1
|
Mubarak AS, Ameen ZS, Hassan AS, Ozsahin DU. Enhancing tuberculosis vaccine development: a deconvolution neural network approach for multi-epitope prediction. Sci Rep 2024; 14:10375. [PMID: 38710737 DOI: 10.1038/s41598-024-59291-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Tuberculosis (TB) a disease caused by Mycobacterium tuberculosis (Mtb) poses a significant threat to human life, and current BCG vaccinations only provide sporadic protection, therefore there is a need for developing efficient vaccines. Numerous immunoinformatic methods have been utilized previously, here for the first time a deep learning framework based on Deconvolutional Neural Networks (DCNN) and Bidirectional Long Short-Term Memory (DCNN-BiLSTM) was used to predict Mtb Multiepitope vaccine (MtbMEV) subunits against six Mtb H37Rv proteins. The trained model was used to design MEV within a few minutes against TB better than other machine learning models with 99.5% accuracy. The MEV has good antigenicity, and physiochemical properties, and is thermostable, soluble, and hydrophilic. The vaccine's BLAST search ruled out the possibility of autoimmune reactions. The secondary structure analysis revealed 87% coil, 10% beta, and 2% alpha helix, while the tertiary structure was highly upgraded after refinement. Molecular docking with TLR3 and TLR4 receptors showed good binding, indicating high immune reactions. Immune response simulation confirmed the generation of innate and adaptive responses. In-silico cloning revealed the vaccine is highly expressed in E. coli. The results can be further experimentally verified using various analyses to establish a candidate vaccine for future clinical trials.
Collapse
Affiliation(s)
- Auwalu Saleh Mubarak
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia, 99138, Turkey
- Department of Electrical Engineering, Aliko Dangote University of Science and Technology, Wudil, Kano, Nigeria
| | - Zubaida Said Ameen
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia, 99138, Turkey
- Department of Biochemistry, Yusuf Maitama Sule University, Kano, Nigeria
| | - Abdurrahman Shuaibu Hassan
- Department of Electrical Electronics and Automation Systems Engineering, Kampala International University, Kampala, Uganda.
| | - Dilber Uzun Ozsahin
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia, 99138, Turkey.
- Department of Medical Diagnostic Imaging, College of Health Science, University of Sharjah, Sharjah, UAE.
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE.
| |
Collapse
|
2
|
Ozsahin DU, Ameen ZS, Hassan AS, Mubarak AS. Enhancing explainable SARS-CoV-2 vaccine development leveraging bee colony optimised Bi-LSTM, Bi-GRU models and bioinformatic analysis. Sci Rep 2024; 14:6737. [PMID: 38509174 PMCID: PMC10954760 DOI: 10.1038/s41598-024-55762-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded RNA virus that caused the outbreak of the coronavirus disease 2019 (COVID-19). The COVID-19 outbreak has led to millions of deaths and economic losses globally. Vaccination is the most practical solution, but finding epitopes (antigenic peptide regions) in the SARS-CoV-2 proteome is challenging, costly, and time-consuming. Here, we proposed a deep learning method based on standalone Recurrent Neural networks to predict epitopes from SARS-CoV-2 proteins easily. We optimised the standalone Bidirectional Long Short-Term Memory (Bi-LSTM) and Bidirectional Gated Recurrent Unit (Bi-GRU) with a bioinspired optimisation algorithm, namely, Bee Colony Optimization (BCO). The study shows that LSTM-based models, particularly BCO-Bi-LSTM, outperform all other models and achieve an accuracy of 0.92 and AUC of 0.944. To overcome the challenge of understanding the model predictions, explainable AI using the Shapely Additive Explanations (SHAP) method was employed to explain how Blackbox models make decisions. Finally, the predicted epitopes led to the development of a multi-epitope vaccine. The multi-epitope vaccine effectiveness evaluation is based on vaccine toxicity, allergic response risk, and antigenic and biochemical characteristics using bioinformatic tools. The developed multi-epitope vaccine is non-toxic and highly antigenic. Codon adaptation, cloning, gel electrophoresis assess genomic sequence, protein composition, expression and purification while docking and IMMSIM servers simulate interactions and immunological response, respectively. These investigations provide a conceptual framework for developing a SARS-CoV-2 vaccine.
Collapse
Affiliation(s)
- Dilber Uzun Ozsahin
- Department of Medical Diagnostic Imaging, College of Health Science, University of Sharjah, Sharjah, UAE
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia, 99138, Turkey
| | - Zubaida Said Ameen
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia, 99138, Turkey
- Department of Biochemistry, Yusuf Maitama Sule University, Kano, Nigeria
| | - Abdurrahman Shuaibu Hassan
- Department of Electrical Electronics and Automation Systems Engineering, Kampala International University, Kampala, Uganda.
| | - Auwalu Saleh Mubarak
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia, 99138, Turkey
- Department of Electrical Engineering, Aliko Dangote University of Science and Technology, Wudil, Kano, Nigeria
| |
Collapse
|
3
|
Andongma BT, Huang Y, Chen F, Tang Q, Yang M, Chou SH, Li X, He J. In silico design of a promiscuous chimeric multi-epitope vaccine against Mycobacterium tuberculosis. Comput Struct Biotechnol J 2023; 21:991-1004. [PMID: 36733703 PMCID: PMC9883148 DOI: 10.1016/j.csbj.2023.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023] Open
Abstract
Tuberculosis (TB) is a global health threat, killing approximately 1.5 million people each year. The eradication of Mycobacterium tuberculosis, the main causative agent of TB, is increasingly challenging due to the emergence of extensive drug-resistant strains. Vaccination is considered an effective way to protect the host from pathogens, but the only clinically approved TB vaccine, Bacillus Calmette-Guérin (BCG), has limited protection in adults. Multi-epitope vaccines have been found to enhance immunity to diseases by selectively combining epitopes from several candidate proteins. This study aimed to design a multi-epitope vaccine against TB using an immuno-informatics approach. Through functional enrichment, we identified eight proteins secreted by M. tuberculosis that are either required for pathogenesis, secreted into extracellular space, or both. We then analyzed the epitopes of these proteins and selected 16 helper T lymphocyte epitopes with interferon-γ inducing activity, 15 cytotoxic T lymphocyte epitopes, and 10 linear B-cell epitopes, and conjugated them with adjuvant and Pan HLA DR-binding epitope (PADRE) using appropriate linkers. Moreover, we predicted the tertiary structure of this vaccine, its potential interaction with Toll-Like Receptor-4 (TLR4), and the immune response it might elicit. The results showed that this vaccine had a strong affinity for TLR4, which could significantly stimulate CD4+ and CD8+ cells to secrete immune factors and B lymphocytes to secrete immunoglobulins, so as to obtain good humoral and cellular immunity. Overall, this multi-epitope protein was predicted to be stable, safe, highly antigenic, and highly immunogenic, which has the potential to serve as a global vaccine against TB.
Collapse
Affiliation(s)
- Binda T. Andongma
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yazheng Huang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Fang Chen
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Qing Tang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Min Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xinfeng Li
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China,Correspondence to: The State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan, Hubei 430070, PR China.
| | - Jin He
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Correspondence to: The State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan, Hubei 430070, PR China.
| |
Collapse
|
4
|
Sei S, Ahadova A, Keskin DB, Bohaumilitzky L, Gebert J, von Knebel Doeberitz M, Lipkin SM, Kloor M. Lynch syndrome cancer vaccines: A roadmap for the development of precision immunoprevention strategies. Front Oncol 2023; 13:1147590. [PMID: 37035178 PMCID: PMC10073468 DOI: 10.3389/fonc.2023.1147590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Hereditary cancer syndromes (HCS) account for 5~10% of all cancer diagnosis. Lynch syndrome (LS) is one of the most common HCS, caused by germline mutations in the DNA mismatch repair (MMR) genes. Even with prospective cancer surveillance, LS is associated with up to 50% lifetime risk of colorectal, endometrial, and other cancers. While significant progress has been made in the timely identification of germline pathogenic variant carriers and monitoring and early detection of precancerous lesions, cancer-risk reduction strategies are still centered around endoscopic or surgical removal of neoplastic lesions and susceptible organs. Safe and effective cancer prevention strategies are critically needed to improve the life quality and longevity of LS and other HCS carriers. The era of precision oncology driven by recent technological advances in tumor molecular profiling and a better understanding of genetic risk factors has transformed cancer prevention approaches for at-risk individuals, including LS carriers. MMR deficiency leads to the accumulation of insertion and deletion mutations in microsatellites (MS), which are particularly prone to DNA polymerase slippage during DNA replication. Mutations in coding MS give rise to frameshift peptides (FSP) that are recognized by the immune system as neoantigens. Due to clonal evolution, LS tumors share a set of recurrent and predictable FSP neoantigens in the same and in different LS patients. Cancer vaccines composed of commonly recurring FSP neoantigens selected through prediction algorithms have been clinically evaluated in LS carriers and proven safe and immunogenic. Preclinically analogous FSP vaccines have been shown to elicit FSP-directed immune responses and exert tumor-preventive efficacy in murine models of LS. While the immunopreventive efficacy of "off-the-shelf" vaccines consisting of commonly recurring FSP antigens is currently investigated in LS clinical trials, the feasibility and utility of personalized FSP vaccines with individual HLA-restricted epitopes are being explored for more precise targeting. Here, we discuss recent advances in precision cancer immunoprevention approaches, emerging enabling technologies, research gaps, and implementation barriers toward clinical translation of risk-tailored prevention strategies for LS carriers. We will also discuss the feasibility and practicality of next-generation cancer vaccines that are based on personalized immunogenic epitopes for precision cancer immunoprevention.
Collapse
Affiliation(s)
- Shizuko Sei
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
- *Correspondence: Shizuko Sei, ; Steven M. Lipkin, ; Matthias Kloor,
| | - Aysel Ahadova
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Derin B. Keskin
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Broad Institute of The Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Lena Bohaumilitzky
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Steven M. Lipkin
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY, United States
- *Correspondence: Shizuko Sei, ; Steven M. Lipkin, ; Matthias Kloor,
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
- *Correspondence: Shizuko Sei, ; Steven M. Lipkin, ; Matthias Kloor,
| |
Collapse
|
5
|
Walker A, Schwarz T, Brinkmann-Paulukat J, Wisskirchen K, Menne C, Alizei ES, Kefalakes H, Theissen M, Hoffmann D, Schulze zur Wiesch J, Maini MK, Cornberg M, Kraft ARM, Keitel V, Bock HH, Horn PA, Thimme R, Wedemeyer H, Heinemann FM, Luedde T, Neumann-Haefelin C, Protzer U, Timm J. Immune escape pathways from the HBV core 18-27 CD8 T cell response are driven by individual HLA class I alleles. Front Immunol 2022; 13:1045498. [PMID: 36439181 PMCID: PMC9686862 DOI: 10.3389/fimmu.2022.1045498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Background and aims There is growing interest in T cell-based immune therapies for a functional cure of chronic HBV infection including check-point inhibition, T cell-targeted vaccines or TCR-grafted effector cells. All these approaches depend on recognition of HLA class I-presented viral peptides. The HBV core region 18-27 is an immunodominant target of CD8+ T cells and represents the prime target for T cell-based therapies. Here, a high-resolution analysis of the core18-27 specific CD8+ T cell and the selected escape pathways was performed. Methods HLA class I typing and viral sequence analyses were performed for 464 patients with chronic HBV infection. HBV-specific CD8+ T-cell responses against the prototype and epitope variants were characterized by flow cytometry. Results Consistent with promiscuous presentation of the core18-27 epitope, antigen-specific T cells were detected in patients carrying HLA-A*02:01, HLA-B*35:01, HLA-B*35:03 or HLA-B*51:01. Sequence analysis confirmed reproducible selection pressure on the core18-27 epitope in the context of these alleles. Interestingly, the selected immune escape pathways depend on the presenting HLA-class I-molecule. Although cross-reactive T cells were observed, some epitope variants achieved functional escape by impaired TCR-interaction or disturbed antigen processing. Of note, selection of epitope variants was exclusively observed in HBeAg negative HBV infection and here, detection of variants associated with significantly greater magnitude of the CD8 T cell response compared to absence of variants. Conclusion The core18-27 epitope is highly variable and under heavy selection pressure in the context of different HLA class I-molecules. Some epitope variants showed evidence for impaired antigen processing and reduced presentation. Viruses carrying such escape substitutions will be less susceptible to CD8+ T cell responses and should be considered for T cell-based therapy strategies.
