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Salerno-Gonçalves R, Tettelin H, Luo D, Guo Q, Ardito MT, Martin WD, De Groot AS, Sztein MB. Differential functional patterns of memory CD4 + and CD8 + T-cells from volunteers immunized with Ty21a typhoid vaccine observed using a recombinant Escherichia coli system expressing S. Typhi proteins. Vaccine 2019; 38:258-270. [PMID: 31629569 DOI: 10.1016/j.vaccine.2019.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/03/2019] [Accepted: 10/07/2019] [Indexed: 02/01/2023]
Abstract
It is widely accepted that CD4+ and CD8+ T-cells play a significant role in protection against Salmonella enterica serovar Typhi (S. Typhi), the causative agent of the typhoid fever. However, the antigen specificity of these T-cells remains largely unknown. Previously, we demonstrated the feasibility of using a recombinant Escherichia coli (E. coli) expression system to uncover the antigen specificity of CD4+ and CD8+ T cells. Here, we expanded these studies to include the evaluation of 12 additional S. Typhi proteins: 4 outer membrane proteins (OmpH, OmpL, OmpR, OmpX), 3 Vi-polysaccharide biosynthesis proteins (TviA, TviB, TviE), 3 cold shock proteins (CspA, CspB, CspC), and 2 conserved hypothetical proteins (Chp 1 and Chp2), all selected based on the bioinformatic analyses of the content of putative T-cell epitopes. CD4+ and CD8+ T cells from 15 adult volunteers, obtained before and 42 days after immunization with oral live attenuated Ty21a vaccine, were assessed for their functionality (i.e., production of cytokines and cytotoxic expression markers in response to stimulation with selected antigens) as measured by flow cytometry. Although volunteers differed on their T-cell antigen specificity, we observed T-cell immune responses against all S. Typhi proteins evaluated. These responses included 9 proteins, OmpH, OmpR, TviA, TviE, CspA, CspB, CspC, Chp 1 and Chp 2, which have not been previously reported to elicit T-cell responses. Interestingly, we also observed that, regardless of the protein, the functional patterns of the memory T-cells were different between CD4+ and CD8+ T cells. In sum, these studies demonstrated the feasibility of using bioinformatic analysis and the E. coli expressing system described here to uncover novel immunogenic T-cell proteins that could serve as potential targets for the production of protein-based vaccines.
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Affiliation(s)
- Rosângela Salerno-Gonçalves
- Center for Vaccine Development and Global Health (CVD), Department of Pediatrics, University of Maryland School of Medicine, 685 West Baltimore Street, HSF1, Baltimore, MD 21201, USA.
| | - Hervé Tettelin
- Department of Microbiology and Immunology and Institute for Genome Sciences (IGS), University of Maryland School of Medicine, 670 West Baltimore Street, HSF3, Baltimore, MD 21201, USA
| | - David Luo
- Center for Vaccine Development and Global Health (CVD), Department of Pediatrics, University of Maryland School of Medicine, 685 West Baltimore Street, HSF1, Baltimore, MD 21201, USA
| | - Qin Guo
- Department of Microbiology and Immunology and Institute for Genome Sciences (IGS), University of Maryland School of Medicine, 670 West Baltimore Street, HSF3, Baltimore, MD 21201, USA
| | - Matthew T Ardito
- Institute for Immunology and Informatics (iCubed), Department of Cell and Molecular Biology, University of Rhode Island, 80 Washington Street, Providence, RI, USA; EpiVax, Inc., 188 Valley Street Suite 424, Providence, RI, USA
| | - William D Martin
- Institute for Immunology and Informatics (iCubed), Department of Cell and Molecular Biology, University of Rhode Island, 80 Washington Street, Providence, RI, USA; EpiVax, Inc., 188 Valley Street Suite 424, Providence, RI, USA
| | - Anne S De Groot
- Institute for Immunology and Informatics (iCubed), Department of Cell and Molecular Biology, University of Rhode Island, 80 Washington Street, Providence, RI, USA; EpiVax, Inc., 188 Valley Street Suite 424, Providence, RI, USA
| | - Marcelo B Sztein
- Center for Vaccine Development and Global Health (CVD), Department of Pediatrics, University of Maryland School of Medicine, 685 West Baltimore Street, HSF1, Baltimore, MD 21201, USA
