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Anandhan G, Narkhede YB, Mohan M, Paramasivam P. Immunoinformatics aided approach for predicting potent cytotoxic T cell epitopes of respiratory syncytial virus. J Biomol Struct Dyn 2023; 41:12093-12105. [PMID: 36935101 DOI: 10.1080/07391102.2023.2191136] [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: 10/18/2022] [Accepted: 12/27/2022] [Indexed: 03/21/2023]
Abstract
Respiratory syncytial virus (RSV) is an infectious viral pathogen that causing serious respiratory infection in adults and neonates. The only approved therapies for RSV are the monoclonal antibodies palivizumab and its derivative motavizumab. Both treatments are expensive and require a hospital setting for administration. A vaccine represents a safe, effective and cheaper alternative for preventing RSV infection. In silico prediction methods have proven to be valuable in speeding up the process of vaccine design. In this study, reverse vaccinology methods were used to predict the cytotoxic T lymphocytes (CTL) epitopes from the entire proteome of RSV strain A. From amongst 3402 predicted binders to 12 high frequency alleles from the Immune Epitope Database (IEDB), 567 had positive processing scores while 327 epitopes were predicted to be immunogenic. A thorough examination of the 327 epitopes for possible antigenicity, allergenicity and toxicity resulted in 95 epitopes with desirable properties. A BLASTp analysis revealed 94 unique and non-homologous epitopes that were subjected to molecular docking across the 12 high frequency alleles. The final dataset of 70 epitopes contained 13 experimentally proven and 57 unique epitopes from a total of 11 RSV proteins. From our findings on selected T-cell-specific RSV antigen epitopes, notably the four epitopes confirmed to exhibit stable binding by molecular dynamics. The prediction pipeline used in this study represents an effective way to screen the immunogenic epitopes from other pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gayathri Anandhan
- Department of Nanoscience and Technology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | | | - Manikandan Mohan
- College of Pharmacy, University of Georgia, Athens, USA
- Vaxigen International Research Center, Coimbatore, Tamil Nadu, India
| | - Premasudha Paramasivam
- Department of Nanoscience and Technology, Bharathiar University, Coimbatore, Tamil Nadu, India
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102
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Wang Y, Wang B, Zhao Z, Xu J, Zhang Z, Zhang J, Chen Y, Song X, Zheng W, Hou L, Wu S, Chen W. Effects of SARS-CoV-2 Omicron BA.1 Spike Mutations on T-Cell Epitopes in Mice. Viruses 2023; 15:763. [PMID: 36992472 PMCID: PMC10056712 DOI: 10.3390/v15030763] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 02/15/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
T-cell immunity plays an important role in the control of SARS-CoV-2 and has a great cross-protective effect on the variants. The Omicron BA.1 variant contains more than 30 mutations in the spike and severely evades humoral immunity. To understand how Omicron BA.1 spike mutations affect cellular immunity, the T-cell epitopes of SARS-CoV-2 wild-type and Omicron BA.1 spike in BALB/c (H-2d) and C57BL/6 mice (H-2b) were mapped through IFNγ ELISpot and intracellular cytokine staining assays. The epitopes were identified and verified in splenocytes from mice vaccinated with the adenovirus type 5 vector encoding the homologous spike, and the positive peptides involved in spike mutations were tested against wide-type and Omicron BA.1 vaccines. A total of eleven T-cell epitopes of wild-type and Omicron BA.1 spike were identified in BALB/c mice, and nine were identified in C57BL/6 mice, only two of which were CD4+ T-cell epitopes and most of which were CD8+ T-cell epitopes. The A67V and Del 69-70 mutations in Omicron BA.1 spike abolished one epitope in wild-type spike, and the T478K, E484A, Q493R, G496S and H655Y mutations resulted in three new epitopes in Omicron BA.1 spike, while the Y505H mutation did not affect the epitope. These data describe the difference of T-cell epitopes in SARS-CoV-2 wild-type and Omicron BA.1 spike in H-2b and H-2d mice, providing a better understanding of the effects of Omicron BA.1 spike mutations on cellular immunity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Shipo Wu
- Correspondence: (S.W.); (W.C.); Tel.: +86-10-66948692 (S.W.)
| | - Wei Chen
- Correspondence: (S.W.); (W.C.); Tel.: +86-10-66948692 (S.W.)
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103
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Zhu W, Zhou B, Chen L, Zhao J, Rao H. Combinations but Not a Single PlpE Epitope Induces Host Protective Immunity against Pasteurella multocida. Infect Immun 2023; 91:e0027222. [PMID: 36815793 PMCID: PMC10016081 DOI: 10.1128/iai.00272-22] [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: 07/07/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Pasteurella multocida is the causative agent of a wide range of diseases (pasteurellosis) and a zoonotic pathogen in humans. Recombinant subunit vaccines are hot spots in recent pasteurellosis vaccine development. A chimeric vaccine is also constructed for rabbit hemorrhagic disease virus (RHDV) protective antigen VP60 chimeric with fragments of Pasteurella multocida protective antigen PlpE. The protective efficacy of the chimeric vaccine against P. multocida is not as high as that of PlpE, and the reason is not well known. In this study, we analyzed the linear B-cell epitopes of PlpE and then assessed the protective efficacy of these epitopes and their combinations. It was found that the immunodominant region of PlpE was mainly located in the region between the 21st to the 185th amino acids from the N terminus. Overlapping peptide scanning results demonstrated that this region contained six nonoverlapping epitopes, and epitope E was the predominant epitope. Chimeric protein antigens were constructed of single nonoverlapping PlpE epitopes or their combinations chimeric with the RHDV VP60 P domain. Immunization with recombinant antigen chimeric with a single PlpE epitope exhibited poor immunoprotection, whereas immunization with recombinant antigen chimeric with PlpE epitope combinations (epitopes A and E; epitopes C and E; epitopes A, C, and E; and epitopes B, D, and F) exhibited significant immunoprotection. In a word, P. multocida protective antigen PlpE contained six nonoverlapping linear B-cell epitopes, and combinations but not a single epitope induced host protective immunity. Our work will give help for future chimeric vaccine design.
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Affiliation(s)
- Weifeng Zhu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Banghui Zhou
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Lu Chen
- College of Animal Science, Tibetan Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Juan Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Huaqin Rao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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104
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Abstract
Background IL-23 is central to the pathogenesis of psoriasis, and is structurally comprised of p19 and p40 subunits. "Targeted" IL-23 inhibitors risankizumab, tildrakizumab, and guselkumab differ mechanistically from ustekinumab because they bind p19, whereas ustekinumab binds p40; however, a knowledge gap exists regarding the structural composition of their epitopes and how these molecular properties relate to their clinical efficacy. Objectives To characterize and differentiate the structural epitopes of the IL-23 inhibitors risankizumab, guselkumab, tildrakinumab, and ustekinumab, and correlate their molecular characteristics with clinical response in plaque psoriasis therapy. Methods We utilized epitope data derived from hydrogen-deuterium exchange studies for risankizumab, tildrakizumab, and guselkumab, and crystallographic data for ustekinumab to map drug epitope locations, hydrophobicity, and surface charge onto the IL-23 molecular surface (Protein Data Bank ID Code 3D87) using UCSF Chimera. PDBePISA was used to calculate solvent accessible surface area (SASA). Epitope composition was determined by classifying residues as acidic, basic, polar, or hydrophobic and calculating their contribution to epitope SASA. Linear regression and analysis of variance was performed. Results All the p19-specific inhibitor epitopes differ in location and size, with risankizumab and guselkumab having large epitope surface areas (SA), and tildrakizumab and ustekinumab having smaller SA. The tildrakizumab epitope was mostly hydrophobic (56%), while guselkumab, risankizumab, and ustekinumab epitopes displayed >50% non-hydrophobic residues. Risankizumab and ustekinumab exhibited acidic surface charges, while tildrakizumab and guselkumab were net neutral. Each inhibitor binds an epitope with a unique size and composition, and with mostly distinct locations except for a 10-residue overlap region that lies outside of the IL-23 receptor epitope. We observed a strong correlation between epitope SA and PASI-90 rates (R2 = 0.9969, p = 0.0016), as well as between epitope SA and KD (R2 = 0.9772, p = 0.0115). In contrast, we found that total epitope hydrophobicity, polarity, and charge content do not correlate with clinical efficacy. Conclusions Structural analysis of IL-23 inhibitor epitopes reveals strong association between epitope SA and early drug efficacy in plaque psoriasis therapy, exemplifying how molecular data can explain clinical observations, inform future innovation, and help clinicians in specific drug selection for patients.
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Affiliation(s)
- Stefano G. Daniele
- Medical Scientist Training Program (MD/PhD), Yale School of Medicine, New Haven, CT 06511, USA
| | - Sherif A. Eldirany
- Department of Dermatology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Minh Ho
- Department of Dermatology and Program in Translational Biomedicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Christopher G. Bunick
- Department of Dermatology and Program in Translational Biomedicine, Yale School of Medicine, New Haven, CT 06520, USA
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105
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Emmert V, Lendvai-Emmert D, Eklics K, Prémusz V, Tóth GP. Current Practice in Pediatric Cow's Milk Protein Allergy-Immunological Features and Beyond. Int J Mol Sci 2023; 24:ijms24055025. [PMID: 36902457 PMCID: PMC10003246 DOI: 10.3390/ijms24055025] [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: 01/31/2023] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023] Open
Abstract
Cow's milk protein allergy is one of the most common pediatric food allergies. It poses a significant socioeconomic burden in industrialized countries and has a profound effect on the quality of life of affected individuals and their families. Diverse immunologic pathways can lead to the clinical symptoms of cow's milk protein allergy; some of the pathomechanisms are known in detail, but others need further elucidation. A comprehensive understanding of the development of food allergies and the features of oral tolerance could have the potential to unlock more precise diagnostic tools and novel therapeutic approaches for patients with cow's milk protein allergy.
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Affiliation(s)
- Vanessza Emmert
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, 7621 Pécs, Hungary
- Erzsébet Teaching Hospital and Rehabilitation Institute, 9400 Sopron, Hungary
- Correspondence:
| | - Dominika Lendvai-Emmert
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, 7621 Pécs, Hungary
- Department of Neurosurgery, Medical School, University of Pécs, 7623 Pécs, Hungary
- Neurotrauma Research Group, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary
| | - Kata Eklics
- Department of Languages for Biomedical Purposes, Medical School, University of Pécs, 7624 Pécs, Hungary
| | - Viktória Prémusz
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, 7621 Pécs, Hungary
- Institute of Physiotherapy and Sport Sciences, Faculty of Health Sciences, University of Pécs, 7621 Pécs, Hungary
| | - Gergely Péter Tóth
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, 7621 Pécs, Hungary
- Erzsébet Teaching Hospital and Rehabilitation Institute, 9400 Sopron, Hungary
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106
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Zhang XD, Lin CX, Cui Z, Gu QH, Yan BJ, Liu L, Song WC, Shi Y, Debiec H, Ronco P, Zhao MH. Mapping the T cell epitopes of the M-type transmembrane phospholipase A2 receptor in primary membranous nephropathy. Kidney Int 2023; 103:580-592. [PMID: 36549363 DOI: 10.1016/j.kint.2022.11.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 12/12/2021] [Revised: 10/09/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022]
Abstract
The M-type phospholipase A2 receptor (PLA2R) is the major autoantigen of primary membranous nephropathy (MN). Despite many studies on B-cell epitopes recognized by antibodies, little is known about T-cell epitopes. Herein, we synthesized 123 linear peptides, each consisting of 15-22 amino acids with 8-12 amino acid overlaps, across ten domains of PLA2R. Their binding capacity to risk (DRB1∗1501, DRB1∗0301) and protective (DRB1∗0901, DRB1∗0701) HLA molecules was then assessed by flow cytometry. Proliferation of CD4+ T cells from patients with anti-PLA2R positive MN was analyzed after peptide stimulation. Cytokines produced by activated peripheral blood mononuclear cells were measured by cytometric bead arrays. We identified 17 PLA2R peptides that bound to both DRB1∗1501 and DRB1∗0301 molecules with high capacity. Some of these peptides showed decreased binding to heterozygous DRB1∗1501/0901 and DRB1∗0301/0701. Ten of the 17 peptides (CysR1, CysR10, CysR12, FnII-3, CTLD3-9, CTLD3-10, CTLD3-11, CTLD5-2-1, CTLD7-1 and CTLD7-2) induced significant proliferation of CD4+ T cells from patients with MN than cells from healthy individuals. Upon activation by these peptides, peripheral blood mononuclear cells from patients with MN produced higher levels of pro-inflammatory cytokines, predominantly IL-6, TNF-α, IL-10, IL-9 and IL-17. Thus, we mapped and identified ten peptides in the CysR, FnII, CTLD3, CTLD5, and CTLD7 domains of PLA2R as potential T-cell epitopes of MN. These findings are a first step towards developing peptide-specific immunotherapies.
