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Luo H, Ma Y, Bi J, Li Z, Wang Y, Su Z, Gerstweiler L, Ren Y, Zhang S. Experimental and molecular dynamics simulation studies on the physical properties of three HBc-VLP derivatives as nanoparticle protein vaccine candidates. Vaccine 2024:S0264-410X(24)00599-1. [PMID: 38811268 DOI: 10.1016/j.vaccine.2024.05.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Self-assembling virus-like particles (VLPs) are promising platforms for vaccine development. However, the unpredictability of the physical properties, such as self-assembly capability, hydrophobicity, and overall stability in engineered protein particles fused with antigens, presents substantial challenges in their downstream processing. We envision that these challenges can be addressed by combining more precise computer-aided molecular dynamics (MD) simulations with experimental studies on the modified products, with more to-date forcefield descriptions and larger models closely resembling real assemblies, realized by rapid advancement in computing technology. In this study, three chimeric designs based on the hepatitis B core (HBc) protein as model vaccine candidates were constructed to study and compare the influence of inserted epitopes as well as insertion strategy on HBc modifications. Large partial VLP models containing 17 chains for the HBc chimeric model vaccines were constructed based on the wild-type (wt) HBc assembly template. The findings from our simulation analysis have demonstrated good consistency with experimental results, pertaining to the surface hydrophobicity and overall stability of the chimeric vaccine candidates. Furthermore, the different impact of foreign antigen insertions on the HBc scaffold was investigated through simulations. It was found that separately inserting two epitopes into the HBc platform at the N-terminal and the major immunogenic regions (MIR) yields better results compared to a serial insertion at MIR in terms of protein structural stability. This study substantiates that an MD-guided design approach can facilitate vaccine development and improve its manufacturing efficiency by predicting products with extreme surface hydrophobicity or structural instability.
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Affiliation(s)
- Hong Luo
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia; State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, PR China
| | - Yanyan Ma
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Jingxiu Bi
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia
| | - Zhengjun Li
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yingli Wang
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, PR China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Lukas Gerstweiler
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia.
| | - Ying Ren
- State Key Laboratory of Mesoscience and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
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Khan MA, Amin A, Farid A, Ullah A, Waris A, Shinwari K, Hussain Y, Alsharif KF, Alzahrani KJ, Khan H. Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics 2022; 15:pharmaceutics15010152. [PMID: 36678781 PMCID: PMC9863128 DOI: 10.3390/pharmaceutics15010152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Infectious diseases continue to be a leading cause of morbidity and mortality worldwide. The majority of infectious diseases are caused by intracellular pathogenic bacteria (IPB). Historically, conventional vaccination drives have helped control the pathogenesis of intracellular bacteria and the emergence of antimicrobial resistance, saving millions of lives. However, in light of various limitations, many diseases that involve IPB still do not have adequate vaccines. In response to increasing demand for novel vaccine development strategies, a new area of vaccine research emerged following the advent of genomics technology, which changed the paradigm of vaccine development by utilizing the complete genomic data of microorganisms against them. It became possible to identify genes related to disease virulence, genetic patterns linked to disease virulence, as well as the genetic components that supported immunity and favorable vaccine responses. Complete genomic databases, and advancements in transcriptomics, metabolomics, structural genomics, proteomics, immunomics, pan-genomics, synthetic genomics, and population biology have allowed researchers to identify potential vaccine candidates and predict their effects in patients. New vaccines have been created against diseases for which previously there were no vaccines available, and existing vaccines have been improved. This review highlights the key issues and explores the evolution of vaccines. The increasing volume of IPB genomic data, and their application in novel genome-based techniques for vaccine development, were also examined, along with their characteristics, and the opportunities and obstacles involved. Critically, the application of genomics technology has helped researchers rapidly select and evaluate candidate antigens. Novel vaccines capable of addressing the limitations associated with conventional vaccines have been developed and pressing healthcare issues are being addressed.
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Affiliation(s)
- Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- Correspondence: (M.A.K.); or (H.K.)
| | - Aftab Amin
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Awais Farid
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Hong Kong, China
| | - Amin Ullah
- Molecular Virology Laboratory, Department of Microbiology and Biotechnology, Abasyn University, Peshawar 25000, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Khyber Shinwari
- Institute of Chemical Engineering, Department Immuno-Chemistry, Ural Federal University, Yekaterinbiurg 620002, Russia
| | - Yaseen Hussain
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Khalaf F. Alsharif
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Khalid J. Alzahrani
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Haroon Khan
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence: (M.A.K.); or (H.K.)
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Abstract
Immune principles formulated by Jenner, Pasteur, and early immunologists served as fundamental propositions for vaccine discovery against many dreadful pathogens. However, decisive success in the form of an efficacious vaccine still eludes for diseases such as tuberculosis, leishmaniasis, and trypanosomiasis. Several antileishmanial vaccine trials have been undertaken in past decades incorporating live, attenuated, killed, or subunit vaccination, but the goal remains unmet. In light of the above facts, we have to reassess the principles of vaccination by dissecting factors associated with the hosts' immune response. This chapter discusses the pathogen-associated perturbations at various junctures during the generation of the immune response which inhibits antigenic processing, presentation, or remodels memory T cell repertoire. This can lead to ineffective priming or inappropriate activation of memory T cells during challenge infection. Thus, despite a protective primary response, vaccine failure can occur due to altered immune environments in the presence of pathogens.
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Affiliation(s)
| | - Sunil Kumar
- National Centre for Cell Science, Pune, Maharashtra, India
| | | | - Bhaskar Saha
- National Centre for Cell Science, Pune, Maharashtra, India.
- Trident Academy of Creative Technology, Bhubaneswar, Odisha, India.
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Immunoinformatics and reverse vaccinomic approaches for effective design. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300457 DOI: 10.1016/b978-0-323-91172-6.00004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The emergence of mutagenic strains of severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) worst hit the world which already suffered from the Coronavirus disease-2019 (COVID-19) pandemic for 2 years. Due to recent advances in vaccinomics, many vaccine candidates are available but their efficacy against a mutant version of SARS-CoV-2 has remained uncertain. The immune-informatics-based reverse vaccinomic approaches have shown promising investigations recently for the development of cost-effective vaccinomics candidates in a very short period of time. The strategic vaccine development of selected epitopes using artificial intelligence for both B- and T-cells is a very crucial step in this process. This approach provides a highly effective and immunogenic vaccine that offers immunological safety against autoimmunity and other adverse effects over ethnicities, pregnant women, and vulnerable age groups. Several researchers have developed effective vaccine candidates using computational vaccinology and the immune-informatics approach. In this process, a unique peptide sequence of viral proteins such as Nucleocapsid, spike, envelope protein was identified by various in silico tools which are acting as immunological epitopes against TLRs, T-cells, and B-cells. While the conventional immunological vaccine studies take years for vaccine candidature, the immunoinformatics approach is a time-efficient way for the next generation research to study host-pathogen interactions and vaccine development. It is also cost-effective and leads to a better understanding of disease pathogenesis, diagnosis, and immunological response. Owing to the advantage of immunoinformatics-based vaccine approaches the present chapter aimed to discuss vaccine development using immunoinformatics approaches. Besides, the current challenges and future aspects have also been discussed herewith.
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Jain R, Jain A, Verma SK. Prediction of Epitope based Peptides for Vaccine Development from Complete Proteome of Novel Corona Virus (SARS-COV-2) Using Immunoinformatics. Int J Pept Res Ther 2021; 27:1729-1740. [PMID: 33897313 PMCID: PMC8051835 DOI: 10.1007/s10989-021-10205-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2021] [Indexed: 12/19/2022]
Abstract
COVID-19 is an infectious disease caused by a newly discovered corona virus SARS-COV-2. It is the most dangerous epidemic existing currently all over the world. To date, there is no licensed vaccine and not any particular efficient therapeutic agent available to prevent or cure the disease. So development of an effective vaccine is the urgent need of the time. The proposed study aims to identify potential vaccine candidates by screening the complete proteome of SARS-COV-2 using the computational approach. From 14 protein entries in UniProtKB, 4 proteins were screened for epitope prediction based on consensus antigenicity predictions and various physico-chemical criteria like transmembrane domain, allergenicity, GRAVY value, toxicity, stability index. Comprehensive analysis of these 4 antigens revealed that spike protein (P0DTC2) and nucleoprotein (P0DTC9) show the greatest potential for experimental immunogenicity analysis. These 2 proteins have several potential CD4+ and CD8+ T-cell epitopes, as well as high probability of B-cell epitope regions as compared to well-characterized antigen the matrix protein 1 [Influenza A virus (H5N1)]. In addition, the epitope SIIAYTMSL predicted from spike protein (P0DTC2) and epitope SPRWYFYYL predicted from nucleoprotein (P0DTC9) exhibited more than 60% population coverage in the target populations Europe, North America, South Asia, Northeast Asia taken in this study. These epitopes have also been found to exhibit highly significant TCR–pMHC interactions having a joint Z value of 4.51 and 4.37 respectively. Therefore, this analysis suggests that the predicted epitopes might be suitable vaccine candidates and should be subjected to further in-vivo and in-vitro studies.
