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da Silva OLT, da Silva MK, Rodrigues-Neto JF, Santos Lima JPM, Manzoni V, Akash S, Fulco UL, Bourhia M, Dawoud TM, Nafidi HA, Sitotaw B, Akter S, Oliveira JIN. Advancing molecular modeling and reverse vaccinology in broad-spectrum yellow fever virus vaccine development. Sci Rep 2024; 14:10842. [PMID: 38735993 PMCID: PMC11089047 DOI: 10.1038/s41598-024-60680-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
Yellow fever outbreaks are prevalent, particularly in endemic regions. Given the lack of an established treatment for this disease, significant attention has been directed toward managing this arbovirus. In response, we developed a multiepitope vaccine designed to elicit an immune response, utilizing advanced immunoinformatic and molecular modeling techniques. To achieve this, we predicted B- and T-cell epitopes using the sequences from all structural (E, prM, and C) and nonstructural proteins of 196 YFV strains. Through comprehensive analysis, we identified 10 cytotoxic T-lymphocyte (CTL) and 5T-helper (Th) epitopes that exhibited overlap with B-lymphocyte epitopes. These epitopes were further evaluated for their affinity to a wide range of human leukocyte antigen system alleles and were rigorously tested for antigenicity, immunogenicity, allergenicity, toxicity, and conservation. These epitopes were linked to an adjuvant ( β -defensin) and to each other using ligands, resulting in a vaccine sequence with appropriate physicochemical properties. The 3D structure of this sequence was created, improved, and quality checked; then it was anchored to the Toll-like receptor. Molecular Dynamics and Quantum Mechanics/Molecular Mechanics simulations were employed to enhance the accuracy of docking calculations, with the QM portion of the simulations carried out utilizing the density functional theory formalism. Moreover, the inoculation model was able to provide an optimal codon sequence that was inserted into the pET-28a( +) vector for in silico cloning and could even stimulate highly relevant humoral and cellular immunological responses. Overall, these results suggest that the designed multi-epitope vaccine can serve as prophylaxis against the yellow fever virus.
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Affiliation(s)
- Ohana Leticia Tavares da Silva
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande Do Norte, Natal, RN, 59064-741, Brazil
| | - Maria Karolaynne da Silva
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande Do Norte, Natal, RN, 59064-741, Brazil
| | - Joao Firmino Rodrigues-Neto
- Multicampi School of Medical Sciences, Federal University of Rio Grande do Norte, Caicó, RN, 59300-000, Brazil
| | - Joao Paulo Matos Santos Lima
- Department of Biochemistry, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, 59064-741, Brazil
| | - Vinicius Manzoni
- Physics Institute, Federal University of Alagoas, Maceio, AL, 57072-970, Brazil
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Sukrabad, Dhaka, 1207, Bangladesh
| | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande Do Norte, Natal, RN, 59064-741, Brazil
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, 70000, Laayoune, Morocco
| | - Turki M Dawoud
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, 2325, Quebec City, QC, G1V 0A6, Canada
| | - Baye Sitotaw
- Department of Biology, Bahir Dar University, P.O. Box 79, Bahir Dar, Ethiopia.
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande Do Norte, Natal, RN, 59064-741, Brazil.
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In Silico Studies to Support Vaccine Development. Pharmaceutics 2023; 15:pharmaceutics15020654. [PMID: 36839975 PMCID: PMC9963741 DOI: 10.3390/pharmaceutics15020654] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
The progress that has been made in computer science positioned in silico studies as an important and well-recognized methodology in the drug discovery and development process. It has numerous advantages in terms of costs and also plays a huge impact on the way the research is conducted since it can limit the use of animal models leading to more sustainable research. Currently, human trials are already being partly replaced by in silico trials. EMA and FDA are both endorsing these studies and have been providing webinars and guidance to support them. For instance, PBPK modeling studies are being used to gather data on drug interactions with other drugs and are also being used to support clinical and regulatory requirements for the pediatric population, pregnant women, and personalized medicine. This trend evokes the need to understand the role of in silico studies in vaccines, considering the importance that these products achieved during the pandemic and their promising hope in oncology. Vaccines are safer than other current oncology treatments. There is a huge variety of strategies for developing a cancer vaccine, and some of the points that should be considered when designing the vaccine technology are the following: delivery platforms (peptides, lipid-based carriers, polymers, dendritic cells, viral vectors, etc.), adjuvants (to boost and promote inflammation at the delivery site, facilitating immune cell recruitment and activation), choice of the targeted antigen, the timing of vaccination, the manipulation of the tumor environment, and the combination with other treatments that might cause additive or even synergistic anti-tumor effects. These and many other points should be put together to outline the best vaccine design. The aim of this article is to perform a review and comprehensive analysis of the role of in silico studies to support the development of and design of vaccines in the field of oncology and infectious diseases. The authors intend to perform a literature review of all the studies that have been conducted so far in preparing in silico models and methods to support the development of vaccines. From this point, it was possible to conclude that there are few in silico studies on vaccines. Despite this, an overview of how the existing work could support the design of vaccines is described.
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Global Research Trend in Vaccine Design. Vaccines (Basel) 2022; 10:vaccines10122034. [PMID: 36560444 PMCID: PMC9787551 DOI: 10.3390/vaccines10122034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022] Open
Abstract
The current study established a research mapping of the vaccine design using bibliometric indicators and network visualization. For an analysis of the result, the study retrieved a total of 5379 documents from Scopus from 1983 to 2021. The study used the VOS Viewer and the RStudio tools for data visualization. The findings revealed that there has been significant growth in literature on vaccine design in the last two decades; in the last ten years, the year with the most publications were 2020, with 477 publications, and the highest had a total of 14,145 citations. D.R. Burton was ranked as the most prolific author, with 86 publications and 18,449 total citations and was observed as the most frequently published author in the domain. The National Institute of Health (NIH) was the most productive organization in the domain, with 266 publications. The document entitled "Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae" received a total of 1398 citations, and was the most cited document in the field of vaccine design. In network visualization, an analysis of the co-occurrence of keywords showed that "vaccine" and "vaccine design" occurred the most, which was 761 and 335 times, respectively. The study also observed that there were five clusters of author collaboration with a maximum of 18 authors and a minimum of two authors. The findings of the study will aid scholarly coalitions in the domains of medicine and health, information science and bibliometric professionals to carry out further research in the area of vaccine design.