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Coxiella burnetii Epitope-Specific T-Cell Responses in Patients with Chronic Q Fever. Infect Immun 2019; 87:IAI.00213-19. [PMID: 31331958 DOI: 10.1128/iai.00213-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
Infection with Coxiella burnetii, the causative agent of Q fever, can result in life-threatening persistent infection. Reactogenicity hinders worldwide implementation of the only licensed human Q fever vaccine. We previously demonstrated long-lived immunoreactivity in individuals with past symptomatic and asymptomatic Coxiella infection (convalescents) to promiscuous HLA class II C. burnetii epitopes, providing the basis for a novel T-cell targeted subunit vaccine. In this study, we investigated in a cohort of 22 individuals treated for persistent infection (chronic Q fever) whether they recognize the same set of epitopes or distinct epitopes that could be candidates for a therapeutic vaccine or aid in the diagnosis of persistent infection. In cultured enzyme-linked immunosorbent spot (ELISpot) assays, individuals with chronic Q fever showed strong class II epitope-specific responses that were largely overlapping with the peptide repertoire identified previously for convalescents. Five additional peptides were recognized more frequently by chronic subjects, but there was no combination of epitopes uniquely recognized by or nonreactive in subjects with chronic Q fever. Consistent with more recent/prolonged exposure, we found, however, stronger ex vivo responses by direct ELISpot to both whole-cell C. burnetii and individual peptides in chronic patients than in convalescents. In conclusion, we have validated and expanded a previously published set of candidate epitopes for a novel T-cell targeted subunit Q fever vaccine in treated patients with chronic Q fever and demonstrated that they successfully mounted a T-cell response comparable to that of convalescents. Finally, we demonstrated that individuals treated for chronic Q fever mount a broader ex vivo response to class II epitopes than convalescents, which could be explored for diagnostic purposes.
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Hoffmann PR, Hoffmann FW, Premeaux TA, Fujita T, Soprana E, Panigada M, Chew GM, Richard G, Hindocha P, Menor M, Khadka VS, Deng Y, Moise L, Ndhlovu LC, Siccardi A, Weinberg AD, De Groot AS, Bertino P. Multi-antigen Vaccination With Simultaneous Engagement of the OX40 Receptor Delays Malignant Mesothelioma Growth and Increases Survival in Animal Models. Front Oncol 2019; 9:720. [PMID: 31428586 PMCID: PMC6688537 DOI: 10.3389/fonc.2019.00720] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/19/2019] [Indexed: 01/09/2023] Open
Abstract
Malignant Mesothelioma (MM) is a rare and highly aggressive cancer that develops from mesothelial cells lining the pleura and other internal cavities, and is often associated with asbestos exposure. To date, no effective treatments have been made available for this pathology. Herein, we propose a novel immunotherapeutic approach based on a unique vaccine targeting a series of antigens that we found expressed in different MM tumors, but largely undetectable in normal tissues. This vaccine, that we term p-Tvax, is comprised of a series of immunogenic peptides presented by both MHC-I and -II to generate robust immune responses. The peptides were designed using in silico algorithms that discriminate between highly immunogenic T cell epitopes and other harmful epitopes, such as suppressive regulatory T cell epitopes and autoimmune epitopes. Vaccination of mice with p-Tvax led to antigen-specific immune responses that involved both CD8+ and CD4+ T cells, which exhibited cytolytic activity against MM cells in vitro. In mice carrying MM tumors, p-Tvax increased tumor infiltration of CD4+ T cells. Moreover, combining p-Tvax with an OX40 agonist led to decreased tumor growth and increased survival. Mice treated with this combination immunotherapy displayed higher numbers of tumor-infiltrating CD8+ and CD4+ T cells and reduced T regulatory cells in tumors. Collectively, these data suggest that the combination of p-Tvax with an OX40 agonist could be an effective strategy for MM treatment.
