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Lybeck K, Tollefsen S, Mikkelsen H, Sjurseth SK, Lundegaard C, Aagaard C, Olsen I, Jungersen G. Selection of vaccine-candidate peptides from Mycobacterium avium subsp. paratuberculosis by in silico prediction, in vitro T-cell line proliferation, and in vivo immunogenicity. Front Immunol 2024; 15:1297955. [PMID: 38352876 PMCID: PMC10861761 DOI: 10.3389/fimmu.2024.1297955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is a global concern in modern livestock production worldwide. The available vaccines against paratuberculosis do not offer optimal protection and interfere with the diagnosis of bovine tuberculosis. The aim of this study was to identify immunogenic MAP-specific peptides that do not interfere with the diagnosis of bovine tuberculosis. Initially, 119 peptides were selected by either (1) identifying unique MAP peptides that were predicted to bind to bovine major histocompatibility complex class II (MHC-predicted peptides) or (2) selecting hydrophobic peptides unique to MAP within proteins previously shown to be immunogenic (hydrophobic peptides). Subsequent testing of peptide-specific CD4+ T-cell lines from MAP-infected, adult goats vaccinated with peptides in cationic liposome adjuvant pointed to 23 peptides as being most immunogenic. These peptides were included in a second vaccine trial where three groups of eight healthy goat kids were vaccinated with 14 MHC-predicted peptides, nine hydrophobic peptides, or no peptides in o/w emulsion adjuvant. The majority of the MHC-predicted (93%) and hydrophobic peptides (67%) induced interferon-gamma (IFN-γ) responses in at least one animal. Similarly, 86% of the MHC-predicted and 89% of the hydrophobic peptides induced antibody responses in at least one goat. The immunization of eight healthy heifers with all 119 peptides formulated in emulsion adjuvant identified more peptides as immunogenic, as peptide specific IFN-γ and antibody responses in at least one heifer was found toward 84% and 24% of the peptides, respectively. No peptide-induced reactivity was found with commercial ELISAs for detecting antibodies against Mycobacterium bovis or MAP or when performing tuberculin skin testing for bovine tuberculosis. The vaccinated animals experienced adverse reactions at the injection site; thus, it is recommend that future studies make improvements to the vaccine formulation. In conclusion, immunogenic MAP-specific peptides that appeared promising for use in a vaccine against paratuberculosis without interfering with surveillance and trade tests for bovine tuberculosis were identified by in silico analysis and ex vivo generation of CD4+ T-cell lines and validated by the immunization of goats and cattle. Future studies should test different peptide combinations in challenge trials to determine their protective effect and identify the most MHC-promiscuous vaccine candidates.
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Affiliation(s)
- Kari Lybeck
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
| | - Stig Tollefsen
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
| | - Heidi Mikkelsen
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Claus Lundegaard
- Department of Systems Biology, Centre for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Claus Aagaard
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Ingrid Olsen
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
| | - Gregers Jungersen
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Brenner EP, Sreevatsan S. Attenuated but immunostimulatory Mycobacterium tuberculosis variant bovis strain Ravenel shows variation in T cell epitopes. Sci Rep 2023; 13:12402. [PMID: 37524777 PMCID: PMC10390569 DOI: 10.1038/s41598-023-39578-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/27/2023] [Indexed: 08/02/2023] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis complex (MTBC) organisms, affects a range of humans and animals globally. Mycobacterial pathogenesis involves manipulation of the host immune system, partially through antigen presentation. Epitope sequences across the MTBC are evolutionarily hyperconserved, suggesting their recognition is advantageous for the bacterium. Mycobacterium tuberculosis var. bovis (MBO) strain Ravenel is an isolate known to provoke a robust immune response in cattle, but typically fails to produce lesions and persist. Unlike attenuated MBO BCG strains that lack the critical RD1 genomic region, Ravenel is classic-type MBO structurally, suggesting genetic variation is responsible for defective pathogenesis. This work explores variation in epitope sequences in MBO Ravenel by whole genome sequencing, and contrasts such variation against a fully virulent clinical isolate, MBO strain 10-7428. Validated MTBC epitopes (n = 4818) from the Immune Epitope Database were compared to their sequences in MBO Ravenel and MBO 10-7428. Ravenel yielded 3 modified T cell epitopes, in genes rpfB, argC, and rpoA. These modifications were predicted to have little effect on protein stability. In contrast, T cells epitopes in 10-7428 were all WT. Considering T cell epitope hyperconservation across MTBC variants, these altered MBO Ravenel epitopes support their potential contribution to overall strain attenuation. The affected genes may provide clues on basic pathogenesis, and if so, be feasible targets for reverse vaccinology.