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Zhang J, Askenase P, Crumpacker CS. Systems Vaccinology in HIV Vaccine Development. Vaccines (Basel) 2022; 10:vaccines10101624. [PMID: 36298489 PMCID: PMC9611490 DOI: 10.3390/vaccines10101624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Themes of discussions in the Special Issue of T Cell Immunity and HIV-1 Pathogenicity are outlined here [...]
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Ghafouri F, Ahangari Cohan R, Samimi H, Hosseini Rad S M A, Naderi M, Noorbakhsh F, Haghpanah V. Development of a Multiepitope Vaccine Against SARS-CoV-2: Immunoinformatics Study. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2022; 3:e36100. [PMID: 35891920 PMCID: PMC9302570 DOI: 10.2196/36100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 05/16/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022]
Abstract
Background Since the first appearance of SARS-CoV-2 in China in December 2019, the world witnessed the emergence of the SARS-CoV-2 outbreak. Due to the high transmissibility rate of the virus, there is an urgent need to design and develop vaccines against SARS-CoV-2 to prevent more cases affected by the virus. Objective A computational approach is proposed for vaccine design against the SARS-CoV-2 spike (S) protein, as the key target for neutralizing antibodies, and envelope (E) protein, which contains a conserved sequence feature. Methods We used previously reported epitopes of S protein detected experimentally and further identified a collection of predicted B-cell and major histocompatibility (MHC) class II–restricted T-cell epitopes derived from E proteins with an identical match to SARS-CoV-2 E protein. Results The in silico design of our candidate vaccine against the S and E proteins of SARS-CoV-2 demonstrated a high affinity to MHC class II molecules and effective results in immune response simulations. Conclusions Based on the results of this study, the multiepitope vaccine designed against the S and E proteins of SARS-CoV-2 may be considered as a new, safe, and efficient approach to combatting the COVID-19 pandemic.
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Affiliation(s)
- Fatemeh Ghafouri
- Department of Biotechnology Faculty of Life Sciences and Biotechnology Shahid Beheshti University Tehran Iran
| | - Reza Ahangari Cohan
- Department of Nanobiotechnology New Technologies Research Group Pasteur Institute of Iran Tehran Iran
| | - Hilda Samimi
- Endocrinology and Metabolism Research Center Endocrinology and Metabolism Clinical Sciences Institute Tehran University of Medical Sciences Tehran Iran
| | | | - Mahmood Naderi
- Digestive Diseases Research Center Digestive Diseases Research Institute Tehran University of Medical Sciences Tehran Iran
| | - Farshid Noorbakhsh
- Department of Immunology School of Medicine Tehran University of Medical Sciences Tehran Iran
| | - Vahid Haghpanah
- Endocrinology and Metabolism Research Center Endocrinology and Metabolism Clinical Sciences Institute Tehran University of Medical Sciences Tehran Iran
- Personalized Medicine Research Center Endocrinology and Metabolism Clinical Sciences Institute Tehran University of Medical Sciences Tehran Iran
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Huffman A, Ong E, Hur J, D’Mello A, Tettelin H, He Y. COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. Brief Bioinform 2022; 23:bbac190. [PMID: 35649389 PMCID: PMC9294427 DOI: 10.1093/bib/bbac190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 12/11/2022] Open
Abstract
Rational vaccine design, especially vaccine antigen identification and optimization, is critical to successful and efficient vaccine development against various infectious diseases including coronavirus disease 2019 (COVID-19). In general, computational vaccine design includes three major stages: (i) identification and annotation of experimentally verified gold standard protective antigens through literature mining, (ii) rational vaccine design using reverse vaccinology (RV) and structural vaccinology (SV) and (iii) post-licensure vaccine success and adverse event surveillance and its usage for vaccine design. Protegen is a database of experimentally verified protective antigens, which can be used as gold standard data for rational vaccine design. RV predicts protective antigen targets primarily from genome sequence analysis. SV refines antigens through structural engineering. Recently, RV and SV approaches, with the support of various machine learning methods, have been applied to COVID-19 vaccine design. The analysis of post-licensure vaccine adverse event report data also provides valuable results in terms of vaccine safety and how vaccines should be used or paused. Ontology standardizes and incorporates heterogeneous data and knowledge in a human- and computer-interpretable manner, further supporting machine learning and vaccine design. Future directions on rational vaccine design are discussed.
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Affiliation(s)
- Anthony Huffman
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202, USA
| | - Adonis D’Mello
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. Pathogens 2022; 11:pathogens11070743. [PMID: 35889989 PMCID: PMC9320269 DOI: 10.3390/pathogens11070743] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/11/2022] [Accepted: 06/25/2022] [Indexed: 01/25/2023] Open
Abstract
COVID-19 vaccines have been instrumental tools in reducing the impact of SARS-CoV-2 infections around the world by preventing 80% to 90% of hospitalizations and deaths from reinfection, in addition to preventing 40% to 65% of symptomatic illnesses. However, the simultaneous large-scale vaccination of the global population will indubitably unveil heterogeneity in immune responses as well as in the propensity to developing post-vaccine adverse events, especially in vulnerable individuals. Herein, we applied a systems biology workflow, integrating vaccine transcriptional signatures with chemogenomics, to study the pharmacological effects of mRNA vaccines. First, we derived transcriptional signatures and predicted their biological effects using pathway enrichment and network approaches. Second, we queried the Connectivity Map (CMap) to prioritize adverse events hypotheses. Finally, we accepted higher-confidence hypotheses that have been predicted by independent approaches. Our results reveal that the mRNA-based BNT162b2 vaccine affects immune response pathways related to interferon and cytokine signaling, which should lead to vaccine success, but may also result in some adverse events. Our results emphasize the effects of BNT162b2 on calcium homeostasis, which could be contributing to some frequently encountered adverse events related to mRNA vaccines. Notably, cardiac side effects were signaled in the CMap query results. In summary, our approach has identified mechanisms underlying both the expected protective effects of vaccination as well as possible post-vaccine adverse effects. Our study illustrates the power of systems biology approaches in improving our understanding of the comprehensive biological response to vaccination against COVID-19.