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Affiliation(s)
- Peter R Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Fukun W Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Thomas A Premeaux
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Tsuyoshi Fujita
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Elisa Soprana
- Department of Molecular Immunology, San Raffaele University and Research Institute, Milan, Italy
| | - Maddalena Panigada
- Department of Molecular Immunology, San Raffaele University and Research Institute, Milan, Italy
| | - Glen M Chew
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | | | | | - Mark Menor
- Bioinformatics Core, Department of Complementary and Integrative Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Vedbar S Khadka
- Bioinformatics Core, Department of Complementary and Integrative Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Youping Deng
- Bioinformatics Core, Department of Complementary and Integrative Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Lenny Moise
- EpiVax, Inc., Providence, RI, United States.,Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, United States
| | - Lishomwa C Ndhlovu
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Antonio Siccardi
- Department of Molecular Immunology, San Raffaele University and Research Institute, Milan, Italy
| | - Andrew D Weinberg
- Robert W. Franz Cancer Research Center, Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Anne S De Groot
- EpiVax, Inc., Providence, RI, United States.,Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, United States
| | - Pietro Bertino
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
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54
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Eickhoff CS, Terry FE, Peng L, Meza KA, Sakala IG, Van Aartsen D, Moise L, Martin WD, Schriewer J, Buller RM, De Groot AS, Hoft DF. Highly conserved influenza T cell epitopes induce broadly protective immunity. Vaccine 2019; 37:5371-5381. [PMID: 31331771 DOI: 10.1016/j.vaccine.2019.07.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 12/30/2022]
Abstract
Influenza world-wide causes significant morbidity and mortality annually, and more severe pandemics when novel strains evolve to which humans are immunologically naïve. Because of the high viral mutation rate, new vaccines must be generated based on the prevalence of circulating strains every year. New approaches to induce more broadly protective immunity are urgently needed. Previous research has demonstrated that influenza-specific T cells can provide broadly heterotypic protective immunity in both mice and humans, supporting the rationale for developing a T cell-targeted universal influenza vaccine. We used state-of-the art immunoinformatic tools to identify putative pan-HLA-DR and HLA-A2 supertype-restricted T cell epitopes highly conserved among > 50 widely diverse influenza A strains (representing hemagglutinin types 1, 2, 3, 5, 7 and 9). We found influenza peptides that are highly conserved across influenza subtypes that were also predicted to be class I epitopes restricted by HLA-A2. These peptides were found to be immunoreactive in HLA-A2 positive but not HLA-A2 negative individuals. Class II-restricted T cell epitopes that were highly conserved across influenza subtypes were identified. Human CD4+ T cells were reactive with these conserved CD4 epitopes, and epitope expanded T cells were responsive to both H1N1 and H3N2 viruses. Dendritic cell vaccines pulsed with conserved epitopes and DNA vaccines encoding these epitopes were developed and tested in HLA transgenic mice. These vaccines were highly immunogenic, and more importantly, vaccine-induced immunity was protective against both H1N1 and H3N2 influenza challenges. These results demonstrate proof-of-principle that conserved T cell epitopes expressed by widely diverse influenza strains can induce broadly protective, heterotypic influenza immunity, providing strong support for further development of universally relevant multi-epitope T cell-targeting influenza vaccines.
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Affiliation(s)
- Christopher S Eickhoff
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Frances E Terry
- EpiVax, Inc., 188 Valley Street, Suite 424, Providence, RI 02909, United States
| | - Linda Peng
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Krystal A Meza
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Isaac G Sakala
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Daniel Van Aartsen
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Leonard Moise
- EpiVax, Inc., 188 Valley Street, Suite 424, Providence, RI 02909, United States; University of Rhode Island, Institute for Immunology and Informatics, Department of Cell and Molecular Biology, 80 Washington Street, Providence, RI 02903, United States
| | - William D Martin
- EpiVax, Inc., 188 Valley Street, Suite 424, Providence, RI 02909, United States
| | - Jill Schriewer
- Saint Louis University, Department of Molecular Microbiology & Immunology, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - R Mark Buller
- Saint Louis University, Department of Molecular Microbiology & Immunology, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Anne S De Groot
- EpiVax, Inc., 188 Valley Street, Suite 424, Providence, RI 02909, United States; University of Rhode Island, Institute for Immunology and Informatics, Department of Cell and Molecular Biology, 80 Washington Street, Providence, RI 02903, United States
| | - Daniel F Hoft
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States; Saint Louis University, Department of Molecular Microbiology & Immunology, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States.