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Affiliation(s)
- Evan P Brenner
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, East Lansing, MI, 48824, USA
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, East Lansing, MI, 48824, USA.
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3
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Sunita, Singh Y, Beamer G, Sun X, Shukla P. Recent developments in systems biology and genetic engineering toward design of vaccines for TB. Crit Rev Biotechnol 2022; 42:532-547. [PMID: 34641752 PMCID: PMC11208086 DOI: 10.1080/07388551.2021.1951649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
Tuberculosis (TB) is one of the most prevalent diseases worldwide. The currently available Bacillus Calmette-Guérin vaccine is not sufficient in protecting against pulmonary TB. Although many vaccines have been evaluated in clinical trials, but none of them yet has proven to be more successful. Thus, new strategies are urgently needed to design more effective TB vaccines. The emergence of new technologies will undoubtedly accelerate the process of vaccine development. This review summarizes the potential and validated applications of emerging technologies, including: systems biology (genomics, proteomics, and transcriptomics), genetic engineering, and other computational tools to discover and develop novel vaccines against TB. It also discussed that the significant implementation of these approaches will play crucial roles in the development of novel vaccines to cure and control TB.
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Affiliation(s)
- Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Gillian Beamer
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, MA, USA
| | - Xingmin Sun
- Department of Molecular Medicine, College of Medicine (COM), University of South Florida, Tampa, FL, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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4
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Antonelli ACB, Almeida VP, de Castro FOF, Silva JM, Pfrimer IAH, Cunha-Neto E, Maranhão AQ, Brígido MM, Resende RO, Bocca AL, Fonseca SG. In silico construction of a multiepitope Zika virus vaccine using immunoinformatics tools. Sci Rep 2022; 12:53. [PMID: 34997041 PMCID: PMC8741764 DOI: 10.1038/s41598-021-03990-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 12/01/2021] [Indexed: 01/02/2023] Open
Abstract
Zika virus (ZIKV) is an arbovirus from the Flaviviridae family and Flavivirus genus. Neurological events have been associated with ZIKV-infected individuals, such as Guillain-Barré syndrome, an autoimmune acute neuropathy that causes nerve demyelination and can induce paralysis. With the increase of ZIKV infection incidence in 2015, malformation and microcephaly cases in newborns have grown considerably, which suggested congenital transmission. Therefore, the development of an effective vaccine against ZIKV became an urgent need. Live attenuated vaccines present some theoretical risks for administration in pregnant women. Thus, we developed an in silico multiepitope vaccine against ZIKV. All structural and non-structural proteins were investigated using immunoinformatics tools designed for the prediction of CD4 + and CD8 + T cell epitopes. We selected 13 CD8 + and 12 CD4 + T cell epitopes considering parameters such as binding affinity to HLA class I and II molecules, promiscuity based on the number of different HLA alleles that bind to the epitopes, and immunogenicity. ZIKV Envelope protein domain III (EDIII) was added to the vaccine construct, creating a hybrid protein domain-multiepitope vaccine. Three high scoring continuous and two discontinuous B cell epitopes were found in EDIII. Aiming to increase the candidate vaccine antigenicity even further, we tested secondary and tertiary structures and physicochemical parameters of the vaccine conjugated to four different protein adjuvants: flagellin, 50S ribosomal protein L7/L12, heparin-binding hemagglutinin, or RS09 synthetic peptide. The addition of the flagellin adjuvant increased the vaccine's predicted antigenicity. In silico predictions revealed that the protein is a probable antigen, non-allergenic and predicted to be stable. The vaccine’s average population coverage is estimated to be 87.86%, which indicates it can be administered worldwide. Peripheral Blood Mononuclear Cells (PBMC) of individuals with previous ZIKV infection were tested for cytokine production in response to the pool of CD4 and CD8 ZIKV peptide selected. CD4 + and CD8 + T cells showed significant production of IFN-γ upon stimulation and IL-2 production was also detected by CD8 + T cells, which indicated the potential of our peptides to be recognized by specific T cells and induce immune response. In conclusion, we developed an in silico universal vaccine predicted to induce broad and high-coverage cellular and humoral immune responses against ZIKV, which can be a good candidate for posterior in vivo validation.