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Affiliation(s)
- Richa Jain
- Institute of Engineering and Technology, Lucknow, Uttar Pradesh India
| | - Ankit Jain
- Indian Meteorological Department, Lucknow, India
| | - Santosh Kumar Verma
- Department of Civil Engineering, National Institute of Technology, Hamirpur, India
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Sharma A, Sanduja P, Anand A, Mahajan P, Guzman CA, Yadav P, Awasthi A, Hanski E, Dua M, Johri AK. Advanced strategies for development of vaccines against human bacterial pathogens. World J Microbiol Biotechnol 2021; 37:67. [PMID: 33748926 PMCID: PMC7982316 DOI: 10.1007/s11274-021-03021-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 02/17/2021] [Indexed: 12/18/2022]
Abstract
Infectious diseases are one of the main grounds of death and disabilities in human beings globally. Lack of effective treatment and immunization for many deadly infectious diseases and emerging drug resistance in pathogens underlines the need to either develop new vaccines or sufficiently improve the effectiveness of currently available drugs and vaccines. In this review, we discuss the application of advanced tools like bioinformatics, genomics, proteomics and associated techniques for a rational vaccine design.
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Affiliation(s)
- Abhinay Sharma
- School of Life Sciences, Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Vaccinology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research, Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Pooja Sanduja
- School of Life Sciences, Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Aparna Anand
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research, Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Pooja Mahajan
- School of Life Sciences, Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Carlos A Guzman
- Department of Vaccinology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendragarh, Harayana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad-Gurgaon Expressway, PO box #04, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121001, India
| | - Emanuel Hanski
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research, Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Meenakshi Dua
- School of Environmental Sciences, Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Atul Kumar Johri
- School of Life Sciences, Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Haynes AM, Fernandez M, Romeis E, Mitjà O, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Giacani L. Transcriptional and immunological analysis of the putative outer membrane protein and vaccine candidate TprL of Treponema pallidum. PLoS Negl Trop Dis 2021; 15:e0008812. [PMID: 33497377 PMCID: PMC7864442 DOI: 10.1371/journal.pntd.0008812] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/05/2021] [Accepted: 01/09/2021] [Indexed: 11/29/2022] Open
Abstract
Background An effective syphilis vaccine should elicit antibodies to Treponema pallidum subsp. pallidum (T. p. pallidum) surface antigens to induce pathogen clearance through opsonophagocytosis. Although the combination of bioinformatics, structural, and functional analyses of T. p. pallidum genes to identify putative outer membrane proteins (OMPs) resulted in a list of potential vaccine candidates, still very little is known about whether and how transcription of these genes is regulated during infection. This knowledge gap is a limitation to vaccine design, as immunity generated to an antigen that can be down-regulated or even silenced at the transcriptional level without affecting virulence would not induce clearance of the pathogen, hence allowing disease progression. Principal findings We report here that tp1031, the T. p. pallidum gene encoding the putative OMP and vaccine candidate TprL is differentially expressed in several T. p. pallidum strains, suggesting transcriptional regulation. Experimental identification of the tprL transcriptional start site revealed that a homopolymeric G sequence of varying length resides within the tprL promoter and that its length affects promoter activity compatible with phase variation. Conversely, in the closely related pathogen T. p. subsp. pertenue, the agent of yaws, where a naturally-occurring deletion has eliminated the tprL promoter region, elements necessary for protein synthesis, and part of the gene ORF, tprL transcription level are negligible compared to T. p. pallidum strains. Accordingly, the humoral response to TprL is absent in yaws-infected laboratory animals and patients compared to syphilis-infected subjects. Conclusion The ability of T. p. pallidum to stochastically vary tprL expression should be considered in any vaccine development effort that includes this antigen. The role of phase variation in contributing to T. p. pallidum antigenic diversity should be further studied. Syphilis is still an endemic disease in many low- and middle-income countries and has been resurgent in high-income nations for almost two decades now. In endemic areas, syphilis still causes significant morbidity and mortality in patients, particularly when its causative agent, the bacterium Treponema pallidum subsp. pallidum is transmitted to the fetus during pregnancy. Although there are significant ongoing efforts to identify an effective syphilis vaccine to bring into clinical trials within the decade in the U.S., such efforts are partially hindered by the lack of knowledge on transcriptional regulation of many genes encoding vaccine candidates. Here, we start addressing this knowledge gap for the putative outer membrane protein (OMP) and vaccine candidates TprL, encoded by the tp1031 gene. As we previously reported for other putative OMP-encoding genes of the syphilis agent, tprL transcription level appears to be affected by the length of a homopolymeric sequence of guanosines (Gs) located within the gene promoter. This is a mechanism known as phase variation and often involved in altering the surface antigenic profile of a bacterial pathogen to facilitate immune evasion and/or adaptation to the host milieu.
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Affiliation(s)
- Austin M. Haynes
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Mark Fernandez
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Emily Romeis
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Oriol Mitjà
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias I Pujol, Badalona, Barcelona, Spain
- Lihir Medical Centre-International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Kelika A. Konda
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- David Geffen School of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, United States of America
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- School of Public Health and Administration “Carlos Vidal Layseca”, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- David Geffen School of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, United States of America
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Abstract
The application of the fields of pharmacogenomics and pharmacogenetics to vaccine design, profoundly combined with bioinformatics, has been recently termed "vaccinomics." The enormous amount of information generated by whole genome sequencing projects and the rise of bioinformatics has triggered the birth of a new era of vaccine research and development, leading to a "third generation" of vaccines, which are based on the application of vaccinomics science to vaccinology. The first example of such an approach is reverse vaccinology. Reverse vaccinology reduces the period of vaccine target detection and evaluation to 1-2 years. This approach targets the genomic sequence and predicts those antigens that are most likely to be vaccine candidates. This approach allows not only the identification of all the antigens obtained by the previous methods but also the discovery of new antigens that work on a totally different paradigm. Hence this method helps in the discovery of novel mechanisms of immune intervention. Epitope-based immune-derived vaccines (IDV) are generally considered to be safe when compared to other vectored or attenuated live vaccines. Epitope-based IDV may also provide essential T-cell help for antibody-directed vaccines. Such vaccines may have a significant advantage over earlier vaccine design approaches, as the cautious assortment of the components may diminish.
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Charlton Hume HK, Vidigal J, Carrondo MJT, Middelberg APJ, Roldão A, Lua LHL. Synthetic biology for bioengineering virus-like particle vaccines. Biotechnol Bioeng 2018; 116:919-935. [PMID: 30597533 PMCID: PMC7161758 DOI: 10.1002/bit.26890] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/08/2018] [Accepted: 11/29/2018] [Indexed: 12/13/2022]
Abstract
Vaccination is the most effective method of disease prevention and control. Many viruses and bacteria that once caused catastrophic pandemics (e.g., smallpox, poliomyelitis, measles, and diphtheria) are either eradicated or effectively controlled through routine vaccination programs. Nonetheless, vaccine manufacturing remains incredibly challenging. Viruses exhibiting high antigenic diversity and high mutation rates cannot be fairly contested using traditional vaccine production methods and complexities surrounding the manufacturing processes, which impose significant limitations. Virus‐like particles (VLPs) are recombinantly produced viral structures that exhibit immunoprotective traits of native viruses but are noninfectious. Several VLPs that compositionally match a given natural virus have been developed and licensed as vaccines. Expansively, a plethora of studies now confirms that VLPs can be designed to safely present heterologous antigens from a variety of pathogens unrelated to the chosen carrier VLPs. Owing to this design versatility, VLPs offer technological opportunities to modernize vaccine supply and disease response through rational bioengineering. These opportunities are greatly enhanced with the application of synthetic biology, the redesign and construction of novel biological entities. This review outlines how synthetic biology is currently applied to engineer VLP functions and manufacturing process. Current and developing technologies for the identification of novel target‐specific antigens and their usefulness for rational engineering of VLP functions (e.g., presentation of structurally diverse antigens, enhanced antigen immunogenicity, and improved vaccine stability) are described. When applied to manufacturing processes, synthetic biology approaches can also overcome specific challenges in VLP vaccine production. Finally, we address several challenges and benefits associated with the translation of VLP vaccine development into the industry.