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55
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Hewitt JS, Karuppannan AK, Tan S, Gauger P, Halbur PG, Gerber PF, De Groot AS, Moise L, Opriessnig T. A prime-boost concept using a T-cell epitope-driven DNA vaccine followed by a whole virus vaccine effectively protected pigs in the pandemic H1N1 pig challenge model. Vaccine 2019; 37:4302-4309. [PMID: 31248687 DOI: 10.1016/j.vaccine.2019.06.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 01/08/2023]
Abstract
Influenza A virus (IAV) vaccines in pigs generally provide homosubtypic protection but fail to prevent heterologous infections. In this pilot study, the efficacy of an intradermal pDNA vaccine composed of conserved SLA class I and class II T cell epitopes (EPITOPE) against a homosubtypic challenge was compared to an intramuscular commercial inactivated whole virus vaccine (INACT) and a heterologous prime boost approach using both vaccines. Thirty-nine IAV-free, 3-week-old pigs were randomly assigned to one of five groups including NEG-CONTROL (unvaccinated, sham-challenged), INACT-INACT-IAV (vaccinated with FluSure XP® at 4 and 7 weeks, pH1N1 challenged), EPITOPE-INACT-IAV (vaccinated with PigMatrix EDV at 4 and FluSure XP® at 7 weeks, pH1N1 challenged), EPITOPE-EPITOPE-IAV (vaccinated with PigMatrix EDV at 4 and 7 weeks, pH1N1 challenged), and a POS-CONTROL group (unvaccinated, pH1N1 challenged). The challenge was done at 9 weeks of age and pigs were necropsied at day post challenge (dpc) 5. At the time of challenge, all INACT-INACT-IAV pigs, and by dpc 5 all EPITOPE-INACT-IAV pigs were IAV seropositive. IFNγ secreting cells, recognizing vaccine epitope-specific peptides and pH1N1 challenge virus were highest in the EPITOPE-INACT-IAV pigs at challenge. Macroscopic lung lesion scores were reduced in all EPITOPE-INACT-IAV pigs while INACT-INACT-IAV pigs exhibited a bimodal distribution of low and high scores akin to naïve challenged animals. No IAV antigen in lung tissues was detected at necropsy in the EPITOPE-INACT-IAV group, which was similar to naïve unchallenged pigs and different from all other challenged groups. Results suggest that the heterologous prime boost approach using an epitope-driven DNA vaccine followed by an inactivated vaccine was effective against a homosubtypic challenge, and further exploration of this vaccine approach as a practical control measure against heterosubtypic IAV infections is warranted.
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Affiliation(s)
- Joshua S Hewitt
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Anbu K Karuppannan
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Swan Tan
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Phillip Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Patrick G Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Priscilla F Gerber
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - Anne S De Groot
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA; EpiVax Inc., Providence, RI, USA
| | - Leonard Moise
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA; EpiVax Inc., Providence, RI, USA
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA; The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
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56
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Ning L, He B, Zhou P, Derda R, Huang J. Molecular Design of Peptide-Fc Fusion Drugs. Curr Drug Metab 2019; 20:203-208. [DOI: 10.2174/1389200219666180821095355] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 01/18/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
Abstract
Background:Peptide-Fc fusion drugs, also known as peptibodies, are a category of biological therapeutics in which the Fc region of an antibody is genetically fused to a peptide of interest. However, to develop such kind of drugs is laborious and expensive. Rational design is urgently needed.Methods:We summarized the key steps in peptide-Fc fusion technology and stressed the main computational resources, tools, and methods that had been used in the rational design of peptide-Fc fusion drugs. We also raised open questions about the computer-aided molecular design of peptide-Fc.Results:The design of peptibody consists of four steps. First, identify peptide leads from native ligands, biopanning, and computational design or prediction. Second, select the proper Fc region from different classes or subclasses of immunoglobulin. Third, fuse the peptide leads and Fc together properly. At last, evaluate the immunogenicity of the constructs. At each step, there are quite a few useful resources and computational tools.Conclusion:Reviewing the molecular design of peptibody will certainly help make the transition from peptide leads to drugs on the market quicker and cheaper.