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Affiliation(s)
- Ana Clara Barbosa Antonelli
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil
| | - Vinnycius Pereira Almeida
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil
| | - Fernanda Oliveira Feitosa de Castro
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil.,Departament of Master in Environmental Sciences and Health, School of Medical, Pharmaceutical and Biomedical Sciences, Pontifical Catholic University of Goiás, Goiânia, Brazil
| | | | - Irmtraut Araci Hoffmann Pfrimer
- Departament of Master in Environmental Sciences and Health, School of Medical, Pharmaceutical and Biomedical Sciences, Pontifical Catholic University of Goiás, Goiânia, Brazil
| | - Edecio Cunha-Neto
- Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil.,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil
| | - Andréa Queiroz Maranhão
- Department of Cell Biology, University of Brasília, Brasília, Brazil.,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil
| | - Marcelo Macedo Brígido
- Department of Cell Biology, University of Brasília, Brasília, Brazil.,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil
| | | | | | - Simone Gonçalves Fonseca
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Rua 235 s/n, sala 335, Setor Universitário, Goiânia, GO, 74605-050, Brazil. .,Institute for Investigation in Immunology (iii) - National Institute of Science and Technology (INCT), São Paulo, Brazil.
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5
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Gul N, Khan SU, Ali I, Khan FU. Transmission dynamic of stochastic hepatitis C model by spectral collocation method. Comput Methods Biomech Biomed Engin 2021; 25:578-592. [PMID: 34459684 DOI: 10.1080/10255842.2021.1970143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this research work, we present an exciting mathematical analysis of a stochastic model, using a standard incidence function, for infectious disease hepatitis C transmission dynamics. In this model, we divided the infected population into three different classes with two different infection stages known as chronic class and acute class while the third is an isolation class. We also presents briefly the Legendre spectral method for the numerical solution to the proposed model. It is observed that the disease-free equilibrium is asymptotically stable, when basic reproduction number R0<1. It is also shown that the proposed model has a stable endemic equilibrium when the reproduction number R0>1. Also, sensitivity analysis is carried out to study and identify the effect of parameters on R0. Moreover, we have performed numerical simulations to study the influence of disease free equilibrium and endemic equilibrium. Legendre polynomial and Legendre weight function are used to solve the proposed stochastic system numerically. Numerical results are compared against the basic reproduction number.
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Affiliation(s)
- Naseeb Gul
- Department of Mathematics, City University of Science and Information Technology Peshawar, KP, Pakistan
| | - Sami Ullah Khan
- Department of Mathematics, City University of Science and Information Technology Peshawar, KP, Pakistan
| | - Ishtiaq Ali
- Department of Mathematics and Statistics, College of Science, King Faisal University, Al-Hasa, KSA
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6
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Immunoinformatics Approach to Design Multi-Epitope- Subunit Vaccine against Bovine Ephemeral Fever Disease. Vaccines (Basel) 2021; 9:vaccines9080925. [PMID: 34452050 PMCID: PMC8402647 DOI: 10.3390/vaccines9080925] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/16/2022] Open
Abstract
Bovine ephemeral fever virus (BEFV) is an overlooked pathogen, recently gaining widespread attention owing to its associated enormous economic impacts affecting the global livestock industries. High endemicity with rapid spread and morbidity greatly impacts bovine species, demanding adequate attention towards BEFV prophylaxis. Currently, a few suboptimum vaccines are prevailing, but were confined to local strains with limited protection. Therefore, we designed a highly efficacious multi-epitope vaccine candidate targeted against the geographically distributed BEFV population. By utilizing immunoinformatics technology, all structural proteins were targeted for B- and T-cell epitope prediction against the entire allele population of BoLA molecules. Prioritized epitopes were adjoined by linkers and adjuvants to effectively induce both cellular and humoral immune responses in bovine. Subsequently, the in silico construct was characterized for its physicochemical parameters, high immunogenicity, least allergenicity, and non-toxicity. The 3D modeling, refinement, and validation of ligand (vaccine construct) and receptor (bovine TLR7) then followed molecular docking and molecular dynamic simulation to validate their stable interactions. Moreover, in silico cloning of codon-optimized vaccine construct in the prokaryotic expression vector (pET28a) was explored. This is the first time HTL epitopes have been predicted using bovine datasets. We anticipate that the designed construct could be an effective prophylactic remedy for the BEF disease that may pave the way for future laboratory experiments.
