synthesis. The immunoreactivity of membrane-bound peptides with sera from mice vaccinated with an oral inactivated vaccine (Schankol™) allowed the mapping of continuous B-cell epitopes, topological studies, multi-antigen peptide (MAP) synthesis, and Enzyme-Linked Immunosorbent Assay (ELISA) development. Eighteen IgG epitopes were identified; eight in the CTA, three in the CTB, and seven in the protein P. Three V. cholera specific epitopes, Vc/TxA-3, Vc/TxB-11, and Vc/TxP-16, were synthesized as MAP4 and used to coat ELISA plates in order to screen immunized mouse sera. Sensitivities and specificities of 100% were obtained with the MAP4s of Vc/TxA-3 and Vc/TxB-11. The results revealed a set of peptides whose immunoreactivity reflects the immune response to vaccination. The array of peptide data can be applied to develop improved serological tests in order to detect cholera toxin exposure, as well as next generation vaccines to induce more specific antibodies against the cholera toxin.
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Affiliation(s)
- Salvatore G. De-Simone
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Program of Post-Graduation on Science and Biotechnology, Molecular and Cellular Biology Department, Biology Institute, Federal Fluminense University, Niterói 24020-036, RJ, Brazil
| | - Paloma Napoleão-Pêgo
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
| | - Priscilla S. Gonçalves
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Program of Post-Graduation on Science and Biotechnology, Molecular and Cellular Biology Department, Biology Institute, Federal Fluminense University, Niterói 24020-036, RJ, Brazil
| | - Guilherme C. Lechuga
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
| | - Sergian V. Cardoso
- Department of Health, Graduate Program in Translational Biomedicine (BIOTRANS), University of Grande Rio (UNIGRANRIO), Caxias 25071-202, RJ, Brazil
| | - David W. Provance
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
| | - Carlos M. Morel
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
| | - Flavio R. da Silva
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Xu H, Zhao Z. NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes. Genomics Proteomics Bioinformatics 2022; 20:1002-1012. [PMID: 36526218 PMCID: PMC10025766 DOI: 10.1016/j.gpb.2022.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 10/27/2022] [Accepted: 11/11/2022] [Indexed: 12/15/2022]
Abstract
Identification of B-cell epitopes (BCEs) plays an essential role in the development of peptide vaccines and immuno-diagnostic reagents, as well as antibody design and production. In this work, we generated a large benchmark dataset comprising 124,879 experimentally supported linear epitope-containing regions in 3567 protein clusters from over 1.3 million B cell assays. Analysis of this curated dataset showed large pathogen diversity covering 176 different families. The accuracy in linear BCE prediction was found to strongly vary with different features, while all sequence-derived and structural features were informative. To search more efficient and interpretive feature representations, a ten-layer deep learning framework for linear BCE prediction, namely NetBCE, was developed. NetBCE achieved high accuracy and robust performance with the average area under the curve (AUC) value of 0.8455 in five-fold cross-validation through automatically learning the informative classification features. NetBCE substantially outperformed the conventional machine learning algorithms and other tools, with more than 22.06% improvement of AUC value compared to other tools using an independent dataset. Through investigating the output of important network modules in NetBCE, epitopes and non-epitopes tended to be presented in distinct regions with efficient feature representation along the network layer hierarchy. The NetBCE is freely available at https://github.com/bsml320/NetBCE.
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Affiliation(s)
- Haodong Xu
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA.
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23
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Dewi KS, Chairunnisa S, Swasthikawati S, Yuliawati, Agustiyanti DF, Mustopa AZ, Kusharyoto W, Ningrum RA. Production of codon-optimized Human papillomavirus type 52 L1 virus-like particles in Pichia pastoris BG10 expression system. Prep Biochem Biotechnol 2022; 53:148-156. [PMID: 35302435 DOI: 10.1080/10826068.2022.2048262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cervical cancer caused by Human papillomavirus (HPV) is one of the most common causes of cancer death in women worldwide. Even though the disease can be avoided by immunization, the expensive price of HPV vaccines makes it hard to be accessed by women in middle-low-income countries. Thus, the development of generic HPV vaccines is needed to address inequalities in life-saving access. This study aimed to develop the HPV52 L1 VLP-based recombinant vaccine using Pichia pastoris expression system. The l1 gene was codon-optimized based on P. pastoris codon usage resulting CAI value of 0.804. The gene was inserted into the pD902 plasmid under the regulation of the AOX1 promoter. The linear plasmid was transformed into P. pastoris BG10 genome and screened in YPD medium containing zeocin antibiotic. Colony of transformant that grown on highest zeocin concentration was characterized by genomic PCR and sequencing. The positive clone was selected and expressed using BMGY/BMMY medium induced with various methanol concentrations. The SDS-PAGE and Western blot analyses showed that 55 kDa L1 protein was successfully expressed using an optimum concentration of 1% methanol. The self-assembly of HPV52 L1 protein was also proven using TEM analysis. Moreover, we also analyzed the B-cell epitope of HPV52 L1 protein based on several criteria, including antigenicity, surface accessibility, flexibility, and hydrophilicity. We assumed that epitope 476GLQARPKLKRPASSAPRTSTKKKKV500 could be developed as an epitope-based vaccine with a neutralizing antibody response toward HPV52 infection. Finally, our study provided the alternative for developing low-cost HPV vaccines, either VLP or epitope-based.
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Affiliation(s)
- Kartika Sari Dewi
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Sheila Chairunnisa
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Sri Swasthikawati
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Yuliawati
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Dian Fitria Agustiyanti
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Apon Zainal Mustopa
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Wien Kusharyoto
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Ratih Asmana Ningrum
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
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24
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Sun X, Xing S, Wang S, Zhang X, Yu Y, Wang L. In vitro assembly of chimeric virus-like particles composed of a porcine circovirus 2b capsid protein and a B-cell epitope of infectious bursal disease virus. Biotechnol Lett 2022; 44:429-438. [PMID: 35199255 DOI: 10.1007/s10529-022-03237-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To develop a method for in vitro assembly of recombinant proteins expressed in E. coli into chimeric virus-like particles (cVLPs). RESULTS A fusion protein (Bepi-Cap-A) between capsid protein (Cap) of PCV2b and B cell epitope (Bepi) of IBDV was expressed in E. Coli, and purified. For assembling them into cVLPs (Bepi-Cap-VLP), the Bepi-Cap-A was suspended in buffer C [0.03% ("%" stands for "v/v" unless otherwise indicated) polyethylene glycol, 0.4 M Tris, 10 mM β-mercaptoethanol, 5% glycerol, 0.02% (w/v) gellan gum, 0.1 M glycine, 0.03% Tween 80, 500 mM NaCl], and incubated. After centrifugation, the pellet was resuspended in buffer D [50 mM Na2HPO4, 50 mM NaH2PO4, 0.01% (w/v) gellan gum, 0.05 mM EDTA, 500 mM NaCl, 0.03% Tween 80, pH 6.5], and then dialyzed against dialysis buffer (50 mM Na2HPO4, 50 mM NaH2PO4, 500 mM NaCl, 0.03% Tween 80, pH 6.5). The procedure resulted in typical and immunogenic Bepi-Cap-VLP. CONCLUSIONS The data provide a method which is feasible for in vitro assembly of recombinant proteins into chimeric virus-like particles.
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Affiliation(s)
- Xiaomeng Sun
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, People's Republic of China
- Department of Immunology, School of Changchun Medical College, Changchun, Jilin, 130031, People's Republic of China
| | - Shiyu Xing
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, People's Republic of China
| | - Shengnan Wang
- Department of Molecular Biology, College of Basic Medical Sciences and Institute of Pediatrics in the First Hospital of Jilin University, Jilin University, Changchun, Jilin, 130021, People's Republic of China
| | - Xian Zhang
- Department of Molecular Biology, College of Basic Medical Sciences and Institute of Pediatrics in the First Hospital of Jilin University, Jilin University, Changchun, Jilin, 130021, People's Republic of China
| | - Yongli Yu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, People's Republic of China.
| | - Liying Wang
- Department of Molecular Biology, College of Basic Medical Sciences and Institute of Pediatrics in the First Hospital of Jilin University, Jilin University, Changchun, Jilin, 130021, People's Republic of China.
