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Gupta SK, Osmanoglu Ö, Minocha R, Bandi SR, Bencurova E, Srivastava M, Dandekar T. Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information. Front Med (Lausanne) 2022; 9:1008527. [PMID: 36405591 PMCID: PMC9669072 DOI: 10.3389/fmed.2022.1008527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2023] Open
Abstract
Candida auris is a globally emerging fungal pathogen responsible for causing nosocomial outbreaks in healthcare associated settings. It is known to cause infection in all age groups and exhibits multi-drug resistance with high potential for horizontal transmission. Because of this reason combined with limited therapeutic choices available, C. auris infection has been acknowledged as a potential risk for causing a future pandemic, and thus seeking a promising strategy for its treatment is imperative. Here, we combined evolutionary information with reverse vaccinology approach to identify novel epitopes for vaccine design that could elicit CD4+ T-cell responses against C. auris. To this end, we extensively scanned the family of proteins encoded by C. auris genome. In addition, a pathogen may acquire substitutions in epitopes over a period of time which could cause its escape from the immune response thus rendering the vaccine ineffective. To lower this possibility in our design, we eliminated all rapidly evolving genes of C. auris with positive selection. We further employed highly conserved regions of multiple C. auris strains and identified two immunogenic and antigenic T-cell epitopes that could generate the most effective immune response against C. auris. The antigenicity scores of our predicted vaccine candidates were calculated as 0.85 and 1.88 where 0.5 is the threshold for prediction of fungal antigenic sequences. Based on our results, we conclude that our vaccine candidates have the potential to be successfully employed for the treatment of C. auris infection. However, in vivo experiments are imperative to further demonstrate the efficacy of our design.
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Affiliation(s)
- Shishir K. Gupta
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Evolutionary Genomics Group, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Özge Osmanoglu
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
| | - Rashmi Minocha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sourish Reddy Bandi
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
| | - Mugdha Srivastava
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- BioComputing Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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Dhasmana A, Dhasmana S, Alsulimani A, Kotnala S, Kashyap VK, Haque S, Jaggi M, Yallapu MM, Chauhan SC. In silico CD4 + T-cell multiepitope prediction and HLA distribution analysis for Marburg Virus-A strategy for vaccine designing. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2022; 34:101751. [PMID: 38881729 PMCID: PMC11178283 DOI: 10.1016/j.jksus.2021.101751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Marburg, a RNA virus (MRV), is responsible for causing hemorrhagic fever that affects humans and non-human primates. World Health Organization (WHO), National Institutes of Health (NIH) and Centre of Disease Control and Prevention (CDC) considered this as an extremely dangerous virus, thus categorised as risk group 4, category A priority pathogen and category "A" bioterrorism agent, respectively. Despite of all these alarming concerns, no prophylaxis arrangements are available against this virus till date. In fact, the construction of immunogenic vaccine candidates by traditional molecular immunology methods is time consuming and very expensive. Considering these concerns, herein, we have designed CD4 + T Cell multiepitopes against MRV using in silico approach. The pin-point criteria of the screening and selection of potential epitopes are, non-mutagenic, antigenic, large HLAs coverage, non-toxic and high world population coverage. This kind of methodology and investigations can precisely reduce the expenditure and valuable time for experimental planning in development of vaccines in laboratories. In current scenario, researchers are frequently using in silico approaches to speed up their vaccine-based lab studies. The computational studies are highly valuable for the screening of large epitope dataset into smaller one prior to in vitro and in vivo confirmatory analyses.
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Affiliation(s)
- Anupam Dhasmana
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
- Department of Biosciences, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Dehradun, India
| | - Swati Dhasmana
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Ahmad Alsulimani
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Sudhir Kotnala
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Vivek Kumar Kashyap
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Bursa Uludağ University, Faculty of Medicine, Görükle Campus, 16059 Nilüfer, Bursa, Turkey
| | - Meena Jaggi
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Murali M. Yallapu
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Subhash C. Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
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Zhigis LS, Kotelnikova OV, Zinchenko AA, Karlinsky DM, Prokopenko YA, Rumsh LD. IgA1 Protease as a Vaccine Basis for Prevention of Bacterial Meningitis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s106816202104021x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
The review covers the study of the protective properties of IgA1 protease and the possibility of creating a vaccine preparation for the prevention of bacterial meningitis of various origins on its basis. Bacterial meningitis belongs to the group of socially dangerous diseases and is characterized by a severe course, numerous complications and high mortality. The approaches used at present in world practice to create antimicrobial vaccines are based on a narrow targeting against a specific pathogen. The development of a monocomponent vaccine against a wide range of bacterial pathogens with a common virulence factor is still relevant. IgA1 protease, a protein that is one of the main virulence factors of a number of gram-negative and gram-positive bacteria, can serve as such an antigen. Bacterial IgA1 protease is uniquely specific for immunoglobulins A1 (IgA1), cleaving peptide bonds in the hinge regions of the IgA1 in humans and other higher primates. Bacteria, getting on the mucous membrane, destroy IgA1, which acts as the first barrier to protect the body from infections. Neutralization of IgA1 protease at this stage can become an obstacle to the development of infection, hindering the adhesion of a number of pathogens that produce this protein. The data available in the literature on the mechanism of antibacterial protection are scattered and ambiguous. The review considers the literature data and the results of our own experiments on the protective activity of IgA1 protease. We have shown that the recombinant meningococcal IgA1 protease and some of its fragments protect mice from infection with a live virulent culture not only of meningococci of the main epidemic serogroups (A, B, C, and W135), but also of some of the most common virulent pneumococcal serotypes. The data obtained indicate the possibility of creating a monocomponent vaccine against these and, possibly, other bacterial infections. Currently, significant progress has been made in studying the structure and functions of secreted proteins in the bacteria Neisseria meningitidis and Haemophilus influenzae. In this review we describe protein translocation systems of N. meningitidis, which are related to the secretion of proteins in these bacteria, and also present modern data on the functions of these proteins. Analysis of experimental data on the structure of IgA1 protease of N. meningitidis and the formation of immunity during vaccination is of key importance in the development of prophylactic preparations.