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Affiliation(s)
- Hayley K Charlton Hume
- The University of Queensland, Australian Institute of Bioengineering and Nanotechnology, St Lucia, Queensland, Australia
| | - João Vidigal
- Health & Pharma Division, Animal Cell Technology Unit, Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Health & Pharma Division, Animal Cell Technology Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Manuel J T Carrondo
- Health & Pharma Division, Animal Cell Technology Unit, Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
| | - Anton P J Middelberg
- Faculty of Engineering, Computer and Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - António Roldão
- Health & Pharma Division, Animal Cell Technology Unit, Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Health & Pharma Division, Animal Cell Technology Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Linda H L Lua
- The University of Queensland, St Lucia, Queensland, Australia
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Rana A, Thakur S, Kumar G, Akhter Y. Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens. Front Genet 2018; 9:572. [PMID: 30538722 PMCID: PMC6277634 DOI: 10.3389/fgene.2018.00572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/06/2018] [Indexed: 11/21/2022] Open
Abstract
Mycobacterial infections are one of the deadliest infectious diseases still posing a major health burden worldwide. The battle against these pathogens needs to focus on novel approaches and key interventions. In recent times, availability of genome scale data has revolutionized the fields of computational biology and immunoproteomics. Here, we summarize the cutting-edge ‘omics’ technologies and innovative system scale strategies exploited to mine the available data. These may be targeted using high-throughput technologies to expedite the identification of novel antigenic candidates for the rational next generation vaccines and serodiagnostic development against mycobacterial pathogens for which traditional methods have been failing.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Shweta Thakur
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Girish Kumar
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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Hegde NR, Gauthami S, Sampath Kumar HM, Bayry J. The use of databases, data mining and immunoinformatics in vaccinology: where are we? Expert Opin Drug Discov 2017; 13:117-130. [PMID: 29226722 DOI: 10.1080/17460441.2018.1413088] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Vaccinology has evolved from a sub-discipline focussed on simplistic vaccine development based on antibody-mediated protection to a separate discipline involving epidemiology, host and pathogen biology, immunology, genomics, proteomics, structure biology, protein engineering, chemical biology, and delivery systems. Data mining in combination with bioinformatics has provided a scaffold linking all these disciplines to the design of vaccines and vaccine adjuvants. Areas covered: This review provides background knowledge on immunological aspects which have been exploited with informatics for the in silico analysis of immune responses and the design of vaccine antigens. Furthermore, the article presents various databases and bioinformatics tools, and discusses B and T cell epitope predictions, antigen design, adjuvant research and systems immunology, highlighting some important examples, and challenges for the future. Expert opinion: Informatics and data mining have not only reduced the time required for experimental immunology, but also contributed to the identification and design of novel vaccine candidates and the determination of biomarkers and pathways of vaccine response. However, more experimental data is required for benchmarking immunoinformatic tools. Nevertheless, developments in immunoinformatics and reverse vaccinology, which are nascent fields, are likely to hasten vaccine discovery, although the path to regulatory approval is likely to remain a necessary impediment.
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Affiliation(s)
| | - S Gauthami
- b Ella Foundation, Turkapally , Hyderabad , India
| | - H M Sampath Kumar
- c Council of Scientific and Industrial Research - Indian Institute of Chemical Technology , Hyderabad , India
| | - Jagadeesh Bayry
- d Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1138 , Centre de Recherche des Cordeliers, Paris , France
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Genome-Wide Prediction of Potential Vaccine Candidates for Campylobacter jejuni Using Reverse Vaccinology. Interdiscip Sci 2017; 11:337-347. [PMID: 29128919 DOI: 10.1007/s12539-017-0260-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/01/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
Abstract
Campylobacteriosis is a deadly disease which has developed resistance to most of the available chemotherapeutic agents. Although various studies provide evidence of acquired immunity following exposure to Campylobacter jejuni, no effective vaccine has been developed, still. Hence, there is an urgent need to identify potential vaccine candidates for Campylobacter species. In the proposed study, Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) was taken and computational approach was employed to screen C. jejuni genome for promising vaccine candidates. From 1623 protein-coding sequences, 37 potential antigens were screened for epitope prediction based on surface association, consensus antigenicity predictions, solubility, transmembrane domain, and ortholog analysis. Comprehensive immunogenic analysis of these 37 antigens revealed that antigen Q0PA22 shows the greatest potential for experimental immunogenicity analysis. It has several potential CD4+ and CD8+ T-cell epitopes, as well as high probability of B-cell epitope regions as compared to well-characterized antigen Omp18 (Uniprot ID:Q0PC24). Among the highest scoring predicted epitopes, an optimal set of epitopes with respect to overall immunogenicity in target populations for campylobacteriosis viz. Europe, North America and Southwest Asia was determined. An epitope AMLTYMQWL from antigen no. 6(Q0PA22) binds to the most prevalent allele HLA-A*0201, and this epitope has most immunogenicity for all the target populations. In addition, this epitope exhibited highly significant TCR-pMHC interactions having a joint Z value of 4.87. Homology mapping studies of the predicted epitope show best homology to a well-studied antigenic peptide from influenza virus H5N1. Therefore, the predicted epitope might be a suitable vaccine candidate.
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Márquez-Escobar VA. Current developments and prospects on human metapneumovirus vaccines. Expert Rev Vaccines 2017; 16:419-431. [PMID: 28116910 DOI: 10.1080/14760584.2017.1283223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION Human metapneumovirus (hMPV) has become one of the major pathogens causing acute respiratory infections (ARI) mainly affecting young children, immunocompromised patients, and the elderly. Currently there are no licensed vaccines against this virus. Areas covered: Since the discovery of hMPV in 2001, many groups have focused on developing vaccines against this pathogen. This review presents the outcomes and perspectives derived from preclinical studies performed in cell cultures and animals as well as the only candidate that has reached evaluation in a clinical trial. Limitations of the current vaccine candidates are discussed and perspectives for the development of plant-based vaccines are analyzed. Expert commentary: Several hMPV vaccine candidates are under development with the potential to progress into clinical trials. In parallel, the molecular farming field offers new opportunities to generate innovative vaccines that will offer several advantages in the fight against hMPV.
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Affiliation(s)
- Verónica Araceli Márquez-Escobar
- a Facultad de Ciencias Químicas , Universidad Autónoma de San Luis Potosí , Av. Dr. Manuel Nava 6, San Luis Potosí 78210 , SLP , Mexico
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14
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The development of veterinary vaccines: a review of traditional methods and modern biotechnology approaches. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.biori.2017.10.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Mehla K, Ramana J. Identification of epitope-based peptide vaccine candidates against enterotoxigenic Escherichia coli: a comparative genomics and immunoinformatics approach. MOLECULAR BIOSYSTEMS 2016; 12:890-901. [PMID: 26766131 DOI: 10.1039/c5mb00745c] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Enterotoxigenic Escherichia coli (ETEC) associated diarrhea remains a global killer with an estimated annual incidence rate of 840 million infections and 3 800 000 deaths worldwide. There are no vaccines available for ETEC and the traditional vaccine development approach is arduous and time consuming. Thus, alternative in silico approaches for epitope prediction have engrossed the interest of researchers to reduce resources and time of vaccine development. Computational approaches are playing a crucial role in fighting against rapidly growing infectious organisms. In this study we employed an integrated comparative genomics and immunoinformatics approach for proteome scale identification of peptide vaccine candidates. The proteins shared between both ETEC E24377A and H10407 strains, but lacking in commensal E. coli SE11, were subjected to immunoinformatics analysis. For a protein pool shared between different pathogenic ETEC strains, we investigated varied physicochemical and immunogenic properties to prioritize potential vaccine candidates. Epitopes were further tested using docking studies to bind in the MHC-I binding cleft. Predicted epitopes provided more than a 95% population coverage in diarrhea endemic regions presented by major MHC-I supertypes, and bind efficiently to a MHC molecule. We conclude by accentuating that the epitopes predicted in this study are believed to accelerate the development of successful vaccines to control or prevent ETEC infections, albeit the results require experimental validation using model organisms. This study underscores that in silico approaches, together with omics data, hold great potential to be utilized for rapid and reliable genome-wide screening for identification of vaccine candidates against devastating infectious diseases.