Collapse
Affiliation(s)
- Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tatjana Schwarz
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Janine Brinkmann-Paulukat
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karin Wisskirchen
- Institute of Virology, School of Medicine, Technical University of Munich, Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Site Munich, Munich, Germany
| | - Christopher Menne
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Elahe Salimi Alizei
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Helenie Kefalakes
- Institute of Virology, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Martin Theissen
- Research Group Bioinformatics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Research Group Bioinformatics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Julian Schulze zur Wiesch
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg, Hamburg, Germany
| | - Mala K. Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Markus Cornberg
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover, Hannover, Germany
| | - Anke RM Kraft
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover, Hannover, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Hans H. Bock
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter A. Horn
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Robert Thimme
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover, Hannover, Germany
| | - Falko M. Heinemann
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christoph Neumann-Haefelin
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Site Munich, Munich, Germany
| | - Jörg Timm
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
6
|
Pley C, Lourenço J, McNaughton AL, Matthews PC. Spacer Domain in Hepatitis B Virus Polymerase: Plugging a Hole or Performing a Role? J Virol 2022; 96:e0005122. [PMID: 35412348 PMCID: PMC9093120 DOI: 10.1128/jvi.00051-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/14/2022] [Indexed: 11/25/2022] Open
Abstract
Hepatitis B virus (HBV) polymerase is divided into terminal protein, spacer, reverse transcriptase, and RNase domains. Spacer has previously been considered dispensable, merely acting as a tether between other domains or providing plasticity to accommodate deletions and mutations. We explore evidence for the role of spacer sequence, structure, and function in HBV evolution and lineage, consider its associations with escape from drugs, vaccines, and immune responses, and review its potential impacts on disease outcomes.
Collapse
Affiliation(s)
- Caitlin Pley
- School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
- Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
| | - Anna L. McNaughton
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Nuffield Department of Medicine, University of Oxford Medawar Building, Oxford, United Kingdom
| | - Philippa C. Matthews
- Nuffield Department of Medicine, University of Oxford Medawar Building, Oxford, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| |
Collapse
|
7
|
Ding Y, Zhou Z, Li X, Zhao C, Jin X, Liu X, Wu Y, Mei X, Li J, Qiu J, Shen C. Screening and Identification of HBV Epitopes Restricted by Multiple Prevalent HLA-A Allotypes. Front Immunol 2022; 13:847105. [PMID: 35464415 PMCID: PMC9021956 DOI: 10.3389/fimmu.2022.847105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/15/2022] [Indexed: 12/21/2022] Open
Abstract
Although host T cell immune responses to hepatitis B virus (HBV) have been demonstrated to have important influences on the outcome of HBV infection, the development of T cell epitope-based vaccine and T cell therapy and the clinical evaluation of specific T cell function are currently hampered markedly by the lack of validated HBV T cell epitopes covering broad patients. This study aimed to screen T cell epitopes spanning overall HBsAg, HBeAg, HBx and HBpol proteins and presenting by thirteen prevalent human leukocyte antigen (HLA)-A allotypes which gather a total gene frequency of around 95% in China and Northeast Asia populations. 187 epitopes were in silico predicted. Of which, 62 epitopes were then functionally validated as real-world HBV T cell epitopes by ex vivo IFN-γ ELISPOT assay and in vitro co-cultures using peripheral blood mononuclear cells (PBMCs) from HBV infected patients. Furthermore, the HLA-A cross-restrictions of each epitope were identified by peptide competitive binding assay using transfected HMy2.CIR cell lines, and by HLA-A/peptide docking as well as molecular dynamic simulation. Finally, a peptide library containing 105 validated epitopes which cross-binding by 13 prevalent HLA-A allotypes were used in ELISPOT assay to enumerate HBV-specific T cells for 116 patients with HBV infection. The spot forming units (SFUs) was significantly correlated with serum HBsAg level as confirmed by multivariate linear regression analysis. This study functionally validated 62 T cell epitopes from HBV main proteins and elucidated their HLA-A restrictions and provided an alternative ELISPOT assay using validated epitope peptides rather than conventional overlapping peptides for the clinical evaluation of HBV-specific T cell responses.
Collapse
Affiliation(s)
- Yan Ding
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China
| | - Zining Zhou
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China
| | - Xingyu Li
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Chen Zhao
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China
| | - Xiaoxiao Jin
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China
| | - Xiaotao Liu
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China
| | - Yandan Wu
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China
| | - Xueyin Mei
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jian Li
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jie Qiu
- Division of Hepatitis, Nanjing Second Hospital, Nanjing Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China
| |
Collapse
|
8
|
Brooks BD, Beland A, Aguero G, Taylor N, Towne FD. Moving beyond Titers. Vaccines (Basel) 2022; 10:vaccines10050683. [PMID: 35632439 PMCID: PMC9144832 DOI: 10.3390/vaccines10050683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 01/27/2023] Open
Abstract
Vaccination to prevent and even eliminate disease is amongst the greatest achievements of modern medicine. Opportunities remain in vaccine development to improve protection across the whole population. A next step in vaccine development is the detailed molecular characterization of individual humoral immune responses against a pathogen, especially the rapidly evolving pathogens. New technologies such as sequencing the immune repertoire in response to disease, immunogenomics/vaccinomics, particularly the individual HLA variants, and high-throughput epitope characterization offer new insights into disease protection. Here, we highlight the emerging technologies that could be used to identify variation within the human population, facilitate vaccine discovery, improve vaccine safety and efficacy, and identify mechanisms of generating immunological memory. In today’s vaccine-hesitant climate, these techniques used individually or especially together have the potential to improve vaccine effectiveness and safety and thus vaccine uptake rates. We highlight the importance of using these techniques in combination to understand the humoral immune response as a whole after vaccination to move beyond neutralizing titers as the standard for immunogenicity and vaccine efficacy, especially in clinical trials.
Collapse
Affiliation(s)
- Benjamin D. Brooks
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT 84738, USA
- Inovan Inc., Fargo, ND 58103, USA
- Correspondence: ; Tel.: +1-(435)-222-1304
| | - Alexander Beland
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Gabriel Aguero
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Nicholas Taylor
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Francina D. Towne
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| |
Collapse
|
9
|
Baron M, Soulié C, Lavolé A, Assoumou L, Abbar B, Fouquet B, Rousseau A, Veyri M, Samri A, Makinson A, Choquet S, Mazières J, Brosseau S, Autran B, Costagliola D, Katlama C, Cadranel J, Marcelin AG, Lambotte O, Spano JP, Guihot A. Impact of Anti PD-1 Immunotherapy on HIV Reservoir and Anti-Viral Immune Responses in People Living with HIV and Cancer. Cells 2022; 11:cells11061015. [PMID: 35326466 PMCID: PMC8946896 DOI: 10.3390/cells11061015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
The role of immune checkpoints (ICPs) in both anti-HIV T cell exhaustion and HIV reservoir persistence, has suggested that an HIV cure therapeutic strategy could involve ICP blockade. We studied the impact of anti-PD-1 therapy on HIV reservoirs and anti-viral immune responses in people living with HIV and treated for cancer. At several timepoints, we monitored CD4 cell counts, plasma HIV-RNA, cell associated (CA) HIV-DNA, EBV, CMV, HBV, HCV, and HHV-8 viral loads, activation markers, ICP expression and virus-specific T cells. Thirty-two patients were included, with median follow-up of 5 months. The CA HIV-DNA tended to decrease before cycle 2 (p = 0.049). Six patients exhibited a ≥0.5 log10 HIV-DNA decrease at least once. Among those, HIV-DNA became undetectable for 10 months in one patient. Overall, no significant increase in HIV-specific immunity was observed. In contrast, we detected an early increase in CTLA-4 + CD4+ T cells in all patients (p = 0.004) and a greater increase in CTLA-4+ and TIM-3 + CD8+ T cells in patients without HIV-DNA reduction compared to the others (p ≤ 0.03). Our results suggest that ICP replacement compensatory mechanisms might limit the impact of anti-PD-1 monotherapy on HIV reservoirs, and pave the way for combination ICP blockade in HIV cure strategies.
Collapse
Affiliation(s)
- Marine Baron
- INSERM U1135, CIMI, Département d’Immunologie, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (B.A.); (B.F.); (A.R.); (A.S.); (B.A.); (A.G.)
- Correspondence:
| | - Cathia Soulié
- INSERM UMR_S 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Département de Virologie, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (C.S.); (A.-G.M.)
| | - Armelle Lavolé
- GRC #04 Theranoscan, Département de Pneumologie et Oncologie Thoracique, AP-HP, Hôpital Tenon, Sorbonne Université, F-75020 Paris, France; (A.L.); (J.C.)
| | - Lambert Assoumou
- INSERM UMR_S 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Sorbonne Université, F-75013 Paris, France; (L.A.); (D.C.)
| | - Baptiste Abbar
- INSERM U1135, CIMI, Département d’Immunologie, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (B.A.); (B.F.); (A.R.); (A.S.); (B.A.); (A.G.)
| | - Baptiste Fouquet
- INSERM U1135, CIMI, Département d’Immunologie, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (B.A.); (B.F.); (A.R.); (A.S.); (B.A.); (A.G.)
| | - Alice Rousseau
- INSERM U1135, CIMI, Département d’Immunologie, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (B.A.); (B.F.); (A.R.); (A.S.); (B.A.); (A.G.)
| | - Marianne Veyri
- Département d’Oncologie Médicale, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (M.V.); (J.-P.S.)
| | - Assia Samri
- INSERM U1135, CIMI, Département d’Immunologie, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (B.A.); (B.F.); (A.R.); (A.S.); (B.A.); (A.G.)
| | - Alain Makinson
- INSERM U1175, Département de Maladies Infectieuses, Centre Hospitalier Universitaire de Montpellier, Université de Montpellier, F-34090 Montpellier, France;
| | - Sylvain Choquet
- Département d’Hématologie Clinique, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France;
| | - Julien Mazières
- Département de Pneumologie, Centre Hospitalier Universitaire de Toulouse, F-31000 Toulouse, France;
| | - Solenn Brosseau
- Département de Pneumologie, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France;
| | - Brigitte Autran
- INSERM U1135, CIMI, Département d’Immunologie, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (B.A.); (B.F.); (A.R.); (A.S.); (B.A.); (A.G.)
| | - Dominique Costagliola
- INSERM UMR_S 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Sorbonne Université, F-75013 Paris, France; (L.A.); (D.C.)
| | - Christine Katlama
- Département de Maladies Infectieuses, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France;
| | - Jacques Cadranel
- GRC #04 Theranoscan, Département de Pneumologie et Oncologie Thoracique, AP-HP, Hôpital Tenon, Sorbonne Université, F-75020 Paris, France; (A.L.); (J.C.)
| | - Anne-Geneviève Marcelin
- INSERM UMR_S 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Département de Virologie, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (C.S.); (A.-G.M.)
| | - Olivier Lambotte
- Département d’Immunologie Clinique, AP-HP, Hôpital Bicêtre, Université Paris-Saclay, F-94270 Le Kremlin Bicêtre, France;
- INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IDMIT/IMVA-HB), UMR1184, Université Paris-Saclay, F-94270 Le Kremlin Bicêtre, France
| | - Jean-Philippe Spano
- Département d’Oncologie Médicale, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (M.V.); (J.-P.S.)
| | - Amélie Guihot
- INSERM U1135, CIMI, Département d’Immunologie, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, F-75013 Paris, France; (B.A.); (B.F.); (A.R.); (A.S.); (B.A.); (A.G.)
| | | | | |
Collapse
|
10
|
A Systematic Review of T Cell Epitopes Defined from the Proteome of Hepatitis B Virus. Vaccines (Basel) 2022; 10:vaccines10020257. [PMID: 35214714 PMCID: PMC8878595 DOI: 10.3390/vaccines10020257] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) infection remains a worldwide health problem and no eradicative therapy is currently available. Host T cell immune responses have crucial influences on the outcome of HBV infection, however the development of therapeutic vaccines, T cell therapies and the clinical evaluation of HBV-specific T cell responses are hampered markedly by the lack of validated T cell epitopes. This review presented a map of T cell epitopes functionally validated from HBV antigens during the past 33 years; the human leukocyte antigen (HLA) supertypes to present these epitopes, and the methods to screen and identify T cell epitopes. To the best of our knowledge, a total of 205 CD8+ T cell epitopes and 79 CD4+ T cell epitopes have been defined from HBV antigens by cellular functional experiments thus far, but most are restricted to several common HLA supertypes, such as HLA-A0201, A2402, B0702, DR04, and DR12 molecules. Therefore, the currently defined T cell epitope repertoire cannot cover the major populations with HLA diversity in an indicated geographic region. More researches are needed to dissect a more comprehensive map of T cell epitopes, which covers overall HBV proteome and global patients.
Collapse
|
11
|
Aldakheel FM, Abrar A, Munir S, Aslam S, Allemailem KS, Khurshid M, Ashfaq UA. Proteome-Wide Mapping and Reverse Vaccinology Approaches to Design a Multi-Epitope Vaccine against Clostridium perfringens. Vaccines (Basel) 2021; 9:1079. [PMID: 34696187 PMCID: PMC8539331 DOI: 10.3390/vaccines9101079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/30/2022] Open
Abstract
C. perfringens is a highly versatile bacteria of livestock and humans, causing enteritis (a common food-borne illness in humans), enterotoxaemia (in which toxins are formed in the intestine which damage and destroy organs, i.e., the brain), and gangrene (wound infection). There is no particular cure for the toxins of C. perfringens. Supportive care (medical control of pain, intravenous fluids) is the standard treatment. Therefore, a multiple-epitope vaccine (MEV) should be designed to battle against C. perfringens infection. Furthermore, the main objective of this in silico investigation is to design an MEV that targets C. perfringens. For this purpose, we selected the top three proteins that were highly antigenic using immuno-informatics approaches, including molecular docking. B-cells, IFN-gamma, and T cells for target proteins were predicted and the most conserved epitopes were selected for further investigation. For the development of the final MEV, epitopes of LBL5, CTL17, and HTL13 were linked to GPGPG, AAY, and KK linkers. The vaccine N-end was joined to an adjuvant through an EAAK linker to improve immunogenicity. After the attachment of linkers and adjuvants, the final construct was 415 amino acids. B-cell and IFN-gamma epitopes demonstrate that the model structure is enhanced for humoral and cellular immune responses. To validate the immunogenicity and safety of the final construct, various physicochemical properties, and other properties such as antigenicity and non-allergens, were evaluated. Furthermore, molecular docking was carried out for verification of vaccine compatibility with the receptor, evaluated in silico. Also, in silico cloning was employed for the verification of the proper expression and credibility of the construct.