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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.
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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.
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Unni PA, Ali AMMT, Rout M, Thabitha A, Vino S, Lulu SS. Designing of an epitope-based peptide vaccine against walking pneumonia: an immunoinformatics approach. Mol Biol Rep 2018; 46:511-527. [PMID: 30465133 DOI: 10.1007/s11033-018-4505-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/15/2018] [Indexed: 11/25/2022]
Abstract
Mycoplasma pneumoniae is a substantial respiratory pathogen that develops not only pneumonia but also other respiratory diseases, which mimic viral respiratory syndromes. Nevertheless, vaccine development for this pathogen delays behind as immunity correlated with protection is now predominantly unknown. In the present study, an immunoinformatics pipeline is utilized for epitope-based peptide vaccine design, which can trigger a critical immune response against M. pneumoniae. A total of 105 T-cell epitopes from 12 membrane associated proteins and 7 T-cell epitopes from 5 cytadherence proteins of M. pneumoniae were obtained and validated. Thus, 18 peptides with 9-mer core sequence were identified as best T-cell epitopes by considering the number of residues with > 75% in favored region. Further, the crucial screening studies predicted three peptides with good binding affinity towards HLA molecules as best T-cell and B-cell epitopes. Based on this result, visualization, and dynamic simulation for the three epitopes (WIHGLILLF, VILLFLLLF, and LLAWMLVLF) were assessed. The predicted epitopes needs to be further validated for their adept use as vaccine. Collectively, the study opens up a new horizon with extensive therapeutic application against M. pneumoniae and its associated diseases.
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Affiliation(s)
- P Ambili Unni
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - A M Mohamed Thoufic Ali
- Department of Integrative Biology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Madhusmita Rout
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - A Thabitha
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - S Vino
- Department of Bio-Sciences, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - S Sajitha Lulu
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
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Kotel'nikova OV, Alliluev AP, Zinchenko AA, Prokopenko YA, Zhigis LS, Zueva VS, Razgulyaeva OA, Gordeeva EA, Melikhova TD, Nokel' EA, Rumsh LD. Peculiarities of the Formation of Antimeningococcus Immunity in Mice Immunized with Fragments of N. meningitidis IgA1 Protease. Bull Exp Biol Med 2018; 165:763-766. [PMID: 30353335 DOI: 10.1007/s10517-018-4260-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Indexed: 11/25/2022]
Abstract
We studied immunogenicity of two recombinant proteins FR.9 and FR.11-3 created on the basis of fragments of the primary structure of N. meningitidis IgA1 protease with different molecular weights containing different sets of T and B epitopes. The proteins actively protect animals infected with live virulent culture of meningococci, serogroups A, B, and C. Analysis of CD4+, CD8+, and CD19+ lymphocyte populations in mouse blood showed predominant contribution of different cell populations to the formation of immune response to different proteins. Injection of FR.11-3 protein to animals did no affect the immunoregulatory index, hence, this protein can be used for creation of immunologically safe vaccine preparation.
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Affiliation(s)
- O V Kotel'nikova
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - A P Alliluev
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - A A Zinchenko
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yu A Prokopenko
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - L S Zhigis
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - V S Zueva
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - O A Razgulyaeva
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - E A Gordeeva
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - T D Melikhova
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - E A Nokel'
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - L D Rumsh
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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7
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Exploring Highly Antigenic Protein of Campylobacter jejuni for Designing Epitope Based Vaccine: Immunoinformatics Approach. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9764-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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8
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Zinchenko AA, Kotelnikova OV, Gordeeva EA, Prokopenko YA, Razgulyaeva OA, Serova OV, Melikhova TD, Nokel EA, Zhigis LS, Zueva VS, Alliluev AP, Rumsh LD. Immunogenic and Protective Properties of Neisseria meningitidis IgA1 Protease and of Its Truncated Fragments. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018010193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Masforrol Y, Gil J, García D, Noda J, Ramos Y, Betancourt L, Guirola O, González S, Acevedo B, Besada V, Reyes O, González LJ. A deeper mining on the protein composition of VA-MENGOC-BC®: An OMV-based vaccine against N. meningitidis serogroup B and C. Hum Vaccin Immunother 2017; 13:2548-2560. [PMID: 29083947 DOI: 10.1080/21645515.2017.1356961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The protein composition of an Outer Membrane Vesicle (OMV) preparation that constitutes the active pharmaceutical ingredient of VA-MENGOC-BC®, an effective vaccine against Neisseria meningitidis serogroups B, and C is presented. This preparation has a high lipid content and five abundant membrane proteins (FetA, PorA, PorB, RmpM, and Opc), constituting approximately 70% of the total protein mass. The protein composition was determined by combining the use of the Hexapeptide Ligand Library and an orthogonal tandem fractionation of tryptic peptides by reverse-phase chromatography at alkaline and acid pH. This approach equalizes the concentration of tryptic peptides derived from low- and high-abundance proteins as well as considerably simplifying the number of peptides analyzed by LC-MS/MS, enhancing the possibility of identifying low-abundance species. Fifty-one percent of the proteins originally annotated as membrane proteins in the genome of the MC58 strain were identified. One hundred and sixty-eight low-abundance cytosolic proteins presumably occluded within OMV were also identified. Four (NadA, NUbp, GNA2091, and fHbp), out of the five antigens constituting the Bexsero® vaccine, were detected in this OMV preparation. In particular, fHbp is also the active principle of the Trumenba® vaccine developed by Pfizer. The HpuA and HpuB gene products (not annotated in the MC58 genome) were identified in the CU385 strain, a clinical isolate that is used to produce this OMV. Considering the proteins identified here and previous work done by our group, the protein catalogue of this OMV preparation was extended to 266 different protein species.