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25
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Huang HR, Dong Y, Deng Y, Xu YC, Chen MN, Liu Y, Zhang CL. [Analysis of lactate dehydrogenase gene polymorphisms and prediction of B cell epitopes in four human Plasmodium species]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2022; 34:28-35. [PMID: 35266354 DOI: 10.16250/j.32.1374.2021026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To analyze the polymorphism of Plasmodium lactate dehydrogenase (pLDH) gene and predict B-cell epitopes in pLDH peptides in four species of human malaria parasites. METHODS The blood samples and epidemiological characteristics were collected from malaria cases in Yunnan Province registered in the National Notifiable Disease Report System. The pLDH genes of four human Plasmodium species were amplified using nested PCR assay and sequenced. The polymorphisms of pLDH genes was analyzed using the software MEGA version 7.0.26 and DnaSP version 5.10, and the B-cell epitopes were predicted in pLDH peptides using the Immune Epitope Database (IEDB). RESULTS The sequences of P. vivax LDH (PvLDH), P. falciparum LDH (PfLDH), P. ovale LDH (PoLDH) and P. malariae LDH (PmLDH) genes were obtained from 153, 29, 17 and 11 blood samples from patients with P. vivax, P. falciparum, P. ovale and P. malariae malaria, respectively, which included 15, 2, 4 and 2 haplotypes and had a nucleotide diversity (π) of 0.104. A high level of intra-species differentiation was seen in the PoLDH gene (π = 0.012), and the π values were all < 0.001 for PvLDH, PfLDH and PmLDH genes. Active regions of B-cell antigen were predicted in the pLDH peptide chain of four human malaria parasites, of 4 to 5 in each chain, and the activity score was approximately 0.430. Among these peptide chains, the "86-PGKSDKEWNRD-96" short-peptide was a B-cell epitope shared by all four species of human malaria parasites, and the "266-GQYGHS (T)-271" short-peptide was present in PvLDH and PoLDH peptide chains, while "212-EEVEGIFDR-220" was only found in the PvLDH peptide chain, and "208-LISDAE-213" was only seen in the PfLDH peptide chain. CONCLUSIONS The PoLDH gene polymorphism may be derived from the weak negative purification selection, while PvLDH, PfLDH and PmLDH genes may maintain a relatively conservative state. There may be two B-cell epitopes "212-EEVEGIFDR-220" and "208-LISDAE-213" in the proximal region of the C terminal in the pLDH peptide chain, which is feasible to differentiate between P. vivax and P. falciparum infections.
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Affiliation(s)
- H R Huang
- Department of Basic Medical Sciences, Clinical College of Anhui Medical University, Hefei, Anhui 230031, China
| | - Y Dong
- Yunnan Institute of Parasitic Diseases Control, Yunnan Centre of Malaria Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, Yunnan 665000, China
| | - Y Deng
- Yunnan Institute of Parasitic Diseases Control, Yunnan Centre of Malaria Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, Yunnan 665000, China
| | - Y C Xu
- Yunnan Institute of Parasitic Diseases Control, Yunnan Centre of Malaria Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, Yunnan 665000, China
| | - M N Chen
- Yunnan Institute of Parasitic Diseases Control, Yunnan Centre of Malaria Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, Yunnan 665000, China
| | - Y Liu
- Yunnan Institute of Parasitic Diseases Control, Yunnan Centre of Malaria Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, Yunnan 665000, China
| | - C L Zhang
- Yunnan Institute of Parasitic Diseases Control, Yunnan Centre of Malaria Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, Yunnan 665000, China
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26
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Wang H, Zhang X, Zhang H, Chen X, Zhang B, Su Y. [Prokaryotic expression of the GapC protein of Streptococcus uberis and prediction, identification of its B-cell epitopes]. Sheng Wu Gong Cheng Xue Bao 2022; 38:148-159. [PMID: 35142126 DOI: 10.13345/j.cjb.210285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The GapC protein of Streptococcus uberis located on the surface of bacteria is a protein with glyceraldehyde-3-phosphate dehydrogenase activity. It participates in cellular processes and exhibits a variety of biological activities. In addition, it has good antigenicity. The aim of this study was to predict the possible B-cell epitopes of the GapC protein and verify the immunogenicity of candidate epitope peptides. The gapC gene of S. uberis isolate RF5-1 was cloned into a recombinant expression plasmid pET-28a-GapC and inducibly expressed. The purified protein was used to immunize experimental rabbits to produce anti-GapC polyclonal antibodies. The three-dimensional structure and three-dimensional location of the GapC B-cell epitopes and the homology comparison of the GapC protein and its B-cell epitopes were carried out using bioinformatics softwares. The results showed that the 44-kDa GapC protein had a good immunological reactivity. Six linear and 3 conformational dominant B-cell epitopes against the GapC protein were selected and synthesized. Three dimensional analysis indicated that the selected peptides have better antigen epitope formation potential. Rabbit anti-GapC polyclonal antibodies were generated after immunized with the purified GapC protein, and the polyclonal antibodies were used to identify the epitope peptide by an indirect ELISA. The ELISA results showed that all of the 9 epitope peptides could react with anti-GapC polyclonal antibodies with varying titers. Among them, the epitope polypeptide 266AANDSYGYTEDPIVSSD282 reacted with the polyclonal antibodies significantly stronger than with other epitope peptides. This study laid an experimental foundation for in-depth understanding of the immunological properties and utilizing effective epitopes of the GapC protein of S. uberis.
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Affiliation(s)
- Hanqing Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Xuejing Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Huan Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Xiaomeng Chen
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Baojiang Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Yan Su
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
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Anasir MI, Poh CL. Discovery of B-cell epitopes for development of dengue vaccines and antibody therapeutics. Med Microbiol Immunol 2022; 211:1-18. [PMID: 35059822 DOI: 10.1007/s00430-021-00726-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/04/2021] [Indexed: 10/19/2022]
Abstract
Dengue is one of the most frequently transmitted viral infections globally which creates a serious burden to the healthcare system in many countries in the tropical and subtropical regions. To date, no vaccine has demonstrated balanced protection against the four dengue serotypes. Dengvaxia as the only vaccine that has been licensed for use in endemic areas has shown an increased risk in dengue-naïve vaccines to develop severe dengue. A crucial element in protection from dengue infection is the neutralizing antibody responses. Therefore, the identification of protective linear B-cell epitopes can guide vaccine design and facilitate the development of monoclonal antibodies as dengue therapeutics. This review summarizes the identification of dengue B-cell epitopes within the envelope (E) protein of dengue that can be incorporated into peptide vaccine constructs. These epitopes have been identified through approaches such as bioinformatics, three-dimensional structure analysis of antibody-dengue complexes, mutagenesis/alanine scanning and escape mutant studies. Additionally, the therapeutic potential of monoclonal antibodies targeting the E protein of dengue is reviewed. This can provide a basis for the design of future dengue therapies.
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Affiliation(s)
- Mohd Ishtiaq Anasir
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, Shah Alam, Selangor, Malaysia
- Centre for Virus and Vaccine Research, Sunway University, 5, Jalan Universiti, 47500, Bandar Sunway, Selangor, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, Sunway University, 5, Jalan Universiti, 47500, Bandar Sunway, Selangor, Malaysia.