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Affiliation(s)
- Xiao-Dan Zhang
- Renal Division, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing, China
| | - Cai-Xia Lin
- Renal Division, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing, China
| | - Zhao Cui
- Renal Division, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing, China.
| | - Qiu-Hua Gu
- Renal Division, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing, China; Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Bing-Jia Yan
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, China
| | - Lei Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Wen-Chao Song
- Department of Pharmacology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Yi Shi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hanna Debiec
- Sorbonne Université, Paris, France; Institut National de la Santé et de la Recherche Médicale (Inserm), Unité Mixte de Recherche S1155, Paris, France
| | - Pierre Ronco
- Sorbonne Université, Paris, France; Institut National de la Santé et de la Recherche Médicale (Inserm), Unité Mixte de Recherche S1155, Paris, France; Department of Nephrology, Centre Hospitalier du Mans, Le Mans, France
| | - Ming-Hui Zhao
- Renal Division, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing, China; Peking-Tsinghua Center for Life Sciences, Beijing, China
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107
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Tse Sum Bui B, Mier A, Haupt K. Molecularly Imprinted Polymers as Synthetic Antibodies for Protein Recognition: The Next Generation. Small 2023; 19:e2206453. [PMID: 36650929 DOI: 10.1002/smll.202206453] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Molecularly imprinted polymers (MIPs) are chemical antibody mimics obtained by nanomoulding the 3D shape and chemical functionalities of a desired target in a synthetic polymer. Consequently, they possess exquisite molecular recognition cavities for binding the target molecule, often with specificity and affinity similar to those of antigen-antibody interactions. Research on MIPs targeting proteins began in the mid-90s, and this review will evaluate the progress made till now, starting from their synthesis in a monolith bulk format through surface imprinting to biocompatible soluble nanogels prepared by solid-phase synthesis. MIPs in the latter format will be discussed more in detail because of their tremendous potential of replacing antibodies in the biomedical domain like in diagnostics and therapeutics, where the workforce of antibodies is concentrated. Emphasis is also put on the development of epitope imprinting, which consists of imprinting a short surface-exposed fragment of a protein, resulting in MIPs capable of selectively recognizing the whole macromolecule, amidst others in complex biological media, on cells or tissues. Thus selecting the 'best' peptide antigen is crucial and in this context a rational approach, inspired from that used to predict peptide immunogens for peptide antibodies, is described for its unambiguous identification.
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Affiliation(s)
- Bernadette Tse Sum Bui
- Université de Technologie de Compiègne, CNRS Laboratory for Enzyme and Cell Engineering, Rue du Docteur Schweitzer, CS 60319, Compiègne, 60203 Cedex, France
| | - Alejandra Mier
- Université de Technologie de Compiègne, CNRS Laboratory for Enzyme and Cell Engineering, Rue du Docteur Schweitzer, CS 60319, Compiègne, 60203 Cedex, France
| | - Karsten Haupt
- Université de Technologie de Compiègne, CNRS Laboratory for Enzyme and Cell Engineering, Rue du Docteur Schweitzer, CS 60319, Compiègne, 60203 Cedex, France
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108
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Abdulhameed Odhar H, Hashim AF, Humadi SS, Ahjel SW. Design and construction of multi epitope- peptide vaccine candidate for rabies virus. Bioinformation 2023; 19:167-177. [PMID: 37814687 PMCID: PMC10560302 DOI: 10.6026/97320630019167] [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: 02/01/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 09/01/2023] Open
Abstract
Rabies virus is a zoonotic pathogen that causes lethal encephalitis with a case fatality rate of almost 100% in unvaccinated individuals. The currently available vaccines against rabies are composed of inactivated viral particles that only confer a short-term immune response. It is well-known that the entry of rabies virus into host cells is mediated by a trimeric glycoprotein presents on the surface of viral envelope. As the sole viral surface protein, this trimeric glycoprotein represents a promising molecular target to design new vaccines and neutralizing antibodies against rabies virus. Epitope mapping studies had identified several antigenic sites on the surface of trimeric pre-fusion glycoprotein of rabies virus. Therefore, it is of interest to screen the rabies virus glycoprotein by different web-based immuno-informatics tools to identify potential B-cells and T-cells linear epitopes. Here, we present a construct of peptide vaccine that consists of these predicted linear epitopes of rabies virus glycoprotein together with appropriate linkers and adjuvant. Various online prediction tools, molecular docking and dynamics simulation assume that the vaccine construct may be stable, safe and effective. However, validation of these in-silico results is necessary both in vitro and in vivo setting.
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Affiliation(s)
| | | | - Suhad Sami Humadi
- Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq
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109
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Benghouzi P, Louadj L, Pagani A, Garnier M, Fresnais J, Gonzato C, Sabbah M, Griffete N. Synthesis of Fluorescent, Small, Stable and Non-Toxic Epitope-Imprinted Polymer Nanoparticles in Water. Polymers (Basel) 2023; 15:polym15051112. [PMID: 36904354 PMCID: PMC10007256 DOI: 10.3390/polym15051112] [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: 02/07/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Molecularly imprinted polymers (MIPs) are really interesting for nanomedicine. To be suitable for such application, they need to be small, stable in aqueous media and sometimes fluorescent for bioimaging. We report herein, the facile synthesis of fluorescent, small (below 200 nm), water-soluble and water-stable MIP capable of specific and selective recognition of their target epitope (small part of a protein). To synthesize these materials, we used dithiocarbamate-based photoiniferter polymerization in water. The use of a rhodamine-based monomer makes the resulting polymers fluorescent. Isothermal titration calorimetry (ITC) is used to determine the affinity as well as the selectivity of the MIP for its imprinted epitope, according to the significant differences observed when comparing the binding enthalpy of the original epitope with that of other peptides. The toxicity of the nanoparticles is also tested in two breast cancer cell lines to show the possible use of these particle for future in vivo applications. The materials demonstrated a high specificity and selectivity for the imprinted epitope, with a Kd value comparable with the affinity values of antibodies. The synthesized MIP are not toxic, which makes them suitable for nanomedicine.
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Affiliation(s)
- Perla Benghouzi
- Physico-Chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), Sorbonne Université, CNRS, 4 Place Jussieu, 75005 Paris, France
| | - Lila Louadj
- Physico-Chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), Sorbonne Université, CNRS, 4 Place Jussieu, 75005 Paris, France
- Saint-Antoine Research Center (CRSA) INSERM, CNRS, Sorbonne Université, 75012 Paris, France
| | - Aurélia Pagani
- Physico-Chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), Sorbonne Université, CNRS, 4 Place Jussieu, 75005 Paris, France
- Saint-Antoine Research Center (CRSA) INSERM, CNRS, Sorbonne Université, 75012 Paris, France
| | - Maylis Garnier
- Physico-Chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), Sorbonne Université, CNRS, 4 Place Jussieu, 75005 Paris, France
- Saint-Antoine Research Center (CRSA) INSERM, CNRS, Sorbonne Université, 75012 Paris, France
| | - Jérôme Fresnais
- Physico-Chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), Sorbonne Université, CNRS, 4 Place Jussieu, 75005 Paris, France
| | - Carlo Gonzato
- Laboratory for Enzyme and Cell Engineering UMR 7025, CNRS, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, 60203 Compiègne, France
| | - Michèle Sabbah
- Saint-Antoine Research Center (CRSA) INSERM, CNRS, Sorbonne Université, 75012 Paris, France
| | - Nébéwia Griffete
- Physico-Chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), Sorbonne Université, CNRS, 4 Place Jussieu, 75005 Paris, France
- Correspondence:
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110
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El Kenz B, Schmidt KG, Ogungbemi-Alt VK, Bergmann S, Steininger P, Korn K, Spriewald B, Harrer EG, Nganou-Makamdop K, Harrer T. Definition of a New HLA B*52-Restricted Rev CTL Epitope Targeted by an HIV-1-Infected Controller. Viruses 2023; 15. [PMID: 36851781 DOI: 10.3390/v15020567] [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: 01/04/2023] [Revised: 02/05/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The analysis of T-cell responses in HIV-1-infected controllers may contribute to a better understanding of the protective components of the immune system. Here, we analyzed the HIV-1-specific T-cell response in a 59-year-old HIV-1-infected controller, infected for at least seven years, who presented with low viral loads ranging from <20 copies/mL to 200 copies/mL and normal CD4 counts of >800 cells/µL. In γ-IFN-ELISpot assays using freshly isolated PBMCs, he displayed a very strong polyclonal T-cell response to eight epitopes in Gag, Nef and Rev; with the dominant responses directed against the HLA-B*57-epitope AISPRTLNAW and against a so-far-unknown epitope within Rev. Further analyses using peptide-stimulated T-cell lines in γ-IFN-ELISpot assays delineated the peptide RQRQIRSI (Rev-RI8) as a newly defined HLA-B*52-restricted epitope located within a functionally important region of Rev. Peptide-stimulation assays in 15 HLA-B*52-positive HIV-1-infected subjects, including the controller, demonstrated recognition of the Rev-RI8 epitope in 6/15 subjects. CD4 counts before the start of antiviral therapy were significantly higher in subjects with recognition of the Rev-RI8 epitope. Targeting of the Rev-RI8 epitope in Rev by CTL could contribute to the positive association of HLA-B*52 with a more favorable course of HIV-1-infection.
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111
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Miao C, Yang S, Shao J, Zhou G, Ma Y, Wen S, Hou Z, Peng D, Guo H, Liu W, Chang H. Identification of p72 epitopes of African swine fever virus and preliminary application. Front Microbiol 2023; 14:1126794. [PMID: 36819042 PMCID: PMC9935695 DOI: 10.3389/fmicb.2023.1126794] [Citation(s) in RCA: 3] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
African swine fever virus (ASFV) causes a highly lethal hemorrhagic viral disease (ASF) of pigs that results in serious losses in China and elsewhere. The development of a vaccine and diagnosis technology for ASFV is essential to prevent and control the spread of ASF. The p72 protein of ASFV is highly immunogenic and reactive, and is a dominant antigen in ASF vaccine and diagnostic research. In this study, 17 p72 monoclonal antibodies (mAbs) were generated. Epitope mapping by a series of overlapping peptides expressed in Escherichia coli showed that these mAbs recognized a total of seven (1-7) linear B cell epitopes. These mAbs did not show significant neutralizing activity. Epitopes 1 (249HKPHQSKPIL258), 2 (69PVGFEYENKV77), 5 (195VNGNSLDEYSS205), and 7 (223GYKHLVGQEV233) are novel. Sequence alignment analysis revealed that the identified epitopes were highly conserved among 27 ASFV strains from nine genotypes. Preliminary screening using known positive and negative sera indicated the diagnostic potential of mAb-2B8D7. The results provide new insights into the antigenic regions of ASFV p72 and will inform the diagnosis of ASFV.
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Affiliation(s)
- Chun Miao
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Sicheng Yang
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Junjun Shao
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Guangqing Zhou
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yunyun Ma
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Shenghui Wen
- Animal Science and Technology College, Guangxi University, Nanning, Guangxi, China
| | - Zhuo Hou
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Decai Peng
- Animal Science and Technology College, Guangxi University, Nanning, Guangxi, China
| | - HuiChen Guo
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Wei Liu
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China,Wei Liu,
| | - Huiyun Chang
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China,*Correspondence: Huiyun Chang,
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112
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Razim A, Górska S, Gamian A. Non-Toxin-Based Clostridioides difficile Vaccination Approaches. Pathogens 2023; 12. [PMID: 36839507 DOI: 10.3390/pathogens12020235] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 02/05/2023] Open
Abstract
Clostridioides difficile (CD) is a Gram-positive, anaerobic bacterium that infects mainly hospitalized and elderly people who have been treated with long-term antibiotic therapy leading to dysbiosis. The deteriorating demographic structure and the increase in the number of antibiotics used indicate that the problem of CD infections (CDI) will continue to increase. Thus far, there is no vaccine against CD on the market. Unfortunately, clinical trials conducted using the CD toxin-based antigens did not show sufficiently high efficacy, because they did not prevent colonization and transmission between patients. It seems that the vaccine should also include antigens found in the bacterium itself or its spores in order not only to fight the effects of toxins but also to prevent the colonization of the patient. This literature review summarizes the latest advances in research into vaccine antigens that do not contain CD toxins.
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113
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Isoda Y, Tanaka T, Suzuki H, Asano T, Yoshikawa T, Kitamura K, Kudo Y, Ejima R, Ozawa K, Kaneko MK, Kato Y. Epitope Mapping Using the Cell-Based 2 × Alanine Substitution Method About the Anti-mouse CXCR6 Monoclonal Antibody, Cx 6Mab-1. Monoclon Antib Immunodiagn Immunother 2023; 42:22-26. [PMID: 36383116 DOI: 10.1089/mab.2022.0029] [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: 11/17/2022] Open
Abstract
An anti-mouse CXC chemokine receptor 6 (mCXCR6) monoclonal antibody (mAb), Cx6Mab-1, was developed recently. Cx6Mab-1 is applicable for flow cytometry, Western blotting, and enzyme-linked immunosorbent assay. The purpose of this study is to determine the binding epitope of Cx6Mab-1 using 2 × alanine mutated mCXCR6. Analysis of flow cytometry revealed that Cx6Mab-1 did not recognize S8A-A9G, L10A-Y11A, D12A-G13A, and H14A-Y15A mutants of mCXCR6. The results clearly indicate that the binding epitope of Cx6Mab-1 includes Ser8, Ala9, Leu10, Tyr11, Asp12, Gly13, His14, and Tyr15 of mCXCR6. The successful determination of the Cx6Mab-1 epitope might contribute to the pathophysiological investigation of mCXCR6.