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Affiliation(s)
- Yordanka Masforrol
- a Peptide Synthesis Group, Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Jeovanis Gil
- b Mass Spectrometry Laboratory and Department of Proteomics , Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Darien García
- d Vaccine Department, Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Jesús Noda
- b Mass Spectrometry Laboratory and Department of Proteomics , Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Yassel Ramos
- b Mass Spectrometry Laboratory and Department of Proteomics , Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Lázaro Betancourt
- b Mass Spectrometry Laboratory and Department of Proteomics , Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Osmany Guirola
- c Bioinformatics Department, Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Sonia González
- d Vaccine Department, Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Boris Acevedo
- e Quality Assurance Departments, Center for Genetic Engineering and Biotechnology, Havana , Cuba
| | - Vladimir Besada
- b Mass Spectrometry Laboratory and Department of Proteomics , Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Osvaldo Reyes
- a Peptide Synthesis Group, Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Luis Javier González
- b Mass Spectrometry Laboratory and Department of Proteomics , Center for Genetic Engineering and Biotechnology , Havana , Cuba
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Mei Y, Zhao L, Liu Y, Gong H, Song Y, Lei L, Zhu Y, Jin Z, Ma S, Hu B, Sun Q, Liu H. Combining DNA Vaccine and AIDA-1 in Attenuated Salmonella Activates Tumor-Specific CD4 + and CD8 + T-cell Responses. Cancer Immunol Res 2017; 5:503-514. [PMID: 28468915 DOI: 10.1158/2326-6066.cir-16-0240-t] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 03/01/2017] [Accepted: 04/21/2017] [Indexed: 11/16/2022]
Abstract
Stimulation of tumor-specific responses in both CD4+ and CD8+ T cells has been a challenge for effective tumor vaccines. We designed a vaccine vector containing the AIDA-1 autotransporter and DNA vaccine elements, generating a murine melanoma vaccine that was delivered by the attenuated Salmonella strain SL7207. Growth of murine subcutaneous melanoma was significantly inhibited by intranasal immunization with the Salmonella tumor vaccine. The vaccine activated tumor-specific CD4+ and CD8+ T-cell responses, with increased T-cell proliferation, tumor antigen-specific Th1 cytokine production, increased percentages of tetramer positive cells, and cytotoxicity. CD4+ or CD8+ T-cell depletion resulted in the loss of antitumor activity of the Salmonella tumor vaccine, suggesting that the efficacy of the vaccine was dependent on both CD4+ and CD8+ T cells. Lung metastasis of the tumor was also inhibited by vaccine treatment. Similarly, the percentages of tumor-specific Th1 cytokine production by CD4+ and CD8+ T cells in the spleen, tumor, and bronchoalveolar lavage were increased after vaccine treatment. Tumor-specific proliferation of CD4+ and CD8+ T cells was also promoted by the vaccine. Tetramer staining and cytotoxicity assay showed enhanced tumor-specific CD8+ T-cell response after vaccine treatment. Therefore, the Salmonella tumor vaccine could activate both tumor-specific CD4+ and CD8+ T-cell responses. This vaccine strategy may be widely applicable to the development of oral or nasal vaccines against tumors. Cancer Immunol Res; 5(6); 503-14. ©2017 AACR.
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Affiliation(s)
- Yu Mei
- Institute of Blood and Marrow Transplantation, Department of Hematology, Collaborative Innovation Center of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China.,Immunology Programme, Life Sciences Institute and Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
| | - Lixiang Zhao
- College of Basic Medicine and Biological Sciences, Medical Department, Soochow University, Suzhou, P.R. China
| | - Yonghao Liu
- Institute of Blood and Marrow Transplantation, Department of Hematology, Collaborative Innovation Center of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Huanle Gong
- Institute of Blood and Marrow Transplantation, Department of Hematology, Collaborative Innovation Center of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Yuan Song
- Institute of Blood and Marrow Transplantation, Department of Hematology, Collaborative Innovation Center of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Lei Lei
- Institute of Blood and Marrow Transplantation, Department of Hematology, Collaborative Innovation Center of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Ying Zhu
- Institute of Blood and Marrow Transplantation, Department of Hematology, Collaborative Innovation Center of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Ziqi Jin
- Institute of Blood and Marrow Transplantation, Department of Hematology, Collaborative Innovation Center of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Shoubao Ma
- Institute of Blood and Marrow Transplantation, Department of Hematology, Collaborative Innovation Center of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Bo Hu
- Institute of Blood and Marrow Transplantation, Department of Hematology, Collaborative Innovation Center of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Qing Sun
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, P.R. China
| | - Haiyan Liu
- Immunology Programme, Life Sciences Institute and Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore.
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11
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Farhadi T, Ranjbar MM. Designing and modeling of complex DNA vaccine based on MOMP of Chlamydia trachomatis: an in silico approach. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s13721-016-0142-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Sequence-based approach for rapid identification of cross-clade CD8+ T-cell vaccine candidates from all high-risk HPV strains. 3 Biotech 2016; 6:39. [PMID: 28330110 PMCID: PMC4729761 DOI: 10.1007/s13205-015-0352-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 08/13/2015] [Indexed: 11/16/2022] Open
Abstract
Human papilloma virus (HPV) is the primary etiological agent responsible for cervical cancer in women. Although in total 16 high-risk HPV strains have been identified so far. Currently available commercial vaccines are designed by targeting mainly HPV16 and HPV18 viral strains as these are the most common strains associated with cervical cancer. Because of the high level of antigenic specificity of HPV capsid antigens, the currently available vaccines are not suitable to provide cross-protection from all other high-risk HPV strains. Due to increasing reports of cervical cancer cases from other HPV high-risk strains other than HPV16 and 18, it is crucial to design vaccine that generate reasonable CD8+ T-cell responses for possibly all the high-risk strains. With this aim, we have developed a computational workflow to identify conserved cross-clade CD8+ T-cell HPV vaccine candidates by considering E1, E2, E6 and E7 proteins from all the high-risk HPV strains. We have identified a set of 14 immunogenic conserved peptide fragments that are supposed to provide protection against infection from any of the high-risk HPV strains across globe.