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Affiliation(s)
- Lin Ning
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Peng Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Alberta, Canada
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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57
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Nieto-Gómez R, Angulo C, Monreal-Escalante E, Govea-Alonso DO, De Groot AS, Rosales-Mendoza S. Design of a multiepitopic Zaire ebolavirus protein and its expression in plant cells. J Biotechnol 2019; 295:41-48. [PMID: 30826446 DOI: 10.1016/j.jbiotec.2019.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 10/27/2022]
Abstract
The recent Ebola virus disease (EVD) outbreaks make the development of efficacious and low cost vaccines against Ebola virus (EBOV) an urgent goal. Multiepitopic vaccines allow a rational design rendering vaccines able to induce proper immune responses in terms of polarization and potency. In addition, the pathogen variants can be easily covered by including epitopes conserved among relevant isolates. Other important aspects to consider in vaccination are the costs associated to production, distribution, and administration of the vaccine. Plants provide an advantageous platform for this purpose, since they yield biomass at very low costs and some species can be used to formulate purification-free oral vaccines. In the present study, a multiepitopic protein called Zerola, which carries epitopes from the EBOV glycoprotein (GP), was designed based on immunoinformatic approaches and current experimental evidence on B cell protective GP epitopes. Moreover, expression studies performed in nuclear-transformed tobacco lines confirmed the capacity of the plant cell to synthetize the Zerola antigenic protein. The generation of this plant-based candidate vaccine is a step forward in the development of highly efficient and low cost EBOV vaccines.
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Affiliation(s)
- Ricardo Nieto-Gómez
- Laboratorio de Biofarmacéuticos recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP, 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª Sección, San Luis Potosí, 78210, Mexico
| | - Carlos Angulo
- Grupo de Inmunología & Vacunología, Centro de Investigaciones Biológicas del Noroeste, SC., Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.C.S., C.P. 23096, Mexico
| | - Elizabeth Monreal-Escalante
- Laboratorio de Biofarmacéuticos recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP, 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª Sección, San Luis Potosí, 78210, Mexico
| | - Dania O Govea-Alonso
- Laboratorio de Biofarmacéuticos recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP, 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª Sección, San Luis Potosí, 78210, Mexico
| | | | - Sergio Rosales-Mendoza
- Laboratorio de Biofarmacéuticos recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP, 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª Sección, San Luis Potosí, 78210, Mexico.
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58
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Shey RA, Ghogomu SM, Esoh KK, Nebangwa ND, Shintouo CM, Nongley NF, Asa BF, Ngale FN, Vanhamme L, Souopgui J. In-silico design of a multi-epitope vaccine candidate against onchocerciasis and related filarial diseases. Sci Rep 2019; 9:4409. [PMID: 30867498 PMCID: PMC6416346 DOI: 10.1038/s41598-019-40833-x] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/25/2019] [Indexed: 01/02/2023] Open
Abstract
Onchocerciasis is a parasitic disease with high socio-economic burden particularly in sub-Saharan Africa. The elimination plan for this disease has faced numerous challenges. A multi-epitope prophylactic/therapeutic vaccine targeting the infective L3 and microfilaria stages of the parasite's life cycle would be invaluable to achieve the current elimination goal. There are several observations that make the possibility of developing a vaccine against this disease likely. For example, despite being exposed to high transmission rates of infection, 1 to 5% of people have no clinical manifestations of the disease and are thus considered as putatively immune individuals. An immuno-informatics approach was applied to design a filarial multi-epitope subunit vaccine peptide consisting of linear B-cell and T-cell epitopes of proteins reported to be potential novel vaccine candidates. Conservation of the selected proteins and predicted epitopes in other parasitic nematode species suggests that the generated chimera could be helpful for cross-protection. The 3D structure was predicted, refined, and validated using bioinformatics tools. Protein-protein docking of the chimeric vaccine peptide with the TLR4 protein predicted efficient binding. Immune simulation predicted significantly high levels of IgG1, T-helper, T-cytotoxic cells, INF-γ, and IL-2. Overall, the constructed recombinant putative peptide demonstrated antigenicity superior to current vaccine candidates.
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Affiliation(s)
- Robert Adamu Shey
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Gosselies, Belgium.,Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Stephen Mbigha Ghogomu
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Kevin Kum Esoh
- Department of Biochemistry, Faculty of Science, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Neba Derrick Nebangwa
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Cabirou Mounchili Shintouo
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Nkemngo Francis Nongley
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Bertha Fru Asa
- Department of Public Health and Hygiene, Faculty of Health Science, University of Buea, Buea, Cameroon
| | - Ferdinand Njume Ngale
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Gosselies, Belgium.,Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Luc Vanhamme
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
| | - Jacob Souopgui
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Gosselies, Belgium.