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Arora N, Keshri AK, Kaur R, Rawat SS, Prasad A. Immunoinformatic Approaches for Vaccine Designing for Pathogens with Unclear Pathogenesis. Methods Mol Biol 2022; 2412:425-437. [PMID: 34918259 DOI: 10.1007/978-1-0716-1892-9_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Designing a vaccine against a pathogen has been the toughest challenge to fight against any infectious diseases. To overcome this problem, use of artificial neural network with immuno-informatics is emerging as a front runner solution. For a successful designing of a potent vaccine, prediction of T-cell/B-cell epitopes, antigen processing and presentation analysis, antigenic potential analysis of epitopes, usages of linkers, population coverage, codon optimization, allergenicity assessment, toxicity prediction of construct, and finally protein-peptide docking for stability of vaccine are important steps. To achieve this, several bioinformatics software, tools and online web servers have been developed for each application, which have their own advantages and limitations. Scientists must evaluate these parameters and should take the decision to apply more suitable and precise servers for each analysis and prediction based on their accuracy, suitability, and robustness.
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Affiliation(s)
- Naina Arora
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Anand K Keshri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Rimanpreet Kaur
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Suraj Singh Rawat
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Amit Prasad
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India.
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Tian Y, Zhang G, Liu H, Ding P, Jia R, Zhou J, Chen Y, Qi Y, Du J, Liang C, Zhu X, Wang A. Screening and identification of B cell epitope of the nucleocapsid protein in SARS-CoV-2 using the monoclonal antibodies. Appl Microbiol Biotechnol 2022; 106:1151-1164. [PMID: 35037999 PMCID: PMC8762450 DOI: 10.1007/s00253-022-11769-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/10/2021] [Accepted: 01/07/2022] [Indexed: 11/02/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes the coronavirus disease (COVID-19). It is confirmed that nucleocapsid (N) protein is closely related to viral pathogenesis, modulation of host immune response, RNA transcription, and replication and virus packaging. Therefore, the N protein is a preponderant antigen target for virus detection. The codon-optimized N gene was designed according to the encoding characteristics of insect cells and inserted into pFastBacTM1 vector with 6 × His-tag-fused N protein for expression in insect sf21 cells. Six anti-N mAbs (4G3, 5B3, 12B6, 18C7-A2, 21H10-A3, 21H10-E9) were prepared by recombinant N protein. The mAbs showed high titers, antibody affinity, and reactivity with the SARS-CoV-2 N protein. Then, fourteen overlapped peptides that covered the intact N protein were synthesized (N1-N14). Peptide N14 was identified as the main linear B-cell epitope region via peptide-ELISA and dot-blot assay, and this region was truncated gradually until mapping the peptide 401-DFSKQLQQ-408. Simultaneously, compared with the sequence of variants of concern (VOCs) and variants of interest (VOIs) strains among the several countries, epitope 401-DFSKQLQQ-408 is very conservative among them. The findings provide new guidance for the design and detection of COVID-19 targets. KEY POINTS: • The N protein was optimized according to the insect cell codon preference and was highly expressed. • The monoclonal antibodies prepared in this study were shown high antibody titers and high affinity. • Monoclonal antibodies were used to map the epitope 401-408 amino acids of N protein for the first time in this study.
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Affiliation(s)
- Yuanyuan Tian
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Gaiping Zhang
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Hongliang Liu
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Peiyang Ding
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Rui Jia
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Jingming Zhou
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Yumei Chen
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Yanhua Qi
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Jinran Du
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Chao Liang
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Xifang Zhu
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Aiping Wang
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China.
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Thomas S, Doytchinova I. In Silico Identification of the B-Cell and T-Cell Epitopes of the Antigenic Proteins of Staphylococcus aureus for Potential Vaccines. Methods Mol Biol 2022; 2412:439-447. [PMID: 34918260 DOI: 10.1007/978-1-0716-1892-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Staphylococcus aureus is a leading cause of community-acquired, healthcare-associated, and hospital-acquired infections. S. aureus bacteremia is a common and serious infection with significant morbidity and mortality in older patients. The rise of antibiotic-resistant strains of S. aureus has resulted in substantial loss and effective treatment in hospitalized patients. Thus, there is a need in the development of a vaccine that would provide protection against S. aureus. The antigens of our interest include proteins that are essential for bacterial attachment and colonization (ClfA and ClfB), dermonecrosis-driven toxin (Hla), antigens that are essential for abscess formation (EsxA and EsxB), and antigens that are essential for nutrient acquisition and resistance to phagocytes killing induced by reactive oxygen species (FhuD2 and MntC). Development of a structure-based vaccine based on the antigenic protein epitopes is a novel strategy to provide protection against S. aureus. Using bioinformatic tools, we have determined the B-cell and T-cell epitopes of the antigenic proteins of S. aureus. This chapter reports identification of B-cell and T-cell epitopes of the antigenic protein that could be used in the development of effective structure-based vaccines to protect against S. aureus.
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Affiliation(s)
- Sunil Thomas
- Lankenau Institute for Medical Research, Wynnewood, PA, USA.
| | - Irini Doytchinova
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
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31
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Zhang X, Sang S, Guan Q, Tao H, Wang Y, Liu C. Identification of B-Cell Epitopes of HspA from Helicobacter pylori and Detection of Epitope Antibody Profiles in Naturally Infected Persons. Vaccines (Basel) 2021; 10:65. [PMID: 35062726 DOI: 10.3390/vaccines10010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022] Open
Abstract
Helicobacter pylori (H. pylori), heat-shock protein A (HspA), is a bacterial heat-shock chaperone that serves as a nickel ion scavenging protein. Ni2+ is an important co-factor required for the maturation and enzymatic activity of H. pylori urease and [NiFe] hydrogenase, both of which are key virulence factors for pathogen survival and colonization. HspA is an important target molecule for the diagnosis, treatment, and immune prevention of H. pylori. In this work, HspA was truncated into five fragments to determine the location of an antigen immunodominant peptide. A series of overlapping, truncated 11-amino-acid peptides in immunodominant peptide fragments were synthesized chemically and screened by ELISA. The immunogenicity and antigenicity of the screened epitope peptides were verified by ELISA, Western blot, and lymphocyte proliferation tests. Two novel B-cell epitopes were identified, covering amino acids 2–31 of HspA, which are HP11 (2–12; KFQPLGERVLV) and HP19 (18–28; ENKTSSGIIIP). The antiserum obtained from HP11-KLH and HP19-KLH immunized mice can bind to naive HspA in H. pylori SS2000, rHspA expressed in E. coli, and the corresponding GST fusion peptide. Among HspA seropositive persons, the seropositive rates of HP11 and HP19 were 21.4% and 33.3%, respectively. Both of the B-cell epitopes of HspA are highly conserved epitopes with good antigenicity and immunogenicity.
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32
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Ameku WA, Ataide VN, Costa ET, Gomes LR, Napoleão-Pêgo P, William Provance D, Paixão TRLC, Salles MO, De-Simone SG. A Pencil-Lead Immunosensor for the Rapid Electrochemical Measurement of Anti-Diphtheria Toxin Antibodies. Biosensors (Basel) 2021; 11:489. [PMID: 34940247 PMCID: PMC8699316 DOI: 10.3390/bios11120489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/25/2021] [Accepted: 11/28/2021] [Indexed: 05/13/2023]
Abstract
Diphtheria is a vaccine-preventable disease, yet immunization can wane over time to non-protective levels. We have developed a low-cost, miniaturized electroanalytical biosensor to quantify anti-diphtheria toxin (DTx) immunoglobulin G (anti-DTx IgG) antibody to minimize the risk for localized outbreaks. Two epitopes specific to DTx and recognized by antibodies generated post-vaccination were selected to create a bi-epitope peptide, biEP, by synthesizing the epitopes in tandem. The biEP peptide was conjugated to the surface of a pencil-lead electrode (PLE) integrated into a portable electrode holder. Captured anti-DTx IgG was measured by square wave voltammetry from the generation of hydroquinone (HQ) from the resulting immunocomplex. The performance of the biEP reagent presented high selectivity and specificity for DTx. Under the optimized working conditions, a logarithmic calibration curve showed good linearity over the concentration range of 10-5-10-1 IU mL-1 and achieved a limit of detection of 5 × 10-6 IU mL-1. The final device proved suitable for interrogating the immunity level against DTx in actual serum samples. Results showed good agreement with those obtained from a commercial enzyme-linked immunosorbent assay. In addition, the flexibility for conjugating other capture molecules to PLEs suggests that this technology could be easily adapted to the diagnoses of other pathogens.