Collapse
Affiliation(s)
- Fahad M. Aldakheel
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11564, Saudi Arabia;
| | - Amna Abrar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (A.A.); (S.M.); (S.A.)
| | - Samman Munir
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (A.A.); (S.M.); (S.A.)
| | - Sehar Aslam
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (A.A.); (S.M.); (S.A.)
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad 38000, Pakistan;
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (A.A.); (S.M.); (S.A.)
| |
Collapse
|
12
|
Schetelig J, Heidenreich F, Baldauf H, Trost S, Falk B, Hoßbach C, Real R, Roers A, Lindemann D, Dalpke A, Kolditz M, de With K, Bornhäuser M, Bonifacio EE, Rücker-Braun E, Lange V, Markert J, Barth R, Hofmann JA, Sauter J, Bernas SN, Schmidt AH. Individual HLA-A, -B, -C, and -DRB1 Genotypes Are No Major Factors Which Determine COVID-19 Severity. Front Immunol 2021; 12:698193. [PMID: 34381451 PMCID: PMC8350391 DOI: 10.3389/fimmu.2021.698193] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/02/2021] [Indexed: 01/02/2023] Open
Abstract
HLA molecules are key restrictive elements to present intracellular antigens at the crossroads of an effective T-cell response against SARS-CoV-2. To determine the impact of the HLA genotype on the severity of SARS-CoV-2 courses, we investigated data from 6,919 infected individuals. HLA-A, -B, and -DRB1 allotypes grouped into HLA supertypes by functional or predicted structural similarities of the peptide-binding grooves did not predict COVID-19 severity. Further, we did not observe a heterozygote advantage or a benefit from HLA diplotypes with more divergent physicochemical peptide-binding properties. Finally, numbers of in silico predicted viral T-cell epitopes did not correlate with the severity of SARS-CoV-2 infections. These findings suggest that the HLA genotype is no major factor determining COVID-19 severity. Moreover, our data suggest that the spike glycoprotein alone may allow for abundant T-cell epitopes to mount robust T-cell responses not limited by the HLA genotype.
Collapse
Affiliation(s)
- Johannes Schetelig
- Clinical Trials Unit, DKMS, Dresden, Germany.,Division of Hematology, Department of Internal Medicine I, University Hospital Carl Gustav Carus, Technische Universität (TU), Dresden, Dresden, Germany
| | - Falk Heidenreich
- Clinical Trials Unit, DKMS, Dresden, Germany.,Division of Hematology, Department of Internal Medicine I, University Hospital Carl Gustav Carus, Technische Universität (TU), Dresden, Dresden, Germany
| | | | - Sarah Trost
- Clinical Trials Unit, DKMS, Dresden, Germany
| | - Bose Falk
- Clinical Trials Unit, DKMS, Dresden, Germany
| | | | - Ruben Real
- Clinical Trials Unit, DKMS, Dresden, Germany
| | - Axel Roers
- Institute for Immunology, TU Dresden, Dresden, Germany
| | - Dirk Lindemann
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Alexander Dalpke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Martin Kolditz
- Division of Pulmonology, Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Katja de With
- Division of Infectious Diseases, TU Dresden, Dresden, Germany
| | - Martin Bornhäuser
- Division of Hematology, Department of Internal Medicine I, University Hospital Carl Gustav Carus, Technische Universität (TU), Dresden, Dresden, Germany
| | - Ezio E Bonifacio
- Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany
| | - Elke Rücker-Braun
- Clinical Trials Unit, DKMS, Dresden, Germany.,Division of Hematology, Department of Internal Medicine I, University Hospital Carl Gustav Carus, Technische Universität (TU), Dresden, Dresden, Germany
| | | | - Jan Markert
- DKMS, Stem Cell Donor Registry, Tübingen, Germany
| | - Ralf Barth
- DKMS, Stem Cell Donor Registry, Tübingen, Germany
| | | | | | | | - Alexander H Schmidt
- Clinical Trials Unit, DKMS, Dresden, Germany.,DKMS Life Science Lab, Dresden, Germany.,DKMS, Stem Cell Donor Registry, Tübingen, Germany
| |
Collapse
|
13
|
Yashvardhini N, Kumar A, Jha DK. Immunoinformatics Identification of B- and T-Cell Epitopes in the RNA-Dependent RNA Polymerase of SARS-CoV-2. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2021; 2021:6627141. [PMID: 33936347 PMCID: PMC8061227 DOI: 10.1155/2021/6627141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/22/2021] [Accepted: 04/02/2021] [Indexed: 12/31/2022]
Abstract
SARS-CoV-2 (Severe acute respiratory syndrome coronavirus-2) is a newly emerged beta coronavirus and etiolating agent of COVID-19. Considering the unprecedented increasing number of COVID-19 cases, the World Health Organization declared a public health emergency internationally on 11th March 2020. However, existing drugs are insufficient in dealing with this contagious virus infection; therefore, a vaccine is exigent to curb this pandemic disease. In the present study, B- and T-cell immune epitopes were identified for RdRp (RNA-dependent RNA polymerase) protein using immunoinformatic techniques, which is proved to be a rapid and efficient method to explore the candidate peptide vaccine. Subsequently, antigenicity and interactions with HLA (human leukocyte antigen) alleles were estimated. Further, physicochemical properties, allergenicity, toxicity, and stability of RdRp protein were evaluated to demonstrate the specificity of the epitope candidates. Interestingly, we identified a total of 36 B-cell and 16 T-cell epitopes using epitopes predictive tools. Among the predicted epitopes, 26 B-cell and 9 T-cell epitopes showed non-allergenic, non-toxic, and highly antigenic properties. Altogether, our study revealed that RdRp of SARS-CoV-2 (an epitope-based peptide fragment) can be a potentially good candidate for the development of a vaccine against SARS-CoV-2.
Collapse
Affiliation(s)
- Niti Yashvardhini
- Department of Microbiology, Patna Women's College, Patna 800 001, Bihar, India
| | - Amit Kumar
- Department of Botany, Patna University, Patna 800 005, Bihar, India
| | - Deepak Kumar Jha
- Department of Zoology, P. C. Vigyan Mahavidyalaya, Chapra, Bihar 841 301, India
| |
Collapse
|
14
|
Ahmed RA, Almofti YA, Abd-elrahman KA. Structural Analysis of the Polymerase Protein for Multiepitopes Vaccine Prediction against Hepatitis B Virus. BIOSCIENCES BIOTECHNOLOGY RESEARCH ASIA 2021; 18:125-146. [DOI: 10.13005/bbra/2902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Hepatitis B virus (HBV) is the most common cause of hepatocellular carcinoma and liver cirrhosis with significant morbidity and mortality worldwide. DNA polymerase protein of HBV is the immunogenic protein inducing immune response against B and T cells. The aim of this study wasto develop multi-epitope vaccine fromthe polymerase protein elicitingimmune responses.The predicted vaccine comprises epitopes against B and T lymphocytesobtained by IEDB server. The predicted epitopes were linked via suitable spacers (linkers). The 50S ribosomal protein L7/L12 was used as an adjuvant at amino terminal and His-tag at the carboxyl terminal of the vaccine construct. The candidate vaccine contains 457aa and was potentially antigenic and nonallergic. Vaccine molecular weightwas 50.03 KDa with pI of 10.04. The instability index was 25.78 and GRAVY was -0.354 indicating stability andhydrophilicity of the chimeric vaccine,respectively.Vaccine structure (Secondary and tertiary structures) were predicted, refined and used for molecular docking with TLR4.The docking with TLR4 provided energy scores of -1458.7 and -1410.3 for chain A and B, respectively, demonstrated strong binding between the chimeric vaccine and TLR4 chains.The vaccine provided favorable solubility compared to E. coli proteins. Stability via disulfide bonds engineering was predicted to reduce the entropy and mobility regions invaccine construct. Molecular dynamics simulation wasperformed to strengthen the prediction. In silicomolecular cloning was usedto guarantee the efficient clonabilityof the vaccine and translation within suitable vector.
Collapse
Affiliation(s)
- Rolla Abdalkader Ahmed
- Department of Microbiology, Faculty of laboratory science, Omdurman Ahlia University, Khartoum- Sudan
| | - Yassir A. Almofti
- Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum- Sudan
| | - Khoubieb Ali Abd-elrahman
- 3Department of pharmaceutical technology, College of Pharmacy, University of Medical Science and Technology (MUST) Khartoum- Sudan
| |
Collapse
|
15
|
Mahmood M, Javaid A, Shahid F, Ashfaq UA. Rational design of multimeric based subunit vaccine against Mycoplasma pneumonia: Subtractive proteomics with immunoinformatics framework. INFECTION GENETICS AND EVOLUTION 2021; 91:104795. [PMID: 33667723 DOI: 10.1016/j.meegid.2021.104795] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 02/14/2021] [Accepted: 02/27/2021] [Indexed: 02/06/2023]
Abstract
Mycoplasma pneumoniae is the prevalent cause of acquired respiratory infections around the globe. A multi-epitope vaccine (MEV) must be developed to combat infections of M. pneumoniae because there is no specific disease-modifying treatment or vaccination is present. The objective of this research is to design a vaccine that targets M. pneumoniae top five highly antigenic proteins using a combination of immunological techniques and molecular docking. T-cell (HTL & CTL), B-cell, and IFN-γ of target proteins were forecasted and highly conservative epitopes were chosen for further study. For designing of final vaccine, 4LBL, 7CTL, and 5HTL epitopes were joined by linkers of KK, AAY, and GPGPG. The N-end of the vaccine was linked to an adjuvant (Cholera enterotoxin subunit B) with a linker named EAAAK to enhance immunogenicity. After the addition of adjuvants and linkers, the size of the construct was 395 amino acids. The epitopes of IFN-γ and B-cells illustrate that the model construct is optimized for cell-mediated immune or humoral responses. To ensure that the final design is safer and immunogenic, properties like non-allergens, antigenicity, and various physicochemical properties were evaluated. Molecular docking of the vaccine with the toll-like receptor 4 (TLR4) was conducted to check the compatibility of the vaccine with the receptor. Besides, in-silico cloning was utilized for validation of the credibility and proper expression of the vaccine. Furthermore, to confirm that the multi-epitope vaccine created is protective and immunogenic, this research requires experimental validation.
Collapse
Affiliation(s)
- Marvah Mahmood
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Anam Javaid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan.
| |
Collapse
|
16
|
Lin SR, Yang TY, Peng CY, Lin YY, Dai CY, Wang HY, Su TH, Tseng TC, Liu IJ, Cheng HR, Shen YC, Wu FY, Liu CJ, Chen DS, Chen PJ, Yang HC, Kao JH. Whole genome deep sequencing analysis of viral quasispecies diversity and evolution in HBeAg seroconverters. JHEP Rep 2021; 3:100254. [PMID: 33870157 PMCID: PMC8042178 DOI: 10.1016/j.jhepr.2021.100254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/21/2022] Open
Abstract
Background & Aims We aimed to investigate how viral quasispecies of the HBV whole genome evolves and diversifies in response to HBeAg seroconversion and viral control utilising next-generation sequencing (NGS). Methods Fifty HBeAg-positive chronic hepatitis B patients, including 18 treatment-naïve and 32 interferon (IFN)-treated individuals, were recruited. Serial HBV whole genomes in serum were analysed by NGS to determine sequence characteristics and viral quasispecies. Results HBV quasispecies diversity, measured by nucleotide diversity, was negatively correlated with viral load and hepatitis activity. Spontaneous HBeAg seroconverters exhibited significantly greater viral quasispecies diversity than treatment-naïve non-seroconverters from >1 year before seroconversion (0.0112 vs. 0.0060, p <0.01) to >1 year after seroconversion (0.0103 vs. 0.0068, p <0.01). IFN-induced HBeAg seroconverters tended to have higher viral genetic diversity than non-seroconverters along with treatment. Particularly, the IFN responders, defined as IFN-induced HBeAg seroconversion with low viraemia, exhibited significantly greater genetic diversity of whole HBV genome at 6 months post-IFN treatment than IFN non-responders (0.0148 vs. 0.0106, p = 0.048). Moreover, spontaneous HBeAg seroconverters and IFN responders exhibited significantly higher evolutionary rates and more intra-host single-nucleotide variants. Interestingly, in spontaneous HBeAg seroconverters and IFN responders, there were distinct evolutionary patterns in the HBV genome. Conclusions Higher HBV quasispecies diversity is associated with spontaneous HBeAg seroconversion and IFN-induced HBeAg seroconversion with low viraemia, conferring a favourable clinical outcome. Lay summary HBeAg seroconversion is a landmark in the natural history of chronic HBV infection. Using next-generation sequencing, we found that the nucleotide diversity of HBV was negatively correlated with viral load and hepatitis activity. Patients undergoing HBeAg seroconversion had more diverse HBV genomes and a faster viral evolution rate. Our findings suggest HBeAg seroconversion is driven by host selection pressure, likely immune selection pressure. Deep sequencing of whole HBV genome uncovers the quasispecies changes in chronic hepatitis B patients. The nucleotide diversity of HBV negatively correlates with viraemia during HBeAg loss/seroconversion. Viral quasispecies diversity is greater in spontaneous HBeAg seroconverters before and after seroconversion than in treatment-naïve non-seroconverters. Responders to IFN have greater viral quasispecies diversity than non-responders at 24 weeks after treatment. The genome positions of non-synonymous intra-host single nucleotide variants (iSNVs) of HBV tend to be located at possible T cell epitopes.