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8
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Vilela Rodrigues TC, Jaiswal AK, Lemes MR, da Silva MV, Sales-Campos H, Alcântara LCJ, Tosta SFDO, Kato RB, Alzahrani KJ, Barh D, Azevedo VADC, Tiwari S, Soares SDC. An immunoinformatics-based designed multi-epitope candidate vaccine (mpme-VAC/STV-1) against Mycoplasma pneumoniae. Comput Biol Med 2021; 142:105194. [PMID: 35007945 DOI: 10.1016/j.compbiomed.2021.105194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022]
Abstract
Pneumonia is a serious global health problem that accounts for over one million deaths annually. Among the main microorganisms causing pneumonia, Mycoplasma pneumoniae is one of the most common ones for which a vaccine is immediately required. In this context, a multi-epitope vaccine against this pathogen could be the best option that can induce effective immune response avoiding any serious adverse reactions. In this study, using an immunoinformatics approach we have designed a multi-epitope vaccine (mpme-VAC/STV-1) against M. pneumoniae. Our designed mpme-VAC/STV-1 is constructed using CTL (cytotoxic T lymphocyte), HTL (Helper T lymphocyte), and B-cell epitopes. These epitopes are selected from the core proteins of 88 M. pneumoniae genomes that were previously identified through reverse vaccinology approaches. The epitopes were filtered according to their immunogenicity, population coverage, and several other criteria. Sixteen CTL/B- and thirteen HTL/B- epitopes that belong to 5 core proteins were combined together through peptide linkers to develop the mpme-VAC/STV-1. The heat-labile enterotoxin from E. coli was used as an adjuvant. The designed mpme-VAC/STV-1 is predicted to be stable, non-toxic, non-allergenic, non-host homologous, and with required antigenic and immunogenic properties. Docking and molecular dynamic simulation of mpme-VAC/STV-1 shows that it can stimulate TLR2 pathway mediated immunogenic reactions. In silico cloning of mpme-VAC/STV-1 in an expression vector also shows positive results. Finally, the mpme-VAC/STV-1 also shows promising efficacy in immune simulation tests. Therefore, our constructed mpme-VAC/STV-1 could be a safe and effective multi-epitope vaccine for immunization against pneumonia. However, it requires further experimental and clinical validations.
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Affiliation(s)
- Thaís Cristina Vilela Rodrigues
- Programa PG Em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Arun Kumar Jaiswal
- Programa PG Em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcela Rezende Lemes
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Science and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, 38025-180, MG, Brazil
| | - Marcos Vinícius da Silva
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Science and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, 38025-180, MG, Brazil
| | - Helioswilton Sales-Campos
- Institute of Tropical Pathology and Public Health, Federal University of Goias (UFG), Goiânia, 74605-050, GO, Goiás, Brazil
| | | | - Sthephane Fraga de Oliveira Tosta
- Programa PG Em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Bentes Kato
- Programa PG Em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Debmalya Barh
- Programa PG Em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, 721172, India
| | - Vasco Ariston de Carvalho Azevedo
- Programa PG Em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sandeep Tiwari
- Programa PG Em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Science and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, 38025-180, MG, Brazil.
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Andresen AMS, Gjøen T. Chitosan nanoparticle formulation attenuates poly (I:C) induced innate immune responses against inactivated virus vaccine in Atlantic salmon (Salmo salar). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2021; 40:100915. [PMID: 34634571 DOI: 10.1016/j.cbd.2021.100915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Many vaccine formulations, in particular vaccines based on inactivated virus, needs adjuvants to boost immunogenicity. In aquaculture, mineral and plant oil are used as adjuvant in commercial vaccines, and the advent of oil-adjuvanted vaccines was crucial to aquaculture development. Nevertheless, some of these approved vaccines display suboptimal performance in the field compared to experimental conditions. Therefore, there is a need to improve adjuvants and delivery methods for fish vaccines against viruses. We used RNA sequencing of Atlantic salmon head kidney to analyse the difference in gene expression 24 h after injection of different experimental vaccine formulations. We compared five different formulations in addition to a PBS control: inactivated virus alone (group V), soluble poly (I:C) (group P), nanoparticles containing poly (I:C) (group N), soluble poly (I:C) + inactivated virus (group PV) and finally nanoparticles containing poly (I:C) + inactivated virus (group NV). Our results showed poly (I:C)'s ability as adjuvant and its capacity influence innate immune genes expression in Atlantic salmon. Soluble poly (I:C) upregulated multiple immune related genes and was more effective compared to poly (I:C) formulated into chitosan nanoparticles (more than 10 fold increase in differentially expressed genes, DEGs). However, inclusion of inactivated ISA virus in the nanoparticle vaccine, increased the number of DEGs fivefold suggesting a synergistic effect of adjuvant and antigen. Our results indicate that the way poly (I:C) is formulated and the presence of antigen is important for the magnitude of the innate immune response in Atlantic salmon.
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Affiliation(s)
| | - Tor Gjøen
- Department of Pharmacy, Section for Pharmacology and Pharmaceutical Biosciences, University of Oslo, Oslo, Norway.
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10
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Lemon JL, McMenamy MJ. A Review of UK-Registered and Candidate Vaccines for Bovine Respiratory Disease. Vaccines (Basel) 2021; 9:vaccines9121403. [PMID: 34960149 PMCID: PMC8703677 DOI: 10.3390/vaccines9121403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/10/2021] [Accepted: 11/22/2021] [Indexed: 01/11/2023] Open
Abstract
Vaccination is widely regarded as a cornerstone in animal or herd health and infectious disease management. Nineteen vaccines against the major pathogens implicated in bovine respiratory disease are registered for use in the UK by the Veterinary Medicines Directorate (VMD). However, despite annual prophylactic vaccination, bovine respiratory disease is still conservatively estimated to cost the UK economy approximately £80 million per annum. This review examines the vaccine types available, discusses the surrounding literature and scientific rationale of the limitations and assesses the potential of novel vaccine technologies.