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Affiliation(s)
- Kusum Mehla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, PIN-173234, Himachal Pradesh, India.
| | - Jayashree Ramana
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, PIN-173234, Himachal Pradesh, India.
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Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates. Proteomes 2016; 4:proteomes4010011. [PMID: 28248221 PMCID: PMC5217363 DOI: 10.3390/proteomes4010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/05/2016] [Accepted: 03/01/2016] [Indexed: 01/20/2023] Open
Abstract
Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control.
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17
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Couto N, Martins J, Lourenço AM, Pomba C, Varela Coelho A. Identification of vaccine candidate antigens of Staphylococcus pseudintermedius by whole proteome characterization and serological proteomic analyses. J Proteomics 2016; 133:113-124. [DOI: 10.1016/j.jprot.2015.12.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 01/12/2023]
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18
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Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries. PLoS One 2014; 9:e114159. [PMID: 25473968 PMCID: PMC4256389 DOI: 10.1371/journal.pone.0114159] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/04/2014] [Indexed: 12/22/2022] Open
Abstract
There is a need for techniques capable of identifying the antigenic epitopes targeted by polyclonal antibody responses during deliberate or natural immunization. Although successful, traditional phage library screening is laborious and can map only some of the epitopes. To accelerate and improve epitope identification, we have employed massive sequencing of phage-displayed antigen-specific libraries using the Illumina MiSeq platform. This enabled us to precisely identify the regions of a model antigen, the meningococcal NadA virulence factor, targeted by serum antibodies in vaccinated individuals and to rank hundreds of antigenic fragments according to their immunoreactivity. We found that next generation sequencing can significantly empower the analysis of antigen-specific libraries by allowing simultaneous processing of dozens of library/serum combinations in less than two days, including the time required for antibody-mediated library selection. Moreover, compared with traditional plaque picking, the new technology (named Phage-based Representation OF Immuno-Ligand Epitope Repertoire or PROFILER) provides superior resolution in epitope identification. PROFILER seems ideally suited to streamline and guide rational antigen design, adjuvant selection, and quality control of newly produced vaccines. Furthermore, this method is also susceptible to find important applications in other fields covered by traditional quantitative serology.
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Davies DH, Chun S, Hermanson G, Tucker JA, Jain A, Nakajima R, Pablo J, Felgner PL, Liang X. T cell antigen discovery using soluble vaccinia proteome reveals recognition of antigens with both virion and nonvirion association. THE JOURNAL OF IMMUNOLOGY 2014; 193:1812-27. [PMID: 25024392 DOI: 10.4049/jimmunol.1400663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Vaccinia virus (VACV) is a useful model system for understanding the immune response to a complex pathogen. Proteome-wide Ab profiling studies reveal the humoral response to be strongly biased toward virion-associated Ags, and several membrane proteins induce Ab-mediated protection against VACV challenge in mice. Some studies have indicated that the CD4 response is also skewed toward proteins with virion association, whereas the CD8 response is more biased toward proteins with early expression. In this study, we have leveraged a VACV strain Western Reserve (VACV-WR) plasmid expression library, produced previously for proteome microarrays for Ab profiling, to make a solubilized full VACV-WR proteome for T cell Ag profiling. Splenocytes from VACV-WR-infected mice were assayed without prior expansion against the soluble proteome in assays for Th1 and Th2 signature cytokines. The response to infection was polarized toward a Th1 response, with the distribution of reactive T cell Ags comprising both early and late VACV proteins. Interestingly, the proportions of different functional subsets were similar to that present in the whole proteome. In contrast, the targets of Abs from the same mice were enriched for membrane and other virion components, as described previously. We conclude that a "nonbiasing" approach to T cell Ag discovery reveals a T cell Ag profile in VACV that is broader and less skewed to virion association than the Ab profile. The T cell Ag mapping method developed in the present study should be applicable to other organisms where expressible "ORFeome" libraries are also available, and it is readily scalable for larger pathogens.
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Affiliation(s)
- D Huw Davies
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697; Antigen Discovery, Inc., Irvine, CA 92618; and
| | - Sookhee Chun
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697
| | | | - Jo Anne Tucker
- Division of Hematology and Oncology, School of Medicine, University of California, Irvine, Irvine, CA 92697
| | - Aarti Jain
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697
| | - Rie Nakajima
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697
| | - Jozelyn Pablo
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697; Antigen Discovery, Inc., Irvine, CA 92618; and
| | - Philip L Felgner
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697
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Pruneau L, Moumène A, Meyer DF, Marcelino I, Lefrançois T, Vachiéry N. Understanding Anaplasmataceae pathogenesis using "Omics" approaches. Front Cell Infect Microbiol 2014; 4:86. [PMID: 25072029 PMCID: PMC4078744 DOI: 10.3389/fcimb.2014.00086] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 06/10/2014] [Indexed: 11/13/2022] Open
Abstract
This paper examines how "Omics" approaches improve our understanding of Anaplasmataceae pathogenesis, through a global and integrative strategy to identify genes and proteins involved in biochemical pathways key for pathogen-host-vector interactions. The Anaplasmataceae family comprises obligate intracellular bacteria mainly transmitted by arthropods. These bacteria are responsible for major human and animal endemic and emerging infectious diseases with important economic and public health impacts. In order to improve disease control strategies, it is essential to better understand their pathogenesis. Our work focused on four Anaplasmataceae, which cause important animal, human and zoonotic diseases: Anaplasma marginale, A. phagocytophilum, Ehrlichia chaffeensis, and E. ruminantium. Wolbachia spp. an endosymbiont of arthropods was also included in this review as a model of a non-pathogenic Anaplasmataceae. A gap analysis on "Omics" approaches on Anaplasmataceae was performed, which highlighted a lack of studies on the genes and proteins involved in the infection of hosts and vectors. Furthermore, most of the studies have been done on the pathogen itself, mainly on infectious free-living forms and rarely on intracellular forms. In order to perform a transcriptomic analysis of the intracellular stage of development, researchers developed methods to enrich bacterial transcripts from infected cells. These methods are described in this paper. Bacterial genes encoding outer membrane proteins, post-translational modifications, eukaryotic repeated motif proteins, proteins involved in osmotic and oxidative stress and hypothetical proteins have been identified to play a key role in Anaplasmataceae pathogenesis. Further investigations on the function of these outer membrane proteins and hypothetical proteins will be essential to confirm their role in the pathogenesis. Our work underlines the need for further studies in this domain and on host and vector responses to infection.
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Affiliation(s)
- Ludovic Pruneau
- CIRAD, BIOS, UMR CMAEE Petit-Bourg, France ; INRA, BIOS, UMR CMAEE Montpellier, France ; Université des Antilles et de la Guyane Pointe-à-Pitre, France
| | - Amal Moumène
- CIRAD, BIOS, UMR CMAEE Petit-Bourg, France ; INRA, BIOS, UMR CMAEE Montpellier, France ; Université des Antilles et de la Guyane Pointe-à-Pitre, France
| | - Damien F Meyer
- CIRAD, BIOS, UMR CMAEE Petit-Bourg, France ; INRA, BIOS, UMR CMAEE Montpellier, France
| | - Isabel Marcelino
- CIRAD, BIOS, UMR CMAEE Petit-Bourg, France ; INRA, BIOS, UMR CMAEE Montpellier, France ; IBET Apartado, Oeiras, Portugal ; ITQB-UNL, Estação Agronómica Nacional Oeiras, Lisboa, Portugal
| | - Thierry Lefrançois
- CIRAD, BIOS, UMR CMAEE Petit-Bourg, France ; INRA, BIOS, UMR CMAEE Montpellier, France
| | - Nathalie Vachiéry
- CIRAD, BIOS, UMR CMAEE Petit-Bourg, France ; INRA, BIOS, UMR CMAEE Montpellier, France
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21
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He Y. Ontology-supported research on vaccine efficacy, safety and integrative biological networks. Expert Rev Vaccines 2014; 13:825-41. [PMID: 24909153 DOI: 10.1586/14760584.2014.923762] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including Vaccine Ontology, Ontology of Adverse Events and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network ('OneNet') Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms.