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Yang HJ, Zhang JY, Wei C, Yang LY, Zuo QF, Zhuang Y, Feng YJ, Srinivas S, Zeng H, Zou QM. Immunisation With Immunodominant Linear B Cell Epitopes Vaccine of Manganese Transport Protein C Confers Protection against Staphylococcus aureus Infection. PLoS One 2016; 11:e0149638. [PMID: 26895191 PMCID: PMC4764517 DOI: 10.1371/journal.pone.0149638] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/03/2016] [Indexed: 12/15/2022] Open
Abstract
Vaccination strategies for Staphylococcus aureus, particularly methicillin-resistant S. aureus (MRSA) infections have attracted much research attention. Recent efforts have been made to select manganese transport protein C, or manganese binding surface lipoprotein C (MntC), which is a metal ion associated with pathogen nutrition uptake, as potential candidates for an S. aureus vaccine. Although protective humoral immune responses to MntC are well-characterised, much less is known about detailed MntC-specific B cell epitope mapping and particularly epitope vaccines, which are less-time consuming and more convenient. In this study, we generated a recombinant protein rMntC which induced strong antibody response when used for immunisation with CFA/IFA adjuvant. On the basis of the results, linear B cell epitopes within MntC were finely mapped using a series of overlapping synthetic peptides. Further studies indicate that MntC113-136, MntC209-232, and MntC263-286 might be the original linear B-cell immune dominant epitope of MntC, furthermore, three-dimensional (3-d) crystal structure results indicate that the three immunodominant epitopes were displayed on the surface of the MntC antigen. On the basis of immunodominant MntC113-136, MntC209-232, and MntC263-286 peptides, the epitope vaccine for S. aureus induces a high antibody level which is biased to TH2 and provides effective immune protection and strong opsonophagocytic killing activity in vitro against MRSA infection. In summary, the study provides strong proof of the optimisation of MRSA B cell epitope vaccine designs and their use, which was based on the MntC antigen in the development of an MRSA vaccine.
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Affiliation(s)
- Hui-Jie Yang
- National Engineering Research Centre for Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - Jin-Yong Zhang
- National Engineering Research Centre for Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - Chao Wei
- National Engineering Research Centre for Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - Liu-Yang Yang
- National Engineering Research Centre for Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - Qian-Fei Zuo
- National Engineering Research Centre for Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - Yuan Zhuang
- National Engineering Research Centre for Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - You-Jun Feng
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Swaminath Srinivas
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801, United States of America
| | - Hao Zeng
- National Engineering Research Centre for Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
- * E-mail: (HZ); (QMZ)
| | - Quan-Ming Zou
- National Engineering Research Centre for Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
- * E-mail: (HZ); (QMZ)
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Mortier MC, Jongert E, Mettens P, Ruelle JL. Sequence conservation analysis and in silico human leukocyte antigen-peptide binding predictions for the Mtb72F and M72 tuberculosis candidate vaccine antigens. BMC Immunol 2015; 16:63. [PMID: 26493839 PMCID: PMC4619029 DOI: 10.1186/s12865-015-0119-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 09/08/2015] [Indexed: 11/16/2022] Open
Abstract
Background Requisites for an efficacious tuberculosis (TB) vaccine are a minimal genomic diversity among infectious Mycobacterium tuberculosis strains for the selected antigen, and the capability to induce robust T-cell responses in the majority of human populations. A tool in the identification of putative T-cell epitopes is in silico prediction of major histocompatibility complex (MHC)-peptide binding. Candidate TB vaccine antigen Mtb72F and its successor M72 are recombinant fusion proteins derived from Mtb32A and Mtb39A (encoded by Rv0125 and Rv1196, respectively). Adjuvanted Mtb72F and M72 candidate vaccines were shown to induce CD4+ T-cell responses in European, US, African and Asian populations. Methods Sequence conservation of Mtb32A, Mtb39A, Mtb72F and M72 among 46 strains (prevalent Mycobacterium strains causing human TB disease, and H37Ra) was assessed by multiple alignments using ClustalX. For Mtb32A, Mtb39A and Mtb72F, 15-mer human leukocyte antigen (HLA)-class II-binding peptides were predicted for 158 DRB1 alleles prevailing in populations with high TB burden, 6 DRB3/4/5, 8 DQ and 6 DP alleles, using NetMHCII-pan-3.0. Results for 3 DRB1 alleles were compared with previously published allele-matched in vitro binding data. Additional analyses were done for M72. Nonameric MHC class I-binding peptides in Mtb72F were predicted for three alleles representative of class I supertypes A02, A03 and B07, using seven prediction algorithms. Results Sequence identity among strains was ≥98 % for each protein. Residue changes in Mtb39A comprised primarily single residue or nucleotide insertions and/or deletions in repeat regions, and were observed in 67 % of strains. For Mtb72F, 156 DRB1, 6 DRB3/4/5, 7 DQ and 5 DP alleles were predicted to contain at least one MHC class II-binding peptide, and class I-binding peptides were predicted for each HLA-A/B allele. Comparison of predicted MHC-II-binding peptides with experimental data indicated that the algorithm’s sensitivity and specificity were variable among alleles. Conclusions The sequences from which Mtb72F and M72 are derived are highly conserved among representative Mycobacterium strains. Predicted putative T-cell epitopes in M72 and/or Mtb72F covered a wide array of HLA alleles. In silico binding predictions for class I- and II-binding putative epitopes can be complemented with biochemical verification of HLA binding capacity, processing and immunogenicity of the predicted peptides. Electronic supplementary material The online version of this article (doi:10.1186/s12865-015-0119-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Erik Jongert
- GSK Vaccines, Rue de l'Institut 89, 1330, Rixensart, Belgium.
| | - Pascal Mettens
- GSK Vaccines, Rue de l'Institut 89, 1330, Rixensart, Belgium.