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Affiliation(s)
- Joanne L. Lemon
- Sustainable Agri-Food and Sciences Division, Agri-Food and Bioscience Institute, Newforge Lane, Belfast BT9 5PX, UK
- Correspondence:
| | - Michael J. McMenamy
- Veterinary Sciences Division, Agri-Food and Bioscience Institute, Stormont, Belfast BT4 3SD, UK;
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11
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Meldgaard TS, Blengio F, Maffione D, Sammicheli C, Tavarini S, Nuti S, Kratzer R, Medini D, Siena E, Bertholet S. Single-Cell Analysis of Antigen-Specific CD8+ T-Cell Transcripts Reveals Profiles Specific to mRNA or Adjuvanted Protein Vaccines. Front Immunol 2021; 12:757151. [PMID: 34777370 PMCID: PMC8586650 DOI: 10.3389/fimmu.2021.757151] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/05/2021] [Indexed: 12/29/2022] Open
Abstract
CD8+ T cells play a key role in mediating protective immunity after immune challenges such as infection or vaccination. Several subsets of differentiated CD8+ T cells have been identified, however, a deeper understanding of the molecular mechanism that underlies T-cell differentiation is lacking. Conventional approaches to the study of immune responses are typically limited to the analysis of bulk groups of cells that mask the cells' heterogeneity (RNA-seq, microarray) and to the assessment of a relatively limited number of biomarkers that can be evaluated simultaneously at the population level (flow and mass cytometry). Single-cell analysis, on the other hand, represents a possible alternative that enables a deeper characterization of the underlying cellular heterogeneity. In this study, a murine model was used to characterize immunodominant hemagglutinin (HA533-541)-specific CD8+ T-cell responses to nucleic- and protein-based influenza vaccine candidates, using single-cell sorting followed by transcriptomic analysis. Investigation of single-cell gene expression profiles enabled the discovery of unique subsets of CD8+ T cells that co-expressed cytotoxic genes after vaccination. Moreover, this method enabled the characterization of antigen specific CD8+ T cells that were previously undetected. Single-cell transcriptome profiling has the potential to allow for qualitative discrimination of cells, which could lead to novel insights on biological pathways involved in cellular responses. This approach could be further validated and allow for more informed decision making in preclinical and clinical settings.
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Affiliation(s)
- Trine Sundebo Meldgaard
- Research & Development, GSK, Siena, Italy
- Biochemistry & Molecular Biology, University of Siena, Siena, Italy
| | - Fabiola Blengio
- Chemical & Biological Sciences, University of Torino, Torino, Italy
| | - Denise Maffione
- Chemical & Biological Sciences, University of Torino, Torino, Italy
| | | | | | - Sandra Nuti
- Research & Development, GSK, Siena, Italy
- Research & Development, GSK, Rockville, MD, United States
| | | | | | | | - Sylvie Bertholet
- Research & Development, GSK, Siena, Italy
- Research & Development, GSK, Rockville, MD, United States
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Ruseska I, Fresacher K, Petschacher C, Zimmer A. Use of Protamine in Nanopharmaceuticals-A Review. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1508. [PMID: 34200384 PMCID: PMC8230241 DOI: 10.3390/nano11061508] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022]
Abstract
Macromolecular biomolecules are currently dethroning classical small molecule therapeutics because of their improved targeting and delivery properties. Protamine-a small polycationic peptide-represents a promising candidate. In nature, it binds and protects DNA against degradation during spermatogenesis due to electrostatic interactions between the negatively charged DNA-phosphate backbone and the positively charged protamine. Researchers are mimicking this technique to develop innovative nanopharmaceutical drug delivery systems, incorporating protamine as a carrier for biologically active components such as DNA or RNA. The first part of this review highlights ongoing investigations in the field of protamine-associated nanotechnology, discussing the self-assembling manufacturing process and nanoparticle engineering. Immune-modulating properties of protamine are those that lead to the second key part, which is protamine in novel vaccine technologies. Protamine-based RNA delivery systems in vaccines (some belong to the new class of mRNA-vaccines) against infectious disease and their use in cancer treatment are reviewed, and we provide an update on the current state of latest developments with protamine as pharmaceutical excipient for vaccines.
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Affiliation(s)
| | | | | | - Andreas Zimmer
- Department of Pharmaceutical Technology and Biopharmacy, Institute of Pharmaceutical Sciences, Karl-Franzens-University Graz, Universitätsplatz 1, 8010 Graz, Austria; (I.R.); (K.F.); (C.P.)
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Khan MT, Islam MJ, Parihar A, Islam R, Jerin TJ, Dhote R, Ali MA, Laura FK, Halim MA. Immunoinformatics and molecular modeling approach to design universal multi-epitope vaccine for SARS-CoV-2. INFORMATICS IN MEDICINE UNLOCKED 2021; 24:100578. [PMID: 33898733 PMCID: PMC8057924 DOI: 10.1016/j.imu.2021.100578] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 02/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmittable and pathogenic human coronavirus that caused a pandemic situation of acute respiratory syndrome, called COVID-19, which has posed a significant threat to global health security. The aim of the present study is to computationally design an effective peptide-based multi-epitope vaccine (MEV) against SARS-CoV-2. The overall model quality of the vaccine candidate, immunogenicity, allergenicity, and physiochemical analysis have been conducted and validated. Molecular dynamics studies confirmed the stability of the candidate vaccine. The docked complexes during the simulation revealed a strong and stable binding interactions of MEV with human and mice toll-like receptors (TLR), TLR3 and TLR4. Finally, candidate vaccine codons have been optimized for their in silico cloning in E. coli expression system, to confirm increased expression. The proposed MEV can be a potential candidate against SARS-CoV-2, but experimental validation is needed to ensure its safety and immunogenicity status.