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Affiliation(s)
- Yu Isoda
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Tomohiro Tanaka
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Hiroyuki Suzuki
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Teizo Asano
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Takeo Yoshikawa
- Department of Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Kaishi Kitamura
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yuma Kudo
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Ryo Ejima
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Kazuki Ozawa
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.,Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.,Department of Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
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114
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Meyer S, Blaas I, Bollineni RC, Delic-Sarac M, Tran TT, Knetter C, Dai KZ, Madssen TS, Vaage JT, Gustavsen A, Yang W, Nissen-Meyer LSH, Douvlataniotis K, Laos M, Nielsen MM, Thiede B, Søraas A, Lund-Johansen F, Rustad EH, Olweus J. Prevalent and immunodominant CD8 T cell epitopes are conserved in SARS-CoV-2 variants. Cell Rep 2023; 42:111995. [PMID: 36656713 PMCID: PMC9826989 DOI: 10.1016/j.celrep.2023.111995] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 08/14/2022] [Revised: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
The emergence of SARS-CoV-2 variants of concern (VOC) is driven by mutations that mediate escape from neutralizing antibodies. There is also evidence that mutations can cause loss of T cell epitopes. However, studies on viral escape from T cell immunity have been hampered by uncertain estimates of epitope prevalence. Here, we map and quantify CD8 T cell responses to SARS-CoV-2-specific minimal epitopes in blood drawn from April to June 2020 from 83 COVID-19 convalescents. Among 37 HLA ligands eluted from five prevalent alleles and an additional 86 predicted binders, we identify 29 epitopes with an immunoprevalence ranging from 3% to 100% among individuals expressing the relevant HLA allele. Mutations in VOC are reported in 10.3% of the epitopes, while 20.6% of the non-immunogenic peptides are mutated in VOC. The nine most prevalent epitopes are conserved in VOC. Thus, comprehensive mapping of epitope prevalence does not provide evidence that mutations in VOC are driven by escape of T cell immunity.
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Affiliation(s)
- Saskia Meyer
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Isaac Blaas
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Ravi Chand Bollineni
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Marina Delic-Sarac
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Trung T. Tran
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Cathrine Knetter
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Ke-Zheng Dai
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | | | - John T. Vaage
- Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Alice Gustavsen
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Weiwen Yang
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | | | - Karolos Douvlataniotis
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Maarja Laos
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Morten Milek Nielsen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - Arne Søraas
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Fridtjof Lund-Johansen
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway,ImmunoLingo Convergence Center, University of Oslo, 0372 Oslo, Norway
| | - Even H. Rustad
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Corresponding author
| | - Johanna Olweus
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Corresponding author
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115
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Qin Y, Wu Q, Sheng H, Li T, Liu X, Yang X, Lin B, Zhou X, Jin J, Wang L, Huang B, He Q, Hu Z. Quantitative detection of anti-PLA2R antibodies targeting different epitopes and its clinical application in primary membranous nephropathy. Clin Chem Lab Med 2023; 61:251-259. [PMID: 36351699 DOI: 10.1515/cclm-2022-0720] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 07/26/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVES This study aimed to establish time-resolved fluorescence immunoassays to quantitatively detect the autoantibodies targeting different epitopes of M-type phospholipase A2 receptor (PLA2R) and evaluate its clinical application in primary membranous nephropathy (PMN). METHODS PLA2R and its reactive epitope-specific IgG/IgG4 time-resolved fluorescence immunoassays (TRFIAs) were established using europium-labeled anti-human IgG/IgG4 antibodies, recombinant proteins, and patient serum. The levels of IgG/IgG4 targeting PLA2R and its epitopes in PMN patient serum were detected, and the relationship between epitope spreading of PLA2R and the severity of patients with PMN was evaluated. RESULTS The TRFIAs established in this study could quantitatively detect PLA2R and its epitope-specific IgG and IgG4. Sera from 59 patients with PMN were subjected to detection using anti-PLA2R IgG and anti-PLA2R IgG4. Among them, 46 and 54 patients were found positive for PLA2R antibodies, respectively. Moreover, the levels of PLA2R antibodies were strongly correlated with the severity of patients with PMN. Patients who were detected to have two or more epitopes had more serious renal injury. CONCLUSIONS PLA2R domain-specific IgG/IgG4 TRFIAs were established in this study, and detection with anti-PLA2R IgG4 could more sensitively screen the reactivity of patients to the PLA2R domain. Moreover, detection epitope spreading of PLA2R was confirmed which is related to the severity of patients with PMN.
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Affiliation(s)
- Yuan Qin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, P.R. China
| | - Qingqing Wu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, P.R. China
| | - Huiming Sheng
- Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Ting Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, P.R. China
| | - Xiaobin Liu
- Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, P.R. China
| | - Xue Yang
- Wuxi Children's Hospital, Wuxi, P.R. China
| | - Bo Lin
- Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, P.R. China
| | - Xiumei Zhou
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, P.R. China
| | - Juan Jin
- Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, P.R. China
| | - Liang Wang
- Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, P.R. China
| | - Biao Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, P.R. China
| | - Qiang He
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang, P.R. China
| | - Zhigang Hu
- Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, P.R. China
- Wuxi Children's Hospital, Wuxi, P.R. China
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116
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Vijver SV, Danklmaier S, Pipperger L, Gronauer R, Floriani G, Hackl H, Das K, Wollmann G. Prediction and validation of murine MHC class I epitopes of the recombinant virus VSV-GP. Front Immunol 2023; 13:1100730. [PMID: 36741416 PMCID: PMC9893851 DOI: 10.3389/fimmu.2022.1100730] [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: 11/17/2022] [Accepted: 12/30/2022] [Indexed: 01/20/2023] Open
Abstract
Oncolytic viruses are currently tested as a novel platform for cancer therapy. These viruses preferentially replicate in and kill malignant cells. Due to their microbial origin, treatment with oncolytic viruses naturally results in anti-viral responses and general immune activation. Consequently, the oncolytic virus treatment also induces anti-viral T cells. Since these can constitute the dominant activated T cell pool, monitoring of the anti-viral T cell response may aid in better understanding of the immune responses post oncolytic virotherapy. This study aimed to identify the anti-viral T cells raised by VSV-GP virotherapy in C57BL/6J mice, one of the most widely used models for preclinical studies. VSV-GP is a novel oncolytic agent that recently entered a clinical phase I study. To identify the VSV-GP epitopes to which mouse anti-viral T cells react, we used a multilevel adapted bioinformatics viral epitope prediction approach based on the tools netMHCpan, MHCflurry and netMHCstabPan, which are commonly used in neoepitope identification. Predicted viral epitopes were ranked based on consensus binding strength categories, predicted stability, and dissimilarity to the mouse proteome. The top ranked epitopes were selected and included in the peptide candidate matrix in order to use a matrix deconvolution approach. Using ELISpot, we showed which viral epitopes presented on C57BL/6J mouse MHC-I alleles H2-Db and H2-Kb trigger IFN-γ secretion due to T cell activation. Furthermore, we validated these findings using an intracellular cytokine staining. Collectively, identification of the VSV-GP T cell epitopes enables monitoring of the full range of anti-viral T cell responses upon VSV-GP virotherapy in future studies with preclinical mouse models to more comprehensively delineate anti-viral from anti-tumor T cell responses. These findings also support the development of novel VSV-GP variants expressing immunomodulatory transgenes and can improve the assessment of anti-viral immunity in preclinical models.
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Affiliation(s)
- Saskia V. Vijver
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
| | - Sarah Danklmaier
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
| | - Lisa Pipperger
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
| | - Raphael Gronauer
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriel Floriani
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Hubert Hackl
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Guido Wollmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
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117
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Bi Z, Wang W, Xia X. Structure and function of a novel lineage-specific neutralizing epitope on H protein of canine distemper virus. Front Microbiol 2023; 13:1088243. [PMID: 36713169 PMCID: PMC9875009 DOI: 10.3389/fmicb.2022.1088243] [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: 11/03/2022] [Accepted: 12/28/2022] [Indexed: 01/13/2023] Open
Abstract
Canine distemper virus (CDV) infects many sensitive species worldwide and its host range is expanding. The hemagglutinin (H) protein, the major neutralizing target, binds to cellular receptors and subsequently triggers fusion for initial viral infection. So it's necessary to clarify the precise neutralizing epitopes of H protein and extend the knowledge of mechanisms of virus neutralization. In this study, a neutralizing monoclonal antibody (mAb) 2D12 against CDV H protein, which had different reactivity with different CDV strains, was generated and characterized. A series of truncated H proteins were screened to define the minimal linear epitope 238DIEREFD244 recognized by 2D12. Further investigation revealed that the epitope was highly conserved in America-1 vaccine lineage of CDV strains, but different substitutions in the epitope appeared in CDV strains of the other lineages and two substitutions (D238Y and R241G) caused the change of antigenicity. Thus, the epitope represents a novel lineage-specific neutralizing target on H protein of CDV for differentiation of America-1 vaccine lineage and the other lineages of CDV strains. The epitope was identified to localize at the surface of H protein in two different positions in a three-dimensional (3D) structure, but not at the position of the receptor-binding site (RBS), so the mAb 2D12 that recognized the epitope did not inhibit binding of H protein to the receptor. But mAb 2D12 interfered with the H-F interaction for inhibiting membrane fusion, suggesting that the mAb plays key roles for formation of H-F protein oligomeric structure. Our data will contribute to the understanding of the structure, function, and antigenicity of CDV H protein and mechanisms of virus neutralization.
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Affiliation(s)
- Zhenwei Bi
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China,Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China,*Correspondence: Zhenwei Bi,
| | - Wenjie Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China,Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xingxia Xia
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, National Center for Engineering Research of Veterinary Bio-products, Nanjing, China,Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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118
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Harmsen MM, Li H, Sun S, van der Poel WHM, Dekker A. Mapping of foot-and-mouth disease virus antigenic sites recognized by single-domain antibodies reveals different 146S particle specific sites and particle flexibility. Front Vet Sci 2023; 9:1040802. [PMID: 36699337 PMCID: PMC9869066 DOI: 10.3389/fvets.2022.1040802] [Citation(s) in RCA: 3] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
Vaccination with intact (146S) foot-and-mouth disease virus (FMDV) particles is used to control FMD. However, 146S particles easily dissociate into stable pentameric 12S particles which are less immunogenic. We earlier isolated several single-domain antibody fragments (VHHs) that specifically bind either 146S or 12S particles. These particle-specific VHHs are excellent tools for vaccine quality control. In this study we mapped the antigenic sites recognized by these VHHs by competition ELISAs, virus neutralization, and trypsin sensitivity of epitopes. We included two previously described monoclonal antibodies (mAbs) that are either 12S specific (mAb 13A6) or 146S specific (mAb 9). Although both are 12S specific, the VHH M3F and mAb 13A6 were found to bind independent antigenic sites. M3F recognized a non-neutralizing and trypsin insensitive site whereas mAb 13A6 recognized the trypsin sensitive VP2 N-terminus. The Asia1 146S-specific site was trypsin sensitive, neutralizing and also recognized by the VHH M8F, suggesting it involves the VP1 GH-loop. The type A 146S-specific VHHs recognized two independent antigenic sites that are both also neutralizing but trypsin insensitive. The major site was further mapped by cross-linking mass spectrometry (XL-MS) of two broadly strain reactive 146S-specific VHHs complexed to FMDV. The epitopes were located close to the 2-fold and 3-fold symmetry axes of the icosahedral virus 3D structure, mainly on VP2 and VP3, overlapping the earlier identified mAb 9 site. Since the epitopes were located on a single 12S pentamer, the 146S specificity cannot be explained by the epitope being split due to 12S pentamer dissociation. In an earlier study the cryo-EM structure of the 146S-specific VHH M170 complexed to type O FMDV was resolved. The 146S specificity was reported to be caused by an altered conformation of this epitope in 12S and 146S particles. This mechanism probably also explains the 146S-specific binding by the two type A VHHs mapped by XL-MS since their epitopes overlapped with the epitope recognized by M170. Surprisingly, residues internal in the 146S quaternary structure were also cross-linked to VHH. This probably reflects particle flexibility in solution. Molecular studies of virus-antibody interactions help to further optimize vaccines and improve their quality control.