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59
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Khan S, Parrillo M, Gutierrez AH, Terry FE, Moise L, Martin WD, De Groot AS. Immune escape and immune camouflage may reduce the efficacy of RTS,S vaccine in Malawi. Hum Vaccin Immunother 2019; 16:214-227. [PMID: 30614773 PMCID: PMC7062414 DOI: 10.1080/21645515.2018.1560772] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The RTS,S/AS01 malaria vaccine will undergo a pilot vaccination study in sub-Saharan Africa beginning in 2019. RTS,S/AS01 Phase III trials reported an efficacy of 28.3% (children 5–17 months) and 18.3% (infants 6–12 weeks), with substantial variability across study sites. We postulated that the relatively low efficacy of the RTS,S vaccine and variability across sites may be due to lack of T-cell epitopes in the vaccine antigen, and due to the HLA distribution of the vaccinated population, and/or due to ‘immune camouflage’, an immune escape mechanism. To examine these hypotheses, we used immunoinformatics tools to compare T helper epitopes contained in RTS,S vaccine antigens with Plasmodium falciparum circumsporozoite protein (CSP) variants isolated from infected individuals in Malawi. The prevalence of epitopes restricted by specific HLA-DRB1 alleles was inversely associated with prevalence of the HLA-DRB1 allele in the Malawi study population, suggesting immune escape. In addition, T-cell epitopes in the CSP of strains circulating in Malawi were more often restricted by low-frequency HLA-DRB1 alleles in the population. Furthermore, T-cell epitopes that were highly conserved across CSP variants in Malawi possessed TCR-facing residues that were highly conserved in the human proteome, potentially reducing T-cell help through tolerance. The CSP component of the RTS,S vaccine also exhibited a low degree of T-cell epitope relatedness to circulating variants. These results suggest that RTS,S vaccine efficacy may be impacted by low T-cell epitope content, reduced presentation of T-cell epitopes by prevalent HLA-DRB1, high potential for human-cross-reactivity, and limited conservation with the CSP of circulating malaria strains.
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Affiliation(s)
- Sundos Khan
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Matthew Parrillo
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | | | | | - Leonard Moise
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA.,EpiVax, Inc., Providence, RI, USA
| | | | - Anne S De Groot
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA.,EpiVax, Inc., Providence, RI, USA
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60
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Scholzen A, Richard G, Moise L, Baeten LA, Reeves PM, Martin WD, Brauns TA, Boyle CM, Raju Paul S, Bucala R, Bowen RA, Garritsen A, De Groot AS, Sluder AE, Poznansky MC. Promiscuous Coxiella burnetii CD4 Epitope Clusters Associated With Human Recall Responses Are Candidates for a Novel T-Cell Targeted Multi-Epitope Q Fever Vaccine. Front Immunol 2019; 10:207. [PMID: 30828331 PMCID: PMC6384241 DOI: 10.3389/fimmu.2019.00207] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/23/2019] [Indexed: 12/13/2022] Open
Abstract
Coxiella burnetii, the causative agent of Q fever, is a Gram-negative intracellular bacterium transmitted via aerosol. Regulatory approval of the Australian whole-cell vaccine Q-VAX® in the US and Europe is hindered by reactogenicity in previously exposed individuals. The aim of this study was to identify and rationally select C. burnetii epitopes for design of a safe, effective, and less reactogenic T-cell targeted human Q fever vaccine. Immunoinformatic methods were used to predict 65 HLA class I epitopes and 50 promiscuous HLA class II C. burnetii epitope clusters, which are conserved across strains of C. burnetii. HLA binding assays confirmed 89% of class I and 75% of class II predictions, and 11 HLA class II epitopes elicited IFNγ responses following heterologous DNA/DNA/peptide/peptide prime-boost immunizations of HLA-DR3 transgenic mice. Human immune responses to the predicted epitopes were characterized in individuals naturally exposed to C. burnetii during the 2007–2010 Dutch Q fever outbreak. Subjects were divided into three groups: controls with no immunological evidence of previous infection and individuals with responses to heat-killed C. burnetii in a whole blood IFNγ release assay (IGRA) who remained asymptomatic or who experienced clinical Q fever during the outbreak. Recall responses to C. burnetii epitopes were assessed by cultured IFNγ ELISpot. While HLA class I epitope responses were sparse in this cohort, we identified 21 HLA class II epitopes that recalled T-cell IFNγ responses in 10–28% of IGRA+ subjects. IGRA+ individuals with past asymptomatic and symptomatic C. burnetii infection showed a comparable response pattern and cumulative peptide response which correlated with IGRA responses. None of the peptides elicited reactogenicity in a C. burnetii exposure-primed guinea pig model. These data demonstrate that a substantial proportion of immunoinformatically identified HLA class II epitopes show long-lived immunoreactivity in naturally infected individuals, making them desirable candidates for a novel human multi-epitope Q fever vaccine.