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Affiliation(s)
- Md Tahsin Khan
- Division of Infectious Diseases, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious Diseases, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Arpana Parihar
- Department of Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Rahatul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Tarhima Jahan Jerin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Rupali Dhote
- Department of Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Md Ackas Ali
- Division of Infectious Diseases, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Fariha Khan Laura
- Division of Infectious Diseases, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Mohammad A Halim
- Division of Infectious Diseases, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, AR, USA
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Ghafouri F, Cohan RA, Noorbakhsh F, Samimi H, Haghpanah V. An in-silico approach to develop of a multi-epitope vaccine candidate against SARS-CoV-2 envelope (E) protein. RESEARCH SQUARE 2020. [PMID: 32702713 PMCID: PMC7336711 DOI: 10.21203/rs.3.rs-30374/v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Since the first appearance of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS- CoV-2) in China on December 2019, the world has now witnessed the emergence of the SARS- CoV-2 outbreak. Therefore, due to the high transmissibility rate of virus, there is an urgent need to design and develop vaccines against SARS-CoV-2 to prevent more cases affected by the virus. In this study, a computational approach is proposed for vaccine design against the envelope (E) protein of SARS-CoV-2, which contains a conserved sequence feature. First, we sought to gain potential B-cell and T-cell epitopes for vaccine designing against SARS-CoV-2. Second, we attempted to develop a multi-epitope vaccine. Immune targeting of such epitopes could theoretically provide defense against SARS-CoV-2. Finally, we evaluated the affinity of the vaccine to major histocompatibility complex (MHC) molecules to stimulate the immune system response to this vaccine. We also identified a collection of B-cell and T-cell epitopes derived from E proteins that correspond identically to SARS-CoV-2 E proteins. The in-silico design of our potential vaccine against E protein of SARS-CoV-2 demonstrated a high affinity to MHC molecules, and it can be a candidate to make a protection against this pandemic event.
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15
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Hodgson SH, Muller J, Lockstone HE, Hill AVS, Marsh K, Draper SJ, Knight JC. Use of gene expression studies to investigate the human immunological response to malaria infection. Malar J 2019; 18:418. [PMID: 31835999 PMCID: PMC6911278 DOI: 10.1186/s12936-019-3035-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 11/26/2019] [Indexed: 01/02/2023] Open
Abstract
Background Transcriptional profiling of the human immune response to malaria has been used to identify diagnostic markers, understand the pathogenicity of severe disease and dissect the mechanisms of naturally acquired immunity (NAI). However, interpreting this body of work is difficult given considerable variation in study design, definition of disease, patient selection and methodology employed. This work details a comprehensive review of gene expression profiling (GEP) of the human immune response to malaria to determine how this technology has been applied to date, instances where this has advanced understanding of NAI and the extent of variability in methodology between studies to allow informed comparison of data and interpretation of results. Methods Datasets from the gene expression omnibus (GEO) including the search terms; ‘plasmodium’ or ‘malaria’ or ‘sporozoite’ or ‘merozoite’ or ‘gametocyte’ and ‘Homo sapiens’ were identified and publications analysed. Datasets of gene expression changes in relation to malaria vaccines were excluded. Results Twenty-three GEO datasets and 25 related publications were included in the final review. All datasets related to Plasmodium falciparum infection, except two that related to Plasmodium vivax infection. The majority of datasets included samples from individuals infected with malaria ‘naturally’ in the field (n = 13, 57%), however some related to controlled human malaria infection (CHMI) studies (n = 6, 26%), or cells stimulated with Plasmodium in vitro (n = 6, 26%). The majority of studies examined gene expression changes relating to the blood stage of the parasite. Significant heterogeneity between datasets was identified in terms of study design, sample type, platform used and method of analysis. Seven datasets specifically investigated transcriptional changes associated with NAI to malaria, with evidence supporting suppression of the innate pro-inflammatory response as an important mechanism for this in the majority of these studies. However, further interpretation of this body of work was limited by heterogeneity between studies and small sample sizes. Conclusions GEP in malaria is a potentially powerful tool, but to date studies have been hypothesis generating with small sample sizes and widely varying methodology. As CHMI studies are increasingly performed in endemic settings, there will be growing opportunity to use GEP to understand detailed time-course changes in host response and understand in greater detail the mechanisms of NAI.
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Affiliation(s)
- Susanne H Hodgson
- The Jenner Institute, University of Oxford, Old Road Campus Road Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK. .,Department of Infectious Diseases & Microbiology, Oxford University Hospitals Trust, Oxford, UK.
| | - Julius Muller
- The Jenner Institute, University of Oxford, Old Road Campus Road Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Helen E Lockstone
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adrian V S Hill
- The Jenner Institute, University of Oxford, Old Road Campus Road Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kevin Marsh
- Department of Tropical Medicine, University of Oxford, Oxford, UK
| | - Simon J Draper
- The Jenner Institute, University of Oxford, Old Road Campus Road Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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Qiu X, Duvvuri VR, Bahl J. Computational Approaches and Challenges to Developing Universal Influenza Vaccines. Vaccines (Basel) 2019; 7:E45. [PMID: 31141933 PMCID: PMC6631137 DOI: 10.3390/vaccines7020045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/15/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022] Open
Abstract
The traditional design of effective vaccines for rapidly-evolving pathogens, such as influenza A virus, has failed to provide broad spectrum and long-lasting protection. With low cost whole genome sequencing technology and powerful computing capabilities, novel computational approaches have demonstrated the potential to facilitate the design of a universal influenza vaccine. However, few studies have integrated computational optimization in the design and discovery of new vaccines. Understanding the potential of computational vaccine design is necessary before these approaches can be implemented on a broad scale. This review summarizes some promising computational approaches under current development, including computationally optimized broadly reactive antigens with consensus sequences, phylogenetic model-based ancestral sequence reconstruction, and immunomics to compute conserved cross-reactive T-cell epitopes. Interactions between virus-host-environment determine the evolvability of the influenza population. We propose that with the development of novel technologies that allow the integration of data sources such as protein structural modeling, host antibody repertoire analysis and advanced phylodynamic modeling, computational approaches will be crucial for the development of a long-lasting universal influenza vaccine. Taken together, computational approaches are powerful and promising tools for the development of a universal influenza vaccine with durable and broad protection.
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Affiliation(s)
- Xueting Qiu
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Venkata R Duvvuri
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA 30606, USA.
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore.
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17
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Oh SJ, Choi YK, Shin OS. Systems Biology-Based Platforms to Accelerate Research of Emerging Infectious Diseases. Yonsei Med J 2018; 59:176-186. [PMID: 29436184 PMCID: PMC5823818 DOI: 10.3349/ymj.2018.59.2.176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 12/29/2022] Open
Abstract
Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs.