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15
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Gasparini R, Panatto D, Bragazzi NL, Lai PL, Bechini A, Levi M, Durando P, Amicizia D. How the Knowledge of Interactions between Meningococcus and the Human Immune System Has Been Used to Prepare Effective Neisseria meningitidis Vaccines. J Immunol Res 2015; 2015:189153. [PMID: 26351643 PMCID: PMC4553322 DOI: 10.1155/2015/189153] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/09/2015] [Indexed: 01/17/2023] Open
Abstract
In the last decades, tremendous advancement in dissecting the mechanisms of pathogenicity of Neisseria meningitidis at a molecular level has been achieved, exploiting converging approaches of different disciplines, ranging from pathology to microbiology, immunology, and omics sciences (such as genomics and proteomics). Here, we review the molecular biology of the infectious agent and, in particular, its interactions with the immune system, focusing on both the innate and the adaptive responses. Meningococci exploit different mechanisms and complex machineries in order to subvert the immune system and to avoid being killed. Capsular polysaccharide and lipooligosaccharide glycan composition, in particular, play a major role in circumventing immune response. The understanding of these mechanisms has opened new horizons in the field of vaccinology. Nowadays different licensed meningococcal vaccines are available and used: conjugate meningococcal C vaccines, tetravalent conjugate vaccines, an affordable conjugate vaccine against the N. menigitidis serogroup A, and universal vaccines based on multiple antigens each one with a different and peculiar function against meningococcal group B strains.
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Affiliation(s)
- R. Gasparini
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - D. Panatto
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - N. L. Bragazzi
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - P. L. Lai
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - A. Bechini
- Department of Health Sciences, University of Florence, Viale G.B. Morgagni 48, 50134 Florence, Italy
| | - M. Levi
- Department of Health Sciences, University of Florence, Viale G.B. Morgagni 48, 50134 Florence, Italy
| | - P. Durando
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - D. Amicizia
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
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In silico epitope analysis of unique and membrane associated proteins from Mycobacterium avium subsp. paratuberculosis for immunogenicity and vaccine evaluation. J Theor Biol 2015; 384:1-9. [PMID: 26279134 DOI: 10.1016/j.jtbi.2015.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/27/2015] [Accepted: 08/04/2015] [Indexed: 11/24/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of paratuberculosis disease affecting ruminants worldwide. The aim of this study was to identify potential candidate antigens and epitopes by bio and immuno-informatic tools which could be later evaluated as vaccines and/or diagnosis. 110 protein sequences were selected from MAP K-10 genome database: 48 classified as putative enzymes involved in surface polysaccharide and lipopolysaccharide synthesis, as membrane associated and secreted proteins, 32 as conserved membrane proteins, and 30 as absent from other mycobacterial genomes. These 110 proteins were preliminary screened for Major Histocompatibility Complex (MHC) class II affinity and promiscuity using ProPred program. In addition, subcellular localization and host protein homology was analyzed. From these analyses, 23 MAP proteins were selected for a more accurate inmunoinformatic analysis (i.e. T cell and B cell epitopes analysis) and for homology with mycobacterial proteins. Finally, eleven MAP proteins were identified as potential candidates for further immunogenic evaluation: six proteins (MAP0228c, MAP1239c, MAP2232, MAP3080, MAP3131 and MAP3890) were identified as presenting potential T cell epitopes, while 5 selected proteins (MAP0232c, MAP1240c, MAP1738, MAP2239 and MAP3641c) harbored a large numbers of epitopes predicted to induce both cell- and antibody-mediated immune responses. Moreover, immunogenicity of selected epitopes from MAP1239c were evaluated in IFN-γ release assay. In summary, eleven M. avium subsp. paratuberculosis proteins were identified by in silico analysis and need to be further evaluated for their immunodiagnostic and vaccine potential in field and mice model.
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Gupta SK, Jaitly T, Schmitz U, Schuler G, Wolkenhauer O, Vera J. Personalized cancer immunotherapy using Systems Medicine approaches. Brief Bioinform 2015; 17:453-67. [DOI: 10.1093/bib/bbv046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Indexed: 12/27/2022] Open
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18
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Designing of Complex Multi-epitope Peptide Vaccine Based on Omps of Klebsiella pneumoniae: An In Silico Approach. Int J Pept Res Ther 2015. [DOI: 10.1007/s10989-015-9461-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Yang J, Dai LX, Pan X, Wang H, Li B, Zhu J, Li MY, Shi XL, Wang BN. Protection against Helicobacter pylori infection in BALB/c mice by oral administration of multi-epitope vaccine of CTB-UreI-UreB. Pathog Dis 2015; 73:ftv026. [PMID: 25846576 DOI: 10.1093/femspd/ftv026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2015] [Indexed: 12/26/2022] Open
Abstract
Chronic gastric infection by the Gram-negative bacterium Helicobacter pylori (H. pylori) is strongly associated with gastritis, gastric ulcer and the development of distal gastric carcinoma and gastric mucosal lymphoma in humans. Antibiotic treatment of H. pylori is becoming less effective because of increasing antibiotic resistance; other treatment approaches such as specifically targeted methods, etc. to destroy this organism would be beneficial. An epitope vaccine is a promising option for protection against H. pylori infection. In this study, a multi-epitope vaccine was constructed by linking cholera toxin B subunit (CTB), two antigenic fragments of H. pylori urease I subunit (UreI20-29, UreI98-107) and four antigenic fragments of H. pylori urease B subunit (UreB12-23, UreB229-251, UreB327-400, UreB515-561), resulting in the recombinant CTB-UreI-UreB (BIB). Its protective effect against H. pylori infection was evaluated in BALB/c mice. Significant protection against H. pylori challenge was achieved in BALB/c mice immunized with BIB (15/18, 83.3%), rIB plus rCTB (6/18, 33.3%) and rIB (2/18, 11.1%) separately, while no protective effect was found in the mice immunized with either adjuvant rCTB alone or PBS. The induction of significant protection against H. pylori is possibly mediated by specific serum IgA and mucosal sIgA antibodies, and a mixed Th1/Th2/Th17 cells response. This multi-epitope vaccine might be a promising vaccine candidate that helps to control H. pylori infection.