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Affiliation(s)
- Michiel M. Harmsen
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, Netherlands,*Correspondence: Michiel M. Harmsen ✉
| | - Haozhou Li
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands,State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shiqi Sun
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Wim H. M. van der Poel
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, Netherlands,Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Aldo Dekker
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, Netherlands
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Li L, Qiao S, Liu J, Zhou Y, Tong W, Dong S, Liu C, Jiang Y, Guo Z, Zheng H, Zhao R, Tong G, Li G, Gao F. A highly efficient indirect ELISA and monoclonal antibody established against African swine fever virus pK205R. Front Immunol 2023; 13:1103166. [PMID: 36700212 PMCID: PMC9868132 DOI: 10.3389/fimmu.2022.1103166] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 11/20/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
African swine fever (ASF) is a contagious infectious disease with high lethality which continuously threatens the global pig industry causing huge economic losses. Currently, there are no commercially available vaccines or antiviral drugs that can effectively control ASF. The pathogen of ASF, ASF virus (ASFV) is a double-stranded DNA virus with a genome ranging from 170 to 193 kb and 151 to 167 open reading frames in various strains, which encodes 150-200 proteins. An effective method of monitoring ASFV antibodies, and specific antibodies against ASFV to promote the development of prevention techniques are urgently needed. In the present study, pK205R of ASFV was successfully expressed in mammalian cells using a suspension culture system. An indirect enzyme-linked immunosorbent assay (ELISA) based on the purified pK205R was established and optimized. The monoclonal antibody (mAb) against pK205R recognized a conservative linear epitope (2VEPREQFFQDLLSAV16) and exhibited specific reactivity, which was conducive to the identification of the recombinant porcine reproductive and respiratory syndrome virus (PRRSV) expressing pK205R. The ELISA method efficiently detected clinical ASFV infection and revealed good application prospects in monitoring the antibody level in vivo for recombinant PRRSV live vector virus expressing the ASFV antigen protein. The determination of the conserved linear epitope of pK205R would contribute to further research on the structural biology and function of pK205R. The indirect ELISA method and mAb against ASFV pK205R revealed efficient detection and promising application prospects, making them ideal for epidemiological surveillance and vaccine research on ASF.
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Affiliation(s)
- Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Sina Qiao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China,College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jiachen Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yanjun Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Shishan Dong
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yifeng Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ziqiang Guo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Haihong Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ran Zhao
- Xiamen Center for Animal Disease Control and Prevention, Xiamen, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Guoxin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China,*Correspondence: Guoxin Li, ; Fei Gao,
| | - Fei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China,*Correspondence: Guoxin Li, ; Fei Gao,
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Kronfel CM, Cheng H, McBride JK, Nesbit JB, Krouse R, Burns P, Cabanillas B, Crespo JF, Ryan R, Simon RJ, Maleki SJ, Hurlburt BK. IgE epitopes of Ara h 9, Jug r 3, and Pru p 3 in peanut-allergic individuals from Spain and the US. Front Allergy 2023; 3:1090114. [PMID: 36698378 PMCID: PMC9869384 DOI: 10.3389/falgy.2022.1090114] [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: 11/04/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Non-specific lipid transfer proteins (LTPs) are well studied allergens that can lead to severe reactions, but often cause oral allergy syndrome in the Mediterranean area and other European countries. However, studies focused on LTP reactivity in allergic individuals from the United States are lacking because they are not considered major allergens. The goal of this study is to determine if differences in immunoglobulin (Ig) E binding patterns to the peanut allergen Ara h 9 and two homologous LTPs (walnut Jug r 3 and peach Pru p 3) between the US and Spain contribute to differences observed in allergic reactivity. Synthetic overlapping 15-amino acid-long peptides offset by five amino acids from Ara h 9, Jug r 3, and Pru p 3 were synthesized, and the intact proteins were attached to microarray slides. Sera from 55 peanut-allergic individuals from the US were tested for IgE binding to the linear peptides and IgE binding to intact proteins using immunofluorescence. For comparison, sera from 17 peanut-allergic individuals from Spain were also tested. Similar IgE binding profiles for Ara h 9, Jug r 3, and Pru p 3 were identified between the US and Spain, with slight differences. Certain regions of the proteins, specifically helices 1 and 2 and the C-terminal coil, were recognized by the majority of the sera more often than other regions of the proteins. While serum IgE from peanut-allergic individuals in the US binds to peptides of Ara h 9 and its homologs, only IgE from the Spanish subjects bound to the intact LTPs. This study identifies Ara h 9, Jug r 3, and Pru p 3 linear epitopes that were previously unidentified using sera from peanut-allergic individuals from the US and Spain. Certain regions of the LTPs are recognized more often in US subjects, indicating that they represent conserved and possible cross-reactive regions. The location of the epitopes in 3D structure models of the LTPs may predict the location of potential conformational epitopes bound by a majority of the Spanish patient sera. These findings are potentially important for development of peptide or protein-targeting diagnostic and therapeutic tools for food allergy.
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Affiliation(s)
- Christina M. Kronfel
- United States Department of Agriculture, Agriculture Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Hsiaopo Cheng
- United States Department of Agriculture, Agriculture Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Jane K. McBride
- United States Department of Agriculture, Agriculture Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Jacqueline B. Nesbit
- United States Department of Agriculture, Agriculture Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | | | - Preston Burns
- Rho Federal Systems Division, Durham, NC, United States
| | - Beatriz Cabanillas
- Department of Allergy, Research Institute Hospital 12 de Octubre, Madrid, Spain
| | - Jesus F. Crespo
- Department of Allergy, Research Institute Hospital 12 de Octubre, Madrid, Spain
| | - Robert Ryan
- Aimmune Therapeutics, a Nestlé Health Science Company, Brisbane, CA, United States
| | - Reyna J. Simon
- Aimmune Therapeutics, a Nestlé Health Science Company, Brisbane, CA, United States
| | - Soheila J. Maleki
- United States Department of Agriculture, Agriculture Research Service, Southern Regional Research Center, New Orleans, LA, United States,Correspondence: Soheila J. Maleki
| | - Barry K. Hurlburt
- United States Department of Agriculture, Agriculture Research Service, Southern Regional Research Center, New Orleans, LA, United States
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Huang M, Yang F, Wu Y, Meng X, Shi L, Chen H, Li X. Identification of peptides sequence and conformation contributed to potential allergenicity of main allergens in yogurts. Front Nutr 2023; 9:1038466. [PMID: 36687717 PMCID: PMC9849743 DOI: 10.3389/fnut.2022.1038466] [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: 09/07/2022] [Accepted: 11/21/2022] [Indexed: 01/07/2023] Open
Abstract
Yogurts provide a good source of nutrition and may induce tolerance in people with cow's milk allergy (CMA). This study aimed to investigate the IgE-binding capacity of main allergens in the different yogurts which provide a reference for people with a high risk of CMA, and analyze the epitopes of major allergen peptides in yogurt. We assessed the degradation and the allergenic properties of major allergens in six commercial yogurts and fresh milk. The degradation of major allergens was analyzed by SDS-PAGE and RP-HPLC. Western blot and ELISA experiments detected allergenic characteristics by using specific sera. The results showed that β-lactoglobulin (Bos d 5) and α-lactalbumin (Bos d 4) were obviously degraded in yogurts but caseins were still present in abundance, which indicated that the proteases in yogurts were specific to whey proteins. IgE and IgG binding ability of major allergens were obviously reduced in yogurts, especially GuMi yogurt. In addition, 17 peptides of major allergens in GuMi yogurt were identified by LC-MS/MS and most of them were located in the interior of the spatial structure of proteins. Among them, 8 peptides had specific biological functions for health benefits, such as antibacterial, antioxidant, and ACE-inhibitory. We also found that 6 and 14 IgE epitopes of Bos d 5 and caseins were destroyed in GuMi yogurt, which could lead to the reduction of IgE-binding capacity. Meanwhile, peptides [Bos d 5 (AA15-40), Bos d 9 (AA120-151, AA125-151)] also preserved T cell epitopes, which might also induce the development of oral tolerance. Therefore, this study suggested that the sequence and conformation of peptides in yogurts contributed to hypoallergenicity.
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Affiliation(s)
- Meijia Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China,School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Fan Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China,School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Yong Wu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China,Sino-German Joint Research Institute (Jiangxi-OAI), Nanchang University, Nanchang, China,Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, China
| | - Xuanyi Meng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China,Sino-German Joint Research Institute (Jiangxi-OAI), Nanchang University, Nanchang, China,Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, China
| | - Linbo Shi
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Hongbing Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China,Sino-German Joint Research Institute (Jiangxi-OAI), Nanchang University, Nanchang, China,Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, China
| | - Xin Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China,School of Food Science and Technology, Nanchang University, Nanchang, China,Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, China,*Correspondence: Xin Li,
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Zhou J, Ni Y, Wang D, Fan B, Zhu X, Zhou J, Hu Y, Li L, Li B. Development of a Competitive Enzyme-Linked Immunosorbent Assay Targeting the-p30 Protein for Detection of Antibodies against African Swine Fever Virus. Viruses 2023; 15:154. [PMID: 36680193 PMCID: PMC9861063 DOI: 10.3390/v15010154] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 12/20/2022] [Revised: 12/31/2022] [Accepted: 12/31/2022] [Indexed: 01/05/2023] Open
Abstract
African swine fever (ASF) is a highly contagious hemorrhagic viral disease of domestic and wild pigs of all breeds and ages, caused by African swine fever virus (ASFV). Due to the absence of a safe and efficacious vaccine, accurate laboratory diagnosis is critical for the control of ASF prevention. The p30 protein is immunogenic and stimulates a high level of antibody response to ASFV infection. We developed a panel of 4 monoclonal antibodies (mAbs) against p30 protein, and mAb-2B4 showed the highest percent of inhibition (PI) of 70% in the solid phase blocking ELISA (bELISA). Epitope mapping revealed the mAb-2B4 recognized the epitope of aa 12-18 of p30, which is conserved among various ASFV genotypes. Subsequently, a competitive enzyme-linked immunosorbent assay (cELISA) was established using HRP-labeled mAb-2B4. The cutoff for discrimination between 98 negative sera and 40 positive sera against ASFV was determined by plotting a receiver operating characteristic (ROC) curve. It yielded the area under the curve (AUC) of 0.998, and a diagnostic specificity of 97.96% and a sensitivity of 97.5% were achieved when the cutoff value was determined at 37.1%. Furthermore, the results showed an excellent repeatability of the established cELISA and no cross-reaction to antisera against six other pig pathogens. Additionally, the cELISA detected a titer of 1:256 in the positive standard serum. Overall, mAb-2B4 showed a conserved epitope and high ability to be inhibited by positive sera in ASFV antibody detection. The cELISA based on HRP-labeled mAb-2B4 offers an alternative to other assays for a broader diagnostic coverage of ASFV infection.
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Affiliation(s)
- Junming Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
| | - Yanxiu Ni
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
| | - Dandan Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
| | - Xuejiao Zhu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
| | - Jinzhu Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
| | - Yiyi Hu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
| | - Li Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
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Qi Y, Zheng P, Huang G. DeepLBCEPred: A Bi-LSTM and multi-scale CNN-based deep learning method for predicting linear B-cell epitopes. Front Microbiol 2023; 14:1117027. [PMID: 36910218 PMCID: PMC9992402 DOI: 10.3389/fmicb.2023.1117027] [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: 12/06/2022] [Accepted: 01/17/2023] [Indexed: 02/24/2023] Open
Abstract
The epitope is the site where antigens and antibodies interact and is vital to understanding the immune system. Experimental identification of linear B-cell epitopes (BCEs) is expensive, is labor-consuming, and has a low throughput. Although a few computational methods have been proposed to address this challenge, there is still a long way to go for practical applications. We proposed a deep learning method called DeepLBCEPred for predicting linear BCEs, which consists of bi-directional long short-term memory (Bi-LSTM), feed-forward attention, and multi-scale convolutional neural networks (CNNs). We extensively tested the performance of DeepLBCEPred through cross-validation and independent tests on training and two testing datasets. The empirical results showed that the DeepLBCEPred obtained state-of-the-art performance. We also investigated the contribution of different deep learning elements to recognize linear BCEs. In addition, we have developed a user-friendly web application for linear BCEs prediction, which is freely available for all scientific researchers at: http://www.biolscience.cn/DeepLBCEPred/.
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Affiliation(s)
- Yue Qi
- School of Information Engineering, Shaoyang University, Shaoyang, Hunan, China
| | - Peijie Zheng
- School of Information Engineering, Shaoyang University, Shaoyang, Hunan, China
| | - Guohua Huang
- School of Information Engineering, Shaoyang University, Shaoyang, Hunan, China
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Zhou L, Mo C, Yang Y, Zhou Z, You A, Fan Y, Liu W, Li X, Zhou R, Tian X. Characterization and application of a series of monoclonal antibodies against SARS-CoV-2 nucleocapsid protein. J Med Virol 2023; 95:e28225. [PMID: 36238992 PMCID: PMC9874425 DOI: 10.1002/jmv.28225] [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: 06/07/2022] [Revised: 09/29/2022] [Accepted: 10/11/2022] [Indexed: 01/27/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic has a significant global social and economic impact, and the emergence of new and more destructive mutant strains highlights the need for accurate virus detection. Here, 90 monoclonal antibodies (MAbs) that exclusively reacted with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (NP) were generated. These MAbs did not cross-react with NPs of common human coronaviruses (HCoVs, i.e., 229E, OC43, HKU1, and NL63) and Middle East Respiratory Syndrome Coronavirus. Subsequently, overlapped peptides in individual fragments (N1-N4) of NP were synthesized. N1-3 (25-GSNQNGERSGARSKQ-39), N3-1 (217-AALALLLLDRLNQL-230), and N4-8 (393-TLLPAADLDDFSKQL-407) were identified as major epitopes using enzyme-linked immunoassay (ELISA) and recognized by 47, 1, and 18 MAbs, respectively. The 24 remaining MAbs exhibited no reactivity with all synthetic peptides. Among MAb-epitope pairs, only MAbs targeting epitope N1-3 displayed no cross-reaction with NPs of SARS-CoV-1 and other SARS-related CoVs. All Omicron variants contained a three-amino acid deletion (31ERS33) in the N1-3 region. Thus, MAbs targeting N1-3 failed to recognize these variants. Furthermore, a double-antibody sandwich ELISA for antigen detection was established using the optimal MAbs. Overall, a series of MAbs targeting SARS-CoV-2 NP was prepared, characterized with epitope mapping, and applied for the detection of SARS-CoV-2 antigens, and some novel B-cell epitopes of the viral NP were identified.