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Affiliation(s)
- Soo Jin Oh
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Young Ki Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea
| | - Ok Sarah Shin
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Korea.
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18
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van den Berg RA, Coccia M, Ballou WR, Kester KE, Ockenhouse CF, Vekemans J, Jongert E, Didierlaurent AM, van der Most RG. Predicting RTS,S Vaccine-Mediated Protection from Transcriptomes in a Malaria-Challenge Clinical Trial. Front Immunol 2017; 8:557. [PMID: 28588574 PMCID: PMC5440508 DOI: 10.3389/fimmu.2017.00557] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/25/2017] [Indexed: 12/24/2022] Open
Abstract
The RTS,S candidate malaria vaccine can protect against controlled human malaria infection (CHMI), but how protection is achieved remains unclear. Here, we have analyzed longitudinal peripheral blood transcriptome and immunogenicity data from a clinical efficacy trial in which healthy adults received three RTS,S doses 4 weeks apart followed by CHMI 2 weeks later. Multiway partial least squares discriminant analysis (N-PLS-DA) of transcriptome data identified 110 genes that could be used in predictive models of protection. Among the 110 genes, 42 had known immune-related functions, including 29 that were related to the NF-κB-signaling pathway and 14 to the IFN-γ-signaling pathway. Post-dose 3 serum IFN-γ concentrations were also correlated with protection; and N-PLS-DA of IFN-γ-signaling pathway transcriptome data selected almost all (44/45) of the representative genes for predictive models of protection. Hence, the identification of the NF-κB and IFN-γ pathways provides further insight into how vaccine-mediated protection may be achieved.
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Affiliation(s)
| | | | | | - Kent E Kester
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | - Erik Jongert
- GSK Vaccines, Rue de l'Institut, Rixensart, Belgium
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19
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Vibert J, Thomas-Vaslin V. Modelling T cell proliferation: Dynamics heterogeneity depending on cell differentiation, age, and genetic background. PLoS Comput Biol 2017; 13:e1005417. [PMID: 28288157 PMCID: PMC5367836 DOI: 10.1371/journal.pcbi.1005417] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/27/2017] [Accepted: 02/16/2017] [Indexed: 12/03/2022] Open
Abstract
Cell proliferation is the common characteristic of all biological systems. The immune system insures the maintenance of body integrity on the basis of a continuous production of diversified T lymphocytes in the thymus. This involves processes of proliferation, differentiation, selection, death and migration of lymphocytes to peripheral tissues, where proliferation also occurs upon antigen recognition. Quantification of cell proliferation dynamics requires specific experimental methods and mathematical modelling. Here, we assess the impact of genetics and aging on the immune system by investigating the dynamics of proliferation of T lymphocytes across their differentiation through thymus and spleen in mice. Our investigation is based on single-cell multicolour flow cytometry analysis revealing the active incorporation of a thymidine analogue during S phase after pulse-chase-pulse experiments in vivo, versus cell DNA content. A generic mathematical model of state transition simulates through Ordinary Differential Equations (ODEs) the evolution of single cell behaviour during various durations of labelling. It allows us to fit our data, to deduce proliferation rates and estimate cell cycle durations in sub-populations. Our model is simple and flexible and is validated with other durations of pulse/chase experiments. Our results reveal that T cell proliferation is highly heterogeneous but with a specific “signature” that depends upon genetic origins, is specific to cell differentiation stages in thymus and spleen and is altered with age. In conclusion, our model allows us to infer proliferation rates and cell cycle phase durations from complex experimental 5-ethynyl-2'-deoxyuridine (EdU) data, revealing T cell proliferation heterogeneity and specific signatures. We assess the impact of genetics and aging on immune system dynamics by investigating the dynamics of proliferation of T lymphocytes across their differentiation through thymus and spleen in mice. Understanding cell proliferation dynamics requires specific experimental methods and mathematical modelling. Our investigation is based upon single-cell multicolour flow cytometry analysis thereby revealing the active incorporation in DNA of a thymidine analogue during S phase after pulse-chase experiments in vivo, versus cell DNA content. A generic mathematical model that simulates the evolution of single cell behaviour during the experiment allows us to fit our data, to deduce proliferation rates and mean cell cycle phase durations in sub-populations. This reveals that T cell proliferation is constrained by genetic influences, declines with age, and is specific to cell differentiation stage, revealing a specific “signature” of cell proliferation. Our model is simple and flexible and can be used with other pulse/chase experiments.
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Affiliation(s)
- Julien Vibert
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Immunology-Immunopathology-Immunotherapy (I3) UMRS959; Paris, France
| | - Véronique Thomas-Vaslin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Immunology-Immunopathology-Immunotherapy (I3) UMRS959; Paris, France
- * E-mail:
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20
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Designing an efficient multi-epitope peptide vaccine against Vibrio cholerae via combined immunoinformatics and protein interaction based approaches. Comput Biol Chem 2016; 62:82-95. [DOI: 10.1016/j.compbiolchem.2016.04.006] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/15/2016] [Accepted: 04/15/2016] [Indexed: 12/18/2022]
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21
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Galassie AC, Link AJ. Proteomic contributions to our understanding of vaccine and immune responses. Proteomics Clin Appl 2015; 9:972-89. [PMID: 26172619 PMCID: PMC4713355 DOI: 10.1002/prca.201500054] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/24/2015] [Accepted: 07/07/2015] [Indexed: 01/19/2023]
Abstract
Vaccines are one of the greatest public health successes; yet, due to the empirical nature of vaccine design, we have an incomplete understanding of how the genes and proteins induced by vaccines contribute to the development of both protective innate and adaptive immune responses. While the advent of genomics has enabled new vaccine development and facilitated understanding of the immune response, proteomics identifies potentially new vaccine antigens with increasing speed and sensitivity. In addition, as proteomics is complementary to transcriptomic approaches, a combination of both approaches provides a more comprehensive view of the immune response after vaccination via systems vaccinology. This review details the advances that proteomic strategies have made in vaccine development and reviews how proteomics contributes to the development of a more complete understanding of human vaccines and immune responses.