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7
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Li Z, Lu G, Li Z, Wu B, Luo E, Qiu X, Guo J, Xia Z, Zheng C, Su Q, Zeng Y, Chan WY, Su X, Cai Q, Xu Y, Chen Y, Wang M, Poon WS, Luo X. Altered Actinobacteria and Firmicutes Phylum Associated Epitopes in Patients With Parkinson's Disease. Front Immunol 2021; 12:632482. [PMID: 34276644 PMCID: PMC8284394 DOI: 10.3389/fimmu.2021.632482] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/11/2021] [Indexed: 01/10/2023] Open
Abstract
Recent evidence suggests that inflammation was participated in the pathogenesis of PD, thus, to understand the potential mechanism of gut microbiota in the pathogenesis of Parkinson’s disease (PD), we performed a metagenomic analysis of fecal samples from PD patient and controls. Using a two-stage metagenome-wide association strategy, fecal DNA samples from 69 PD patients and 244 controls in three groups (comprising 66 spouses, 97 age-matched, and 81 normal samples, respectively) were analyzed, and differences between candidate gut microbiota and microbiota-associated epitopes (MEs) were compared. In the study, 27 candidate bacterial biomarkers and twenty-eight candidate epitope peptides were significantly different between the PD patients and control groups. Further, enriched 4 and 13 MEs in PD were positively associated with abnormal inflammatory indicators [neutrophil percentage (NEUT.1), monocyte count/percentage (MONO/MONO.1), white blood cell count (WBC)] and five candidate bacterial biomarkers (c_Actinobacteria, f_Bifidobacteriaceae, g_Bifidobacterium, o_Bifidobacteriales, p_Actinobacteria) from Actinobacteria phylum, and they were also positively associated with histidine degradation and proline biosynthesis pathways, respectively. Additionally, enriched 2 MEs and 1 ME in PD were positively associated with above inflammatory indicators and two bacteria (f_Lactobacillaceae, g_Lactobacillus) from Firmicutes phylum, and they were also positively associated with pyruvate fermentation to propanoate I and negatively associated with isopropanol biosynthesis, respectively. Of these MEs, two MEs from GROEL2, RPSC were derived from Mycobacterium tuberculosis, triggered the T cell immune response, as previously reported. Additionally, other candidate epitope peptides derived from Mycobacterium tuberculosis and Mycobacterium leprae may also have potential immune effects in PD. In all, the altered MEs in PD may relate to abnormalities in immunity and glutamate and propionate metabolism, which furthers our understanding of the pathogenesis of PD.
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Affiliation(s)
- Zhuo Li
- Genetic Testing Lab, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Gang Lu
- The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Zhe Li
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Bin Wu
- Genetic Testing Lab, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Enli Luo
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinmin Qiu
- Genetic Testing Lab, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianwen Guo
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhangyong Xia
- Department of Neurology, Liaocheng People's Hospital, Liaocheng, China.,Department of Neurology, Liaocheng Clinical School of Shandong First Medical University, Liaocheng, China
| | - Chunye Zheng
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiaozhen Su
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yan Zeng
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wai Yee Chan
- The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Xianwei Su
- The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Qiaodi Cai
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yanjuan Xu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yingjun Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mingbang Wang
- Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
| | - Wai Sang Poon
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Xiaodong Luo
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Couto J, Seixas G, Stutzer C, Olivier NA, Maritz-Olivier C, Antunes S, Domingos A. Probing the Rhipicephalusbursa Sialomes in Potential Anti-Tick Vaccine Candidates: A Reverse Vaccinology Approach. Biomedicines 2021; 9:363. [PMID: 33807386 PMCID: PMC8067113 DOI: 10.3390/biomedicines9040363] [Citation(s) in RCA: 6] [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: 01/15/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 11/16/2022] Open
Abstract
In the wake of the 'omics' explosion of data, reverse vaccinology approaches are being applied more readily as an alternative for the discovery of candidates for next generation diagnostics and vaccines. Promising protective antigens for the control of ticks and tick-borne diseases can be discovered by mining available omics data for immunogenic epitopes. The present study aims to explore the previously obtained Rhipicephalus bursa sialotranscriptome during both feeding and Babesia infection, to select antigenic targets that are either membrane-associated or a secreted protein, as well as unique to the ectoparasite and not present in the mammalian host. Further, they should be capable of stimulating T and B cells for a potential robust immune response, and be non-allergenic or toxic to the host. From the R. bursa transcriptome, 5706 and 3025 proteins were identified as belonging to the surfaceome and secretome, respectively. Following a reverse genetics immunoinformatics pipeline, nine preferred candidates, consisting of one transmembrane-related and eight secreted proteins, were identified. These candidates showed a higher predicted antigenicity