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Affiliation(s)
- Jing Yang
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China Sichuan Vaccine Technology Co. Ltd, Chengdu, Sichuan 610041, People's Republic of China Department of Infectious Disease, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, People's Republic of China Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, People's Republic of China
| | - Lv-xia Dai
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China Experiment Teaching Center of Clinical Medicine, Chengdu College of Medicine, Chengdu, Sichuan 610500, People's Republic of China
| | - Xing Pan
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China Sichuan Vaccine Technology Co. Ltd, Chengdu, Sichuan 610041, People's Republic of China
| | - Hongren Wang
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Bei Li
- Department of Infectious Disease, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, People's Republic of China Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, People's Republic of China
| | - Jie Zhu
- Sichuan Vaccine Technology Co. Ltd, Chengdu, Sichuan 610041, People's Republic of China
| | - Ming-yuan Li
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Xin-Li Shi
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, People's Republic of China
| | - Bao-ning Wang
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
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Ranjbar MM, Gupta SK, Ghorban K, Nabian S, Sazmand A, Taheri M, Esfandyari S, Taheri M. Designing and Modeling of Complex DNA Vaccine Based on Tropomyosin Protein of Boophilus Genus Tick. Appl Biochem Biotechnol 2014; 175:323-39. [DOI: 10.1007/s12010-014-1245-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 09/10/2014] [Indexed: 12/13/2022]
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Newcombe J, Mendum TA, Ren CP, McFadden J. Identification of the immunoproteome of the meningococcus by cell surface immunoprecipitation and MS. MICROBIOLOGY-SGM 2013; 160:429-438. [PMID: 24275101 DOI: 10.1099/mic.0.071829-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Most healthy adults are protected from meningococcal disease by the presence of naturally acquired anti-meningococcal antibodies; however, the identity of the target antigens of this protective immunity remains unclear, particularly for protection against serogroup B disease. To identify the protein targets of natural protective immunity we developed an immunoprecipitation and proteomics approach to define the immunoproteome of the meningococcus. Sera from 10 healthy individuals showing serum bactericidal activity against both a meningococcal C strain (L91543) and the B strain MC58, together with commercially available pooled human sera, were used as probe antisera. Immunoprecipitation was performed with each serum sample and live cells from both meningococcal strains. Immunoprecipitated proteins were identified by MS. Analysis of the immunoproteome from each serum demonstrated both pan-reactive antigens that were recognized by most sera as well as subject-specific antigens. Most antigens were found in both meningococcal strains, but a few were strain-specific. Many of the immunoprecipitated proteins have been characterized previously as surface antigens, including adhesins and proteases, several of which have been recognized as vaccine candidate antigens, e.g. factor H-binding protein, NadA and neisserial heparin-binding antigen. The data demonstrate clearly the presence of meningococcal antibodies in healthy individuals with no history of meningococcal infection and a wide diversity of immune responses. The identification of the immunoreactive proteins of the meningococcus provides a basis for understanding the role of each antigen in the natural immunity associated with carriage and may help to design vaccination strategies.
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Affiliation(s)
- Jane Newcombe
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Tom A Mendum
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Chuan-Peng Ren
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Johnjoe McFadden
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
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22
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Santos AR, Pereira VB, Barbosa E, Baumbach J, Pauling J, Röttger R, Turk MZ, Silva A, Miyoshi A, Azevedo V. Mature Epitope Density--a strategy for target selection based on immunoinformatics and exported prokaryotic proteins. BMC Genomics 2013; 14 Suppl 6:S4. [PMID: 24564223 PMCID: PMC3908659 DOI: 10.1186/1471-2164-14-s6-s4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Current immunological bioinformatic approaches focus on the prediction of allele-specific epitopes capable of triggering immunogenic activity. The prediction of major histocompatibility complex (MHC) class I epitopes is well studied, and various software solutions exist for this purpose. However, currently available tools do not account for the concentration of epitope products in the mature protein product and its relation to the reliability of target selection. Results We developed a computational strategy based on measuring the epitope's concentration in the mature protein, called Mature Epitope Density (MED). Our method, though simple, is capable of identifying promising vaccine targets. Our online software implementation provides a computationally light and reliable analysis of bacterial exoproteins and their potential for vaccines or diagnosis projects against pathogenic organisms. We evaluated our computational approach by using the Mycobacterium tuberculosis (Mtb) H37Rv exoproteome as a gold standard model. A literature search was carried out on 60 out of 553 Mtb's predicted exoproteins, looking for previous experimental evidence concerning their possible antigenicity. Half of the 60 proteins were classified as highest scored by the MED statistic, while the other half were classified as lowest scored. Among the lowest scored proteins, ~13% were confirmed as not related to antigenicity or not contributing to the bacterial pathogenicity, and 70% of the highest scored proteins were confirmed as related. There was no experimental evidence of antigenic or pathogenic contributions for three of the highest MED-scored Mtb proteins. Hence, these three proteins could represent novel putative vaccine and drug targets for Mtb. A web version of MED is publicly available online at http://med.mmci.uni-saarland.de/. Conclusions The software presented here offers a practical and accurate method to identify potential vaccine and diagnosis candidates against pathogenic bacteria by "reading" results from well-established reverse vaccinology software in a novel way, considering the epitope's concentration in the mature portion of the protein.