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Affiliation(s)
| | - Andrew J. Link
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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22
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Munang’andu HM, Mutoloki S, Evensen Ø. An Overview of Challenges Limiting the Design of Protective Mucosal Vaccines for Finfish. Front Immunol 2015; 6:542. [PMID: 26557121 PMCID: PMC4617105 DOI: 10.3389/fimmu.2015.00542] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 10/08/2015] [Indexed: 01/18/2023] Open
Abstract
Research in mucosal vaccination in finfish has gained prominence in the last decade in pursuit of mucosal vaccines that would lengthen the duration of protective immunity in vaccinated fish. However, injectable vaccines have continued to dominate in the vaccination of finfish because they are perceived to be more protective than mucosal vaccines. Therefore, it has become important to identify the factors that limit developing protective mucosal vaccines in finfish as an overture to identifying key areas that require optimization in mucosal vaccine design. Some of the factors that limit the success for designing protective mucosal vaccines for finfish identified in this review include the lack optimized protective antigen doses for mucosal vaccines, absence of immunostimulants able to enhance the performance of non-replicative mucosal vaccines, reduction of systemic antibodies due to prolonged exposure to oral vaccination and the lack of predefined correlates of protective immunity for use in the optimization of newly developed mucosal vaccines. This review also points out the need to develop prime-boost vaccination regimes able to induce long-term protective immunity in vaccinated fish. By overcoming some of the obstacles identified herein, it is anticipated that future mucosal vaccines shall be designed to induce long-term protective immunity in finfish.
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Affiliation(s)
- Hetron Mweemba Munang’andu
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Stephen Mutoloki
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Øystein Evensen
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway
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23
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Boianelli A, Pettini E, Prota G, Medaglini D, Vicino A. A Stochastic Model for CD4+ T Cell Proliferation and Dissemination Network in Primary Immune Response. PLoS One 2015; 10:e0135787. [PMID: 26301680 PMCID: PMC4547705 DOI: 10.1371/journal.pone.0135787] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/27/2015] [Indexed: 01/29/2023] Open
Abstract
The study of the initial phase of the adaptive immune response after first antigen encounter provides essential information on the magnitude and quality of the immune response. This phase is characterized by proliferation and dissemination of T cells in the lymphoid organs. Modeling and identifying the key features of this phenomenon may provide a useful tool for the analysis and prediction of the effects of immunization. This knowledge can be effectively exploited in vaccinology, where it is of interest to evaluate and compare the responses to different vaccine formulations. The objective of this paper is to construct a stochastic model based on branching process theory, for the dissemination network of antigen-specific CD4+ T cells. The devised model is validated on in vivo animal experimental data. The model presented has been applied to the vaccine immunization context making references to simple proliferation laws that take into account division, death and quiescence, but it can also be applied to any context where it is of interest to study the dynamic evolution of a population.
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Affiliation(s)
- Alessandro Boianelli
- Systems Medicine of Infectious Diseases group and Braunschweig Integrated Centre of Systems Biology, Department of Systems Immunology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- * E-mail:
| | - Elena Pettini
- Laboratorio di Microbiologia Molecolare e Biotecnologie, Dipartimento di Biotecnologie Mediche, Università di Siena, Viale Bracci 1, 53100 Siena, Italy
| | - Gennaro Prota
- Laboratorio di Microbiologia Molecolare e Biotecnologie, Dipartimento di Biotecnologie Mediche, Università di Siena, Viale Bracci 1, 53100 Siena, Italy
| | - Donata Medaglini
- Laboratorio di Microbiologia Molecolare e Biotecnologie, Dipartimento di Biotecnologie Mediche, Università di Siena, Viale Bracci 1, 53100 Siena, Italy
| | - Antonio Vicino
- Dipartimento di Ingegneria dell’Informazione e Science Matematiche, Università di Siena, Via Roma 56, 53100 Siena, Italy
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Cherryholmes GA, Stanton SE, Disis ML. Current methods of epitope identification for cancer vaccine design. Vaccine 2015; 33:7408-7414. [PMID: 26238725 DOI: 10.1016/j.vaccine.2015.06.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/23/2015] [Indexed: 01/05/2023]
Abstract
The importance of the immune system in tumor development and progression has been emerging in many cancers. Previous cancer vaccines have not shown long-term clinical benefit possibly because were not designed to avoid eliciting regulatory T-cell responses that inhibit the anti-tumor immune response. This review will examine different methods of identifying epitopes derived from tumor associated antigens suitable for immunization and the steps used to design and validate peptide epitopes to improve efficacy of anti-tumor peptide-based vaccines. Focusing on in silico prediction algorithms, we survey the advantages and disadvantages of current cancer vaccine prediction tools.
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Affiliation(s)
- Gregory A Cherryholmes
- Tumor Vaccine Group, Center for Translational Medicine in Women's Health, University of Washington, 850 Republican Street, Seattle, WA 98109, United States.
| | - Sasha E Stanton
- Tumor Vaccine Group, Center for Translational Medicine in Women's Health, University of Washington, 850 Republican Street, Seattle, WA 98109, United States.
| | - Mary L Disis
- Tumor Vaccine Group, Center for Translational Medicine in Women's Health, University of Washington, 850 Republican Street, Seattle, WA 98109, United States.