than the Bm86 antigen, with no homology to mammalian hosts and exposed regions. Only four were functionally annotated and selected for further in silico analysis, which examined their protein structure, surface accessibility, flexibility, hydrophobicity, and putative linear B and T-cell epitopes. Regions with overlapping coincident epitopes groups (CEGs) were evaluated to select peptides that were further analyzed for their physicochemical characteristics, potential allergenicity, toxicity, solubility, and potential propensity for crystallization. Following these procedures, a set of three peptides from the three R. bursa proteins were selected. In silico results indicate that the designed epitopes could stimulate a protective and long-lasting immune response against those tick proteins, reflecting its potential as anti-tick vaccines. The immunogenicity of these peptides was evaluated in a pilot immunization study followed by tick feeding to evaluate its impact on tick behavior and pathogen transmission. Combining in silico methods with in vivo immunogenicity evaluation enabled the screening of vaccine candidates prior to expensive infestation studies on the definitive ovine host animals.
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Affiliation(s)
- Joana Couto
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal; (G.S.); (A.D.)
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (GHTM-IHMT-UNL), Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - Gonçalo Seixas
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal; (G.S.); (A.D.)
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (GHTM-IHMT-UNL), Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - Christian Stutzer
- Division of Genetics, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.S.); (C.M.-O.)
| | - Nicholas A. Olivier
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria 0002, South Africa;
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Christine Maritz-Olivier
- Division of Genetics, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.S.); (C.M.-O.)
| | - Sandra Antunes
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal; (G.S.); (A.D.)
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (GHTM-IHMT-UNL), Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - Ana Domingos
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal; (G.S.); (A.D.)
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (GHTM-IHMT-UNL), Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
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9
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Farrell D. epitopepredict: a tool for integrated MHC binding prediction. GIGABYTE 2021; 2021:gigabyte13. [PMID: 36824339 PMCID: PMC9631954 DOI: 10.46471/gigabyte.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/19/2021] [Indexed: 11/09/2022] Open
Abstract
A key step in the cellular adaptive immune response is the presentation of antigens to T cells. Computational prediction of T cell epitopes has many applications in vaccine design and immuno-diagnostics. This is the basis of immunoinformatics, which allows in silico screening of peptides before experiments are performed. With the availability of whole genomes for many microbial species it is now feasible to computationally screen whole proteomes for candidate peptides. epitopepredict is a programmatic framework and command line tool designed to aid this process. It provides access to multiple binding prediction algorithms under a single interface and scales for whole genomes using multiple target MHC alleles. A web interface is provided to assist visualization and filtering of the results. The software is freely available under an open-source license from https://github.com/dmnfarrell/epitopepredict.
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Affiliation(s)
- Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Ireland, E-mail:
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10
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Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble. Pathogens 2020; 9:pathogens9121078. [PMID: 33371523 PMCID: PMC7767518 DOI: 10.3390/pathogens9121078] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/12/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022] Open
Abstract
African swine fever virus is the etiological agent of African swine fever, a transmissible severe hemorrhagic disease that affects pigs, causing massive economic losses. There is neither a treatment nor a vaccine available, and the only method to control its spread is by extensive culling of pigs. So far, classical vaccine development approaches have not yielded sufficiently good results in terms of concomitant safety and efficacy. Nowadays, thanks to advances in genomic and proteomic techniques, a reverse vaccinology strategy can be explored to design alternative vaccine formulations. In this study, ASFV protein sequences were analyzed using an in-house pipeline based on publicly available immunoinformatic tools to identify epitopes of interest for a prospective vaccine ensemble. These included experimentally validated sequences from the Immune Epitope Database, as well as de novo predicted sequences. Experimentally validated and predicted epitopes were prioritized following a series of criteria that included evolutionary conservation, presence in the virulent and currently circulating variant Georgia 2007/1, and lack of identity to either the pig proteome or putative proteins from pig gut microbiota. Following this strategy, 29 B-cell, 14 CD4+ T-cell and 6 CD8+ T-cell epitopes were selected, which represent a starting point to investigating the protective capacity of ASFV epitope-based vaccines.