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Affiliation(s)
- Wilson A. Ameku
- Oswaldo Cruz Foundation (FIOCRUZ), Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Populations Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (W.A.A.); (L.R.G.); (P.N.-P.); (D.W.P.J.)
| | - Vanessa N. Ataide
- Electronic Languages and Electrochemical Sensors Laboratory, Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil; (V.N.A.); (E.T.C.); (T.R.L.C.P.)
| | - Eric T. Costa
- Electronic Languages and Electrochemical Sensors Laboratory, Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil; (V.N.A.); (E.T.C.); (T.R.L.C.P.)
| | - Larissa R. Gomes
- Oswaldo Cruz Foundation (FIOCRUZ), Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Populations Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (W.A.A.); (L.R.G.); (P.N.-P.); (D.W.P.J.)
| | - Paloma Napoleão-Pêgo
- Oswaldo Cruz Foundation (FIOCRUZ), Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Populations Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (W.A.A.); (L.R.G.); (P.N.-P.); (D.W.P.J.)
| | - David William Provance
- Oswaldo Cruz Foundation (FIOCRUZ), Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Populations Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (W.A.A.); (L.R.G.); (P.N.-P.); (D.W.P.J.)
| | - Thiago R. L. C. Paixão
- Electronic Languages and Electrochemical Sensors Laboratory, Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil; (V.N.A.); (E.T.C.); (T.R.L.C.P.)
- National Institute of Bioanalytical Science and Technology, Campinas 13084-971, Brazil
| | - Maiara O. Salles
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Salvatore Giovanni De-Simone
- Oswaldo Cruz Foundation (FIOCRUZ), Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Populations Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (W.A.A.); (L.R.G.); (P.N.-P.); (D.W.P.J.)
- Cellular and Molecular Department, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil
- Epidemiology and Molecular Systematics Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
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Chen M, Chen L, Wang J, Mou C, Chen Z. Identification of a B-Cell Epitope in the VP3 Protein of Senecavirus A. Viruses 2021; 13:2300. [PMID: 34835106 DOI: 10.3390/v13112300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/03/2022] Open
Abstract
Senecavirus A (SVA) is a member of the genus Senecavirus of the family Picornaviridae. SVA-associated vesicular disease (SAVD) outbreaks have been extensively reported since 2014–2015. Characteristic symptoms include vesicular lesions on the snout and feet as well as lameness in adult pigs and even death in piglets. The capsid protein VP3, a structural protein of SVA, is involved in viral replication and genome packaging. Here, we developed and characterized a mouse monoclonal antibody (mAb) 3E9 against VP3. A motif 192GWFSLHKLTK201 was identified as the linear B-cell epitope recognized by mAb 3E9 by using a panel of GFP-tagged epitope polypeptides. Sequence alignments show that 192GWFSLHKLTK201 was highly conserved in all SVA strains. Subsequently, alanine (A)-scanning mutagenesis indicated that W193, F194, L196, and H197 were the critical residues recognized by mAb 3E9. Further investigation with indirect immunofluorescence assay indicated that the VP3 protein was present in the cytoplasm during SVA replication. In addition, the mAb 3E9 specifically immunoprecipitated the VP3 protein from SVA-infected cells. Taken together, our results indicate that mAb 3E9 could be a powerful tool to work on the function of the VP3 protein during virus infection.
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Zhang W, Wang W, Liu X, Chen Y, Ouyang K, Wei Z, Liu H, Huang W. Identification of novel B-cell epitopes on the capsid protein of type 1 porcine astrovirus, using monoclonal antibodies. Int J Biol Macromol 2021; 189:939-947. [PMID: 34464644 DOI: 10.1016/j.ijbiomac.2021.08.129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Porcine astrovirus (PAstV) is prevalent in pigs worldwide and could cause clinical symptoms such as diarrhea and encephalitis. The capsid protein (Cap) of PAstV plays a determinant role for virus immunological characteristics. In this study, the major antigenic regions of PAstV1 Cap were expressed through prokaryotic expression systems and immunized to BALB/c mice. Finally, two anti-Cap monoclonal antibodies (named mAb F4-4 and D3F10) were screened by indirect immune-fluorescence assay (IFA). A series of truncated GST-fused or artificially synthesized peptides were used to detect their reactivity with the mAbs and PAstV positive serum. Two novel B cell epitopes (120-GNNTFG-125, 485-RISDPTWFSA-494) were identified by using these two mAbs. Moreover, sequence alignment result showed that epitope 120-GNNTFG-125 was highly conserved in type 1 PAstV capsid protein. Cross-reactivity analysis further confirmed the genotype-specificity of mAb F4-4. The results of this study demonstrated to be the first description of monoclonal antibody preparation and B-cell epitope mapping on PAstV capsid protein, which may provide new information on the biological significance of PAstV capsid protein and lay a foundation for the development of PAstV immunological tests and genotype diagnostic methods.
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Affiliation(s)
- Wenchao Zhang
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Weiyi Wang
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Xin Liu
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Ying Chen
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Kang Ouyang
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Zuzhang Wei
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Huan Liu
- Department of Scientific Research, The First Affiliated Hospital of Guangxi University of Chinese Medicine, No. 89-9 Dongge Road, Nanning 530024, China.
| | - Weijian Huang
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China.
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35
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D'haeseleer P, Collette NM, Lao V, Segelke BW, Branda SS, Franco M. Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei. Front Immunol 2021; 12:716676. [PMID: 34659206 PMCID: PMC8513525 DOI: 10.3389/fimmu.2021.716676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Peptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of linear compared to conformational epitopes are their simple structure, ease of synthesis, and ability to stimulate immune responses by means that do not require complex 3D conformation. Prediction of linear epitopes through use of computational tools is fast and cost-effective, but typically of low accuracy, necessitating extensive experimentation to verify results. On the other hand, identification of linear epitopes through experimental screening has been an inefficient process that requires thorough characterization of previously identified full-length protein antigens, or laborious techniques involving genetic manipulation of organisms. In this study, we apply a newly developed generalizable screening method that enables efficient identification of B-cell epitopes in the proteomes of pathogenic bacteria. As a test case, we used this method to identify epitopes in the proteome of Francisella tularensis (Ft), a Select Agent with a well-characterized immunoproteome. Our screen identified many peptides that map to known antigens, including verified and predicted outer membrane proteins and extracellular proteins, validating the utility of this approach. We then used the method to identify seroreactive peptides in the less characterized immunoproteome of Select Agent Burkholderia pseudomallei (Bp). This screen revealed known Bp antigens as well as proteins that have not been previously identified as antigens. Although B-cell epitope prediction tools Bepipred 2.0 and iBCE-EL classified many of our seroreactive peptides as epitopes, they did not score them significantly higher than the non-reactive tryptic peptides in our study, nor did they assign higher scores to seroreactive peptides from known Ft or Bp antigens, highlighting the need for experimental data instead of relying on computational epitope predictions alone. The present workflow is easily adaptable to detecting peptide targets relevant to the immune systems of other mammalian species, including humans (depending upon the availability of convalescent sera from patients), and could aid in accelerating the discovery of B-cell epitopes and development of vaccines to counter emerging biological threats.