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Affiliation(s)
- Liling Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Chuncong Mo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina,Guangzhou LaboratoryGuangzhouChina
| | - Yujie Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Aiping You
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Ye Fan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Xiao Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Rong Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina,Guangzhou LaboratoryGuangzhouChina
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
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Qasim A, Jaan S, Wara TU, Shehroz M, Nishan U, Shams S, Shah M, Ojha SC. Computer-aided genomic data analysis of drug-resistant Neisseria gonorrhoeae for the Identification of alternative therapeutic targets. Front Cell Infect Microbiol 2023; 13:1017315. [PMID: 37033487 PMCID: PMC10080061 DOI: 10.3389/fcimb.2023.1017315] [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: 08/11/2022] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
Neisseria gonorrhoeae is an emerging multidrug resistance pathogen that causes sexually transmitted infections in men and women. The N. gonorrhoeae has demonstrated an emerging antimicrobial resistance against reported antibiotics, hence fetching the attention of researchers to address this problem. The present in-silico study aimed to find putative novel drug and vaccine targets against N. gonorrhoeae infection by the application of bioinformatics approaches. Core genes set of 69 N. gonorrhoeae strains was acquired from complete genome sequences. The essential and non-homologous metabolic pathway proteins of N. gonorrhoeae were identified. Moreover, different bioinformatics databases were used for the downstream analysis. The DrugBank database scanning identified 12 novel drug targets in the prioritized list. They were preferred as drug targets against this bacterium. A viable vaccine is unavailable so far against N. gonorrhoeae infection. In the current study, two outer-membrane proteins were prioritized as vaccine candidates via reverse vaccinology approach. The top lead B and T-cells overlapped epitopes were utilized to generate a chimeric vaccine construct combined with immune-modulating adjuvants, linkers, and PADRE sequences. The top ranked prioritized vaccine construct (V7) showed stable molecular interaction with human immune cell receptors as inferred during the molecular docking and MD simulation analyses. Considerable response for immune cells was interpreted by in-silico immune studies. Additional tentative validation is required to ensure the effectiveness of the prioritized vaccine construct against N. gonorrhoeae infection. The identified proteins can be used for further rational drug and vaccine designing to develop potential therapeutic entities against the multi-drug resistant N. gonorrhoeae.
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Affiliation(s)
- Aqsa Qasim
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Samavia Jaan
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Tehreem Ul Wara
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University, Murree, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
- *Correspondence: Suvash Chandra Ojha, ; Mohibullah Shah, ;
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Suvash Chandra Ojha, ; Mohibullah Shah, ;
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Abstract
Leptospirosis is one of the neglected diseases caused by the spirochete, Leptospira interrogans. Leptospiral surface adhesion (Lsa) proteins are surface exposed outer membrane proteins present in the pathogen. It acts as laminin and plasminogen binding proteins which enable them to infect host cells. The major target for the development of vaccine in the current era focuses on surface exposed outer membrane proteins, as they can induce strong and fast immune response in hosts. Therefore, the present study mapped the potential epitopes of the Leptospiral outer membrane proteins, mainly the surface adhesion proteins. Protein sequence analysis of Lsa proteins was done by in silico methods. The primary protein sequence analysis revealed Lsa46 as a suitable target which can be a potent Leptospiral vaccine candidate. Its structure was modelled by threading based method in I-TASSER server and validated by Ramachandran plot. The predicted epitope's interactions with human IgG, IgM(Fab) and T-cell receptor TCR(αβ) were performed by molecular docking studies using Biovia Discovery studio 2018. One of the predicted B-cell epitopes and the IgG showed desirable binding interactions, while four of the predicted B-cell epitopes and T-cell epitopes showed desirable binding interactions with IgM and TCR respectively. The molecular dynamic simulation studies carried out with the molecular docked complexes gave minimized energies indicating stable interactions. The structural analysis of the entire simulated complex showed a stable nature except for one of the Epitope-IgM complex. Further the binding free energy calculation of eight receptor-ligand complex predicted them energetically stable. The results of the study help in elucidating the structural and functional characterization of Lsa46 for epitope-based vaccine design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Junaida M Ibrahim
- Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Shanitha A
- Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Achuthsankar S Nair
- Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Oommen V Oommen
- Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Perumana R Sudhakaran
- Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
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Lewis SA, Peters B. T-cell epitope discovery and single-cell technologies to advance food allergy research. J Allergy Clin Immunol 2023; 151:15-20. [PMID: 36411114 PMCID: PMC9825656 DOI: 10.1016/j.jaci.2022.10.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 07/01/2022] [Revised: 09/13/2022] [Accepted: 10/06/2022] [Indexed: 11/19/2022]
Abstract
There is good evidence for a role of T cells in food allergy, but there is a lack of mechanistic understanding and phenotypic markers of the specific T cells contributing to pathology. Recent technologic advancements have allowed for a new experimental paradigm where we can find and pull out rare antigen-specific T cells and characterize them at the single-cell level. However, studies in infectious disease and broader allergy have shown that these techniques benefit greatly from precisely defined T-cell epitopes. Food allergens have fewer epitopes currently available, but it is growing and promises to overcome this gap. With growing use of this experimental design, it will be important to unbiasedly map T-cell phenotypes across food allergy and look for commonalities and contrasts to other allergic and infectious diseases. Once a pathologic phenotype for T cells has been established, the frequencies of these cells can be monitored with simpler techniques that could be applied to the clinic and used in diagnosis, prediction of treatment responsiveness, and discovery of targets for new treatments.
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Affiliation(s)
- Sloan A Lewis
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, Calif
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, Calif; Department of Medicine, University of California San Diego, La Jolla, Calif.
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128
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Sun B, Zhang J, Li Z, Xie M, Luo C, Wang Y, Chen L, Wang Y, Jiang D, Yang K. Integration: Gospel for immune bioinformatician on epitope-based therapy. Front Immunol 2023; 14:1075419. [PMID: 36798136 PMCID: PMC9927647 DOI: 10.3389/fimmu.2023.1075419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Affiliation(s)
- Baozeng Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China
| | - Junqi Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China
| | - Zhikui Li
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China
| | - Mingyang Xie
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China
| | - Cheng Luo
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China
| | - Yongkai Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China
| | - Longyu Chen
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China
| | - Yueyue Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China
| | - Dongbo Jiang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China.,The Key Laboratory of Bio-hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China.,Department of Microbiology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China
| | - Kun Yang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China.,The Key Laboratory of Bio-hazard Damage and Prevention Medicine, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China.,Department of Rheumatology, Tangdu Hospital, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, China
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129
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Malisheni MM, Chong CS, Murali TM, Purushotorman K, Qian X, Laiman A, Tan YJ, MacAry PA. Switching Heavy Chain Constant Domains Denatures the Paratope 3D Architecture of Influenza Monoclonal Antibodies. Pathogens 2022; 12. [PMID: 36678399 DOI: 10.3390/pathogens12010051] [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: 10/25/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
Several human monoclonal Abs for treating Influenza have been evaluated in clinical trials with limited success despite demonstrating superiority in preclinical animal models including mice. To conduct efficacy studies in mice, human monoclonal Abs are genetically engineered to contain mouse heavy chain constant domain to facilitate the engagement of Fc-receptors on mouse immune effector cells. Although studies have consistently reported discrepancies in Ab effectiveness following genetic engineering, the structural and mechanistic basis for these inconsistencies remain uncharacterized. Here, we use homology modeling to predict variable region (VR) analogous monoclonal Abs possessing human IgG1, mouse IgG1, and mouse IgG2a heavy chain constant domains. We then examine predicted 3D structures for variations in the spatial location and orientation of corresponding paratope amino acid residues. By structurally aligning crystal structures of Fabs in complex with hemagglutinin (HA), we show that corresponding paratope amino acid residues for VR-analogous human IgG1, mouse IgG1, and mouse IgG2a monoclonal Abs interact differentially with HA suggesting that their epitopes might not be identical. To demonstrate that variations in the paratope 3D fine architecture have implications for Ab specificity and effectiveness, we genetically engineered VR-analogous human IgG1, human IgG4, mouse IgG1, and mouse IgG2a monoclonal Abs and explored their specificity and effectiveness in protecting MDCK cells from infection by pandemic H1N1 and H3N2 Influenza viruses. We found that VR-analogous monoclonal Abs placed on mouse heavy chain constant domains were more efficacious at protecting MDCK cells from Influenza virus infection relative to those on human heavy chain constant domains. Interestingly, mouse but not human heavy chain constant domains increased target breadth in some monoclonal Abs. These data suggest that heavy chain constant domain sequences play a role in shaping Ab repertoires that go beyond class or sub-class differences in immune effector recruitment. This represents a facet of Ab biology that can potentially be exploited to improve the scope and utilization of current therapeutic or prophylactic candidates for influenza.
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130
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Mahapatra SR, Dey J, Kushwaha GS, Puhan P, Mohakud NK, Panda SK, Lata S, Misra N, Suar M. Immunoinformatic approach employing modeling and simulation to design a novel vaccine construct targeting MDR efflux pumps to confer wide protection against typhoidal Salmonella serovars. J Biomol Struct Dyn 2022; 40:11809-11821. [PMID: 34463211 DOI: 10.1080/07391102.2021.1964600] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 12/31/2022]
Abstract
Overcoming multi drug resistance is one of the crucial challenges to control enteric typhoid fever caused by Salmonella typhi and Salmonella paratyphi. Overexpression of efflux pumps predominantly causes drug resistance in microorganisms. Therefore, immunotherapy targeting the various efflux pumps antigens could be a promising strategy to increase the success of vaccines. An immunoinformatic approach was employed to design a Salmonellosis multi-epitope subunit vaccine peptide consisting of linear B-cell and T-cell epitopes of multidrug resistance protein families including ATP Binding Cassette (ABC), major facilitator superfamily (MFS), resistance nodulation cell division (RND), small multidrug resistance (SMR), and multidrug and toxin extrusion (MATE). The selected epitopes exhibited conservation in both S. typhi and S. paratyphi and thus could be helpful for cross-protection. Further, the final vaccine construct encompassing the peptides, adjuvants and specific linker sequences showed high immunogenicity, solubility, non-allergenic, nontoxic, and wide population coverage due to strong binding affinity to maximum HLA alleles. The three-dimensional structure was predicted, and validated using various structure validation tools. Additionally, protein-protein docking of the chimeric vaccine construct with the TLR-2 protein and molecular dynamics demonstrated stable and efficient binding. Conclusively, the immunoinformatic study showed that the novel multi epitopic vaccine construct can simulate the both T-cell and B-cell immune responses in typhoidal Salmonella serovars and could potentially be used for prophylactic or therapeutic applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumya Ranjan Mahapatra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Jyotirmayee Dey
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Gajraj Singh Kushwaha
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.,Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Puspasree Puhan
- Science and Technology Department, Government of Odisha, Bhubaneswar, India
| | - Nirmal Kumar Mohakud
- Kalinga Institute of Medical Sciences, KIIT, Deemed to Be University, Bhubaneswar, India
| | - Santosh Kumar Panda
- Kalinga Institute of Medical Sciences, KIIT, Deemed to Be University, Bhubaneswar, India
| | - S Lata
- Kalinga Institute of Dental Sciences, KIIT Deemed to Be University, Bhubaneswar, India
| | - Namrata Misra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.,KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.,KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
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131
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Li L, Qiao S, Li G, Tong W, Dong S, Liu J, Guo Z, Zheng H, Zhao R, Tong G, Zhou Y, Gao F. The Indirect ELISA and Monoclonal Antibody against African Swine Fever Virus p17 Revealed Efficient Detection and Application Prospects. Viruses 2022; 15:50. [PMID: 36680090 PMCID: PMC9865993 DOI: 10.3390/v15010050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 12/09/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Since 2018, the outbreak and prevalence of the African swine fever virus (ASFV) in China have caused huge economic losses. Less virulent ASFVs emerged in 2020, which led to difficulties and challenges for early diagnosis and control of African swine fever (ASF) in China. An effective method of monitoring ASFV antibodies and specific antibodies against ASFV to promote the development of prevention techniques are urgently needed. In the present study, ASFV p17 was successfully expressed in CHO cells using a suspension culture system. An indirect enzyme-linked immunosorbent assay (ELISA) based on purified p17 was established and optimized. The monoclonal antibody (mAb) against p17 recognized a conservative linear epitope (3TETSPLLSH11) and exhibited specific reactivity, which was conducive to the identification of recombinant porcine reproductive and respiratory syndrome virus (PRRSV) expressing p17. The ELISA method efficiently detected clinical ASFV infection and effectively monitored the antibody levels in vivo after recombinant PRRSV live vector virus expressing p17 vaccination. Overall, the determination of the conserved linear epitope of p17 would contribute to the in-depth exploration of the biological function of the ASFV antigen protein. The indirect ELISA method and mAb against ASFV p17 revealed efficient detection and promising application prospects, making them ideal for epidemiological surveillance and vaccine research on ASF.