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Affiliation(s)
- Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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22
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Impacto de la investigación infectológica en la salud y el bienestar del ser humano. REVISTA MÉDICA CLÍNICA LAS CONDES 2014. [PMCID: PMC7148812 DOI: 10.1016/s0716-8640(14)70054-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
La prolongación de la vida, así como el avance en su calidad, acaecido de manera formidable durante las últimas décadas se debe en gran parte al control de las enfermedades infecciosas. Este control se ha logrado en buena parte gracias al progreso de la investigación biomédica, a estas alturas más que centenaria, fruto del esfuerzo de miles de investigadores que han aportado sus “granos de arena”, generando una sumatoria de nuevo conocimiento. En determinadas ocasiones el conocimiento generado permite una especie de “salto cuántico” o “breakthroughs” con un impacto rápido y evidente en la disminución de la mortalidad y/o morbilidad. Esta es una revisión no sistemática basada en la reflexión personal, con los sesgos que esta conlleva, sobre los hitos en la investigación infectológica reciente que han impactado en la salud humana y lo que podría esperarse en el futuro cercano. Al final se incluye literatura recomendada que profundiza varios de los tópicos presentados.
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Dodet B. Current barriers, challenges and opportunities for the development of effective STI vaccines: Point of view of vaccine producers, biotech companies and funding agencies. Vaccine 2014; 32:1624-9. [DOI: 10.1016/j.vaccine.2013.08.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 08/06/2013] [Accepted: 08/12/2013] [Indexed: 10/26/2022]
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24
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Schussek S, Trieu A, Doolan DL. Genome- and proteome-wide screening strategies for antigen discovery and immunogen design. Biotechnol Adv 2014; 32:403-14. [DOI: 10.1016/j.biotechadv.2013.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 11/04/2013] [Accepted: 12/16/2013] [Indexed: 01/17/2023]
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25
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Broutet N, Fruth U, Deal C, Gottlieb SL, Rees H. Vaccines against sexually transmitted infections: the way forward. Vaccine 2014; 32:1630-7. [PMID: 24480024 DOI: 10.1016/j.vaccine.2014.01.053] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
| | - Uli Fruth
- World Health Organization, Geneva, Switzerland
| | - Carolyn Deal
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | | | - Helen Rees
- Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa
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Jacob D, Ruffie C, Dubois M, Combredet C, Amino R, Formaglio P, Gorgette O, Pehau-Arnaudet G, Guery C, Puijalon O, Barale JC, Ménard R, Tangy F, Sala M. Whole Pichia pastoris yeast expressing measles virus nucleoprotein as a production and delivery system to multimerize Plasmodium antigens. PLoS One 2014; 9:e86658. [PMID: 24475165 PMCID: PMC3903550 DOI: 10.1371/journal.pone.0086658] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/11/2013] [Indexed: 12/13/2022] Open
Abstract
Yeasts are largely used as bioreactors for vaccine production. Usually, antigens are produced in yeast then purified and mixed with adjuvants before immunization. However, the purification costs and the safety concerns recently raised by the use of new adjuvants argue for alternative strategies. To this end, the use of whole yeast as both production and delivery system appears attractive. Here, we evaluated Pichia pastoris yeast as an alternative vaccine production and delivery system for the circumsporozoite protein (CS) of Plasmodium, the etiologic agent of malaria. The CS protein from Plasmodium berghei (Pb) was selected given the availability of the stringent C57Bl/6 mouse model of infection by Pb sporozoites, allowing the evaluation of vaccine efficacy in vivo. PbCS was multimerized by fusion to the measles virus (MV) nucleoprotein (N) known to auto-assemble in yeast in large-size ribonucleoprotein rods (RNPs). Expressed in P. pastoris, the N-PbCS protein generated highly multimeric and heterogenic RNPs bearing PbCS on their surface. Electron microscopy and immunofluorescence analyses revealed the shape of these RNPs and their localization in peripheral cytoplasmic inclusions. Subcutaneous immunization of C57Bl/6 mice with heat-inactivated whole P. pastoris expressing N-PbCS RNPs provided significant reduction of parasitemia after intradermal challenge with a high dose of parasites. Thus, in the absence of accessory adjuvants, a very low amount of PbCS expressed in whole yeast significantly decreased clinical damages associated with Pb infection in a highly stringent challenge model, providing a proof of concept of the intrinsic adjuvancy of this vaccine strategy. In addition to PbCS multimerization, the N protein contributed by itself to parasitemia delay and long-term mice survival. In the future, mixtures of whole recombinant yeasts expressing relevant Plasmodium antigens would provide a multivalent formulation applicable for antigen combination screening and possibly for large-scale production, distribution and delivery of a malaria vaccine in developing countries.
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Affiliation(s)
- Daria Jacob
- Institut Pasteur, Viral Genomics and Vaccination Unit, Paris, France
- CNRS, URA3015, Paris, France
| | - Claude Ruffie
- Institut Pasteur, Viral Genomics and Vaccination Unit, Paris, France
- CNRS, URA3015, Paris, France
| | - Myriam Dubois
- Institut Pasteur, Viral Genomics and Vaccination Unit, Paris, France
- CNRS, URA3015, Paris, France
| | - Chantal Combredet
- Institut Pasteur, Viral Genomics and Vaccination Unit, Paris, France
- CNRS, URA3015, Paris, France
| | - Rogerio Amino
- Institut Pasteur, Malaria Biology and Genetics Unit, Paris, France
| | | | - Olivier Gorgette
- Institut Pasteur, Molecular Immunology of Parasites Unit, Paris, France
- CNRS, URA2581, Paris, France
- Institut Pasteur, Malaria Biology and Genetics Unit, Team Malaria Targets and Drug Development, Paris, France
| | | | - Charline Guery
- Institut Pasteur, Viral Genomics and Vaccination Unit, Paris, France
- CNRS, URA3015, Paris, France
| | - Odile Puijalon
- Institut Pasteur, Molecular Immunology of Parasites Unit, Paris, France
- CNRS, URA2581, Paris, France
| | - Jean-Christophe Barale
- Institut Pasteur, Molecular Immunology of Parasites Unit, Paris, France
- CNRS, URA2581, Paris, France
- Institut Pasteur, Malaria Biology and Genetics Unit, Team Malaria Targets and Drug Development, Paris, France
| | - Robert Ménard
- Institut Pasteur, Malaria Biology and Genetics Unit, Paris, France
| | - Frédéric Tangy
- Institut Pasteur, Viral Genomics and Vaccination Unit, Paris, France
- CNRS, URA3015, Paris, France
| | - Monica Sala
- Institut Pasteur, Viral Genomics and Vaccination Unit, Paris, France
- CNRS, URA3015, Paris, France
- * E-mail:
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27
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Kuhn ML, Prachi P, Minasov G, Shuvalova L, Ruan J, Dubrovska I, Winsor J, Giraldi M, Biagini M, Liberatori S, Savino S, Bagnoli F, Anderson WF, Grandi G. Structure and protective efficacy of the Staphylococcus aureus autocleaving protease EpiP. FASEB J 2014; 28:1780-93. [PMID: 24421400 DOI: 10.1096/fj.13-241737] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Despite the global medical needs associated with Staphylococcus aureus infections, no licensed vaccines are currently available. We identified and characterized a protein annotated as an epidermin leader peptide processing serine protease (EpiP), as a novel S. aureus vaccine candidate. In addition, we determined the structure of the recombinant protein (rEpiP) by X-ray crystallography. The crystal structure revealed that rEpiP was cleaved somewhere between residues 95 and 100, and we found that the cleavage occurs through an autocatalytic intramolecular mechanism. The protein expressed by S. aureus cells also appeared to undergo a similar processing event. To determine whether the protein acts as a serine protease, we mutated the hypothesized catalytic serine 393 residue to alanine, generating rEpiP-S393A. The crystal structure of this mutant protein showed that the polypeptide chain was not cleaved and was not interacting stably with the active site. Indeed, rEpiP-S393A was shown to be impaired in its protease activity. Mice vaccinated with rEpiP were protected from S. aureus infection (34% survival, P=0.0054). Moreover, the protective efficacy generated by rEpiP and rEpiP-S393A was comparable, implying that the noncleaving mutant could be used for vaccination purposes.