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Benedictus L, Steinbach S, Holder T, Bakker D, Vrettou C, Morrison WI, Vordermeier M, Connelley T. Hydrophobic Mycobacterial Antigens Elicit Polyfunctional T Cells in Mycobacterium bovis Immunized Cattle: Association With Protection Against Challenge? Front Immunol 2020; 11:588180. [PMID: 33281817 PMCID: PMC7688591 DOI: 10.3389/fimmu.2020.588180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/20/2020] [Indexed: 01/09/2023] Open
Abstract
Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a chronic disease of cattle with a detrimental impact on food quality and production. Research on bTB vaccines has predominantly been focused on proteinaceous antigens. However, mycobacteria have a thick and intricate lipid outer layer and lipids as well as lipopeptides are important for immune-evasion and virulence. In humans, lipid extracts of M. tuberculosis have been shown to elicit immune responses effective against M. tuberculosis in vitro. Chloroform-methanol extraction (CME) was applied to M. bovis BCG to obtain a hydrophobic antigen extract (CMEbcg) containing lipids and lipopeptides. CMEbcg stimulated IFN-γ+IL-2+ and IL-17A+IL-22+ polyfunctional T cells and elicited T cell responses with a Th1 and Th17 cytokine release profile in both M. bovis BCG vaccinated and M. bovis challenged calves. Lipopeptides were shown to be the immunodominant antigens in CMEbcg, stimulating CD4 T cells via MHC class II. CMEbcg expanded T cells killed CMEbcg loaded monocytes and the CMEbcg-specific CD3 T cell proliferative response following M. bovis BCG vaccination was the best predictor for reduced pathology following challenge with M. bovis. Although the high predictive value of CMEbcg-specific immune responses does not confirm a causal relationship with protection against M. bovis challenge, when taking into account the in vitro antimycobacterial phenotype of CMEbcg-specific T cells (e.g. Th1/Th17 cytokine profile), it is indicative that CMEbcg-specific immune responses could play a functional role in immunity against M. bovis. Based on these findings we conclude that lipopeptides of M. bovis are potential novel subunit vaccine candidates and that further studies into the functional characterization of lipopeptide-specific immune responses together with their role in protection against bovine tuberculosis are warranted.
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Affiliation(s)
- Lindert Benedictus
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, United Kingdom
| | - Sabine Steinbach
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Thomas Holder
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Douwe Bakker
- Independent Researcher and Technical Consultant, Lelystad, Netherlands
| | - Christina Vrettou
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, United Kingdom
| | - W Ivan Morrison
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, United Kingdom
| | - Martin Vordermeier
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,Centre for Bovine Tuberculosis, Institute for Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Timothy Connelley
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, United Kingdom
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Design of an Epitope-Based Vaccine Ensemble for Animal Trypanosomiasis by Computational Methods. Vaccines (Basel) 2020; 8:vaccines8010130. [PMID: 32188062 PMCID: PMC7157688 DOI: 10.3390/vaccines8010130] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/29/2020] [Accepted: 03/13/2020] [Indexed: 12/22/2022] Open
Abstract
African animal trypanosomiasis is caused by vector-transmitted parasites of the genus Trypanosoma. T. congolense and T. brucei brucei are predominant in Africa; T. evansi and T. vivax in America and Asia. They have in common an extracellular lifestyle and livestock tropism, which provokes huge economic losses in regions where vectors are endemic. There are licensed drugs to treat the infections, but adherence to treatment is poor and appearance of resistances common. Therefore, the availability of a prophylactic vaccine would represent a major breakthrough towards the management and control of the disease. Selection of the most appropriate antigens for its development is a bottleneck step, especially considering the limited resources allocated. Herein we propose a vaccine strategy based on multiple epitopes from multiple antigens to counteract the parasites´ biological complexity. Epitopes were identified by computer-assisted genome-wide screenings, considering sequence conservation criteria, antigens annotation and sub-cellular localization, high binding affinity to antigen presenting molecules, and lack of cross-reactivity to proteins in cattle and other breeding species. We ultimately provide 31 B-cell, 8 CD4 T-cell, and 15 CD8 T-cell epitope sequences from 30 distinct antigens for the prospective design of a genetic ensemble vaccine against the four trypanosome species responsible for African animal trypanosomiasis.
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