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Affiliation(s)
- Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Nicole M Collette
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Victoria Lao
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Brent W Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Steven S Branda
- Molecular and Microbiology Department, Sandia National Laboratories, Livermore, CA, United States
| | - Magdalena Franco
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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Adhikari UK, Tayebi M. Epitope-specific anti-PrP antibody toxicity: a comparative in-silico study of human and mouse prion proteins. Prion 2021; 15:155-176. [PMID: 34632945 PMCID: PMC8900626 DOI: 10.1080/19336896.2021.1964326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Despite having therapeutic potential, anti-PrP antibodies caused a major controversy due to their neurotoxic effects. For instance, treating mice with ICSM antibodies delayed prion disease onset, but both were found to be either toxic or innocuous to neurons by researchers following cross-linking PrPC. In order to elucidate and understand the reasons that led to these contradictory outcomes, we conducted a comprehensive in silico study to assess the antibody-specific toxicity. Since most therapeutic anti-PrP antibodies were generated against human truncated recombinant PrP91-231 or full-length mouse PrP23-231, we reasoned that host specificity (human vs murine) of PrPC might influence the nature of the specific epitopes recognized by these antibodies at the structural level possibly explaining the 'toxicity' discrepancies reported previously. Initially, molecular dynamics simulation and pro-motif analysis of full-length human (hu)PrP and mouse (mo)PrP 3D structure displayed conspicuous structural differences between huPrP and moPrP. We identified 10 huPrP and 6 moPrP linear B-cell epitopes from the prion protein 3D structure where 5 out of 10 huPrP and 3 out of 6 moPrP B-cell epitopes were predicted to be potentially toxic in immunoinformatics approaches. Herein, we demonstrate that some of the predicted potentially 'toxic' epitopes identified by the in silico analysis were similar to the epitopes recognized by the toxic antibodies such as ICSM18 (146-159), POM1 (138-147), D18 (133-157), ICSM35 (91-110), D13 (95-103) and POM3 (95-100). This in silico study reveals the role of host specificity of PrPC in epitope-specific anti-PrP antibody toxicity.
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Affiliation(s)
| | - Mourad Tayebi
- School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
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Nordin ML, Mohamad Norpi AS, Ng PY, Yusoff K, Abu N, Lim KP, Azmi F. HER2/neu-Based Peptide Vaccination-Pulsed with B-Cell Epitope Induced Efficient Prophylactic and Therapeutic Antitumor Activities in TUBO Breast Cancer Mice Model. Cancers (Basel) 2021; 13:4958. [PMID: 34638441 PMCID: PMC8507975 DOI: 10.3390/cancers13194958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Breast cancer is the most common invasive cancer diagnosed among women. A cancer vaccine has been recognized as a form of immunotherapy with a prominent position in the prevention and treatment of breast cancer. The majority of current breast cancer vaccination strategies aim to stimulate antitumor T-cell responses of the HER2/neu oncogene, which is abnormally expressed in breast cancer cells. However, the role of the B-cell humoral response is often underappreciated in the cancer vaccine design. We have advanced this idea by elucidating the role of B-cells in cancer vaccination by designing a chimeric antigenic peptide possessing both cytotoxic T lymphocytes (GP2) and B-cell (P4) peptide epitopes derived from HER2/neu. The chimeric peptide (GP2-P4) was further conjugated to a carrier protein (KLH), forming a KLH-GP2-P4 conjugate. The immunogenicity of KLH-GP2-P4 was compared with KLH-GP2 (lacking the B-cell epitope) in BALB/c mice. Mice immunized with KLH-GP2-P4 elicited more potent antigen-specific neutralizing antibodies against syngeneic TUBO cells (cancer cell line overexpressing HER2/neu) that was governed by a balanced Th1/Th2 polarization in comparison to KLH-GP2. Subsequently, these immune responses led to greater inhibition of tumor growth and longer survival in TUBO tumor-bearing mice in both prophylactic and therapeutic challenge experiments. Overall, our data demonstrated that the B-cell epitope has a profound effect in orchestrating an efficacious antitumor immunity. Thus, a multi-epitope peptide vaccine encompassing cytotoxic T-lymphocytes, T-helper and B-cell epitopes represents a promising strategy in developing cancer vaccines with a preventive and therapeutic modality for the effective management of breast cancer.
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Affiliation(s)
- Muhammad Luqman Nordin
- Centre for Drug Delivery Technology, Faculty of Pharmacy, Universiti Kebangsaan Malaysia (UKM) Kuala Lumpur Campus, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Malaysia; (M.L.N.); (A.S.M.N.)
- Department of Clinical Studies, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan (UMK), Pengkalan Chepa, Kota Bharu 16100, Kelantan, Malaysia
| | - Abdin Shakirin Mohamad Norpi
- Centre for Drug Delivery Technology, Faculty of Pharmacy, Universiti Kebangsaan Malaysia (UKM) Kuala Lumpur Campus, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Malaysia; (M.L.N.); (A.S.M.N.)
- Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, No.3 Jalan Greentown, Ipoh 30450, Perak, Malaysia
| | - Pei Yuen Ng
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia (UKM), Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Malaysia;
| | - Khatijah Yusoff
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia (UPM), Serdang, Seri Kembangan 43400, Selangor, Malaysia;
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Jalan Ya’acob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia;
| | - Kue Peng Lim
- Cancer Immunology & Immunotherapy Unit, Cancer Research Malaysia, No. 1 Jalan SS12/1A, Subang Jaya 47500, Selangor, Malaysia;
| | - Fazren Azmi
- Centre for Drug Delivery Technology, Faculty of Pharmacy, Universiti Kebangsaan Malaysia (UKM) Kuala Lumpur Campus, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Malaysia; (M.L.N.); (A.S.M.N.)
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Fontes SDS, Maia FM, Ataides LS, Conte FP, Lima-Junior JDC, Rozental T, da Silva Assis MR, Júnior AAP, Fernandes J, de Lemos ERS, Rodrigues-da-Silva RN. Identification of Immunogenic Linear B-Cell Epitopes in C. burnetii Outer Membrane Proteins Using Immunoinformatics Approaches Reveals Potential Targets of Persistent Infections. Pathogens 2021; 10:1250. [PMID: 34684199 DOI: 10.3390/pathogens10101250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
Coxiella burnetii is a global, highly infectious intracellular bacterium, able to infect a wide range of hosts and to persist for months in the environment. It is the etiological agent of Q fever—a zoonosis of global priority. Currently, there are no national surveillance data on C. burnetii’s seroprevalence for any South American country, reinforcing the necessity of developing novel and inexpensive serological tools to monitor the prevalence of infections among humans and animals—especially cattle, goats, and sheep. In this study, we used immunoinformatics and computational biology tools to predict specific linear B-cell epitopes in three C. burnetii outer membrane proteins: OMP-H (CBU_0612), Com-1 (CBU_1910), and OMP-P1 (CBU_0311). Furthermore, predicted epitopes were tested by ELISA, as synthetic peptides, against samples of patients reactive to C. burnetii in indirect immunofluorescence assay, in order to evaluate their natural immunogenicity. In this way, two linear B-cell epitopes were identified in each studied protein (OMP-H(51–59), OMP-H(91–106), Com-1(57–76), Com-1(191–206), OMP-P1(197–209), and OMP-P1(215–227)); all of them were confirmed as naturally immunogenic by the presence of specific antibodies in 77% of studied patients against at least one of the identified epitopes. Remarkably, a higher frequency of endocarditis cases was observed among patients who presented an intense humoral response to OMP-H and Com-1 epitopes. These data confirm that immunoinformatics applied to the identification of specific B-cell epitopes can be an effective strategy to improve and accelerate the development of surveillance tools against neglected diseases.