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Affiliation(s)
- Misty L Kuhn
- 2G.G., Novartis Vaccines, via Fiorentina 1, 53100, Siena, Italy.
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28
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Rhee JH. Towards Vaccine 3.0: new era opened in vaccine research and industry. Clin Exp Vaccine Res 2013; 3:1-4. [PMID: 24427757 PMCID: PMC3890443 DOI: 10.7774/cevr.2014.3.1.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 11/15/2022] Open
Affiliation(s)
- Joon Haeng Rhee
- Department of Microbiology and Clinical Vaccine R&D Center, Chonnam National University Medical School, Gwangju, Korea
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29
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Bartlett G, Antoun J, Zgheib NK. Theranostics in primary care: pharmacogenomics tests and beyond. Expert Rev Mol Diagn 2013; 12:841-55. [PMID: 23249202 DOI: 10.1586/erm.12.115] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Theranostics represents a broadening in the scope of personalized medicine to include companion diagnostics for health interventions ranging from drugs to vaccines, as well as individual susceptibility to disease. Surprisingly, in the course of this broadening of personalized medicine discourse, relatively little attention has been paid to primary care (as compared with tertiary healthcare settings) despite its vast patient population and being a crucial entry point to health services. Recent advances in pharmacogenomics (PGx), a classical theranostics application whereby genotyping and/or gene expression-based tests are used for targeted or optimal therapy, revealed new opportunities to characterize more precisely human genomic variation and the ways in which it contributes to person-to-person and population variations in drug response. In the immediate foreseeable future, the primary-care physicians are expected to play an ever increasing crucial role in PGx-based prescribing in order to reduce the rates of adverse drug events and improve drug efficacy, yet PGx testing in primary care remains limited. In this article, the authors review the advances in PGx applications, the barriers for their adoption in the clinic from a primary care point of view and the efforts that are being undertaken to move PGx forward in this hitherto neglected application context of theranostic medicine. Finally, the authors propose several salient recommendations, including a 5-year forecast, to accelerate the current convergence between PGx and primary care.
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Affiliation(s)
- Gillian Bartlett
- Department of Family Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
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Gomez G, Adams LG, Rice-Ficht A, Ficht TA. Host-Brucella interactions and the Brucella genome as tools for subunit antigen discovery and immunization against brucellosis. Front Cell Infect Microbiol 2013; 3:17. [PMID: 23720712 PMCID: PMC3655278 DOI: 10.3389/fcimb.2013.00017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 04/26/2013] [Indexed: 01/18/2023] Open
Abstract
Vaccination is the most important approach to counteract infectious diseases. Thus, the development of new and improved vaccines for existing, emerging, and re-emerging diseases is an area of great interest to the scientific community and general public. Traditional approaches to subunit antigen discovery and vaccine development lack consideration for the critical aspects of public safety and activation of relevant protective host immunity. The availability of genomic sequences for pathogenic Brucella spp. and their hosts have led to development of systems-wide analytical tools that have provided a better understanding of host and pathogen physiology while also beginning to unravel the intricacies at the host-pathogen interface. Advances in pathogen biology, host immunology, and host-agent interactions have the potential to serve as a platform for the design and implementation of better-targeted antigen discovery approaches. With emphasis on Brucella spp., we probe the biological aspects of host and pathogen that merit consideration in the targeted design of subunit antigen discovery and vaccine development.
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Affiliation(s)
- Gabriel Gomez
- Department of Veterinary Pathobiology, Texas A&M University College Station, TX 77843, USA.
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Gomez G, Pei J, Mwangi W, Adams LG, Rice-Ficht A, Ficht TA. Immunogenic and invasive properties of Brucella melitensis 16M outer membrane protein vaccine candidates identified via a reverse vaccinology approach. PLoS One 2013; 8:e59751. [PMID: 23533646 PMCID: PMC3606113 DOI: 10.1371/journal.pone.0059751] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 02/18/2013] [Indexed: 01/18/2023] Open
Abstract
Brucella is the etiologic agent of brucellosis, one of the most common and widely distributed zoonotic diseases. Its highly infectious nature, the insidious, systemic, chronic, debilitating aspects of the disease and the lack of an approved vaccine for human use in the United States are features that make Brucella a viable threat to public health. One of the main impediments to vaccine development is identification of suitable antigens. In order to identify antigens that could potentially be used in a vaccine formulation, we describe a multi-step antigen selection approach. We initially used an algorithm (Vaxign) to predict ORF encoding outer membrane proteins with antigenic determinants. Differential gene expression during acute infection and published evidence for a role in virulence were used as criteria for down-selection of the candidate antigens that resulted from in silico prediction. This approach resulted in the identification of nine Brucella melitensis outer membrane proteins, 5 of which were recombinantly expressed and used for validation. Omp22 and Hia had the highest in silico scores for adhesin probability and also conferred invasive capacity to E. coli overexpressing recombinant proteins. With the exception of FlgK in the goat, all proteins reacted to pooled sera from exposed goats, mice, and humans. BtuB, Hia and FlgK stimulated a mixed Th1-Th2 response in splenocytes from immunized mice while BtuB and Hia elicited NO release from splenocytes of S19 immunized mice. The results support the applicability of the current approach to the identification of antigens with immunogenic and invasive properties. Studies to assess immunogenicity and protective efficacy of individual proteins in the mouse are currently underway.
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Affiliation(s)
- Gabriel Gomez
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, United States of America.
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Prachi P, Donati C, Masciopinto F, Rappuoli R, Bagnoli F. Deep sequencing in pre- and clinical vaccine research. Public Health Genomics 2013; 16:62-8. [PMID: 23548719 DOI: 10.1159/000345611] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Vaccine research has experienced a quantum leap after the beginning of the genomics era. High-throughput sequencing techniques, unlimited computing resources, as well as new bioinformatic algorithms are now changing the way we perform genomic studies. Whole genome sequencing will soon become the gold standard for phylogenetic and epidemiology studies and is already shedding new light on the dynamics of bacterial evolution. We believe that deep sequencing projects, together with structural studies on vaccine candidates, will allow targeting constant epitopes and avoid vaccine failure due to antigenic variability. Systems biology, which is expected to revolutionize vaccine research and clinical studies, greatly relies on high-throughput technologies such as RNA-seq. Furthermore, genomics is a key element to develop safer vaccines, and the accuracy of deep sequencing will allow monitoring vaccine coverage after their introduction on the market.
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Affiliation(s)
- P Prachi
- Novartis Vaccines, Research Center, Siena, Italy
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Tekle YI, Nielsen KM, Liu J, Pettigrew MM, Meyers LA, Galvani AP, Townsend JP. Controlling antimicrobial resistance through targeted, vaccine-induced replacement of strains. PLoS One 2012; 7:e50688. [PMID: 23227198 PMCID: PMC3515573 DOI: 10.1371/journal.pone.0050688] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/22/2012] [Indexed: 12/18/2022] Open
Abstract
Vaccination has proven effective in controlling many infectious diseases. However, differential effectiveness with regard to pathogen genotype is a frequent reason for failures in vaccine development. Often, insufficient immune response is induced to prevent infection by the diversity of existing serotypes present in pathogenic populations of bacteria. These vaccines that target a too narrow spectrum of serotypes do not offer sufficient prevention of infections, and can also lead to undesirable strain replacements. Here, we examine a novel idea to specifically exploit the narrow spectrum coverage of some vaccines to combat specific, emerging multi- and pan-resistant strains of pathogens. Application of a narrow-spectrum vaccine could serve to prevent infections by some strains that are hard to treat, rather than offer the vaccinated individual protection against infections by the pathogenic species as such. We suggest that vaccines targeted to resistant serotypes have the potential to become important public health tools, and would represent a new approach toward reducing the burden of particular multi-resistant strains occurring in hospitals. Vaccines targeting drug-resistant serotypes would also be the first clinical intervention with the potential to drive the evolution of pathogenic populations toward drug-sensitivity. We illustrate the feasibility of this approach by modeling a hypothetical vaccine that targets a subset of methicillin-resistant Staphylococcus aureus (MRSA) genotypes, in combination with drug treatment targeted at drug-sensitive genotypes. We find that a combined intervention strategy can limit nosocomial outbreaks, even when vaccine efficacy is imperfect. The broader utility of vaccine-based resistance control strategies should be further explored taking into account population structure, and the resistance and transmission patterns of the pathogen considered.