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Li HB, Zhang JY, He YF, Chen L, Li B, Liu KY, Yang WC, Zhao Z, Zou QM, Wu C. Systemic immunization with an epitope-based vaccine elicits a Th1-biased response and provides protection against Helicobacter pylori in mice. Vaccine 2012; 31:120-6. [PMID: 23137845 DOI: 10.1016/j.vaccine.2012.10.091] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/09/2012] [Accepted: 10/25/2012] [Indexed: 12/12/2022]
Abstract
Vaccine-mediated Th1-biased CD4+ T cell responses have been shown to be crucial for protection against Helicobacter pylori (H. pylori). In this study, we investigated whether a vaccine composed of CD4+ T cell epitopes together with Th1 adjuvants could confer protection against H. pylori in a mouse model. We constructed an epitope-based vaccine, designated Epivac, which was composed of predicted immunodominant CD4+ T cell epitopes from H. pylori adhesin A (HpaA), urease B (UreB) and cytotoxin-associated gene A product (CagA). Together with four different Th1 adjuvants, Epivac was administered subcutaneously and the prophylactic potential was examined. Compared to non-immunized mice, immunization with Epivac alone or with a Th1 adjuvant significantly reduced H. pylori colonization, and better protection was observed when an adjuvant was used. Immunized mice exhibited a strong local and systemic Th1-biased immune response, which may contribute to the inhibition of H. pylori colonization. Though a significant specific antibody response was induced by the vaccine, no correlation was found between the intensity of the humoral response and the protective effect. Our results suggest that a vaccine containing CD4+ T cell epitopes is a promising candidate for protection against H. pylori infection.
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Affiliation(s)
- Hai-Bo Li
- Department of Clinical Microbiology and Immunology, College of Medical Laboratory, Third Military Medical University, Chongqing 400038, China
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Gupta SK, Srivastava M, Akhoon BA, Gupta SK, Grabe N. In silico accelerated identification of structurally conserved CD8+ and CD4+ T-cell epitopes in high-risk HPV types. INFECTION GENETICS AND EVOLUTION 2012; 12:1513-8. [DOI: 10.1016/j.meegid.2012.02.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 02/06/2012] [Accepted: 02/12/2012] [Indexed: 01/18/2023]
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25
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Sundaramurthi JC, Brindha S, Shobitha SR, Swathi A, Ramanandan P, Hanna LE. In silico identification of potential antigenic proteins and promiscuous CTL epitopes in Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2012; 12:1312-8. [PMID: 22484107 DOI: 10.1016/j.meegid.2012.03.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 03/23/2012] [Accepted: 03/28/2012] [Indexed: 01/11/2023]
Abstract
Cell-mediated immunity is critical for the control of Mycobacterium tuberculosis infection. We hypothesized that those proteins of M. tuberculosis (MTB) that do not have homologs in humans as well as human gut flora, would mount a good antigenic response in man, and employed a bioinformatics approach to identify MTB antigens capable of inducing a robust cell-mediated immune response in humans. In the first step we identified 624 MTB proteins that had no homologs in humans. Comparison of this set of proteins with the proteome of 77 different microbes that comprise the human gut flora narrowed down the list to 180 proteins unique to MTB. Twenty nine of the 180 proteins are known to be associated with dormancy. Since dormancy associated proteins are known to harbor CTL epitopes, we selected four representative unique proteins and subjected them to epitope analysis using ProPred1. Nineteen novel promiscuous epitopes were identified in the four proteins. Population coverage for 7 of the 19 shortlisted epitopes including Rv3852 (58-KPAEAPVSL, 112-VPLIVAVTL, 118-VTLSLLALL and 123-LALLLIRQL), Rv2706c (66-RPLSGVSFL) Rv3466 (8- RIVEVFDAL and 38-RSLERLECL) was >74%. These novel promiscuous epitopes are conserved in other virulent MTB strains, and can therefore be further investigated for their immunological relevance and usefulness as vaccine candidates.
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Affiliation(s)
- Jagadish Chandrabose Sundaramurthi
- ICMR-Biomedical Informatics Centre, Department of Clinical Research, National Institute for Research in Tuberculosis (Formerly Tuberculosis Research Centre), Indian Council of Medical Research, Chennai 600 031, Tamil Nadu, India
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Nakayasu ES, Sobreira TJP, Torres R, Ganiko L, Oliveira PSL, Marques AF, Almeida IC. Improved proteomic approach for the discovery of potential vaccine targets in Trypanosoma cruzi. J Proteome Res 2012; 11:237-46. [PMID: 22115061 PMCID: PMC3253764 DOI: 10.1021/pr200806s] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chagas disease, caused by Trypanosoma cruzi, is a devastating parasitic infection affecting millions of people. Although many efforts have been made for the development of immunotherapies, there is no available vaccine against this deadly infection. One major hurdle for the rational approach to develop a T. cruzi vaccine is the limited information about the proteins produced by different phylogenetic lineages, strains, and stages of the parasite. Here, we have adapted a 1D nanoHPLC system to perform online 2D LC-MS/MS, using the autosampler to inject the eluting salt solutions in the first dimension separation. The application of this methodology for the proteomic analysis of the infective trypomastigote stage of T. cruzi led to the identification of 1448 nonredundant proteins. Furthermore, about 14% of the identified sequences comprise surface proteins, most of them glycosylphosphatidylinositol (GPI)-anchored and related to parasite pathogenesis. Immunoinformatic analysis revealed thousands of potential peptides with predicted high-binding affinity for major histocompatibility complex (MHC) class I and II molecules. The high diversity of proteins expressed on the trypomastigote surface may have many implications for host-cell invasion and immunoevasion mechanisms triggered by the parasite. Finally, we performed a rational approach to filter potential T-cell epitopes that could be further tested and validated for development of a Chagas disease vaccine.