Collapse
Key Words
- ALT, alanine aminotransferase
- AUC, area under curve
- BCP, basal core promoter
- C, core
- CHB, chronic hepatitis B
- Chronic hepatitis B
- EOT, end of treatment
- HBeAg seroconversion
- IFN, interferon
- IFN-NR, IFN-non-responders
- IFN-No-eSC, IFN-treated HBeAg non-seroconverters
- IFN-RS, IFN-responders
- IFN-eSC, IFN-treated HBeAg seroconverters
- Intra-host single nucleotide variants
- NGS, next-generation sequencing
- ORFs, open reading frames
- P, polymerase
- S, surface
- TN-No-eSC, treatment-naïve non-seroconverters
- TN-eSC, treatment-naïve HBeAg seroconverters
- dN, nonsynonymous substitution rate
- dS, synonymous substitution rate
- iSNVs, intra-host single-nucleotide variants
Collapse
Affiliation(s)
- Su-Ru Lin
- Department of Microbiology, National Taiwan University, Taipei, Taiwan
| | - Ta-Yu Yang
- Department of Microbiology, National Taiwan University, Taipei, Taiwan
| | - Cheng-Yuan Peng
- School of Medicine, China Medical University, Taichung, Taiwan.,Department of Internal Medicine, Center for Digestive Medicine, China Medical University Hospital, Taichung, Taiwan
| | - You-Yu Lin
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Yen Dai
- Department of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Hepato-Biliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tung-Hung Su
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tai-Chung Tseng
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - I-Jung Liu
- Cardinal Tien Junior College of Healthcare and Management, New Taipei City, Taiwan
| | - Huei-Ru Cheng
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yueh-Chi Shen
- Department of Microbiology, National Taiwan University, Taipei, Taiwan
| | - Fang-Yi Wu
- Department of Microbiology, National Taiwan University, Taipei, Taiwan
| | - Chun-Jen Liu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University, Taipei, Taiwan.,Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Ding-Shinn Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University, Taipei, Taiwan.,Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Hung-Chih Yang
- Department of Microbiology, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jia-Horng Kao
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University, Taipei, Taiwan.,Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| |
Collapse
|
17
|
A comprehensive screening of the whole proteome of hantavirus and designing a multi-epitope subunit vaccine for cross-protection against hantavirus: Structural vaccinology and immunoinformatics study. Microb Pathog 2020; 150:104705. [PMID: 33352214 DOI: 10.1016/j.micpath.2020.104705] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/18/2020] [Accepted: 12/10/2020] [Indexed: 11/23/2022]
Abstract
Hantaviruses are an emerging zoonotic group of rodent-borne viruses that are having serious implications on global public health due to the increase in outbreaks. Since there is no permanent cure, there is increasing interest in developing a vaccine against the hantavirus. This research aimed to design a robust cross-protective subunit vaccine using a novel immunoinformatics approach. After careful evaluation, the best predicted cytotoxic & helper T-cell and B-cell epitopes from nucleocapsid proteins, glycoproteins, RdRp proteins, and non-structural proteins were considered as potential vaccine candidates. Among the four generated vaccine models with different adjuvant, the model with toll-like receptor-4 (TLR-4) agonist adjuvant was selected because of its high antigenicity, non-allergenicity, and structural quality. The selected model was 654 amino acids long and had a molecular weight of 70.5 kDa, which characterizes the construct as a good antigenic vaccine candidate. The prediction of the conformational B-lymphocyte (CBL) epitope secured its ability to induce the humoral response. Thereafter, disulfide engineering improved vaccine stability. Afterwards, the molecular docking confirmed a good binding affinity of -1292 kj/mol with considered immune receptor TLR-4 and the dynamics simulation showed high stability of the vaccine-receptor complex. Later, the in silico cloning confirmed the better expression of the constructed vaccine protein in E. coli K12. Finally, in in silico immune simulation, significantly high levels of immunoglobulin M (IgM), immunoglobulin G1 (IgG1), cytotoxic & helper T lymphocyte (CTL & HTL) populations, and numerous cytokines such as interferon-γ (IFN-γ), interleukin-2 (IL-2) etc. were found as coherence with actual immune response and also showed faster antigen clearance for repeated exposures. Nonetheless, experimental validation can demonstrate the safety and cross-protective ability of the proposed vaccine to fight against hantavirus infection.
Collapse
|
18
|
Bazhan SI, Antonets DV, Starostina EV, Ilyicheva TN, Kaplina ON, Marchenko VY, Volkova OY, Bakulina AY, Karpenko LI. In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice. J Biomol Struct Dyn 2020; 40:3196-3212. [PMID: 33222632 DOI: 10.1080/07391102.2020.1845978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The polyepitope strategy is promising approach for successfully creating a broadly protective flu vaccine, which targets T-lymphocytes (both CD4+ and CD8+) to recognise the most conserved epitopes of viral proteins. In this study, we employed a computer-aided approach to develop several artificial antigens potentially capable of evoking immune responses to different virus subtypes. These antigens included conservative T-cell epitopes of different influenza A virus proteins. To design epitope-based antigens we used experimentally verified information regarding influenza virus T-cell epitopes from the Immune Epitope Database (IEDB) (http://www.iedb.org). We constructed two "human" and two "murine" variants of polyepitope antigens. Amino acid sequences of target polyepitope antigens were designed using our original TEpredict/PolyCTLDesigner software. Immunogenic and protective features of DNA constructs encoding "murine" target T-cell immunogens were studied in BALB/c mice. We showed that mice groups immunised with a combination of computer-generated "murine" DNA immunogens had a 37.5% survival rate after receiving a lethal dose of either A/California/4/2009 (H1N1) virus or A/Aichi/2/68 (H3N2) virus, while immunisation with live flu H1N1 and H3N2 vaccine strains provided protection against homologous viruses and failed to protect against heterologous viruses. These results demonstrate that mechanisms of cross-protective immunity may be associated with the stimulation of specific T-cell responses. This study demonstrates that our computer-aided approach may be successfully used for rational designing artificial polyepitope antigens capable of inducing virus-specific T-lymphocyte responses and providing partial protection against two different influenza virus subtypes.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sergei I Bazhan
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Denis V Antonets
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Ekaterina V Starostina
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Tatyana N Ilyicheva
- Department of zoonotic infections and Influenza, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Olga N Kaplina
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Vasiliy Yu Marchenko
- Department of zoonotic infections and Influenza, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Olga Yu Volkova
- Immunogenetics laboratory, Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya Yu Bakulina
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia.,Laboratory of structural bioinformatics and molecular modeling, Novosibirsk State University, Novosibirsk, Russia
| | - Larisa I Karpenko
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| |
Collapse
|
19
|
Rehman HM, Mirza MU, Ahmad MA, Saleem M, Froeyen M, Ahmad S, Gul R, Alghamdi HA, Aslam MS, Sajjad M, Bhinder MA. A Putative Prophylactic Solution for COVID-19: Development of Novel Multiepitope Vaccine Candidate against SARS-COV-2 by Comprehensive Immunoinformatic and Molecular Modelling Approach. BIOLOGY 2020; 9:E296. [PMID: 32962156 PMCID: PMC7563440 DOI: 10.3390/biology9090296] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/13/2022]
Abstract
The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the World Health Organization has declared it a pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. The urgency of the situation requires the development of SARS-CoV-2-based vaccines. Immunoinformatic and molecular modelling are time-efficient methods that are generally used to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines has proved to be a promising immunization strategy against viruses and pathogens, thus inducing more comprehensive protective immunity. The current study demonstrated a comprehensive in silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in Escherichia coli. Despite that this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can be present as a better prophylactic solution against COVID-19.
Collapse
Affiliation(s)
- Hafiz Muzzammel Rehman
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
| | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.U.M.); (M.F.)
| | - Mian Azhar Ahmad
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
- Department of Health, Government of the Punjab, Lahore 54590, Punjab, Pakistan
| | - Mahjabeen Saleem
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.U.M.); (M.F.)
| | - Sarfraz Ahmad
- Drug Design and Development Research Group (DDDRG), Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore 54590, Punjab, Pakistan;
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha 61413, Saudi Arabia;
| | - Muhammad Shahbaz Aslam
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan;
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
| |
Collapse
|
20
|
Discovery and Selection of Hepatitis B Virus-Derived T Cell Epitopes for Global Immunotherapy Based on Viral Indispensability, Conservation, and HLA-Binding Strength. J Virol 2020; 94:JVI.01663-19. [PMID: 31852786 PMCID: PMC7081907 DOI: 10.1128/jvi.01663-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022] Open
Abstract
Multiple HBV-derived T cell epitopes have been reported, which can be useful in a therapeutic vaccination strategy. However, these epitopes are largely restricted to HLA-A*02, which is not dominantly expressed in populations with high HBV prevalence. Thus, current epitopes are falling short in the development of a global immunotherapeutic approach. Therefore, we aimed to identify novel epitopes for 6 HLA supertypes most prevalent in the infected population. Moreover, established epitopes might not all be equally effective as they can be subject to different levels of immune escape. It is therefore important to identify targets that are crucial in viral replication and conserved in the majority of the infected population. Here, we applied a stringent selection procedure to compose a combined overview of existing and novel HBV-derived T cell epitopes most promising for viral eradication. This set of T cell epitopes now lays the basis for the development of globally effective HBV antigen-specific immunotherapies. Immunotherapy represents an attractive option for the treatment of chronic hepatitis B virus (HBV) infection. The HBV proteins polymerase (Pol) and HBx are of special interest for antigen-specific immunotherapy because they are essential for viral replication and have been associated with viral control (Pol) or are still expressed upon viral DNA integration (HBx). Here, we scored all currently described HBx- and Pol-derived epitope sequences for viral indispensability and conservation across all HBV genotypes. This yielded 7 HBx-derived and 26 Pol-derived reported epitopes with functional association and high conservation. We subsequently predicted novel HLA-binding peptides for 6 HLA supertypes prevalent in HBV-infected patients. Potential epitopes expected to be the least prone to immune escape were subjected to a state-of-the-art in vitro assay to validate their HLA-binding capacity. Using this method, a total of 13 HLA binders derived from HBx and 33 binders from Pol were identified across HLA types. Subsequently, we demonstrated interferon gamma (IFN-γ) production in response to 5 of the novel HBx-derived binders and 17 of the novel Pol-derived binders. In addition, we validated several infrequently described epitopes. Collectively, these results specify a set of highly potent T cell epitopes that represent a valuable resource for future HBV immunotherapy design. IMPORTANCE Multiple HBV-derived T cell epitopes have been reported, which can be useful in a therapeutic vaccination strategy. However, these epitopes are largely restricted to HLA-A*02, which is not dominantly expressed in populations with high HBV prevalence. Thus, current epitopes are falling short in the development of a global immunotherapeutic approach. Therefore, we aimed to identify novel epitopes for 6 HLA supertypes most prevalent in the infected population. Moreover, established epitopes might not all be equally effective as they can be subject to different levels of immune escape. It is therefore important to identify targets that are crucial in viral replication and conserved in the majority of the infected population. Here, we applied a stringent selection procedure to compose a combined overview of existing and novel HBV-derived T cell epitopes most promising for viral eradication. This set of T cell epitopes now lays the basis for the development of globally effective HBV antigen-specific immunotherapies.