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Affiliation(s)
- Yonas I Tekle
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, United States of America.
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34
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Abstract
Infectious diseases are responsible for an overwhelming number of deaths worldwide and their clinical management is often hampered by the emergence of multi-drug-resistant strains. Therefore, prevention through vaccination currently represents the best course of action to combat them. However, immune escape and evasion by pathogens often render vaccine development difficult. Furthermore, most currently available vaccines were empirically designed. In this review, we discuss why rational design of vaccines is not only desirable but also necessary. We introduce recent developments towards specifically tailored antigens, adjuvants, and delivery systems, and discuss the methodological gaps and lack of knowledge still hampering true rational vaccine design. Finally, we address the potential and limitations of different strategies and technologies for advancing vaccine development.
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Affiliation(s)
- Christine Rueckert
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Carlos A. Guzmán
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- * E-mail:
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35
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Atzingen MV, Vieira ML, Oliveira R, Domingos RF, Mendes RS, Barros AT, Gonçales AP, de Morais ZM, Vasconcellos SA, Nascimento AL. Evaluation of immunoprotective activity of six leptospiral proteins in the hamster model of leptospirosis. Open Microbiol J 2012; 6:79-87. [PMID: 23173023 PMCID: PMC3502890 DOI: 10.2174/1874285801206010079] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/23/2012] [Accepted: 07/18/2012] [Indexed: 01/26/2023] Open
Abstract
Leptospirosis is a worldwide zoonosis caused by pathogenic Leptospira. The whole-genome sequence of L. interrogans serovar Copenhageni together with bioinformatics tools represent a great opportunity to search for novel antigen candidates that could be used as subunit vaccine against leptospirosis. We focused on six genes encoding for conserved hypothetical proteins predicted to be exported to the outer membrane. The genes were amplified by PCR from Leptospira interrogans genomic DNA and were cloned and expressed in Escherichia coli. The recombinant proteins tagged with N-terminal hexahistidine were purified by metal-charged chromatography. The immunization of hamsters followed by challenge with lethal dose of virulent strain of Leptospira showed that the recombinant proteins Lsa21, Lsa66 and rLIC11030 elicited partial protection to animals. These proteins could be used combined or in a mixture with novel adjuvants in order to improve their effectiveness.
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Affiliation(s)
- Marina V Atzingen
- Centro de Biotecnologia, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900, São Paulo, SP, Brazil
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36
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Prachi P, Biagini M, Bagnoli F. Vaccinology Is Turning into an Omics-Based Science. Drug Dev Res 2012. [DOI: 10.1002/ddr.21048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Prachi Prachi
- Novartis Vaccines; Research Center; via Fiorentina 1; 53100; Siena; Italy
| | | | - Fabio Bagnoli
- Novartis Vaccines; Research Center; via Fiorentina 1; 53100; Siena; Italy
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Mishra RPN, Oviedo-Orta E, Prachi P, Rappuoli R, Bagnoli F. Vaccines and antibiotic resistance. Curr Opin Microbiol 2012; 15:596-602. [PMID: 22981392 DOI: 10.1016/j.mib.2012.08.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 08/08/2012] [Accepted: 08/14/2012] [Indexed: 12/29/2022]
Abstract
Vaccines and antibiotics have significantly contributed to improve health and also to increase the longevity of human beings. The fast-acting effect of antibiotics makes them indispensable to treat infected patients. Likewise, when the causative agent of the infection is unknown and in cases of superinfections with different species of bacteria, antibiotics appear to be the only therapeutic option. On the contrary, vaccines are usually not efficacious in people already infected and their action is generally limited to a much narrowed range of pathogens. However, vaccines have contributed to the eradication of some of the most deadly infectious agents worldwide, can generate immunity to infections lasting for several years or life-long, and are able to induce herd immunity. Nonetheless, infectious diseases are still among the leading causes of morbidity and mortality worldwide. This is mainly owing to the emergence of bacterial resistance to antibiotics and the lack of efficacious medications to treat several other infectious diseases. Development of new vaccines appears to be a promising solution to these issues. Indeed, with the advent of new discovery approaches and adjuvants, today is possible to make vaccines virtually against every pathogen. In addition, while vaccine-resistant bacteria have never been reported, accumulating literature is providing evidence that vaccination can reduce the raise of antibiotic resistant strains by decreasing their use.
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Affiliation(s)
- Ravi P N Mishra
- Novartis Vaccines, Research Center, via Fiorentina 1, 53100, Siena, Italy
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38
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Seib KL, Zhao X, Rappuoli R. Developing vaccines in the era of genomics: a decade of reverse vaccinology. Clin Microbiol Infect 2012; 18 Suppl 5:109-16. [PMID: 22882709 DOI: 10.1111/j.1469-0691.2012.03939.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Vaccines have a significant impact on public health, and vaccinology in the era of genomics is taking advantage of new technologies to tackle diseases for which vaccine development has so far been unsuccessful. Almost all existing vaccines were developed based on traditional vaccinology methods, which relied on empirical screening of a few candidates at a time, based on known features of the pathogen. However, the ability to sequence a pathogen's genome provides access to its entire antigenic repertoire. As such, genomics has catalysed a shift in vaccine development towards sequence-based 'Reverse Vaccinology' approaches, which use high-throughput in silico screening of the entire genome of a pathogen to identify genes that encode proteins with the attributes of good vaccine targets. Furthermore, the increasing availability of genome sequences has led to the development and application of additional technologies to vaccine discovery, including comparative genomics, transcriptomics, proteomics, immunomics and structural genomics. Vaccine candidates identified from a pathogen's genome or proteome can then be expressed as recombinant proteins and tested in appropriate in vitro or in vivo models to assess immunogenicity and protection. The process of reverse vaccinology has been applied to several pathogens, including serogroup B Neisseria meningitidis, Streptococcus agalactiae, Streptococcus pyogenes, Streptococcus pneumoniae and pathogenic Escherichia coli, and has provided scores of new candidate antigens for preclinical and clinical investigation. As novel genome-based technologies continue to emerge, it is expected that new vaccines for unmet diseases will be within reach.
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Affiliation(s)
- K L Seib
- Novartis Vaccines and Diagnostics, Siena, Italy
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39
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Mishra RPN, Mariotti P, Fiaschi L, Nosari S, Maccari S, Liberatori S, Fontana MR, Pezzicoli A, De Falco MG, Falugi F, Altindis E, Serruto D, Grandi G, Bagnoli F. Staphylococcus aureus FhuD2 is involved in the early phase of staphylococcal dissemination and generates protective immunity in mice. J Infect Dis 2012; 206:1041-9. [PMID: 22829645 DOI: 10.1093/infdis/jis463] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Iron availability plays an essential role in staphylococcal pathogenesis. We selected FhuD2, a lipoprotein involved in iron-hydroxamate uptake, as a novel vaccine candidate against Staphylococcus aureus. Unprecedented for staphylococcal lipoproteins, the protein was demonstrated to have a discrete, punctate localization on the bacterial surface. FhuD2 vaccination generated protective immunity against diverse clinical S. aureus isolates in murine infection models. Protection appeared to be associated with functional antibodies that were shown to mediate opsonophagocytosis, to be effective in passive transfer experiments, and to potentially block FhuD2-mediated siderophore uptake. Furthermore, the protein was found to be up-regulated in infected tissues and was required for staphylococcal dissemination and abscess formation. Herein we show that the staphylococcal iron-hydroxamate uptake system is important in invasive infection and functions as an efficacious vaccine target.