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Affiliation(s)
| | | | - Leonard Moise
- EpiVax, Inc., Providence, RI, United States.,Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, United States
| | - Laurie A Baeten
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Patrick M Reeves
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
| | | | - Timothy A Brauns
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
| | | | - Susan Raju Paul
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
| | - Richard Bucala
- Department of Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Richard A Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | | | - Anne S De Groot
- EpiVax, Inc., Providence, RI, United States.,Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, United States
| | - Ann E Sluder
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
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61
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Shi W, Zhao L, Xu Y, Xu G, Zeng Y. Identification of mimotope of Mycoplasma pneumoniae P1 protein and its potential value in serodiagnosis. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1638299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Wenyuan Shi
- Department of Clinical Laboratory, Chenzhou First People's Hospital, Chenzhou, PR China
- Institute of Translational Medicine, University of South China, Chenzhou, PR China
- Chenzhou Hospital Affiliated to Southern Medical University, Chenzhou, PR China
| | - Lanhua Zhao
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, PR China
| | - Yujuan Xu
- Department of Clinical Laboratory, Chenzhou First People's Hospital, Chenzhou, PR China
- Institute of Translational Medicine, University of South China, Chenzhou, PR China
- Chenzhou Hospital Affiliated to Southern Medical University, Chenzhou, PR China
| | - Guizhen Xu
- Department of Clinical Laboratory, Chenzhou First People's Hospital, Chenzhou, PR China
- Institute of Translational Medicine, University of South China, Chenzhou, PR China
- Chenzhou Hospital Affiliated to Southern Medical University, Chenzhou, PR China
| | - Yanhua Zeng
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, PR China
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62
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Bragazzi NL, Gianfredi V, Villarini M, Rosselli R, Nasr A, Hussein A, Martini M, Behzadifar M. Vaccines Meet Big Data: State-of-the-Art and Future Prospects. From the Classical 3Is ("Isolate-Inactivate-Inject") Vaccinology 1.0 to Vaccinology 3.0, Vaccinomics, and Beyond: A Historical Overview. Front Public Health 2018; 6:62. [PMID: 29556492 PMCID: PMC5845111 DOI: 10.3389/fpubh.2018.00062] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 02/16/2018] [Indexed: 12/20/2022] Open
Abstract
Vaccines are public health interventions aimed at preventing infections-related mortality, morbidity, and disability. While vaccines have been successfully designed for those infectious diseases preventable by preexisting neutralizing specific antibodies, for other communicable diseases, additional immunological mechanisms should be elicited to achieve a full protection. “New vaccines” are particularly urgent in the nowadays society, in which economic growth, globalization, and immigration are leading to the emergence/reemergence of old and new infectious agents at the animal–human interface. Conventional vaccinology (the so-called “vaccinology 1.0”) was officially born in 1796 thanks to the contribution of Edward Jenner. Entering the twenty-first century, vaccinology has shifted from a classical discipline in which serendipity and the Pasteurian principle of the three Is (isolate, inactivate, and inject) played a major role to a science, characterized by a rational design and plan (“vaccinology 3.0”). This shift has been possible thanks to Big Data, characterized by different dimensions, such as high volume, velocity, and variety of data. Big Data sources include new cutting-edge, high-throughput technologies, electronic registries, social media, and social networks, among others. The current mini-review aims at exploring the potential roles as well as pitfalls and challenges of Big Data in shaping the future vaccinology, moving toward a tailored and personalized vaccine design and administration.