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Noori Goodarzi N, Bolourchi N, Fereshteh S, Badmasti F. Introduction of novel putative immunogenic targets against Proteus mirabilis using a reverse vaccinology approach. Infect Genet Evol 2021; 95:105045. [PMID: 34428568 DOI: 10.1016/j.meegid.2021.105045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/04/2021] [Accepted: 08/18/2021] [Indexed: 11/15/2022]
Abstract
Multi-drug resistance of Proteus mirabilis, a frequent cause of catheter-associated urinary tract infections, renders ineffective treatment. Therefore, new advanced strategies are needed to overcome it. In the meantime, vaccination may be the most effective and promising method. In this study antigenicity, allergenicity, subcellular localization, human homology, B-cell epitopes and MHC-II binding sites, conserved domains and protein-protein interactions were predicted using different reverse vaccinology methods and bioinformatics databases to find new putative immunogenic targets against P. mirabilis. Finally, 5 putative immunogenic targets against P. mirabilis were identified. Considering all criteria, QKQ94350.1 (Cell envelope opacity-associated protein A), QKQ94681.1 (Porin), QKQ95001.1 (TonB-dependent hemoglobin/ transferrin/ lactoferrin family receptor), QKQ95221.1 (AsmA) and QKQ94335.1 (N-acetylmuramoyl-L-alanine amidase) are excellent putative immunogenic targets. Finally, a multi-epitope vaccine was designed using the conserved linear epitopes of two OMPs (QKQ94681.1 and QKQ95001.1) and N-acetylmuramoyl-L-alanine amidase (QKQ94335.1), which have promising properties for immunization. These findings can simplify the development of efficient vaccines against P. mirabilis.
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Affiliation(s)
- Narjes Noori Goodarzi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Negin Bolourchi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Lechuga GC, Napoleão-Pêgo P, Gomes LR, da Matta Durans A, Provance DW, De-Simone SG. Nicastrin-Like, a Novel Transmembrane Protein from Trypanosoma cruzi Associated to the Flagellar Pocket. Microorganisms 2021; 9:microorganisms9081750. [PMID: 34442829 PMCID: PMC8400621 DOI: 10.3390/microorganisms9081750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/26/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022] Open
Abstract
Nicastrin (NICT) is a transmembrane protein physically associated with the polytypical aspartyl protease presenilin that plays a vital role in the correct localization and stabilization of presenilin to the membrane-bound γ-secretase complex. This complex is involved in the regulation of a wide range of cellular events, including cell signaling and the regulation of endocytosed membrane proteins for their trafficking and protein processing. Methods: In Trypanosoma cruzi, the causal agent of the Chagas disease, a NICT-like protein (Tc/NICT) was identified with a short C-terminus orthologous to the human protein, a large ectodomain (ECD) with numerous glycosylation sites and a single-core transmembrane domain containing a putative TM-domain (457GSVGA461) important for the γ-secretase complex activity. Results: Using the Spot-synthesis strategy with Chagasic patient sera, five extracellular epitopes were identified and synthetic forms were used to generate rabbit anti-Tc/NICT polyclonal serum that recognized a ~72-kDa molecule in immunoblots of T. cruzi epimastigote extracts. Confocal microscopy suggests that Tc/NICT is localized in the flagellar pocket, which is consistent with data from our previous studies with a T. cruzi presenilin-like protein. Phylogenetically, Tc/NICT was localized within a subgroup with the T. rangeli protein that is clearly detached from the other Trypanosomatidae, such as T. brucei. These results, together with a comparative analysis of the selected peptide sequence regions between the T. cruzi and mammalian proteins, suggest a divergence from the human NICT that might be relevant to Chagas disease pathology. As a whole, our data show that a NICT-like protein is expressed in the infective and replicative stages of T. cruzi and may be considered further evidence for a γ-secretase complex in trypanosomatids.
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Affiliation(s)
- Guilherme Curty Lechuga
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Populations (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (A.d.M.D.); (D.W.P.J.)
| | - Paloma Napoleão-Pêgo
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Populations (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (A.d.M.D.); (D.W.P.J.)
| | - Larissa Rodrigues Gomes
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Populations (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (A.d.M.D.); (D.W.P.J.)
| | - Andressa da Matta Durans
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Populations (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (A.d.M.D.); (D.W.P.J.)
| | - David William Provance
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Populations (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (A.d.M.D.); (D.W.P.J.)
- FIOCRUZ, Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, Brazil
| | - Salvatore Giovanni De-Simone
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Populations (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (A.d.M.D.); (D.W.P.J.)
- Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil
- Correspondence: ; Fax: +55-21-2590-3495
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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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Tung CH, Chang YS, Chang KP, Chu YW. NIgPred: Class-Specific Antibody Prediction for Linear B-Cell Epitopes Based on Heterogeneous Features and Machine-Learning Approaches. Viruses 2021; 13:1531. [PMID: 34452396 DOI: 10.3390/v13081531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Upon invasion by foreign pathogens, specific antibodies can identify specific foreign antigens and disable them. As a result of this ability, antibodies can help with vaccine production and food allergen detection in patients. Many studies have focused on predicting linear B-cell epitopes, but only two prediction tools are currently available to predict the sub-type of an epitope. NIgPred was developed as a prediction tool for IgA, IgE, and IgG. NIgPred integrates various heterologous features with machine-learning approaches. Differently from previous studies, our study considered peptide-characteristic correlation and autocorrelation features. Sixty kinds of classifier were applied to construct the best prediction model. Furthermore, the genetic algorithm and hill-climbing algorithm were used to select the most suitable features for improving the accuracy and reducing the time complexity of the training model. NIgPred was found to be superior to the currently available tools for predicting IgE epitopes and IgG epitopes on independent test sets. Moreover, NIgPred achieved a prediction accuracy of 100% for the IgG epitopes of a coronavirus data set. NIgPred is publicly available at our website.
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Xu LL, Gasset M, Lin H, Yu C, Zhao JL, Dang XW, Li ZX. Identification of the Dominant T-Cell Epitopes of Lit v 1 Shrimp Major Allergen and Their Functional Overlap with Known B-Cell Epitopes. J Agric Food Chem 2021; 69:7420-7428. [PMID: 34170668 DOI: 10.1021/acs.jafc.1c02231] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Development of efficient peptide-based immunotherapy for shrimp allergy relies on the identification of the dominant T-cell epitopes of its major allergen, tropomyosin. In this study, immunoinformatic tools, T-cell proliferation, cytokine release, IgG/IgE binding, and degranulation assays were used to identify and characterize the T-cell epitopes in Lit v 1 in comparison with previously validated B-cell epitopes. The results showed that of the six in silico predicted T-cell epitopes only one (T2: VQESLLKANIQLVEK, 60-74) promoted T-cell proliferation, the release of IL-2, and upregulated secretion of Th2-associated cytokines in the absence of IgG/IgE binding and degranulation activities. These findings support T2 as a candidate for the development of an efficient peptide-based vaccine for the immunotherapy for shrimp-allergic patients.
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Affiliation(s)
- Li Li Xu
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
| | - María Gasset
- Institute of Physical Chemistry Rocasolano (IQFR), Spanish National Research Council (CSIC), 28006 Madrid, Spain
| | - Hong Lin
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
| | - Chuang Yu
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
| | - Jin Long Zhao
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
| | - Xue Wen Dang
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
| | - Zhen Xing Li
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
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Cohen S, Chung S, Spiess C, Lundin V, Stefanich E, Laing ST, Clark V, Brumm J, Zhou Y, Huang C, Guerrero J, Myneni S, Yadav R, Siradze K, Peng K. An integrated approach for characterizing immunogenic responses toward a bispecific antibody. MAbs 2021; 13:1944017. [PMID: 34225571 PMCID: PMC8265794 DOI: 10.1080/19420862.2021.1944017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bispecific antibodies (bsAbs) recognize and bind two different targets or two epitopes of the same antigen, making them an attractive diagnostic and treatment modality. Compared to the production of conventional bivalent monospecific antibodies, bsAbs require greater engineering and manufacturing. Therefore, bsAbs are more likely to differ from endogenous immunoglobulins and contain new epitopes that can increase immunogenic risk. Anti-A/B is a bsAb designed using a ‘knobs-into-holes’ (KIH) format. Anti-A/B exhibited an unexpectedly high immunogenicity in both preclinical and clinical studies, resulting in early termination of clinical development. Here, we used an integrated approach that combined in silico analysis, in vitro assays, and an in vivo study in non-human primates to characterize anti-A/B immunogenicity. Our findings indicated that the immunogenicity is associated with epitopes in the anti-B arm and not with mutations engineered through the KIH process. Our results showed the value of this integrated approach for performing immunogenicity risk assessment during clinical candidate selection to effectively mitigate risks during bsAb development.