Collapse
|
21
|
Hu Y, Tang L, Zhu Z, Meng H, Chen T, Zhao S, Jin Z, Wang Z, Jin G. A novel TLR7 agonist as adjuvant to stimulate high quality HBsAg-specific immune responses in an HBV mouse model. J Transl Med 2020; 18:112. [PMID: 32131853 PMCID: PMC7055022 DOI: 10.1186/s12967-020-02275-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/18/2020] [Indexed: 12/15/2022] Open
Abstract
Background The global burden of hepatitis B virus (HBV) infection in terms of morbidity and mortality is immense. Novel treatments that can induce a protective immune response are urgently needed to effectively control the HBV epidemic and eventually eradicate chronic HBV infection. Methods We designed and evaluated an HBV therapeutic vaccine consisting of a novel Toll-like receptor 7 (TLR7) agonist T7-EA, an Alum adjuvant and a recombinant HBsAg protein. We used RNA-seq, ELISA and hTLR7/8 reporting assays to characterize T7-EA in vitro and real-time PCR to evaluate the tissue-retention characteristics in vivo. To evaluate the adjuvant potential, we administrated T7-EA intraperitoneally in a formulation with an Alum adjuvant and HBsAg in normal and HBV mice, then, we evaluated the HBsAg-specific immune responses by ELISA and Elispot assays. Results T7-EA acted as an hTLR7-specific agonist and induced a similar gene expression pattern as an unmodified TLR7 ligand when Raw 264.7 cells were exposed to T7-EA; however, T7-EA was more potent than the unmodified TLR7 ligand. In vivo studies showed that T7-EA had tissue-retaining activity with stimulating local cytokine and chemokine expression for up to 7 days. T7-EA could induce Th1-type immune responses, as evidenced by an increased HBsAg-specific IgG2a titer and a T-cell response in normal mice compared to mice received traditional Alum-adjuvant HBV vaccine. Importantly, T7-EA could break immune tolerance and induce persistent HBsAg-specific antibody and T-cell responses in an HBV mouse model. Conclusions T7-EA might be a candidate adjuvant in a prophylactic and therapeutic HBV vaccine.
Collapse
Affiliation(s)
- Yunlong Hu
- The Cancer Research Center, School of Medicine, Shenzhen University, Shenzhen, 518055, China. .,National Engineering LAB of Synthetic Biology of Medicine, School of Medicine, Shenzhen University, Shenzhen, 518055, China. .,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| | - Li Tang
- The Cancer Research Center, School of Medicine, Shenzhen University, Shenzhen, 518055, China.,National Engineering LAB of Synthetic Biology of Medicine, School of Medicine, Shenzhen University, Shenzhen, 518055, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518055, China
| | - Zhengyu Zhu
- Shenzhen Kang Tai Biological Products CO., Ltd, Shenzhen, 518060, China
| | - He Meng
- Department of Stomatology, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy, Shenzhen, 518055, China
| | - Tingting Chen
- The Cancer Research Center, School of Medicine, Shenzhen University, Shenzhen, 518055, China.,National Engineering LAB of Synthetic Biology of Medicine, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Sheng Zhao
- The Cancer Research Center, School of Medicine, Shenzhen University, Shenzhen, 518055, China.,National Engineering LAB of Synthetic Biology of Medicine, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Zhenchao Jin
- The Cancer Research Center, School of Medicine, Shenzhen University, Shenzhen, 518055, China.,National Engineering LAB of Synthetic Biology of Medicine, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Zhulin Wang
- The Cancer Research Center, School of Medicine, Shenzhen University, Shenzhen, 518055, China.,National Engineering LAB of Synthetic Biology of Medicine, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Guangyi Jin
- The Cancer Research Center, School of Medicine, Shenzhen University, Shenzhen, 518055, China. .,National Engineering LAB of Synthetic Biology of Medicine, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| |
Collapse
|
22
|
Zhang TY, Guo XR, Wu YT, Kang XZ, Zheng QB, Qi RY, Chen BB, Lan Y, Wei M, Wang SJ, Xiong HL, Cao JL, Zhang BH, Qiao XY, Huang XF, Wang YB, Fang MJ, Zhang YL, Cheng T, Chen YX, Zhao QJ, Li SW, Ge SX, Chen PJ, Zhang J, Yuan Q, Xia NS. A unique B cell epitope-based particulate vaccine shows effective suppression of hepatitis B surface antigen in mice. Gut 2020; 69:343-354. [PMID: 30926653 PMCID: PMC6984059 DOI: 10.1136/gutjnl-2018-317725] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/11/2019] [Accepted: 02/24/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE This study aimed to develop a novel therapeutic vaccine based on a unique B cell epitope and investigate its therapeutic potential against chronic hepatitis B (CHB) in animal models. METHODS A series of peptides and carrier proteins were evaluated in HBV-tolerant mice to obtain an optimised therapeutic molecule. The immunogenicity, therapeutic efficacy and mechanism of the candidate were investigated systematically. RESULTS Among the HBsAg-aa119-125-containing peptides evaluated in this study, HBsAg-aa113-135 (SEQ13) exhibited the most striking therapeutic effects. A novel immunoenhanced virus-like particle carrier (CR-T3) derived from the roundleaf bat HBV core antigen (RBHBcAg) was created and used to display SEQ13, forming candidate molecule CR-T3-SEQ13. Multiple copies of SEQ13 displayed on the surface of this particulate antigen promote the induction of a potent anti-HBs antibody response in mice, rabbits and cynomolgus monkeys. Sera and purified polyclonal IgG from the immunised animals neutralised HBV infection in vitro and mediated efficient HBV/hepatitis B virus surface antigen (HBsAg) clearance in the mice. CR-T3-SEQ13-based vaccination induced long-term suppression of HBsAg and HBV DNA in HBV transgenic mice and eradicated the virus completely in hydrodynamic-based HBV carrier mice. The suppressive effects on HBsAg were strongly correlated with the anti-HBs level after vaccination, suggesting that the main mechanism of CR-T3-SEQ13 vaccination therapy was the induction of a SEQ13-specific antibody response that mediated HBV/HBsAg clearance. CONCLUSIONS The novel particulate protein CR-T3-SEQ13 suppressed HBsAg effectively through induction of a humoural immune response in HBV-tolerant mice. This B cell epitope-based therapeutic vaccine may provide a novel immunotherapeutic agent against chronic HBV infection in humans.
Collapse
Affiliation(s)
- Tian-Ying Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Xue-Ran Guo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Yang-Tao Wu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Xiao-Zhen Kang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Qing-Bing Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Ruo-Yao Qi
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Bin-Bing Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Ying Lan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Min Wei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Shao-Juan Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Hua-Long Xiong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Jia-Li Cao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Bao-Hui Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Xiao-Yang Qiao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Xiao-Fen Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Ying-Bin Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Mu-Jin Fang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Ya-Li Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Tong Cheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Yi-Xin Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Qin-Jian Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Shao-Wei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Sheng-Xiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Pei-Jer Chen
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| | - Ning-shao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health & School of Life Science, Xiamen University, Xiamen, China,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Science, Xiamen University, Xiamen, China
| |
Collapse
|
23
|
Structural Features of a Conformation-dependent Antigen Epitope on ORFV-B2L Recognized by the 2E4 mAb. Sci Rep 2019; 9:16094. [PMID: 31695071 PMCID: PMC6834619 DOI: 10.1038/s41598-019-52446-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/16/2019] [Indexed: 12/03/2022] Open
Abstract
Previously, we successfully prepared a monoclonal antibody (mAb) named 2E4, that directly recognizes the major envelope protein B2L of the orf virus (ORFV), but there is little information about its epitope. Here, we meticulously mapped the 2E4 epitope through combinatorial programs and identified the functional binding domain and a key amino acid residue. Briefly, the simulated epitope peptide closely resembles 84VDVQSKDKDADELR97 located at the N-terminus of B2L, strongly suggesting that the epitope is conformationally or spatially structure-dependent. Subsequently, we combined these findings with the results from the antigenicity prediction of B2L to design three truncated fragments of B2L (F1, F2 and F3) selected using 2E4, and only the F1 fragment was found to be eligible for the advanced stage. Alanine-scanning mutagenesis suggested that the D94 residue is structurally crucial for the 2E4 epitope. The other participating residues, including K61, E62, and D92, together with D94 were responsible for enabling 2E4 binding and served as factors that synergistically enabled binding to the whole 2E4 epitope. In this paper, we describe, for the first time, the architecture of an ORFV conformational epitope, and it is also expected that mAb 2E4 and its epitope can be used for applications relating to orf control.
Collapse
|
24
|
Abdulla F, Adhikari UK, Uddin MK. Exploring T & B-cell epitopes and designing multi-epitope subunit vaccine targeting integration step of HIV-1 lifecycle using immunoinformatics approach. Microb Pathog 2019; 137:103791. [PMID: 31606417 DOI: 10.1016/j.micpath.2019.103791] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/14/2022]
Abstract
Till now, AIDS, caused by the human immunodeficiency virus (HIV) is still a severe health problem worldwide. It weakens the immune system by targeting the T-helper cells. Specifically, the severity of the pandemic HIV-1 makes the emergence of an enduring effective vaccine against HIV-1. Therefore, we have applied a series of immunoinformatics approaches to the four conserved domains of HIV-1 integrase (IN) proteins to design an effective multi-epitope based subunit vaccine which might induce a competent immunity against HIV-1. Therefore, we have selected three peptide fragments that contained all overlapping epitopes (35 CD4+, 8 CD8+ T-cell epitopes, and 3 B-cell epitopes) where the epitopes had a high conservancy score. The cumulative population coverage for combined CD8+ and CD4+ T-cell epitopes and their respective HLA-alleles were found as 98.03% in the world which is also followed by East Asia (96.24%), South Asia (96.31%), North Africa (96.14%), North America (98.99%), and Europe (98.80%). The proposed vaccine composed by an adjuvant (β-defensin) at the N-terminal site of the vaccine constructs and three peptide fragments where the adjuvant was fused by EAAAK linker and the peptide fragments were fused by GPGPG linker. The designed final vaccine construct (length: 159 amino acid) was found to be antigenic and non-allergic, which indicates its safety. The vaccine construct was found as good antigenic, stable, higher thermostable, and hydrophilic in nature. The codon adaptation and in silico cloning ensured the high expression rate of the vaccine constructs in E. coli K12 with CAI value of 1.0. Finally, the binding affinity of the vaccine constructs with the immune receptor TLR3 was confirmed by the lowest energy score of -1026.8 evaluated by molecular docking. However, the proposed in silico vaccine construct needs experimental validation for assuring the safety and immunogenicity profile which will ensure an active immunity against HIV-1.
Collapse
Affiliation(s)
- Faruq Abdulla
- Department of Statistics, Islamic University, Kushtia-7003, Bangladesh
| | - Utpal Kumar Adhikari
- School of Medicine, Western Sydney University, Campbelltown, NSW-2560, Australia
| | - M Kamal Uddin
- Department of Statistics, Islamic University, Kushtia-7003, Bangladesh.
| |
Collapse
|
25
|
Dhal AK, Pani A, Mahapatra RK, Yun SI. An immunoinformatics approach for design and validation of multi-subunit vaccine against Cryptosporidium parvum. Immunobiology 2019; 224:747-757. [PMID: 31522782 DOI: 10.1016/j.imbio.2019.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 12/30/2022]
Abstract
An immunoinformatics-based approach is explored for potential multi-subunit vaccine candidates against Cryptosporidium parvum. We performed protein structure based systematic methodology for the development of a proficient multi-subunit vaccine candidate against C. parvum based on their probability of antigenicity, allergenicity and transmembrane helices as the screening criteria. The best-screened epitopes like B-cell epitopes (BCL), Helper T-lymphocytes (HTL) and cytotoxic T- lymphocytes (CTL) were joined by using the appropriate linkers to intensify and develop the presentation and processing of the antigenic molecules. Modeller software was used to generate the best 3D model of the subunit protein. RAMPAGE and other web servers were employed for the validation of the modeled protein. Furthermore, the predicted modeled structure was docked with the two known receptors like TLR2 and TLR4 through ClusPro web server. Based on the docking score, the multi-subunit vaccine docked with TLR2 was subjected to energy minimization by molecular dynamics (MD) simulation to examine their stability within a solvent system. From the simulation study, we found that the residue Glu-107 of subunit vaccine formed a hydrogen bond interaction with Arg-299 of the TLR2 receptor throughout the time frame of the MD simulation. The overall results showed that the multi-subunit vaccine could be an efficient vaccine candidate against C. parvum.
Collapse
Affiliation(s)
- Ajit Kumar Dhal
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Alok Pani
- Department of Food Science and Technology, Chonbuk National University, Jeonju, 561756, South Korea
| | - Rajani Kanta Mahapatra
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar 751024, Odisha, India.
| | - Soon-Il Yun
- Department of Food Science and Technology, Chonbuk National University, Jeonju, 561756, South Korea.
| |
Collapse
|
26
|
In silico Designed Ebola Virus T-Cell Multi-Epitope DNA Vaccine Constructions Are Immunogenic in Mice. Vaccines (Basel) 2019; 7:vaccines7020034. [PMID: 30934980 PMCID: PMC6630745 DOI: 10.3390/vaccines7020034] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/16/2022] Open
Abstract
Background: The lack of effective vaccines against Ebola virus initiates a search for new approaches to overcoming this problem. The aim of the study was to design artificial polyepitope T-cell immunogens⁻⁻candidate DNA vaccines against Ebola virus and to evaluate their capacity to induce a specific immune response in a laboratory animal model. Method: Design of two artificial polyepitope T-cell immunogens, one of which (EV.CTL) includes cytotoxic and the other (EV.Th)⁻⁻T-helper epitopes of Ebola virus proteins was carried out using original TEpredict/PolyCTLDesigner software. Synthesized genes were cloned in pcDNA3.1 plasmid vector. Target gene expression was estimated by synthesis of specific mRNAs and proteins in cells transfected with recombinant plasmids. Immunogenicity of obtained DNA vaccine constructs was evaluated according to their capacity to induce T-cell response in BALB/c mice using IFNγ ELISpot and ICS. Results: We show that recombinant plasmids pEV.CTL and pEV.Th encoding artificial antigens provide synthesis of corresponding mRNAs and proteins in transfected cells, as well as induce specific responses both to CD4+ and CD8+ T-lymphocytes in immunized animals. Conclusions: The obtained recombinant plasmids can be regarded as promising DNA vaccine candidates in future studies of their capacity to induce cytotoxic and protective responses against Ebola virus.