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Affiliation(s)
- Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Sina Qiao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Guoxin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Shishan Dong
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Jiachen Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Ziqiang Guo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Haihong Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Ran Zhao
- Xiamen Center for Animal Disease Control and Prevention, Xiamen 361009, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yanjun Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Fei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou 225009, China
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132
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Ali MC, Khatun MS, Jahan SI, Das R, Munni YA, Rahman MM, Dash R. In silico design of epitope-based peptide vaccine against non-typhoidal Salmonella through immunoinformatic approaches. J Biomol Struct Dyn 2022; 40:10696-10714. [PMID: 36529187 DOI: 10.1080/07391102.2021.1947381] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Non-typhoidal Salmonella (NTS) is one of the leading bacterial causes of many invasive human infections with a high antibiotic resistance profile. With this concern, the current study aimed to design an effective epitope-based peptide vaccine against NTS species as a successive and substitutive protective measure of invasive NTS disease. To design rationally, the current study considered a comprehensive in silico workflow combination of both immunoinformatics and molecular modeling approaches, including molecular docking and molecular dynamics (MD) simulation. We identified the two most promising T cell epitopes KVLYGIFAI and YGIFAITAL, and three B cell epitopes AAPVQVGEAAGS, TGGGDGSNT, and TGGGDGSNTGTTTT, in the outer membrane of NTS. Using these epitopes, a multiepitope vaccine was subsequently constructed along with appropriate adjuvant and linkers, which showed a good binding affinity and stability with toll-like receptor 2 (TLR2) in both molecular docking and MD simulation. Furthermore, in silico immune simulation described a strong immune response with a high number of antibodies, interferon-γ, and activated B and T cells. This study collectively suggests that predicted vaccine constructs could be considered potential vaccine candidates against common NTS species.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Chayan Ali
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Mst Shanzeda Khatun
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Sultana Israt Jahan
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Raju Das
- Department of Physiology, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Md Mafizur Rahman
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
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133
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Feng L, Gao YY, Sun M, Li ZB, Zhang Q, Yang J, Qiao C, Jin H, Feng HS, Xian YH, Qi J, Gao GF, Liu WJ, Gao FS. The Parallel Presentation of Two Functional CTL Epitopes Derived from the O and Asia 1 Serotypes of Foot-and-Mouth Disease Virus and Swine SLA-2*HB01: Implications for Universal Vaccine Development. Cells 2022; 11:cells11244017. [PMID: 36552780 PMCID: PMC9777387 DOI: 10.3390/cells11244017] [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: 08/31/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) poses a significant threat to the livestock industry. Through their recognition of the conserved epitopes presented by the swine leukocyte antigen (SLA), T cells play a pivotal role in the antiviral immunity of pigs. Herein, based on the peptide binding motif of SLA-2*HB01, from an original SLA-2 allele, a series of functional T-cell epitopes derived from the dominant antigen VP1 of FMDV with high binding capacity to SLA-2 were identified. Two parallel peptides, Hu64 and As64, from the O and Asia I serotypes, respectively, were both crystallized with SLA-2*HB01. Compared to SLA-1 and SLA-3, the SLA-2 structures showed the flexibility of residues in the P4, P6, and P8 positions and in their potential interface with TCR. Notably, the peptides Hu64 and As64 adopted quite similar overall conformation when bound to SLA-2*HB01. Hu64 has two different conformations, a more stable 'chair' conformation and an unstable 'boat' conformation observed in the two molecules of one asymmetric unit, whereas only a single 'chair' conformation was observed for As64. Both Hu64 and As64 could induce similar dominant T-cell activities. Our interdisciplinary study establishes a basis for the in-depth interpretation of the peptide presentation of SLA-I, which can be used toward the development of universal vaccines.
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Affiliation(s)
- Lei Feng
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yong-Yu Gao
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- College of Animal Medicine, Jilin Agricultural University, Changchun 130118, China
| | - Mingwei Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Zi-Bin Li
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, China
| | - Qiang Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Jie Yang
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Cui Qiao
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Hang Jin
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
| | - Hong-Sheng Feng
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
| | - Yu-Han Xian
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Correspondence: (G.F.G.); (W.J.L.); (F.-S.G.)
| | - William J. Liu
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Correspondence: (G.F.G.); (W.J.L.); (F.-S.G.)
| | - Feng-Shan Gao
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- Correspondence: (G.F.G.); (W.J.L.); (F.-S.G.)
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134
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Schwarze M, Luo J, Brakel A, Krizsan A, Lakowa N, Grünewald T, Lehmann C, Wolf J, Borte S, Milkovska-Stamenova S, Gabert J, Scholz M, Hoffmann R. Evaluation of S- and M-Proteins Expressed in Escherichia coli and HEK Cells for Serological Detection of Antibodies in Response to SARS-CoV-2 Infections and mRNA-Based Vaccinations. Pathogens 2022; 11:pathogens11121515. [PMID: 36558849 PMCID: PMC9782079 DOI: 10.3390/pathogens11121515] [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: 11/04/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
This study investigated the IgG and IgA antibody response against recombinant S1 and receptor binding domains (RBD) of the spike (S-) protein and the membrane (M-) protein using a set of 115 serum samples collected from patients infected with SARS-CoV-2 in Germany before April 2021 using protein and peptide ELISA. As S1- and RBD-proteins expressed in Escherichia coli provided poor sensitivities in ELISA, they were replaced by proteins expressed in HEK cells. The RBD-ELISA provided a sensitivity of 90.6% (N = 85) for samples collected from patients with confirmed SARS-CoV-2 infections more than 14 days after symptom onset or a positive PCR test. In population-based controls, the specificity was 97.9% (N = 94). In contrast, the sensitivities were only 41.2% and 72.6% for M- and N-proteins, respectively, while the specificities were 88.5% and 100%, respectively. Considering also 20 samples collected during the first two weeks of symptom onset or PCR confirmation, the sensitivity of RBD- and N-protein ELISA decreased to 82.6% and 72.6%, respectively. The combination of two data sets, i.e., N- and RBD-, N- and M-, or RBD- and M-proteins increased the sensitivity to 85.8%, 77.9%, and 87.8%, respectively. Peptide mapping mostly confirmed epitopes previously reported for S1- and M-proteins, but they were only recognized by a few samples already tested positive in the corresponding protein ELISA indicating that peptide-based assays will not improve the diagnostic sensitivity.
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Affiliation(s)
- Mandy Schwarze
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Ji Luo
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
- Adversis Pharma GmbH, 04103 Leipzig, Germany
| | - Alexandra Brakel
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Andor Krizsan
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Nicole Lakowa
- Klinik für Infektions- und Tropenmedizin, Klinikum Chemnitz gGmbH, 09113 Chemnitz, Germany
| | - Thomas Grünewald
- Klinik für Infektions- und Tropenmedizin, Klinikum Chemnitz gGmbH, 09113 Chemnitz, Germany
| | - Claudia Lehmann
- Laboratory for Transplantation Immunology, Institute for Transfusion Medicine, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Johannes Wolf
- Department of Laboratory Medicine, Hospital St. Georg gGmbH, 04129 Leipzig, Germany
- Immuno Deficiency Center Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg gGmbH, 04129 Leipzig, Germany
| | - Stephan Borte
- Department of Laboratory Medicine, Hospital St. Georg gGmbH, 04129 Leipzig, Germany
- Immuno Deficiency Center Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg gGmbH, 04129 Leipzig, Germany
| | - Sanja Milkovska-Stamenova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
- Adversis Pharma GmbH, 04103 Leipzig, Germany
| | - Jörg Gabert
- Adversis Pharma GmbH, 04103 Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, Universität Leipzig, 04107 Leipzig, Germany
- LIFE Research Center of Civilization Diseases, Universität Leipzig, 04103 Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
- Correspondence:
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135
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Montemurro A, Jessen LE, Nielsen M. NetTCR-2.1: Lessons and guidance on how to develop models for TCR specificity predictions. Front Immunol 2022; 13:1055151. [PMID: 36561755 PMCID: PMC9763291 DOI: 10.3389/fimmu.2022.1055151] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 09/27/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
T cell receptors (TCR) define the specificity of T cells and are responsible for their interaction with peptide antigen targets presented in complex with major histocompatibility complex (MHC) molecules. Understanding the rules underlying this interaction hence forms the foundation for our understanding of basic adaptive immunology. Over the last decade, efforts have been dedicated to developing assays for high throughput identification of peptide-specific TCRs. Based on such data, several computational methods have been proposed for predicting the TCR-pMHC interaction. The general conclusion from these studies is that the prediction of TCR interactions with MHC-peptide complexes remains highly challenging. Several reasons form the basis for this including scarcity and quality of data, and ill-defined modeling objectives imposed by the high redundancy of the available data. In this work, we propose a framework for dealing with this redundancy, allowing us to address essential questions related to the modeling of TCR specificity including the use of peptide- versus pan-specific models, how to best define negative data, and the performance impact of integrating of CDR1 and 2 loops. Further, we illustrate how and why it is strongly recommended to include simple similarity-based modeling approaches when validating an improved predictive power of machine learning models, and that such validation should include a performance evaluation as a function of "distance" to the training data, to quantify the potential for generalization of the proposed model. The conclusion of the work is that, given current data, TCR specificity is best modeled using peptide-specific approaches, integrating information from all 6 CDR loops, and with negative data constructed from a combination of true and mislabeled negatives. Comparing such machine learning models to similarity-based approaches demonstrated an increased performance gain of the former as the "distance" to the training data was increased; thus demonstrating an improved generalization ability of the machine learning-based approaches. We believe these results demonstrate that the outlined modeling framework and proposed evaluation strategy form a solid basis for investigating the modeling of TCR specificities and that adhering to such a framework will allow for faster progress within the field. The final devolved model, NetTCR-2.1, is available at https://services.healthtech.dtu.dk/service.php?NetTCR-2.1.
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Affiliation(s)
- Alessandro Montemurro
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, 2800 Kgs., Lyngby, Denmark
| | - Leon Eyrich Jessen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, 2800 Kgs., Lyngby, Denmark
| | - Morten Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, 2800 Kgs., Lyngby, Denmark,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina,*Correspondence: Morten Nielsen,
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Dai G, Huang X, Liu Q, Li Y, Zhang L, Han K, Yang J, Liu Y, Xue F, Zhao D. Identification of a linear epitope in the capsid protein of goose astrovirus with monoclonal antibody. Pol J Vet Sci 2022; 25:579-587. [PMID: 36649111 DOI: 10.24425/pjvs.2022.143541] [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] [Indexed: 01/18/2023]
Abstract
Goose astrovirus (GoAstV) is a novel avastrovirus that typically causes gosling gout and results in 2 to 20% mortality. GoAstV capsid protein is the sole structural protein, which is responsible for viral attachment, assembly, maturation as well as eliciting host antibodies. However, the epitopes within capsid protein have not been well studied. In this study, a monoclonal antibody, named 1D7, was generated against GoAstV capsid protein by hybridoma technology. Western blot results showed that this MAb could react with recombinant capsid protein expressed in E. coli. Also, it recognized the precursor of capsid protein, VP90 and VP70, in GoAstV-infected cells. Besides, excellent specificity of MAb 1D7 was further demonstrated in indirect immunofluorescence assay and immunohistochemical analysis. Epitope mapping results revealed that MAb 1D7 recognized the epitope 33QKVY 36 within Cap protein. Sequence alignment indicated that 33QKVY 36 is a conserved epitope among the isolates of goose astrovirus type 2 (GoAstV-2), suggesting the potential for its use in GoAstV-2 specific diagnostic assay. These findings may provide some insight into a function of the GoAstV capsid protein and further contribute to the development of diagnostic methods for GoAstV infection.