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Affiliation(s)
- Sivan Cohen
- Department of BioAnalytical Sciences, Genentech Inc, South San Francisco, CA, USA
| | - Shan Chung
- Department of BioAnalytical Sciences, Genentech Inc, South San Francisco, CA, USA
| | - Christoph Spiess
- Department of Antibody Engineering, Genentech Inc, South San Francisco, CA, USA
| | - Victor Lundin
- Department of Protein Analytical Chemistry, Genentech Inc, South San Francisco, CA, USA
| | | | - Steven T Laing
- Department of Safety Assessment, Genentech Inc, South San Francisco, CA, USA
| | - Vanessa Clark
- Department of Safety Assessment, Genentech Inc, South San Francisco, CA, USA
| | - Jochen Brumm
- Department of Biostatistics, Genentech Inc, South San Francisco, CA, USA
| | - Ying Zhou
- Department of BioAnalytical Sciences, Genentech Inc, South San Francisco, CA, USA
| | - Catherine Huang
- Department of BioAnalytical Sciences, Genentech Inc, South San Francisco, CA, USA
| | - Joyce Guerrero
- Department of BioAnalytical Sciences, Genentech Inc, South San Francisco, CA, USA
| | - Srividya Myneni
- Department of BioAnalytical Sciences, Genentech Inc, South San Francisco, CA, USA
| | | | - Ketevan Siradze
- Department of BioAnalytical Sciences, Genentech Inc, South San Francisco, CA, USA
| | - Kun Peng
- Department of BioAnalytical Sciences, Genentech Inc, South San Francisco, CA, USA
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Guo JY, Liu IJ, Lin HT, Wang MJ, Chang YL, Lin SC, Liao MY, Hsu WC, Lin YL, Liao JC, Wu HC. Identification of COVID-19 B-cell epitopes with phage-displayed peptide library. J Biomed Sci 2021; 28:43. [PMID: 34098950 PMCID: PMC8182997 DOI: 10.1186/s12929-021-00740-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/03/2021] [Indexed: 12/23/2022] Open
Abstract
Background Coronavirus disease 19 (COVID-19) first appeared in the city of Wuhan, in the Hubei province of China. Since its emergence, the COVID-19-causing virus, SARS-CoV-2, has been rapidly transmitted around the globe, overwhelming the medical care systems in many countries and leading to more than 3.3 million deaths. Identification of immunological epitopes on the virus would be highly useful for the development of diagnostic tools and vaccines that will be critical to limiting further spread of COVID-19. Methods To find disease-specific B-cell epitopes that correspond to or mimic natural epitopes, we used phage display technology to determine the targets of specific antibodies present in the sera of immune-responsive COVID-19 patients. Enzyme-linked immunosorbent assays were further applied to assess competitive antibody binding and serological detection. VaxiJen, BepiPred-2.0 and DiscoTope 2.0 were utilized for B-cell epitope prediction. PyMOL was used for protein structural analysis. Results 36 enriched peptides were identified by biopanning with antibodies from two COVID-19 patients; the peptides 4 motifs with consensus residues corresponding to two potential B-cell epitopes on SARS-CoV-2 viral proteins. The putative epitopes and hit peptides were then synthesized for validation by competitive antibody binding and serological detection. Conclusions The identified B-cell epitopes on SARS-CoV-2 may aid investigations into COVID-19 pathogenesis and facilitate the development of epitope-based serological diagnostics and vaccines.
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Affiliation(s)
- Jing-You Guo
- Institute of Biologic Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nangang, Taipei, 11529, Taiwan
| | - I-Ju Liu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nangang, Taipei, 11529, Taiwan
| | - Hsiu-Ting Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nangang, Taipei, 11529, Taiwan
| | - Mei-Jung Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nangang, Taipei, 11529, Taiwan
| | - Yu-Ling Chang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nangang, Taipei, 11529, Taiwan
| | - Shin-Chang Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nangang, Taipei, 11529, Taiwan
| | - Mei-Ying Liao
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nangang, Taipei, 11529, Taiwan
| | - Wei-Chia Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nangang, Taipei, 11529, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - James C Liao
- Institute of Biologic Chemistry, Academia Sinica, Taipei, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nangang, Taipei, 11529, Taiwan.
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Hao Q, Liu HX, Hou XX, Zhang L, Yang XN, Wan KL. Polymorphism of P66 in Borrelia Burgdorferi Strains in China. Biomed Environ Sci 2021; 34:364-371. [PMID: 34059173 DOI: 10.3967/bes2021.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
OBJECTIVE To study the polymorphism in P66 and its human B-cell epitopes of Borrelia burgdorferi strains in China. METHODS Polymerase chain reaction (PCR) and sequencing were used to obtain the P66 sequences of 59 Chinese B. burgdorferi. Then the sequences were analyzed by MEGA 5.10 software and compared with the human B-cell epitope sequences from the Immune Epitope Database (IEDB) based on the reference strain of each genotype. RESULTS Results showed that genetic and amino acid diversity presented in the 66 kD protein of all 59 Chinese strains, especially in Borrelia garinii ( B.g) and Borrelia afzelii ( B.a) strains. B.g strains were divided into three subclusters and two scattered strains JC1-7 and JC2-2 according to the amino acid sequences of P66. The P66 sequences of 15 Xinjiang strains represented by XI91-12 in the B.g subcluster 1, changed from CAA to TAA codon at 508aa position, resulting in early termination. Bases A and C were inserted at sequence position 1 523 bp of strains FP1, LB20, LB21, and SZ21 in the B.a genotype, which resulted to early termination at position 511 aa. G base was inserted at 438 bp of LIP94-11 strain, which led to early termination at position 172 aa. CONCLUSION In P66 of 59 Chinese strains, polymorphisms were widely distributed. More importantly, the P66 amino acid sequences of B.g strains had a certain regional character. One of the characteristics of Xinjiang B.g isolates might be the variation at the 508aa location in 15 Xinjiang B.g strains, which may be related to the strains' pathogenicity in this area.
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Affiliation(s)
- Qin Hao
- State Key Laboratory of Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hui Xin Liu
- The people's hospital of Liaocheng, Liaocheng 252400, Shandong, China
| | - Xue Xia Hou
- State Key Laboratory of Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lin Zhang
- State Key Laboratory of Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiao Na Yang
- State Key Laboratory of Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Kang Lin Wan
- State Key Laboratory of Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Rangel G, Bárcena J, Moreno N, Mata CP, Castón JR, Alejo A, Blanco E. Chimeric RHDV Virus-Like Particles Displaying Foot-and-Mouth Disease Virus Epitopes Elicit Neutralizing Antibodies and Confer Partial Protection in Pigs. Vaccines (Basel) 2021; 9:vaccines9050470. [PMID: 34066934 PMCID: PMC8148555 DOI: 10.3390/vaccines9050470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 12/29/2022] Open
Abstract
Currently there is a clear trend towards the establishment of virus-like particles (VLPs) as a powerful tool for vaccine development. VLPs are tunable nanoparticles that can be engineered to be used as platforms for multimeric display of foreign antigens. We have previously reported that VLPs derived from rabbit hemorrhagic disease virus (RHDV) constitute an excellent vaccine vector, capable of inducing specific protective immune responses against inserted heterologous T-cytotoxic and B-cell epitopes. Here, we evaluate the ability of chimeric RHDV VLPs to elicit immune response and protection against Foot-and-Mouth disease virus (FMDV), one of the most devastating livestock diseases. For this purpose, we generated a set of chimeric VLPs containing two FMDV-derived epitopes: a neutralizing B-cell epitope (VP1 (140-158)) and a T-cell epitope [3A (21-35)]. The epitopes were inserted joined or individually at two different locations within the RHDV capsid protein. The immunogenicity and protection potential of the chimeric VLPs were analyzed in the mouse and pig models. Herein we show that the RHDV engineered VLPs displaying FMDV-derived epitopes elicit a robust neutralizing immune response in mice and pigs, affording partial clinical protection against an FMDV challenge in pigs.