Collapse
|
27
|
Guo ZS, Lu B, Guo Z, Giehl E, Feist M, Dai E, Liu W, Storkus WJ, He Y, Liu Z, Bartlett DL. Vaccinia virus-mediated cancer immunotherapy: cancer vaccines and oncolytics. J Immunother Cancer 2019; 7:6. [PMID: 30626434 PMCID: PMC6325819 DOI: 10.1186/s40425-018-0495-7] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/26/2018] [Indexed: 12/11/2022] Open
Abstract
Cancer vaccines and oncolytic immunotherapy are promising treatment strategies with potential to provide greater clinical benefit to patients with advanced-stage cancer. In particular, recombinant vaccinia viruses (VV) hold great promise as interventional agents. In this article, we first summarize the current understanding of virus biology and viral genes involved in host-virus interactions to further improve the utility of these agents in therapeutic applications. We then discuss recent findings from basic and clinical studies using VV as cancer vaccines and oncolytic immunotherapies. Despite encouraging results gleaned from translational studies in animal models, clinical trials implementing VV vectors alone as cancer vaccines have yielded largely disappointing results. However, the combination of VV vaccines with alternate forms of standard therapies has resulted in superior clinical efficacy. For instance, combination regimens using TG4010 (MVA-MUC1-IL2) with first-line chemotherapy in advanced-stage non-small cell lung cancer or combining PANVAC with docetaxel in the setting of metastatic breast cancer have clearly provided enhanced clinical benefits to patients. Another novel cancer vaccine approach is to stimulate anti-tumor immunity via STING activation in Batf3-dependent dendritic cells (DC) through the use of replication-attenuated VV vectors. Oncolytic VVs have now been engineered for improved safety and superior therapeutic efficacy by arming them with immune-stimulatory genes or pro-apoptotic molecules to facilitate tumor immunogenic cell death, leading to enhanced DC-mediated cross-priming of T cells recognizing tumor antigens, including neoantigens. Encouraging translational and early phase clinical results with Pexa-Vec have matured into an ongoing global phase III trial for patients with hepatocellular carcinoma. Combinatorial approaches, most notably those using immune checkpoint blockade, have produced exciting pre-clinical results and warrant the development of innovative clinical studies. Finally, we discuss major hurdles that remain in the field and offer some perspectives regarding the development of next generation VV vectors for use as cancer therapeutics.
Collapse
Affiliation(s)
- Zong Sheng Guo
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Binfeng Lu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zongbi Guo
- Fujian Tianjian Pharmaceutical Co. Ltd., Sanming, Fujian, China
| | - Esther Giehl
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mathilde Feist
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Enyong Dai
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Weilin Liu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Walter J Storkus
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Dermatology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yukai He
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Zuqiang Liu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - David L Bartlett
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
28
|
Sabetian S, Nezafat N, Dorosti H, Zarei M, Ghasemi Y. Exploring dengue proteome to design an effective epitope-based vaccine against dengue virus. J Biomol Struct Dyn 2018; 37:2546-2563. [PMID: 30035699 DOI: 10.1080/07391102.2018.1491890] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Dengue, a mosquito-borne disease, is caused by four known dengue serotypes. This infection causes a range of symptoms from a mild fever to a sever homorganic fever and death. It is a serious public health problem in subtropical and tropical countries. There is no specific vaccine currently available for clinical use and study on this issue is ongoing. In this study, bioinformatics approaches were used to predict antigenic, immunogenic, non-allergenic, and conserved B and T-cell epitopes as promising targets to design an effective peptide-based vaccine against dengue virus. Molecular docking analysis indicated the deep binding of the identified epitopes in the binding groove of the most popular human MHC I allele (human leukocyte antigens [HLA] A*0201). The final vaccine construct was created by conjugating the B and T-cell identified epitopes using proper linkers and adding an appropriate adjuvant at the N-terminal. The characteristics of the new subunit vaccine demonstrated that the epitope-based vaccine was antigenic, non-toxic, stable, and soluble. Other physicochemical properties of the new designed construct including isoelectric point value, aliphatic index, and grand average of hydropathicity were biologically considerable. Molecular docking of the engineered vaccine with Toll-like receptor 2 (TLR2) model revealed the hydrophobic interaction between the adjuvant and the ligand binding regions in the hydrophobic channel of TLR2. The study results indicated the high potential capability of the new multi-epitope vaccine to induce cellular and humoral immune responses against the dengue virus. Further experimental tests are required to investigate the immune protection capacity of the new vaccine construct in animal models. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Soudabeh Sabetian
- a Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences , Shiraz , Iran
| | - Navid Nezafat
- a Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences , Shiraz , Iran.,b Department of Pharmaceutical Biotechnology, School of Pharmacy , Shiraz University of Medical Sciences , Shiraz , Iran
| | - Hesam Dorosti
- a Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences , Shiraz , Iran.,b Department of Pharmaceutical Biotechnology, School of Pharmacy , Shiraz University of Medical Sciences , Shiraz , Iran
| | - Mahboubeh Zarei
- a Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences , Shiraz , Iran.,b Department of Pharmaceutical Biotechnology, School of Pharmacy , Shiraz University of Medical Sciences , Shiraz , Iran
| | - Younes Ghasemi
- a Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences , Shiraz , Iran.,b Department of Pharmaceutical Biotechnology, School of Pharmacy , Shiraz University of Medical Sciences , Shiraz , Iran.,c Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies , Shiraz University of Medical Sciences , Shiraz , Iran.,d Biotechnology Research Center, Shiraz University of Medical Sciences , Shiraz , Iran
| |
Collapse
|
29
|
Garba B, Bahaman AR, Zakaria Z, Bejo SK, Mutalib AR, Bande F, Suleiman N. Antigenic potential of a recombinant polyvalent DNA vaccine against pathogenic leptospiral infection. Microb Pathog 2018; 124:136-144. [PMID: 30138761 DOI: 10.1016/j.micpath.2018.08.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 08/02/2018] [Accepted: 08/18/2018] [Indexed: 11/18/2022]
Abstract
Leptospirosis is a serious epidemic disease caused by pathogenic Leptospira species. The disease is endemic in most tropical and sub-tropical regions of the world. Currently, there is no effective polyvalent vaccine for prevention against most of the circulating serovars. Moreover, development of an efficient leptospiral vaccine capable of stimulating cross-protective immune responses against a wide range of serovars remains a daunting challenge. This, in part, is associated with the extensive diversity and variation of leptospiral serovars from region to region. In this study, a multi-epitope DNA vaccine encoding highly immunogenic epitopes from LipL32 and LipL41 was designed using in-silico approach. The DNA encoding antigenic epitopes was constructed from conserved pathogenic Leptospira genes (LipL32 and LipL41). Immunization of golden Syrian hamsters with the multi-epitope chimeric DNA vaccine resulted in the production of both agglutinating and neutralizing antibodies as evidence by MAT and in-vitro growth inhibition tests respectively. The antibodies produced reacted against eight different serovars and significantly reduced renal colonization following in vivo challenge. The vaccine was also able to significantly reduce renal colonization which is a very important factor responsible for persistence of leptospires among susceptible and reservoir animal hosts. In conclusion, the leptospiral multi-epitope chimeric DNA vaccine can serve as a potentially effective and safe vaccine against infection with different pathogenic leptospiral serovars.
Collapse
Affiliation(s)
- Bashiru Garba
- Veterinary Public Health Lab, Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, Sokoto, Nigeria; Bacteriology Lab, Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Abdul Rani Bahaman
- Bacteriology Lab, Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Zunita Zakaria
- Bacteriology Lab, Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Siti Khairani Bejo
- Bacteriology Lab, Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Abdul Rahim Mutalib
- Department of Veterinary Laboratory Diagnostics Services Unit, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Faruku Bande
- Bacteriology Lab, Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Veterinary Services, Ministry of Animal Health and Fisheries Development, Usman Faruk Secretariat Complex, 840245, Sokoto State, Nigeria
| | - Nasiru Suleiman
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, Sokoto, Nigeria
| |
Collapse
|
30
|
Yamamiya D, Mizukoshi E, Kaji K, Terashima T, Kitahara M, Yamashita T, Arai K, Fushimi K, Honda M, Kaneko S. Immune responses of human T lymphocytes to novel hepatitis B virus-derived peptides. PLoS One 2018; 13:e0198264. [PMID: 29856876 PMCID: PMC5983448 DOI: 10.1371/journal.pone.0198264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/16/2018] [Indexed: 12/14/2022] Open
Abstract
Background & aims Many individuals are infected with hepatitis B virus (HBV) worldwide, and this virus is commonly controlled by treatments with interferon (IFN)-alpha and nucleoside analogues (NA). However, the complete elimination of HBV by these treatments is difficult and, thus, the development of new treatments is needed. Host immune responses are closely involved in the elimination of HBV, suggesting the usefulness of immunotherapy. In the present study, we attempted to identify novel cytotoxic T-lymphocyte (CTL) epitopes that are useful for immunotherapy against HBV. Methods CTL epitopes were predicted using computer software. Immune responses to each peptide were evaluated by IFN-γ ELISPOT and cytotoxic assays. The relationships between the immune responses to these newly identified CTL epitopes and the clinical backgrounds of patients and administration of NA were analyzed. Peptides were administered to mice as vaccines and peptide-specific T-cell induction was measured in vivo. Results Positive reactions to 10 synthesized peptides were detected in 3 or more patients using the IFN-γ ELISPOT assay, and concentration-dependent cytotoxicity against 2 of these peptides was observed in the cytotoxic assay. Some peptides that correlated with serum ALT, HBsAg, and HBV core-related antigen (HBcrAg) levels were identified. Immune reactions against some peptides were enhanced by the administration of NA. Regarding their effects as a vaccine, peptide-specific T-cells were induced by four peptides in vivo. Conclusions Novel HBV epitopes that correlated with HBsAg and HBcrAg levels were identified. These newly identified epitopes may be useful in the analysis of immune responses to HBV and development of immunotherapy against HBV.
Collapse
Affiliation(s)
- Daisuke Yamamiya
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Eishiro Mizukoshi
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
- * E-mail:
| | - Kiichiro Kaji
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takeshi Terashima
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Masaaki Kitahara
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Tatsuya Yamashita
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kuniaki Arai
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kazumi Fushimi
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Masao Honda
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Ishikawa, Japan
| |
Collapse
|
31
|
Kosinska AD, Bauer T, Protzer U. Therapeutic vaccination for chronic hepatitis B. Curr Opin Virol 2017; 23:75-81. [PMID: 28453967 DOI: 10.1016/j.coviro.2017.03.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 12/17/2022]
Abstract
A therapeutic vaccine is meant to activate the patient's immune system to fight and finally control or ideally eliminate an already established infectious pathogen. Whereas the success of prophylactic vaccination is based on rapid antibody-mediated neutralization of an invading pathogen, control and elimination of persistent viruses such as hepatitis, herpes or papilloma viruses requires multi-specific and polyfunctional effector T cell responses. These are ideally directed against continuously expressed viral antigens to keep the pathogen in check. Activation of a humoral immune response in order to lower viral antigen load and to limit virus spread, however, confers an additional benefit. Therapeutic vaccines are under development for a number of chronic infections and require an intelligent vaccine design. Hepatitis B virus (HBV) infection may serve as a prime example since a spontaneous, immune-mediated recovery of chronic hepatitis B and an elimination of the virus is possible even if it is observed only in very rare cases. In this review, we summarize the current knowledge and potential improvements of therapeutic vaccines for chronic hepatitis B.
Collapse
Affiliation(s)
- Anna D Kosinska
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany; German Center for Infection research (DZIF), Munich Partner Site, Germany
| | - Tanja Bauer
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany; German Center for Infection research (DZIF), Munich Partner Site, Germany
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany; German Center for Infection research (DZIF), Munich Partner Site, Germany.
| |
Collapse
|
32
|
Escalona E, Sáez D, Oñate A. Immunogenicity of a Multi-Epitope DNA Vaccine Encoding Epitopes from Cu-Zn Superoxide Dismutase and Open Reading Frames of Brucella abortus in Mice. Front Immunol 2017; 8:125. [PMID: 28232837 PMCID: PMC5298974 DOI: 10.3389/fimmu.2017.00125] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/25/2017] [Indexed: 01/08/2023] Open
Abstract
Brucellosis is a bacterial zoonotic disease affecting several mammalian species that is transmitted to humans by direct or indirect contact with infected animals or their products. In cattle, brucellosis is almost invariably caused by Brucella abortus. Live, attenuated Brucella vaccines are commonly used to prevent illness in cattle, but can cause abortions in pregnant animals. It is, therefore, desirable to design an effective and safer vaccine against Brucella. We have used specific Brucella antigens that induce immunity and protection against B. abortus. A novel recombinant multi-epitope DNA vaccine specific for brucellosis was developed. To design the vaccine construct, we employed bioinformatics tools to predict epitopes present in Cu-Zn superoxide dismutase and in the open reading frames of the genomic island-3 (BAB1_0260, BAB1_0270, BAB1_0273, and BAB1_0278) of Brucella. We successfully designed a multi-epitope DNA plasmid vaccine chimera that encodes and expresses 21 epitopes. This DNA vaccine induced a specific humoral and cellular immune response in BALB/c mice. It induced a typical T-helper 1 response, eliciting production of immunoglobulin G2a and IFN-γ particularly associated with the Th1 cell subset of CD4+ T cells. The production of IL-4, an indicator of Th2 activation, was not detected in splenocytes. Therefore, it is reasonable to suggest that the vaccine induced a predominantly Th1 response. The vaccine induced a statistically significant level of protection in BALB/c mice when challenged with B. abortus 2308. This is the first use of an in silico strategy to a design a multi-epitope DNA vaccine against B. abortus.