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Affiliation(s)
- G Dai
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing City, Jiangsu Province, 210014, PR China.,College of Veterinary Medicine, Nanjing Agricultural University, No. 1 Tongwei Road, Nanjing City, Jiangsu Province 210095, PR China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing City, Jiangsu Province, 210014, PR China
| | - X Huang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing City, Jiangsu Province, 210014, PR China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing City, Jiangsu Province, 210014, PR China
| | - Q Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing City, Jiangsu Province, 210014, PR China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing City, Jiangsu Province, 210014, PR China
| | - Y Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing City, Jiangsu Province, 210014, PR China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing City, Jiangsu Province, 210014, PR China
| | - L Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing City, Jiangsu Province, 210014, PR China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing City, Jiangsu Province, 210014, PR China
| | - K Han
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing City, Jiangsu Province, 210014, PR China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing City, Jiangsu Province, 210014, PR China
| | - J Yang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing City, Jiangsu Province, 210014, PR China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing City, Jiangsu Province, 210014, PR China
| | - Y Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing City, Jiangsu Province, 210014, PR China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing City, Jiangsu Province, 210014, PR China
| | - F Xue
- College of Veterinary Medicine, Nanjing Agricultural University, No. 1 Tongwei Road, Nanjing City, Jiangsu Province 210095, PR China
| | - D Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing City, Jiangsu Province, 210014, PR China.,College of Veterinary Medicine, Nanjing Agricultural University, No. 1 Tongwei Road, Nanjing City, Jiangsu Province 210095, PR China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing City, Jiangsu Province, 210014, PR China.,Institute of Life Sciences, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, Jiangsu Province, 212013, PR China
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Xu S, Wang Y, Wang Y, Zhang C, Hong Q, Gu C, Xu R, Wang T, Yang Y, Zang J, Zhou Y, Li Z, Liu Q, Zhou B, Bai L, Zhu Y, Deng Q, Wang H, Lavillette D, Wong G, Xie Y, Cong Y, Huang Z. Mapping cross-variant neutralizing sites on the SARS-CoV-2 spike protein. Emerg Microbes Infect 2022; 11:351-367. [PMID: 34964428 PMCID: PMC8794075 DOI: 10.1080/22221751.2021.2024455] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 11/04/2021] [Accepted: 12/28/2021] [Indexed: 12/23/2022]
Abstract
The emergence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern threatens the efficacy of currently approved vaccines and authorized therapeutic monoclonal antibodies (MAbs). It is hence important to continue searching for SARS-CoV-2 broadly neutralizing MAbs and defining their epitopes. Here, we isolate 9 neutralizing mouse MAbs raised against the spike protein of a SARS-CoV-2 prototype strain and evaluate their neutralizing potency towards a panel of variants, including B.1.1.7, B.1.351, B.1.617.1, and B.1.617.2. By using a combination of biochemical, virological, and cryo-EM structural analyses, we identify three types of cross-variant neutralizing MAbs, represented by S5D2, S5G2, and S3H3, respectively, and further define their epitopes. S5D2 binds the top lateral edge of the receptor-binding motif within the receptor-binding domain (RBD) with a binding footprint centred around the loop477-489, and efficiently neutralizes all variant pseudoviruses, but the potency against B.1.617.2 was observed to decrease significantly. S5G2 targets the highly conserved RBD core region and exhibits comparable neutralization towards the variant panel. S3H3 binds a previously unreported epitope located within the evolutionarily stable SD1 region and is able to near equally neutralize all of the variants tested. Our work thus defines three distinct cross-variant neutralizing sites on the SARS-CoV-2 spike protein, providing guidance for design and development of broadly effective vaccines and MAb-based therapies.
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Affiliation(s)
- Shiqi Xu
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Chao Zhang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Qin Hong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Chenjian Gu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Rong Xu
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Tingfeng Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yong Yang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Jinkai Zang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yu Zhou
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Zuyang Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Qixing Liu
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Bingjie Zhou
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Lulu Bai
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yuanfei Zhu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
- BSL-3 Laboratory of Fudan University, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Qiang Deng
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Haikun Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Dimitri Lavillette
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Gary Wong
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
- BSL-3 Laboratory of Fudan University, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Zhong Huang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People’s Republic of China
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Dawe WH, Kapczynski DR, Linnemann EG, Gauthiersloan VR, Sellers HS. Analysis of the Immune Response and Identification of Antibody Epitopes Against the Sigma C Protein of Avian Orthoreovirus Following Immunization with Live or Inactivated Vaccines. Avian Dis 2022; 66:465-478. [PMID: 36715481 DOI: 10.1637/aviandiseases-d-22-99992] [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: 08/15/2022] [Accepted: 09/01/2022] [Indexed: 01/24/2023]
Abstract
Avian orthoreoviruses are causative agents of tenosynovitis and viral arthritis in both chickens and turkeys. Current commercial reovirus vaccines do not protect against disease caused by emerging variants. Custom-made inactivated reovirus vaccines are commonly utilized to help protect commercial poultry against disease. Antibody epitopes located on the viral attachment protein, σC, involved in virus neutralization, have not been clearly identified. In this study, the S1133 vaccine strain (Genetic Cluster 1 [GC1], a GC1 field isolate (117816), and a GC5 field isolate (94826) were determined to be genetically and serologically unrelated. In addition, chickens were vaccinated with either a commercial S1133 vaccine, 117816 GC1, or 94826 GC5, and sera were used in peptide microarrays to identify linear B-cell epitopes within the σC protein. Specific-pathogen-free (SPF) chickens were vaccinated twice with either: 1) live and live, 2) inactivated and inactivated, or 3) a combination of live and inactivated vaccines. Epitope mapping was performed on individual serum samples from birds in each group using S1133, 117816, and 94826 σC sequences translated into an overlapping peptides and spotted onto microarray chips. Vaccination with a combination of live and inactivated viruses resulted in a greater number of B-cell binding sites on the outer-capsid domains of σC for 117816 and 94826, but not for S1133. In contrast, the S1133-vaccinated birds demonstrated fewer epitopes, and those epitopes were located in the stalk region of the protein. However, within each of the vaccinated groups, the highest virus-neutralization titers were observed in the live/inactivated groups. This study demonstrates differences in antibody binding sites within σC between genetically and antigenically distinct reoviruses and provides initial antigenic characterization of avian orthoreoviruses and insight into the inability of vaccine-induced antibodies to provide adequate protection against variant reovirus-induced disease.
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Affiliation(s)
- W H Dawe
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - D R Kapczynski
- U.S. National Poultry Research Center, Agricultural Research Services, U.S. Department of Agriculture, Athens, GA 30605
| | - E G Linnemann
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - V R Gauthiersloan
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - H S Sellers
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602,
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139
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ANAM K, ENDHARTI AT, POERANTO S, PRAWIRO SR. Peptide Sequence of Pili Subunit Protein 49.8 kDa Shigella flexneri as Antigenic Epitope for Shigellosis Vaccine Development. Turk J Pharm Sci 2022; 19:649-656. [PMID: 36544298 PMCID: PMC9780573 DOI: 10.4274/tjps.galenos.2021.75031] [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: 12/31/2022]
Abstract
Objectives This study investigates the amino acid sequence and identifies antigenic epitopes of 49.8 kilodalton (kDa) pili protein Shigella flexneri, which will be used as candidates for the shigellosis vaccine. Materials and Methods Our study is a prospectively descriptive laboratory. We used bacterial isolate of S. flexneri pili isolation was performed using a pili cutter and sodium dodecyl-sulfate polyacrylamide gel electrophoresis. The amino acid sequences were analyzed using liquid chromatography dual mass spectrometry (LC-MS/MS) method in the proteomic laboratory. The target epitope antigenicity analysis was tested using Kolaskar and Tongaonkar Antigenicity software. The Bepired Linear Epitope Prediction software is used for epitope mapping. PymOL software was used for the visualization of proteins and molecular docking. Peptides and antibodies were applied to hemagglutination test and immune response was tested using the dot blot method. Results LC-MS/MS analysis results from the mascot server showed that the 49.8 kDa pili protein is S. flexneri similar to the flagellin protein of S. flexneri 1235-66 (ID I6H2T2). The results of antigenicity analysis and epitope mapping showed that areas of protein that has the most potential and antigenic epitopes are the regions 98-111 and 263-290 with the amino acid sequences, QSSTGTNSQSDLDS (Q-S) and DTTITKAETKTVTKNQVVDTPVTTDAAK (D-K). The results of the molecular docking interaction test between the peptide and the B-cell receptor have a low binding energy. Peptide Q-S and peptide D-K antigens are hemagglutinin molecules because they can agglutinate erythrocytes. The immune response between peptide antigens and anti-peptide antibodies can react based on color gradations in the dotblot method. Conclusion The amino acid sequences Q-S and D-K are potentially antigenic epitopes. These peptides can be used to develop candidates for shigellosis vaccine.
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Affiliation(s)
- Khoirul ANAM
- Universitas Brawijaya, Faculty of Medicine, Doctoral Program in Medical Science, Malang, Indonesia,Institute of Technology and Health Science of Wiyata Husada Samarinda, Medical Laboratory Technology Study Program, Samarinda, Indonesia,* Address for Correspondence: Phone: +6281347175316 E-mail:
| | - Agustina Tri ENDHARTI
- Universitas Brawijaya, Faculty of Medicine, Department of Parasitology, Malang, Indonesia
| | - Sri POERANTO
- Universitas Brawijaya, Faculty of Medicine, Department of Parasitology, Malang, Indonesia
| | - Sumarno Reto PRAWIRO
- Universitas Brawijaya, Faculty of Medicine, Department of Clinical Microbiology, Malang, Indonesia
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140
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Tanaka T, Suzuki H, Asano T, Li G, Nanamiya R, Tateyama N, Isoda Y, Okada Y, Kobayashi H, Yoshikawa T, Kaneko MK, Kato Y. Epitope Mapping of an Anti-Mouse CCR2 Monoclonal Antibody (C 2Mab-6) Using Enzyme-Linked Immunosorbent Assay. Monoclon Antib Immunodiagn Immunother 2022; 41:339-342. [PMID: 36346278 DOI: 10.1089/mab.2022.0020] [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: 11/09/2022] Open
Abstract
CC chemokine receptor type-2 (CCR2) is a member of the G protein-coupled receptors, and is mainly expressed on cell surface of immune cells. CCR2 binds to its ligand, C-C motif chemokine 2 (also named as monocyte chemoattractant protein-1), which involves in the tumor progression by modulating the tumor microenvironment. Therefore, the monoclonal antibody (mAb) targeting CCR2 could be one of the strategies for cancer treatment. In this study, we investigated the critical epitope of C2Mab-6, an anti-mouse CCR2 (mCCR2) mAb developed by N-terminal peptides immunization. We first performed enzyme-linked immunosorbent assay (ELISA) using N-terminal peptides of mCCR2 and demonstrated that C2Mab-6 recognizes 1-19 amino acids of mCCR2. We further performed ELISA using 20 alanine-substituted peptides of mCCR2. C2Mab-6 lost the reaction to the alanine-substituted peptides of D3A, N4A, M6A, P8A, Q9A, and F10A. These results indicate that the binding epitope of C2Mab-6 includes Asp3, Asn4, Met6, Pro8, Gln9, and Phe10 of mCCR2.
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Affiliation(s)
- Tomohiro Tanaka
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Hiroyuki Suzuki
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Teizo Asano
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Guanjie Li
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Ren Nanamiya
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Nami Tateyama
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Yu Isoda
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Yuki Okada
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Hiyori Kobayashi
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Takeo Yoshikawa
- Department of Pharmacology, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan.,Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan.,Department of Pharmacology, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan
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141
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Prawiningrum AF, Paramita RI, Panigoro SS. Immunoinformatics Approach for Epitope-Based Vaccine Design: Key Steps for Breast Cancer Vaccine. Diagnostics (Basel) 2022; 12. [PMID: 36552988 DOI: 10.3390/diagnostics12122981] [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: 09/16/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Vaccines are an upcoming medical intervention for breast cancer. By targeting the tumor antigen, cancer vaccines can be designed to train the immune system to recognize tumor cells. Therefore, along with technological advances, the vaccine design process is now starting to be carried out with more rational methods such as designing epitope-based peptide vaccines using immunoinformatics methods. Immunoinformatics methods can assist vaccine design in terms of antigenicity and safety. Common protocols used to design epitope-based peptide vaccines include tumor antigen identification, protein structure analysis, T cell epitope prediction, epitope characterization, and evaluation of protein-epitope interactions. Tumor antigen can be divided into two types: tumor associated antigen and tumor specific antigen. We will discuss the identification of tumor antigens using high-throughput technologies. Protein structure analysis comprises the physiochemical, hydrochemical, and antigenicity of the protein. T cell epitope prediction models are widely available with various prediction parameters as well as filtering tools for the prediction results. Epitope characterization such as allergenicity and toxicity can be done in silico as well using allergenicity and toxicity predictors. Evaluation of protein-epitope interactions can also be carried out in silico with molecular simulation. We will also discuss current and future developments of breast cancer vaccines using an immunoinformatics approach. Finally, although prediction models have high accuracy, the opposite can happen after being tested in vitro and in vivo. Therefore, further studies are needed to ensure the effectiveness of the vaccine to be developed. Although epitope-based peptide vaccines have the disadvantage of low immunogenicity, the addition of adjuvants can be a solution.
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142
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de la Fuente J, Moraga-Fernández A, Alberdi P, Díaz-Sánchez S, García-Álvarez O, Fernández-Melgar R, Contreras M. A Quantum Vaccinomics Approach for the Design and Production of MSP4 Chimeric Antigen for the Control of Anaplasma phagocytophilum Infections. Vaccines (Basel) 2022; 10. [PMID: 36560405 DOI: 10.3390/vaccines10121995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Anaplasma phagocytophilum Major surface protein 4 (MSP4) plays a role during infection and multiplication in host neutrophils and tick vector cells. Recently, vaccination trials with the A. phagocytophilum antigen MSP4 in sheep showed only partial protection against pathogen infection. However, in rabbits immunized with MSP4, this recombinant antigen was protective. Differences between rabbit and sheep antibody responses are probably associated with the recognition of non-protective epitopes by IgG of immunized lambs. To address this question, we applied quantum vaccinomics to identify and characterize MSP4 protective epitopes by a microarray epitope mapping using sera from vaccinated rabbits and sheep. The identified candidate protective epitopes or immunological quantum were used for the design and production of a chimeric protective antigen. Inhibition assays of A. phagocytophilum infection in human HL60 and Ixodes scapularis tick ISE6 cells evidenced protection by IgG from sheep and rabbits immunized with the chimeric antigen. These results supported that the design of new chimeric candidate protective antigens using quantum vaccinomics to improve the protective capacity of antigens in multiple hosts.