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Affiliation(s)
- Ernesto S. Nakayasu
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso TX, 79902, USA
| | - Tiago J. P. Sobreira
- National Laboratory for Biosciences (LNBio), National Center for Research in Energy and Materials, Campinas, SP 13083-970, Brazil
| | - Rafael Torres
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso TX, 79902, USA
| | - Luciane Ganiko
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso TX, 79902, USA
| | - Paulo S. L. Oliveira
- National Laboratory for Biosciences (LNBio), National Center for Research in Energy and Materials, Campinas, SP 13083-970, Brazil
| | - Alexandre F. Marques
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso TX, 79902, USA
| | - Igor C. Almeida
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso TX, 79902, USA
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Misra N, Panda PK, Shah K, Sukla LB, Chaubey P. Population coverage analysis of T-Cell epitopes of Neisseria meningitidis serogroup B from Iron acquisition proteins for vaccine design. Bioinformation 2011; 6:255-61. [PMID: 21738325 PMCID: PMC3124689 DOI: 10.6026/97320630006255] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 06/01/2011] [Indexed: 01/10/2023] Open
Abstract
Although the concept of Reverse Vaccinology was first pioneered for sepsis and meningococcal meningitidis causing bacterium, Neisseria meningitides, no broadly effective vaccine against serogroup B meningococcal disease is yet available. In the present investigation, HLA distribution analysis was undertaken to select three most promiscuous T-cell epitopes out of ten computationally validated epitopes of Iron acquisition proteins from Neisseria MC58 by using the population coverage tool of Immune Epitope Database (IEDB). These epitopes have been determined on the basis of their binding ability with maximum number of HLA alleles along with highest population coverage rate values for all the geographical areas studied. The comparative population coverage analysis of moderately immunogenic and high immunogenic peptides suggests that the former may activate T-cell response in a fairly large proportion of people in most geographical areas, thus indicating their potential for development of epitope-based vaccine.
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Affiliation(s)
- Namrata Misra
- Bioresources Engineering Department, Institute of Minerals and Materials Technology (formerly Regional Research Lab), CSIR, Bhubaneswar-751013, Orissa,India
| | - Prasanna Kumar Panda
- Bioresources Engineering Department, Institute of Minerals and Materials Technology (formerly Regional Research Lab), CSIR, Bhubaneswar-751013, Orissa,India
| | - Kavita Shah
- Environmental Biochemistry and Bioinformatics Lab, Department of Zoology, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi-221 005, India
| | - Lala Bihari Sukla
- Bioresources Engineering Department, Institute of Minerals and Materials Technology (formerly Regional Research Lab), CSIR, Bhubaneswar-751013, Orissa,India
| | - Priyanka Chaubey
- Environmental Biochemistry and Bioinformatics Lab, Department of Zoology, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi-221 005, India
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28
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In silico identification of novel protective VSG antigens expressed by Trypanosoma brucei and an effort for designing a highly immunogenic DNA vaccine using IL-12 as adjuvant. Microb Pathog 2011; 51:77-87. [PMID: 21349321 DOI: 10.1016/j.micpath.2011.01.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 01/24/2011] [Accepted: 01/24/2011] [Indexed: 11/22/2022]
Abstract
African trypanosomiasis continues to be a major health problem, with more adults dying from this disease world-wide. As the sequence diversity of Trypanosoma brucei is extreme, with VSGs having 15-25% identity with most other VSGs, hence it displays a huge diversity of adaptations and host specificities. Therefore the need for an improved vaccine has become an international priority. The highly conserved and specific epitopes acting as both CD8+ and CD4+ T-cell epitopes (FLINKKPAL and FTALCTLAA) were predicted from large bunch of VSGs of T. brucei. Besides, some other potential epitopes with very high affinity for MHC I and II molecules were also determined while taking consideration on the most common HLA in the general population which accounts for major ethnicities. The vaccine candidates were found to be effective even for non-african populations as predicted by population coverage analysis. Hence the migrating travelers acting as a spread means of the infection can probably also be treated successfully after injection of such a multiepitopic vaccine. Exploiting the immunoinformatics approaches, we designed a potential vaccine by using the consensus epitopic sequence of 388 VSG proteins of T. brucei and performed in silico cloning of multiepitopic antigenic DNA sequence in pBI-CMV1 vector. Moreover, various techniques like codon adaptation, CpG optimization, removal of self recognized epitopes, use of adjuvant and co-injection with plasmids expressing immune-stimulatory molecules were implemented to enhance the immunogenicity of the proposed in silico vaccine.
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29
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In silico proteomic characterization of human epidermal growth factor receptor 2 (HER-2) for the mapping of high affinity antigenic determinants against breast cancer. Amino Acids 2011; 42:1349-60. [DOI: 10.1007/s00726-010-0830-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 12/23/2010] [Indexed: 10/18/2022]
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30
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Gupta SK, Srivastava M, Akhoon BA, Smita S, Schmitz U, Wolkenhauer O, Vera J, Gupta SK. Identification of immunogenic consensus T-cell epitopes in globally distributed influenza-A H1N1 neuraminidase. INFECTION GENETICS AND EVOLUTION 2010; 11:308-19. [PMID: 21094280 DOI: 10.1016/j.meegid.2010.10.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/15/2010] [Accepted: 10/18/2010] [Indexed: 02/01/2023]
Abstract
Antigenic drift is the ability of the swine influenza virus to undergo continuous and progressive changes in response to the host immune system. These changes dictate influenza vaccine updates annually to ensure inclusion of antigens of the most current strains. The identification of those peptides that stimulate T-cell responses, termed T-cell epitopes, is essential for the development of successful vaccines. In this study, the highly conserved and specific epitopes from neuraminidase of globally distributed H1N1 strains were predicted so that these potential vaccine candidates may escape with antigenic drift. A total of nine novel CD8(+) T-cell epitopes for MHC class-I and eight novel CD4(+) T-cell epitopes for MHC class-II alleles were proposed as novel epitope based vaccine candidates. Additionally, the epitope FSYKYGNGV was identified as a highly conserved, immunogenic and potential vaccine candidate, capable for generating both CD8(+) and CD4(+) responses.
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Affiliation(s)
- Shishir K Gupta
- Society for Biological Research & Rural Development, Lucknow, UP, India.
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