Collapse
Affiliation(s)
- Emilia Escalona
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Darwin Sáez
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Angel Oñate
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| |
Collapse
|
33
|
Harada N, Fukaya S, Wada H, Goto R, Osada T, Gomori A, Ikizawa K, Sakuragi M, Oda N. Generation of a Novel HLA Class I Transgenic Mouse Model Carrying a Knock-in Mutation at the β2-Microglobulin Locus. THE JOURNAL OF IMMUNOLOGY 2016; 198:516-527. [DOI: 10.4049/jimmunol.1502367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 10/07/2016] [Indexed: 11/19/2022]
|
34
|
Ward H, Tang L, Poonia B, Kottilil S. Treatment of hepatitis B virus: an update. Future Microbiol 2016; 11:1581-1597. [PMID: 27855500 DOI: 10.2217/fmb-2016-0128] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chronic hepatitis B virus infection is a global health concern as it affects over 240 million people worldwide and an estimated 686,000 people die annually as a result of complications of the disease. With the development of newer antiviral drugs, viral suppression of HBV is achievable, however elimination of HBV from infected individuals (functional cure) remains an issue. Due to persistence of HBV DNA (cccDNA) in infected cells, chronically infected patients who discontinue therapy prior to HBsAg loss or seroconversion are likely to relapse. Several novel therapeutic strategies are being researched and studied in clinical trials. Here we review these novel strategies to achieve sustained cure or elimination of HBV. These strategies include the targeting of the host or viral factors required for viral persistence as well as therapeutic vaccines.
Collapse
Affiliation(s)
- Haley Ward
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lydia Tang
- Division of Clinical Care & Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Bhawna Poonia
- Division of Clinical Care & Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Shyam Kottilil
- Division of Clinical Care & Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| |
Collapse
|
35
|
Akbar SMF, Al-Mahtab M, Jahan M, Yoshida O, Hiasa Y. Novel insights into immunotherapy for hepatitis B patients. Expert Rev Gastroenterol Hepatol 2016; 10:267-76. [PMID: 26626120 DOI: 10.1586/17474124.2016.1112266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The possible use of immunotherapy for hepatitis B has emerged for two major reasons: (1) chronic hepatitis B (CHB) is an immune-mediated pathological condition, and (2) commercially available antiviral drugs are of limited efficacy. Although various immunomodulatory agents have been used to treat patients with CHB during the last three decades, there is currently no consensus among physicians and hepatologists regarding the suitability of immunotherapy for patients with CHB. However, new insights into immunotherapy for CHB have emerged; these may facilitate design of effective and tolerable immunotherapy regimens for these patients. This review provides a comprehensive overview of immunotherapy for CHB.
Collapse
Affiliation(s)
| | - Mamun Al-Mahtab
- b Department of Hepatology , Bangabandhu Sheikh Mujib Medical University , Dhaka , Bangladesh
| | - Munira Jahan
- c Department of Virology , Bangabandhu Sheikh Mujib Medical University , Dhaka , Bangladesh
| | - Osamu Yoshida
- d Department of Gastroenterology and Metabology , Ehime University Graduate School of Medicine , Toon , Japan
| | - Yoichi Hiasa
- d Department of Gastroenterology and Metabology , Ehime University Graduate School of Medicine , Toon , Japan
| |
Collapse
|
36
|
A phase 1, randomized, controlled dose-escalation study of EP-1300 polyepitope DNA vaccine against Plasmodium falciparum malaria administered via electroporation. Vaccine 2016; 34:5571-5578. [PMID: 27697302 DOI: 10.1016/j.vaccine.2016.09.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 08/25/2016] [Accepted: 09/21/2016] [Indexed: 01/30/2023]
Abstract
Plasmodium falciparum malaria is one of the leading infectious causes of childhood mortality in Africa. EP-1300 is a polyepitope plasmid DNA vaccine expressing 38 cytotoxic T cell epitopes and 16 helper T cell epitopes derived from P. falciparum antigens expressed predominantly in the liver phase of the parasite's life cycle. We performed a phase 1 randomized, placebo-controlled, dose escalation clinical trial of the EP-1300 DNA vaccine administered via electroporation using the TriGrid Delivery System device (Ichor Medical Systems). Although the delivery of the EP-1300 DNA vaccine via electroporation was safe, tolerability was less than that usually observed with standard needle and syringe intramuscular administration. This was primarily due to acute local discomfort at the administration site during electroporation. Despite the use of electroporation, the vaccine was poorly immunogenic. The reasons for the poor immunogenicity of this polyepitope DNA vaccine remain uncertain. CLINICAL TRIALS REGISTRATION ClinicalTrials.gov NCT01169077.
Collapse
|
37
|
Abstract
String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial. We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44 % compared to designs without spacers.
Collapse
|
38
|
Brahmania M, Feld J, Arif A, Janssen HLA. New therapeutic agents for chronic hepatitis B. THE LANCET. INFECTIOUS DISEASES 2016; 16:e10-21. [PMID: 26795693 DOI: 10.1016/s1473-3099(15)00436-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/13/2015] [Accepted: 11/03/2015] [Indexed: 12/11/2022]
Abstract
The treatment goal for chronic hepatitis B is true eradication of the hepatitis B virus, but this is rarely achieved with first-line treatment regimens because of an inability to disrupt covalently closed circular DNA and an inadequate host immune response. Therefore, new antiviral agents are needed to target various stages of the hepatitis B virus lifecycle and modulation of the immune system. This Review provides a summary of available regimens with their strengths and limitations, and highlights future therapeutic strategies to target the virus and host immune response. These new agents can hopefully lead to a finite duration of treatment, and provide a functional and durable cure for chronic hepatitis B infection.
Collapse
Affiliation(s)
- Mayur Brahmania
- Toronto Centre for Liver Diseases, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Jordan Feld
- Toronto Centre for Liver Diseases, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Ambreen Arif
- Toronto Centre for Liver Diseases, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Harry L A Janssen
- Toronto Centre for Liver Diseases, Toronto Western Hospital, University Health Network, Toronto, ON, Canada; Department of Gastroenterology and Hepatology, Erasmus Medical Center University Hospital, Rotterdam, Netherlands.
| |
Collapse
|
39
|
Yang N, Bertoletti A. Advances in therapeutics for chronic hepatitis B. Hepatol Int 2015; 10:277-85. [PMID: 26363922 DOI: 10.1007/s12072-015-9661-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/07/2015] [Indexed: 02/06/2023]
Abstract
Chronic hepatitis B infection remains a major disease burden globally, and leads to high risk of hepatocellular carcinoma development. Current therapies of nucleot(s)ide analogues and interferon alpha treatment remain limited in their efficacy. Several key findings in the hepatitis B virus (HBV) life cycle have led to the development of novel antiviral drugs to inhibit viral replication and persistence. In addition, recent studies on HBV-specific innate and adaptive immune responses have advanced development of immunotherapy to restore immune mediated virus control in chronic hepatitis B patients. In this review, we discuss potential new therapeutic strategies targeting HBV or the host immune system that might lead to a sustained cure for chronic hepatitis B.
Collapse
Affiliation(s)
- Ninghan Yang
- Viral Hepatitis Laboratory, Singapore Institute of Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Antonio Bertoletti
- Viral Hepatitis Laboratory, Singapore Institute of Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Emerging Infectious Disease (EID) Program, Duke-NUS Graduate Medical School, Singapore, Singapore.
| |
Collapse
|
40
|
Xu Q, Ma X, Wang F, Li H, Zhao X. Evaluation of a multi-epitope subunit vaccine against avian leukosis virus subgroup J in chickens. Virus Res 2015. [PMID: 26196055 DOI: 10.1016/j.virusres.2015.06.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The intricate sequence and antigenic variability of avian leukosis virus subgroup J (ALV-J) have led to unprecedented difficulties in the development of vaccines. Much experimental evidence demonstrates that ALV-J mutants have caused immune evasion and pose a challenge for traditional efforts to develop effective vaccines. To investigate the potential of a multi-epitope vaccination strategy to prevent chickens against ALV-J infections, a recombinant chimeric multi-epitope protein X (rCMEPX) containing both immunodominant B and T epitope concentrated domains selected from the major structural protein of ALV-J using bioinformatics approach was expressed in Escherichia coli Rosetta (DE3). Its immunogenicity and protective efficacy was studied in chickens. The results showed that rCMEPX could elicit neutralizing antibodies and cellular responses, and antibodies induced by rCMEPX could specifically recognize host cell naturally expressed ALV-J proteins, which indicated that the rCMEPX is a good immunogen. Challenge experiments showed 80% chickens that received rCMEPX were well protected against ALV-J challenge. This is the first report of a chimeric multi-epitope protein as a potential immunogen against ALV-J.
Collapse
Affiliation(s)
- Qingqing Xu
- Department of Preventive Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, China
| | - Xingjiang Ma
- Department of Preventive Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, China
| | - Fangkun Wang
- Department of Preventive Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, China
| | - Hongmei Li
- Department of Preventive Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, China
| | - Xiaomin Zhao
- Department of Preventive Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, China.
| |
Collapse
|
41
|
Abstract
PURPOSE OF REVIEW Hepatitis B virus (HBV) causes a large proportion of chronic liver disease worldwide. The limited efficiency of current treatments based on the use of nucleotide/nucleoside analogues or interferon-alpha requires the development of new therapeutic tools for the treatment of chronic HBV. We summarize the most recent therapeutic strategies designed to directly target HBV-infected hepatocytes or to restore antiviral immunity during chronic HBV infection. RECENT FINDINGS Novel therapies directly target HBV-infected hepatocytes by inducing covalently closed circular DNA degradation or by inhibiting HBV entry or the expression of viral proteins. In addition, immunotherapeutic approaches may boost HBV-specific T-cell responses or stimulate the intrahepatic innate response. SUMMARY These new therapeutic approaches have mainly been tested in animal models. In humans, therapeutic strategies could be tailored to different chronic HBV patients in relation to their clinical and virological disease profile.
Collapse
|
42
|
Singh SP, Verma V, Mishra BN. Characterization of Plasmodium falciparum Proteome at Asexual Blood Stages for Screening of Effective Vaccine Candidates: An Immunoinformatics Approach. ACTA ACUST UNITED AC 2015. [DOI: 10.4137/iii.s24755] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Malaria is a complex parasitic disease that is currently causing great concerns globally owing to the resistance to antimalarial drugs and lack of an effective vaccine. The present study involves the characterization of extracellular secretory proteins as vaccine candidates derived from proteome analysis of Plasmodium falciparum at asexual blood stages of malaria. Among the screened 32 proteins, 31 were predicted as antigens by the VaxiJen program, and 26 proteins had less than two transmembrane spanning regions predicted using the THMMM program. Moreover, 10 and 5 proteins were predicted to contain secretory signals by SignalP and TargetP, respectively. T-cell epitope prediction using MULTIPRED2 and NetCTL programs revealed that most of the predicted antigens are immunogenic and contain more than 10% supertype and 5% promiscuous epitopes of HLA-A, -B, or -DR. We anticipate that T-cell immune responses against asexual blood stages of Plasmodium are dispersed on a relatively large number of parasite antigens. This is the first report, to the best of our knowledge, offering new insights, at the proteome level, for the putative screening of effective vaccine candidates against the malaria pathogen. The findings also suggest new ways forward for the modern omics-guided vaccine target discovery using reverse vaccinology.
Collapse
Affiliation(s)
- Satarudra Prakash Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Vishal Verma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | | |
Collapse
|
43
|
da Silva FP, Preuhs Filho G, Finger E, Barbeiro HV, Zampieri FG, Goulart AC, Torggler Filho F, Panajotopoulos N, Velasco IT, Kalil J, de Souza HP, da Cruz Neto LM, Rodrigues H. HLA-A*31 as a marker of genetic susceptibility to sepsis. Rev Bras Ter Intensiva 2015; 25:284-9. [PMID: 24553509 PMCID: PMC4031872 DOI: 10.5935/0103-507x.20130049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 10/31/2013] [Indexed: 12/04/2022] Open
Abstract
Objective The HLA haplotype has been associated with many autoimmune diseases, but no
associations have been described in sepsis. This study aims to investigate the HLA
system as a possible marker of genetic sepsis susceptibility. Methods This is a prospective cohort study including patients admitted to an intensive
care unit and healthy controls from a list of renal transplant donors. Patients
with less 18 years of age; pregnant or HIV positive patients; those with
metastatic malignancies or receiving chemotherapy; or with advanced liver disease;
or with end-of-life conditions were excluded. The DNA was extracted from the whole
blood and HLA haplotypes determined using MiliPlex®
technology. Results From October 2010 to October 2012, 1,121 patients were included (1,078 kidney
donors, 20 patients admitted with severe sepsis and 23 with septic shock).