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143
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Liu C, Lin H, Cao L, Wang K, Sui J. Research progress on unique paratope structure, antigen binding modes, and systematic mutagenesis strategies of single-domain antibodies. Front Immunol 2022; 13:1059771. [PMID: 36479130 PMCID: PMC9720397 DOI: 10.3389/fimmu.2022.1059771] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 10/02/2022] [Accepted: 11/07/2022] [Indexed: 11/22/2022] Open
Abstract
Single-domain antibodies (sdAbs) showed the incredible advantages of small molecular weight, excellent affinity, specificity, and stability compared with traditional IgG antibodies, so their potential in binding hidden antigen epitopes and hazard detection in food, agricultural and veterinary fields were gradually explored. Moreover, its low immunogenicity, easy-to-carry target drugs, and penetration of the blood-brain barrier have made sdAbs remarkable achievements in medical treatment, toxin neutralization, and medical imaging. With the continuous development and maturity of modern molecular biology, protein analysis software and database with different algorithms, and next-generation sequencing technology, the unique paratope structure and different antigen binding modes of sdAbs compared with traditional IgG antibodies have aroused the broad interests of researchers with the increased related studies. However, the corresponding related summaries are lacking and needed. Different antigens, especially hapten antigens, show distinct binding modes with sdAbs. So, in this paper, the unique paratope structure of sdAbs, different antigen binding cases, and the current maturation strategy of sdAbs were classified and summarized. We hope this review lays a theoretical foundation to elucidate the antigen-binding mechanism of sdAbs and broaden the further application of sdAbs.
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144
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Abstract
Milk is an essential source of protein for infants and young children. At the same time, cow's milk is also one of the most common allergenic foods causing food allergies in children. Recently, cow's milk allergy (CMA) has become a common public health issue worldwide. Modern food processing technologies have been developed to reduce the allergenicity of milk proteins and improve the quality of life of patients with CMA. In this review, we summarize the main allergens in cow's milk, and introduce the recent findings on CMA responses. Moreover, the reduced effects and underlying mechanisms of different food processing techniques (such as heating, high pressure, γ-ray irradiation, ultrasound irradiation, hydrolysis, glycosylation, etc.) on the allergenicity of cow's milk proteins, and the application of processed cow's milk in clinical studies, are discussed. In addition, we describe the changes of nutritional value in cow's milk treated by different food processing technologies. This review provides an in-depth understanding of the allergenicity reduction of cow's milk proteins by various food processing techniques.
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Affiliation(s)
- Jing Yang
- Chongqing Engineering Research Center for Processing & Storage of Distinct Agricultural Products, Chongqing Technology and Business University, Chongqing, China
- College of Modern Industry for Nutrition & Health, Chongqing Technology and Business University, Chongqing, China
| | - Hong Kuang
- Chongqing Engineering Research Center for Processing & Storage of Distinct Agricultural Products, Chongqing Technology and Business University, Chongqing, China
| | - Xiaoli Xiong
- Chongqing Engineering Research Center for Processing & Storage of Distinct Agricultural Products, Chongqing Technology and Business University, Chongqing, China
| | - Ning Li
- Chongqing Engineering Research Center for Processing & Storage of Distinct Agricultural Products, Chongqing Technology and Business University, Chongqing, China
| | - Jiajia Song
- College of Food Science, Southwest University, Chongqing, China
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Swetha RG, Basu S, Ramaiah S, Anbarasu A. Multi- Epitope Vaccine for Monkeypox Using Pan-Genome and Reverse Vaccinology Approaches. Viruses 2022; 14. [PMID: 36423113 DOI: 10.3390/v14112504] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Outbreaks of monkeypox virus infections have imposed major health concerns worldwide, with high morbidity threats to children and immunocompromised adults. Although repurposed drugs and vaccines are being used to curb the disease, the evolving traits of the virus, exhibiting considerable genetic dynamicity, challenge the limits of a targeted treatment. A pan-genome-based reverse vaccinology approach can provide fast and efficient solutions to resolve persistent inconveniences in experimental vaccine design during an outbreak-exigency. The approach encompassed screening of available monkeypox whole genomes (n = 910) to identify viral targets. From 102 screened viral targets, viral proteins L5L, A28, and L5 were finalized based on their location, solubility, and antigenicity. The potential T-cell and B-cell epitopes were extracted from the proteins using immunoinformatics tools and algorithms. Multiple vaccine constructs were designed by combining the epitopes. Based on immunological properties, chemical stability, and structural quality, a novel multi-epitopic vaccine construct, V4, was finalized. Flexible-docking and coarse-dynamics simulation portrayed that the V4 had high binding affinity towards human HLA-proteins (binding energy < -15.0 kcal/mol) with low conformational fluctuations (<1 Å). Thus, the vaccine construct (V4) may act as an efficient vaccine to induce immunity against monkeypox, which encourages experimental validation and similar approaches against emerging viral infections.
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146
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Wang Q, Ning J, Chen Y, Li B, Shi L, He T, Zhang F, Chen X, Zhai A, Wu C. The BBIBP-CorV inactivated COVID-19 vaccine induces robust and persistent humoral responses to SARS-CoV-2 nucleocapsid, besides spike protein in healthy adults. Front Microbiol 2022; 13:1008420. [PMID: 36406456 PMCID: PMC9672472 DOI: 10.3389/fmicb.2022.1008420] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/17/2022] [Indexed: 01/15/2024] Open
Abstract
Vaccination is one of the best ways to control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic. Among the various SARS-CoV-2 vaccines approved for use, the BBIBP-CorV inactivated vaccine has been widely used in 93 countries. In order to understand deeply the protective mechanism of inactivated vaccine, which retains all antigenic components of live virus, the analysis of humoral responses triggered by multiple proteins is necessary. In this research, antibody responses were generated with 6 selected recombinant proteins and 68 overlapping peptides that completely covered SARS-CoV-2 nucleocapsid (N) protein in 254 healthy volunteers vaccinated with BBIBP-CorV. As a result, antibody responses to the receptor binding domain (RBD), N, and non-structural protein 8 (NSP8) were induced following immunization by BBIBP-CorV. The antibody responses detected in donors after the 2nd dose vaccination can be maintained for about 6 months. Moreover, specific antibody levels can be restored after the boosting vaccination measured by ELISA. Furthermore, the level of SARS-CoV-2 specific IgG response is independent of age and gender. Moreover, N391-408 was identified as a dominant peptide after vaccination of BBIBP-CorV through peptide screening. Understanding the overview of humoral reactivity of the vaccine will contribute to further research on the protective mechanism of the SARS-CoV-2 inactivated vaccine and provide potential biomarkers for the related application of inactivated vaccine.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Aixia Zhai
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Chao Wu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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147
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Yin D, Geng R, Shao H, Ye J, Qian K, Chen H, Qin A. Identification of novel linear epitopes in P72 protein of African swine fever virus recognized by monoclonal antibodies. Front Microbiol 2022; 13:1055820. [PMID: 36406452 PMCID: PMC9666363 DOI: 10.3389/fmicb.2022.1055820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 09/28/2022] [Accepted: 10/17/2022] [Indexed: 01/13/2024] Open
Abstract
African swine fever (ASF) is one of the highly contagious and lethal diseases among domestic pigs and wild boars. The capsid protein P72 of African swine fever virus (ASFV) is very important for the diagnosis and vaccine development. However, the epitope of the protein is not clear. In this study, capsid protein P72 was expressed in Sf9 cells along with its chaperone B602L. A total of ten monoclonal antibodies (mAbs) specific to P72 protein were developed by fusions between SP2/0 cells and spleen cells of mice immunized with the recombinant-P72&B602L proteins expressed in Sf9 cells. Four linear B cell epitopes 31SNIKNVNKSY40, 41GKPDP45, 56HLVHFNAH63 and 185ERLYE189 were identified. Biological information analysis illustrated that epitopes 31SNIKNVNKSY40, 41GKPDP45 and 185ERLYE189 were highly conserved within different ASFV strains. These findings may lead to a better understanding of the antibody-antigen interaction and provide new insights into the vaccine research and serological diagnosis of ASF.
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Affiliation(s)
- Dan Yin
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, China
| | - Renhao Geng
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, China
| | - Hongxia Shao
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, China
| | - Jianqiang Ye
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, China
| | - Kun Qian
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, China
| | - Hongjun Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, China
| | - Aijian Qin
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, China
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148
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Jabarzadeh S, Samiminemati A, Zeinoddini M. [In silico Design of a New Multi- Epitope Peptide-Based Vaccine Candidate Against Q Fever]. Mol Biol (Mosk) 2022; 56:168-178. [PMID: 35082267 DOI: 10.31857/s0026898422010037] [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: 12/06/2020] [Accepted: 04/15/2021] [Indexed: 06/14/2023]
Abstract
Novel types of the vaccines with high immunogenicity and low risks, including epitope-based vaccines, are sought. Among zoonotic disease, Q fever caused by Coxiella burnetii is an important target due to numerous outbreaks and the pandemic potential. Here we present a synthetic multi-epitope vaccine against Coxiella burnetii. This vaccine was developed using immunoinformatics approach. Antigenic proteins were studied, and five T cell epitopes were selected. Antigenicity, allergenicity, and toxicity of the selected epitopes were evaluated using the VaxiJen 2.0, AllerTOP, and ToxinPred servers, respectively. Selected epitopes were joined in a peptide sequence, with the cholera toxin В subunit (CTXB) as an adjuvant. The affinity of the proposed vaccine to MHCI and II molecules was measured in a molecular docking study. Resultant vaccine has high antigenicity, stability, and a half-life compatible with utilization in vaccination programs. In conclusion, the validated epitope sequences may be used as a potential vaccine to ensure protection against Q fever agent.
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Affiliation(s)
- S Jabarzadeh
- Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran
| | - A Samiminemati
- Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran
| | - M Zeinoddini
- Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran
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149
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García-Machorro J, Ramírez-Salinas GL, Martinez-Archundia M, Correa-Basurto J. The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus. Vaccines (Basel) 2022; 10:1844. [PMID: 36366353 PMCID: PMC9693616 DOI: 10.3390/vaccines10111844] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 10/28/2023] Open
Abstract
After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way to control the SARS-CoV-2 pandemic worldwide. This review describes the importance of bioinformatic and immunoinformatic tools (in silico) for guide vaccine design. In silico strategies permit the identification of epitopes (immunogenic peptides) which could be used as potential vaccines, as well as nonacarriers such as: vector viral based vaccines, RNA-based vaccines and dendrimers through immunoinformatics. Currently, nucleic acid and protein sequential as well structural analyses through bioinformatic tools allow us to get immunogenic epitopes which can induce immune response alone or in complex with nanocarriers. One of the advantages of in silico techniques is that they facilitate the identification of epitopes, while accelerating the process and helping to economize some stages of the development of safe vaccines.
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Affiliation(s)
- Jazmín García-Machorro
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Gema Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - Marlet Martinez-Archundia
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
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150
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Zhang H, Xiao W, Zhao M, Zhao Y, Zhang Y, Lu D, Lu S, Zhang Q, Peng W, Shu L, Zhang J, Liu S, Zong K, Wang P, Ye B, Li S, Tan S, Zhang F, Zhou J, Liu P, Wu G, Lu X, Gao GF, Liu WJ. The CD8+ and CD4+ T Cell Immunogen Atlas of Zika Virus Reveals E, NS1 and NS4 Proteins as the Vaccine Targets. Viruses 2022; 14. [PMID: 36366430 DOI: 10.3390/v14112332] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 02/01/2023] Open
Abstract
Zika virus (ZIKV)-specific T cells are activated by different peptides derived from virus structural and nonstructural proteins, and contributed to the viral clearance or protective immunity. Herein, we have depicted the profile of CD8+ and CD4+ T cell immunogenicity of ZIKV proteins in C57BL/6 (H-2b) and BALB/c (H-2d) mice, and found that featured cellular immunity antigens were variant among different murine alleles. In H-2b mice, the proteins E, NS2, NS3 and NS5 are recognized as immunodominant antigens by CD8+ T cells, while NS4 is dominantly recognized by CD4+ T cells. In contrast, in H-2d mice, NS1 and NS4 are the dominant CD8+ T cell antigen and NS4 as the dominant CD4+ T cell antigen, respectively. Among the synthesized 364 overlapping polypeptides spanning the whole proteome of ZIKV, we mapped 91 and 39 polypeptides which can induce ZIKV-specific T cell responses in H-2b and H-2d mice, respectively. Through the identification of CD8+ T cell epitopes, we found that immunodominant regions E294-302 and NS42351-2360 are hotspots epitopes with a distinct immunodominance hierarchy present in H-2b and H-2d mice, respectively. Our data characterized an overall landscape of the immunogenic spectrum of the ZIKV polyprotein, and provide useful insight into the vaccine development.
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