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40
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Gauci CG, Jayashi CM, Gonzalez AE, Lackenby J, Lightowlers MW. Protection of pigs against Taenia solium cysticercosis by immunization with novel recombinant antigens. Vaccine 2012; 30:3824-8. [PMID: 22521850 PMCID: PMC3383989 DOI: 10.1016/j.vaccine.2012.04.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/23/2012] [Accepted: 04/04/2012] [Indexed: 02/08/2023]
Abstract
Recombinant antigens from the oncosphere stage of the parasite Taenia solium were expressed in Escherichia coli. The TSOL16, TSOL45-1A and TSOL45-1B recombinant antigens, each consisting of fibronectin type III (FnIII) domain S, were produced as fusion proteins with glutathione S-transferase (GST) and maltose binding protein (MBP). Groups of pigs were immunized twice with the GST fusions of the antigens and boosted a third time with the MBP fusions prior to receiving a challenge infection with T. solium eggs. The TSOL16 antigen was found to be capable of inducing high levels of immunity in pigs against a challenge infection with T. solium. Immunological investigations identified differences in immune responses in the pigs vaccinated with the various antigens. The results demonstrate that the TSOL16 antigen could be a valuable adjunct to current porcine vaccination approaches and may allow the further development of new vaccination strategies against T. solium cysticercosis.
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Affiliation(s)
- Charles G Gauci
- University of Melbourne, Faculty of Veterinary Science, Werribee, Victoria 3030, Australia.
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41
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Goh YL, He H, March JC. Engineering commensal bacteria for prophylaxis against infection. Curr Opin Biotechnol 2012; 23:924-30. [PMID: 22459613 DOI: 10.1016/j.copbio.2012.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 03/05/2012] [Indexed: 11/16/2022]
Abstract
Infectious diseases are the leading causes of death worldwide. The development of efficient and low cost prophylactics to prevent pathogenic infection is given high priority in the twenty-first century. Commensal bacteria are largely seen as harmless and can survive symbiotically (in many cases) in niches throughout the human body. Advances in genetic engineering and understanding of pathogenesis have revealed many potential strategies to develop engineered bacteria for prophylaxis purposes: including live vaccines and anti-infective agents. In this review, we discuss recent advances and potentialities of prophylaxis with engineered bacteria.
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Affiliation(s)
- Yih-Lin Goh
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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42
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Marcelino I, de Almeida AM, Ventosa M, Pruneau L, Meyer DF, Martinez D, Lefrançois T, Vachiéry N, Coelho AV. Tick-borne diseases in cattle: applications of proteomics to develop new generation vaccines. J Proteomics 2012; 75:4232-50. [PMID: 22480908 DOI: 10.1016/j.jprot.2012.03.026] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/13/2012] [Accepted: 03/15/2012] [Indexed: 01/11/2023]
Abstract
Tick-borne diseases (TBDs) affect 80% of the world's cattle population, hampering livestock production throughout the world. Livestock industry is important to rural populations not only as food supply, but also as a source of income. Tick control is usually achieved by using acaricides which are expensive, deleterious to the environment and can induce chemical resistance of vectors; the development of more effective and sustainable control methods is therefore required. Theileriosis, babesiosis, anaplasmosis and heartwater are the most important TBDs in cattle. Immunization strategies are currently available but with variable efficacy. To develop a new generation of vaccines which are more efficient, cheaper and safer, it is first necessary to better understand the mechanisms by which these parasites are transmitted, multiply and cause disease; this becomes especially difficult due to their complex life cycles, in vitro culture conditions and the lack of genetic tools to manipulate them. Proteomics and other complementary post-genomic tools such as transcriptomics and metabolomics in a systems biology context are becoming key tools to increase knowledge on the biology of infectious diseases. Herein, we present an overview of the so called "Omics" studies currently available on these tick-borne pathogens, giving emphasis to proteomics and how it may help to discover new vaccine candidates to control TBDs.
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Livermore DM. Fourteen years in resistance. Int J Antimicrob Agents 2012; 39:283-94. [PMID: 22386741 DOI: 10.1016/j.ijantimicag.2011.12.012] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 12/29/2011] [Indexed: 12/31/2022]
Abstract
Resistance trends have changed greatly over the 14 years (1997-2011) whilst I was Director of the UK Antibiotic Resistance Monitoring and Reference Laboratory (ARMRL). Meticillin-resistant Staphylococcus aureus (MRSA) first rose, then fell with improved infection control, although with the decline of one major clone beginning before these improvements. Resistant pneumococci too have declined following conjugate vaccine deployment. If the situation against Gram-positive pathogens has improved, that against Gram-negatives has worsened, with the spread of (i) quinolone- and cephalosporin-resistant Enterobacteriaceae, (ii) Acinetobacter with OXA carbapenemases, (iii) Enterobacteriaceae with biochemically diverse carbapenemases and (iv) gonococci resistant to fluoroquinolones and, latterly, cefixime. Laboratory, clinical and commercial aspects have also changed. Susceptibility testing is more standardised, with pharmacodynamic breakpoints. Treatments regimens are more driven by guidelines. The industry has fewer big profitable companies and more small companies without sales income. There is good and bad here. The quality of routine susceptibility testing has improved, but its speed has not. Pharmacodynamics adds science, but over-optimism has led to poor dose selection in several trials. Guidelines discourage poor therapy but concentrate selection onto a diminishing range of antibiotics, threatening their utility. Small companies are more nimble, but less resilient. Last, more than anything, the world has changed, with the rise of India and China, which account for 33% of the world's population and increasingly provide sophisticated health care, but also have huge resistance problems. These shifts present huge challenges for the future of chemotherapy and for the edifice of modern medicine that depends upon it.
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Affiliation(s)
- David M Livermore
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK.
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44
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Palumbo E, Fiaschi L, Brunelli B, Marchi S, Savino S, Pizza M. Antigen identification starting from the genome: a "Reverse Vaccinology" approach applied to MenB. Methods Mol Biol 2012; 799:361-403. [PMID: 21993656 DOI: 10.1007/978-1-61779-346-2_21] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Most of the vaccines available today, albeit very effective, have been developed using traditional "old-style" methodologies. Technologies developed in recent years have opened up new perspectives in the field of vaccinology and novel strategies are now being used to design improved or new vaccines against infections for which preventive measures do not exist. The Reverse Vaccinology (RV) approach is one of the most powerful examples of biotechnology applied to the field of vaccinology for identifying new protein-based vaccines. RV combines the availability of genomic data, the analyzing capabilities of new bioinformatic tools, and the application of high throughput expression and purification systems combined with serological screening assays for a coordinated screening process of the entire genomic repertoire of bacterial, viral, or parasitic pathogens. The application of RV to Neisseria meningitidis serogroup B represents the first success of this novel approach. In this chapter, we describe how this revolutionary approach can be easily applied to any pathogen.
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45
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Human leukocyte antigen associations with humoral and cellular immunity following a second dose of measles-containing vaccine: persistence, dampening, and extinction of associations found after a first dose. Vaccine 2011; 29:7982-91. [PMID: 21872631 DOI: 10.1016/j.vaccine.2011.08.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 08/11/2011] [Accepted: 08/13/2011] [Indexed: 12/16/2022]
Abstract
Previously we found human leukocyte antigen (HLA) associations with humoral immunity following a single dose of measles-containing vaccine. In this study, we sought to determine if HLA associations exist with humoral and cellular immunity following a second dose of measles-containing vaccine and if the associations we found with humoral immunity after the first dose persist following a second dose. We recruited a population-based sample of 346 schoolchildren, all who previously received two doses of a measles-containing vaccine. Molecular HLA classes I and II typing as well as humoral and cellular immune assays (measles-specific IgG antibody levels and lymphoproliferative response) were performed in these subjects. We found significant associations with class I HLA-B (p=0.05) as well as class II HLA-DPB1 (p=0.01) and -DPA1 (p=0.03) genes for measles vaccine-induced antibody levels after the second dose. Similarly, we found significant associations with class II HLA-DQB1 (p=0.05) and -DRB1 (p=0.01) genes for measles-specific lymphoproliferation after the second dose. While we found HLA associations after the second dose that we previously found after the first dose of measles containing vaccine, fewer alleles had statistically significant associations, suggesting that the second dose had a dampening or extinguishing effect on the HLA associations. It appears that the second dose overcomes HLA restriction through an as yet unknown mechanism. Future studies of HLA associations should consider both the effect of dose and the role that subsequent doses might play on genetic associations found with the response to a first dose.
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