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25
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Díaz-Martín V, Manzano-Román R, Obolo-Mvoulouga P, Oleaga A, Pérez-Sánchez R. Development of vaccines against Ornithodoros soft ticks: An update. Ticks Tick Borne Dis 2015; 6:211-20. [PMID: 25802033 DOI: 10.1016/j.ttbdis.2015.03.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 11/19/2022]
Abstract
Ticks are parasites of great medical and veterinary importance since they are vectors of numerous pathogens that affect humans, livestock and pets. Among the argasids, several species of the genus Ornithodoros transmit serious diseases such as tick-borne human relapsing fever (TBRF) and African Swine Fever (ASF). In particular, Ornithodoros erraticus is the main vector of these two diseases in the Mediterranean while O. moubata is the main vector in Africa. The presence of these Ornithodoros ticks in domestic and peridomestic environments may greatly hinder the eradication of TBRF and ASF from endemic areas. In addition, there is a constant threat of reintroduction and spreading of ASF into countries from where it has been eradicated (Spain and Portugal) or where it was never present (the Caucasus, Russia and Eastern Europe). In these countries, the presence of Ornithodoros vectors could have a tremendous impact on ASF transmission and long-term maintenance. Therefore, elimination of these ticks from at least synanthropic environments would contribute heavily to the prevention and control of the diseases they transmit. Tick control is a difficult task and although several methods for such control have been used, none of them has been fully effective against all ticks and the problems they cause. Nevertheless, immunological control using anti-tick vaccines offers an attractive alternative to the traditional use of acaricides. The aim of the present paper is to offer a brief overview of the current status in control measure development for Ornithodoros soft ticks, paying special attention to the development of vaccines against O. erraticus and O. moubata. Thus, our contribution includes an analysis of the chief attributes that the ideal antigens for an anti-tick vaccine should have, an exhaustive compilation and analysis of the scant anti-soft tick vaccine trials carried out to date using both concealed and salivary antigens and, finally, a brief description of the new reverse vaccinology approaches currently used to identify new and more effective protective tick antigens.
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Affiliation(s)
- Verónica Díaz-Martín
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain.
| | - Raúl Manzano-Román
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain.
| | - Prosper Obolo-Mvoulouga
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain.
| | - Ana Oleaga
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain.
| | - Ricardo Pérez-Sánchez
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain.
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Cui Z, Han D, Sun X, Zhang M, Feng X, Sun C, Gu J, Tong C, Lei L, Han W. Mannose-modified chitosan microspheres enhance OprF-OprI-mediated protection of mice against Pseudomonas aeruginosa infection via induction of mucosal immunity. Appl Microbiol Biotechnol 2014; 99:667-80. [PMID: 25381907 DOI: 10.1007/s00253-014-6147-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 10/07/2014] [Accepted: 10/09/2014] [Indexed: 01/22/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that localizes to and colonizes mucosal tissue. Thus, vaccines that elicit a strong mucosal response against P. aeruginosa should be superior to other vaccination strategies. In this study, to stimulate rapid and enhanced mucosal immune responses, mannose-modified chitosan microspheres loaded with the recombinant outer membrane protein OprF190-342-OprI21-83 (FI) (FI-MCS-MPs) of P. aeruginosa were developed as a potent subunit vaccine for mucosal delivery. FI-MCS-MPs were successfully obtained via the tripolyphosphate ionic crosslinking method. Confocal and immunohistochemical analyses indicated that FI-MCS-MPs exhibited the ability to bind the macrophage mannose receptor (MMR, CD206) in vitro and in vivo. After intranasal immunization of mice with FI-MCS-MPs, FI-specific humoral immune responses were detected, measured as local IgM antibody titers in lung tissue slurry; IgA antibody titers in nasal washes, bronchoalveolar lavage (BAL), and intestinal lavage; and systemic IgA and IgG antibody titers in serum. FI-MCS-MPs induced early and high mucosal and systemic humoral antibody responses comparable to those in the group vaccinated with unmodified mannose. High levels of IFN-γ and IL-4 in addition to T lymphocyte subsets induced a mixed Th1/Th2 response in mice immunized with FI-MCS-MPs, resulting in the establishment of cellular immunity. Additionally, when immunized mice were challenged with P. aeruginosa via the nasal cavity, FI-MCS-MPs demonstrated 75 % protective efficacy. Together, these data indicate that mannose-modified chitosan microspheres are a promising subunit delivery system for vaccines against P. aeruginosa infection.
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Affiliation(s)
- Ziyin Cui
- College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
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Doolan DL, Apte SH, Proietti C. Genome-based vaccine design: the promise for malaria and other infectious diseases. Int J Parasitol 2014; 44:901-13. [PMID: 25196370 DOI: 10.1016/j.ijpara.2014.07.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 01/08/2023]
Abstract
Vaccines are one of the most effective interventions to improve public health, however, the generation of highly effective vaccines for many diseases has remained difficult. Three chronic diseases that characterise these difficulties include malaria, tuberculosis and HIV, and they alone account for half of the global infectious disease burden. The whole organism vaccine approach pioneered by Jenner in 1796 and refined by Pasteur in 1857 with the "isolate, inactivate and inject" paradigm has proved highly successful for many viral and bacterial pathogens causing acute disease but has failed with respect to malaria, tuberculosis and HIV as well as many other diseases. A significant advance of the past decade has been the elucidation of the genomes, proteomes and transcriptomes of many pathogens. This information provides the foundation for new 21st Century approaches to identify target antigens for the development of vaccines, drugs and diagnostic tests. Innovative genome-based vaccine strategies have shown potential for a number of challenging pathogens, including malaria. We advocate that genome-based rational vaccine design will overcome the problem of poorly immunogenic, poorly protective vaccines that has plagued vaccine developers for many years.
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Affiliation(s)
- Denise L Doolan
- Infectious Diseases Programme, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia.
| | - Simon H Apte
- Infectious Diseases Programme, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Carla Proietti
- Infectious Diseases Programme, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
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Gómez CE, Perdiguero B, García-Arriaza J, Esteban M. Clinical applications of attenuated MVA poxvirus strain. Expert Rev Vaccines 2013; 12:1395-416. [PMID: 24168097 DOI: 10.1586/14760584.2013.845531] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The highly attenuated poxvirus strain modified vaccinia virus Ankara (MVA) has reached maturity as a vector delivery system and as a vaccine candidate against a broad spectrum of diseases. This has been largely recognized from research on virus-host cell interactions and immunological studies in pre-clinical and clinical trials. This review addresses the studies of MVA vectors used in phase I/II clinical trials, with the aim to provide the main findings obtained on their behavior when tested against relevant human diseases and cancer and also highlights the strategies currently implemented to improve the MVA immunogenicity. The authors assess that MVA vectors are progressing as strong vaccine candidates either alone or when administered in combination with other vectors.
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Affiliation(s)
- Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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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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Lycke N. Recent progress in mucosal vaccine development: potential and limitations. Nat Rev Immunol 2012; 12:592-605. [DOI: 10.1038/nri3251] [Citation(s) in RCA: 495] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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