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Affiliation(s)
- Giselle Rangel
- Centro de Investigación en Sanidad Animal (CISA, CSIC-INIA), Valdeolmos, 28130 Madrid, Spain; (G.R.); (J.B.); (N.M.); (A.A.)
| | - Juan Bárcena
- Centro de Investigación en Sanidad Animal (CISA, CSIC-INIA), Valdeolmos, 28130 Madrid, Spain; (G.R.); (J.B.); (N.M.); (A.A.)
| | - Noelia Moreno
- Centro de Investigación en Sanidad Animal (CISA, CSIC-INIA), Valdeolmos, 28130 Madrid, Spain; (G.R.); (J.B.); (N.M.); (A.A.)
| | - Carlos P. Mata
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Cantoblanco, 28049 Madrid, Spain; (C.P.M.); (J.R.C.)
| | - José R. Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Cantoblanco, 28049 Madrid, Spain; (C.P.M.); (J.R.C.)
| | - Alí Alejo
- Centro de Investigación en Sanidad Animal (CISA, CSIC-INIA), Valdeolmos, 28130 Madrid, Spain; (G.R.); (J.B.); (N.M.); (A.A.)
| | - Esther Blanco
- Centro de Investigación en Sanidad Animal (CISA, CSIC-INIA), Valdeolmos, 28130 Madrid, Spain; (G.R.); (J.B.); (N.M.); (A.A.)
- Correspondence: ; Tel.: +34-916-202-300
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48
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Galanis KA, Nastou KC, Papandreou NC, Petichakis GN, Pigis DG, Iconomidou VA. Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface. Int J Mol Sci 2021; 22:3210. [PMID: 33809918 PMCID: PMC8004178 DOI: 10.3390/ijms22063210] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/15/2021] [Accepted: 03/19/2021] [Indexed: 12/17/2022] Open
Abstract
Linear B-cell epitope prediction research has received a steadily growing interest ever since the first method was developed in 1981. B-cell epitope identification with the help of an accurate prediction method can lead to an overall faster and cheaper vaccine design process, a crucial necessity in the COVID-19 era. Consequently, several B-cell epitope prediction methods have been developed over the past few decades, but without significant success. In this study, we review the current performance and methodology of some of the most widely used linear B-cell epitope predictors which are available via a command-line interface, namely, BcePred, BepiPred, ABCpred, COBEpro, SVMTriP, LBtope, and LBEEP. Additionally, we attempted to remedy performance issues of the individual methods by developing a consensus classifier, which combines the separate predictions of these methods into a single output, accelerating the epitope-based vaccine design. While the method comparison was performed with some necessary caveats and individual methods might perform much better for specialized datasets, we hope that this update in performance can aid researchers towards the choice of a predictor, for the development of biomedical applications such as designed vaccines, diagnostic kits, immunotherapeutics, immunodiagnostic tests, antibody production, and disease diagnosis and therapy.
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Affiliation(s)
| | | | | | | | | | - Vassiliki A. Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece; (K.A.G.); (K.C.N.); (N.C.P.); (G.N.P.); (D.G.P.)
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49
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Thite A, Agrawal M, Pavitrakar D, Cherian S, Damle R. Delineation of an epitope recognized by a chikungunya virus anti-capsid monoclonal antibody on the protease domain using an immuno-informatics approach. J Biomol Struct Dyn 2021; 40:5623-5633. [PMID: 33480314 DOI: 10.1080/07391102.2021.1872416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The capsid-protein (CP) of chikungunya virus (CHIKV) is reported to generate a primary immune response in infected individuals during disease progression. CP-specific monoclonal antibodies (mAbs) developed in our laboratory, exhibited promising potential in diagnosing recent CHIKV infection in IgM capture ELISA. In this study we focused on the molecular and structural characterization of one such representative mAb ClVE4/D9 to delineate the epitope recognized by it using an immuno-informatics approach. The antigen-antibody interacting residues were found to lie within the dimer interface region of the CP, also predicted as a conformational epitope. This implies that the mAb could interfere during the process of nucleocapsid assembly, ultimately preventing budding and egress of the virus particle. The binding specificity of the mAb highlights the possibility of using this anti-CP antibody for therapeutic or prophylactic treatment against CHIKV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aabha Thite
- NIBEC, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Dhankawadi, Pune, Maharashtra, India.,Department of Bioinformatics & Data Management, National Institute of Virology, Pune, India
| | - Megha Agrawal
- Department of Bioinformatics & Data Management, National Institute of Virology, Pune, India
| | - Daya Pavitrakar
- NIBEC, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Dhankawadi, Pune, Maharashtra, India
| | - Sarah Cherian
- Department of Bioinformatics & Data Management, National Institute of Virology, Pune, India
| | - Rekha Damle
- NIBEC, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Dhankawadi, Pune, Maharashtra, India
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50
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Ghaderi S, Bozorgmehr MR, Ahmadi M, Tarahomjoo S. Identification of Conformational B-cell Epitopes in Diphtheria Toxin at Varying Temperatures Using Molecular Dynamics Simulations. Arch Razi Inst 2021; 75:427-437. [PMID: 33403838 PMCID: PMC8410147 DOI: 10.22092/ari.2019.127251.1377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/15/2019] [Indexed: 09/30/2022]
Abstract
The changes in temperature levels can potentially affect the toxins in terms of stability and immunological properties via alteration of their structures. Diphtheria Toxin (DT) is highly considered by scientists since its mechanism of action is similar to those of most bacterial toxins, such as botulinum, tetanus, and anthrax. The protection of conformational B-cell epitopes is critically important in the process of diphtheria vaccine production. This study aimed to evaluate the conformational changes of the DT structure at three different temperature levels (27˚C, 37˚C, and 47˚C) using molecular dynamic simulations. Secondary structures were analyzed in YASARA software. According to the results, significant decreases were observed in percentages of the β-sheets, turns, and the helices of the DT structure at 47˚C in comparison with those at 27˚C and 37˚C. Furthermore, the tertiary structure of the DT was compared at different temperatures using the contact map. Accordingly, the results showed that the root-mean-square deviation of the DT structure increased upon temperature rising. In addition, amino acids D68, G128, G171, C186, and K534-S535 at 27˚C and 37˚C, as well as amino acids G26, P38, S291, T267, H384, A356, and V518 at 47˚C showed higher root mean square fluctuation values. The finding demonstrated that the stability of the DT structure decreased at high temperature (47˚C). The solvent-accessible surface area diagram showed that the hydrophobicity of the DT structure increased via temperature rising, and the amino acid residues belonging to B-cell epitopes extended through increasing temperature. However, B-cell epitopes belonging to the junction region of chains A and B were only present at 37˚C. The results of this study are expected to be applicable for determining a suitable temperature level for the production process of the diphtheria vaccine.
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Affiliation(s)
- S Ghaderi
- Division of Central Laboratory, Department of Biotechnology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - M R Bozorgmehr
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - M Ahmadi
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Sh Tarahomjoo
- Division of Genomics and Genetic Engineering, Department of Biotechnology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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