HLA-A*31 positive subjects had increased risk of developing sepsis (OR 2.36, 95%CI
1.26-5.35). Considering a p value <0.01, no other significant association was
identified. Conclusion HLA-A*31 expression is associated to risk of developing sepsis.
Collapse
Affiliation(s)
- Fabiano Pinheiro da Silva
- Universidade de São Paulo, Departamento de Emergências Clínicas, São PauloSP, Brasil, Departamento de Emergências Clínicas, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Germano Preuhs Filho
- Universidade de São Paulo, Instituto do Coração, Departamento de Imunologia, São PauloSP, Brasil, Departamento de Imunologia, Instituto do Coração, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Eduardo Finger
- Laboratórios Salomão Zoppi, São PauloSP, Brasil, Laboratórios Salomão Zoppi - São Paulo (SP), Brasil
| | - Hermes Vieira Barbeiro
- Universidade de São Paulo, Departamento de Emergências Clínicas, São PauloSP, Brasil, Departamento de Emergências Clínicas, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Fernando Godinho Zampieri
- Universidade de São Paulo, Departamento de Emergências Clínicas, São PauloSP, Brasil, Departamento de Emergências Clínicas, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Alessandra Carvalho Goulart
- Universidade de São Paulo, Departamento de Emergências Clínicas, São PauloSP, Brasil, Departamento de Emergências Clínicas, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Francisco Torggler Filho
- Universidade de São Paulo, Departamento de Emergências Clínicas, São PauloSP, Brasil, Departamento de Emergências Clínicas, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Nicolas Panajotopoulos
- Universidade de São Paulo, Instituto do Coração, Departamento de Imunologia, São PauloSP, Brasil, Departamento de Imunologia, Instituto do Coração, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Irineu Tadeu Velasco
- Universidade de São Paulo, Departamento de Emergências Clínicas, São PauloSP, Brasil, Departamento de Emergências Clínicas, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Jorge Kalil
- Universidade de São Paulo, Instituto do Coração, Departamento de Imunologia, São PauloSP, Brasil, Departamento de Imunologia, Instituto do Coração, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Heraldo Possolo de Souza
- Universidade de São Paulo, Departamento de Emergências Clínicas, São PauloSP, Brasil, Departamento de Emergências Clínicas, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Luiz Monteiro da Cruz Neto
- Universidade de São Paulo, Departamento de Emergências Clínicas, São PauloSP, Brasil, Departamento de Emergências Clínicas, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| | - Hélcio Rodrigues
- Universidade de São Paulo, Instituto do Coração, Departamento de Imunologia, São PauloSP, Brasil, Departamento de Imunologia, Instituto do Coração, Universidade de São Paulo - USP - São Paulo (SP), Brasil
| |
Collapse
|
44
|
Sánchez-Sampedro L, Perdiguero B, Mejías-Pérez E, García-Arriaza J, Di Pilato M, Esteban M. The evolution of poxvirus vaccines. Viruses 2015; 7:1726-803. [PMID: 25853483 PMCID: PMC4411676 DOI: 10.3390/v7041726] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/16/2015] [Accepted: 03/27/2015] [Indexed: 02/07/2023] Open
Abstract
After Edward Jenner established human vaccination over 200 years ago, attenuated poxviruses became key players to contain the deadliest virus of its own family: Variola virus (VARV), the causative agent of smallpox. Cowpox virus (CPXV) and horsepox virus (HSPV) were extensively used to this end, passaged in cattle and humans until the appearance of vaccinia virus (VACV), which was used in the final campaigns aimed to eradicate the disease, an endeavor that was accomplished by the World Health Organization (WHO) in 1980. Ever since, naturally evolved strains used for vaccination were introduced into research laboratories where VACV and other poxviruses with improved safety profiles were generated. Recombinant DNA technology along with the DNA genome features of this virus family allowed the generation of vaccines against heterologous diseases, and the specific insertion and deletion of poxvirus genes generated an even broader spectrum of modified viruses with new properties that increase their immunogenicity and safety profile as vaccine vectors. In this review, we highlight the evolution of poxvirus vaccines, from first generation to the current status, pointing out how different vaccines have emerged and approaches that are being followed up in the development of more rational vaccines against a wide range of diseases.
Collapse
MESH Headings
- Animals
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- Humans
- Poxviridae/immunology
- Poxviridae/isolation & purification
- Smallpox/prevention & control
- Smallpox Vaccine/history
- Smallpox Vaccine/immunology
- Smallpox Vaccine/isolation & purification
- Vaccines, Attenuated/history
- Vaccines, Attenuated/immunology
- Vaccines, Attenuated/isolation & purification
- Vaccines, Synthetic/history
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/isolation & purification
Collapse
Affiliation(s)
- Lucas Sánchez-Sampedro
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid-28049, Spain.
| | - Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid-28049, Spain.
| | - Ernesto Mejías-Pérez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid-28049, Spain
| | - Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid-28049, Spain
| | - Mauro Di Pilato
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid-28049, Spain.
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid-28049, Spain.
| |
Collapse
|
45
|
Taherkhani R, Farshadpour F, Makvandi M. Design and production of a multiepitope construct derived from hepatitis E virus capsid protein. J Med Virol 2015; 87:1225-34. [PMID: 25784455 PMCID: PMC7159329 DOI: 10.1002/jmv.24171] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2015] [Indexed: 11/15/2022]
Abstract
The aim of this study was to design a high density multiepitope protein, which can be a promising multiepitope vaccine candidate against Hepatitis E virus (HEV). Initially, conserved and antigenic helper T‐lymphocyte (HTL) epitopes in the HEV capsid protein were predicted by in silico analysis. Subsequently, a multiepitope comprising four HTL epitopes with high‐affinity binding to the HLA molecules was designed, and repeated four times as high density multiepitope construct. This construct was synthesized and cloned into pET‐30a (+) vector. Then, it was transformed and expressed in Escherichia coli BL21 cells. The high density multiepitope protein was purified by Ni‐NTA agarose and concentrated using Amicon filters. Finally, the immunological properties of this high density multiepitope protein were evaluated in vitro. The results showed that the high density multiepitope construct was successfully expressed and purified. SDS‐PAGE and Western blot analyses showed the presence of a high density multiepitope protein band of approximately 33 kDa. Approximately 1 mg of the purified protein was obtained from each liter of the culture media. Moreover, the purified multiepitope protein was capable of induction of proliferation responses, IFN‐γ ELISPOT responses and IFN‐γ and IL‐12 cytokines production in a significant level in peripheral blood mononuclear cells (PBMCs) isolated from HEV‐recovered individuals compared to the control group. In conclusion, the newly produced multiepitope protein can induce significant T helper type 1 responses in vitro, and can be considered as a novel strategy for the development of HEV vaccines in the future. J. Med. Virol. 87:1225–1234, 2015. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Reza Taherkhani
- Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran; Persian Gulf Biomedical Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | | | | |
Collapse
|
46
|
Woodchuck hepatitis virus core gene deletions and proliferative responses of peripheral blood mononuclear cells stimulated by an immunodominant epitope: a viral immune escape in the woodchuck model of chronic hepatitis B? Arch Virol 2015; 160:1065-73. [PMID: 25666197 DOI: 10.1007/s00705-015-2346-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 01/21/2015] [Indexed: 10/24/2022]
Abstract
Marmota monax and its natural infection by woodchuck hepatitis virus (WHV) could be used as a predictive model for evaluating mechanisms of viral persistence during chronic hepatitis B virus (HBV) infection. The aim of this study was to investigate the presence of viral variants in the core gene of chronically WHV-infected woodchucks that showed two different patterns of peripheral blood mononuclear cells' (PBMCs') responses after stimulation with a specific WHV core peptide. Sequences' analysis of the WHV core region from eight WHV chronically infected woodchucks have been performed after in vitro stimulation with an immunodominant epitope of the WHV core protein (amino acids [aa] 96-110). Following this stimulation, positive PBMC responses at each point of follow-up were observed for four animals (group A), and weak immune responses at one or a few points of follow-up were observed for the remaining four animals (group B). The WHV core gene sequences contained amino acid deletions (aa 84-126, aa 84-113) in three of four group A animals and in none of group B animals. In the group A animals, the same deletions were observed in liver specimens and in two of four tumor specimens. Hepatocellular carcinoma (HCC) was diagnosed in all group A animals and in one group B animal. In conclusion, internal deletions in the core region correlated with a sustained PBMC response to the immunogenic peptide (96-110) of the core protein. A possible role of this relationship in hepatocarcinogenesis could be hypothesized; however, this needs to be investigated in patients with chronic HBV infection. The evaluation of virus-specific T-cell responses and T-cell epitopes that are possibly related to the mechanisms of viral evasion should be further investigated in order to design combined antiviral and immune approaches to control chronic HBV infection.
Collapse
|
47
|
Sharma M, Dixit A. Identification and immunogenic potential of B cell epitopes of outer membrane protein OmpF of Aeromonas hydrophila in translational fusion with a carrier protein. Appl Microbiol Biotechnol 2015; 99:6277-91. [DOI: 10.1007/s00253-015-6398-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/08/2015] [Accepted: 01/08/2015] [Indexed: 01/10/2023]
|
48
|
Therapeutic vaccines in HBV: lessons from HCV. Med Microbiol Immunol 2015; 204:79-86. [PMID: 25573348 PMCID: PMC4305103 DOI: 10.1007/s00430-014-0376-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/07/2014] [Indexed: 12/15/2022]
Abstract
Currently, millions of people infected with hepatitis B virus (HBV) are committed to decades of treatment with anti-viral therapy to control viral replication. However, new tools for immunotherapy that include both viral vectors and molecular checkpoint inhibitors are now available. This has led to a resurgence of interest in new strategies to develop immunotherapeutic strategies with the aim of inducing HBeAg seroconversion—an end-point that has been associated with a decrease in the rates of disease progression. Ultimately, a true cure will involve the elimination of covalently closed circular DNA which presents a greater challenge for immunotherapy. In this manuscript, I describe the development of immunotherapeutic strategies for HBV that are approaching or currently in clinical studies, and draw on observations of T cell function in natural infection supported by recent animal studies that may lead to additional rational vaccine strategies using checkpoint inhibitors. I also draw on our recent experience in developing potent vaccines for HCV prophylaxis based on simian adenoviral and MVA vectors used in prime–boost strategies in both healthy volunteers and HCV infected patients. I have shown that the induction of T cell immune responses is markedly attenuated when administered to people with persistent HCV viremia. These studies and recently published animal studies using the woodchuck model suggest that potent vaccines based on DNA or adenoviral vectored vaccination represent a rational way forward. However, combining these with drugs to suppress viral replication, alongside checkpoint inhibitors may be required to induce long-term immune control.
Collapse
|
49
|
Koh S, Bertoletti A. Circumventing failed antiviral immunity in chronic hepatitis B virus infection: triggering virus-specific or innate-like T cell response? Med Microbiol Immunol 2014; 204:87-94. [PMID: 25511870 DOI: 10.1007/s00430-014-0377-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 09/15/2014] [Indexed: 02/07/2023]
Abstract
Therapeutic vaccination for the treatment of chronic hepatitis B has thus far been unsatisfactory. In this review, we discuss potential new therapeutic vaccination strategies and other immunotherapeutic approaches that aim to achieve efficient restoration of HBV immunity in chronically infected patients.
Collapse
Affiliation(s)
- Sarene Koh
- Viral Hepatitis Unit, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore,
| | | |
Collapse
|
50
|
Abstract
Chronic HBV infection is a major public health concern affecting over 240 million people worldwide. Although suppression of HBV replication is achieved in the majority of patients with currently available newer antivirals, discontinuation of therapy prior to hepatitis B surface antigen loss or seroconversion is associated with relapse of HBV in the majority of cases. Thus, new therapeutic modalities are needed to achieve eradication of the virus from chronically infected patients in the absence of therapy. The basis of HBV persistence includes viral and host factors. Here, we review novel strategies to achieve sustained cure or elimination of HBV. The novel approaches include targeting the viral and or host factors required for viral persistence, and novel immune-based therapies, including therapeutic vaccines.
Collapse
Affiliation(s)
- Rama Kapoor
- Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research Inc., (formerly SAIC-Frederick, Inc.) Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Laboratory of Immunoregulation, National Institute of Allergy & Infectious Diseases, NIH, Department of Health & Human Services, Bethesda, MD 20892, USA
| | - Shyam Kottilil
- Laboratory of Immunoregulation, National Institute of Allergy & Infectious Diseases, NIH, Department of Health & Human Services, Bethesda, MD 20892, USA
| |
Collapse
|