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Affiliation(s)
- Nicola Luigi Bragazzi
- Department of Health Sciences (DISSAL), School of Public Health, University of Genoa, Genoa, Italy
| | - Vincenza Gianfredi
- Department of Experimental Medicine, Unit of Public Health, School of Specialization in Hygiene and Preventive Medicine, University of Perugia, Perugia, Italy
| | - Milena Villarini
- Unit of Public Health, Department of Pharmaceutical Science, University of Perugia, Perugia, Italy
| | | | - Ahmed Nasr
- Department of Medicine and Surgery, Pathology University Milan Bicocca, San Gerardo Hospital, Monza, Italy
| | - Amr Hussein
- Medical Faculty, University of Parma, Parma, Italy
| | - Mariano Martini
- Section of History of Medicine and Ethics, Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Masoud Behzadifar
- Health Management and Economics Research Center, Iran University of Medical Sciences, Tehran, Iran
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63
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Negahdaripour M, Nezafat N, Eslami M, Ghoshoon MB, Shoolian E, Najafipour S, Morowvat MH, Dehshahri A, Erfani N, Ghasemi Y. Structural vaccinology considerations for in silico designing of a multi-epitope vaccine. INFECTION GENETICS AND EVOLUTION 2018; 58:96-109. [DOI: 10.1016/j.meegid.2017.12.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/05/2017] [Accepted: 12/11/2017] [Indexed: 01/26/2023]
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64
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Reeves PM, Paul SR, Sluder AE, Brauns TA, Poznansky MC. Q-vaxcelerate: A distributed development approach for a new Coxiella burnetii vaccine. Hum Vaccin Immunother 2017; 13:2977-2981. [PMID: 28933682 PMCID: PMC5718828 DOI: 10.1080/21645515.2017.1371377] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Development of vaccines that are both safe and effective remains a costly and time-consuming challenge. To accelerate the pace of development and improve the efficacy and safety of candidate vaccines for both existing and emerging infectious agents, we have used a distributed development approach. This features the managed integration of individual expert groups having the requisite vaccine platforms, pre-clinical models, assays, skills and knowledge pertinent to a specific pathogen into a single, end-to-end development team capable of producing a new vaccine tailored to that particular agent. Distributed development focuses on integrating existing effort across multiple institutions rather than developing new capabilities or consolidating resources within an individual organization. Previously we have used the distributed development strategy to generate vaccine candidates for emerging viral diseases. Coxiella burnetii is a highly infectious and resilient bacterium and the causative agent of Q fever. Treatment for Q fever can require months of antibiotics. The current vaccine for Q-fever is only approved in Australia and requires prescreening due to the potential for severe reactogenicity in previously exposed individuals. Here we discuss Q-VaxCelerate, a distributed development consortium for the development of a new vaccine to prevent Q fever.
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Affiliation(s)
- Patrick M Reeves
- a Vaccine and Immunotherapy Center, Division of Infectious Diseases, Department of Medicine , Massachusetts General Hospital , Boston , MA , USA
| | - Susan Raju Paul
- a Vaccine and Immunotherapy Center, Division of Infectious Diseases, Department of Medicine , Massachusetts General Hospital , Boston , MA , USA
| | - Ann E Sluder
- a Vaccine and Immunotherapy Center, Division of Infectious Diseases, Department of Medicine , Massachusetts General Hospital , Boston , MA , USA
| | - Timothy A Brauns
- a Vaccine and Immunotherapy Center, Division of Infectious Diseases, Department of Medicine , Massachusetts General Hospital , Boston , MA , USA
| | - Mark C Poznansky
- a Vaccine and Immunotherapy Center, Division of Infectious Diseases, Department of Medicine , Massachusetts General Hospital , Boston , MA , USA
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65
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66
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Nezafat N, Eslami M, Negahdaripour M, Rahbar MR, Ghasemi Y. Designing an efficient multi-epitope oral vaccine against Helicobacter pylori using immunoinformatics and structural vaccinology approaches. MOLECULAR BIOSYSTEMS 2017; 13:699-713. [PMID: 28194462 DOI: 10.1039/c6mb00772d] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Helicobacter pylori is the cunning bacterium that can live in the stomachs of many people without any symptoms, but gradually can lead to gastric cancer. Due to various obstacles, which are related to anti-H. pylori antibiotic therapy, recently developing an anti-H. pylori vaccine has attracted more attention. In this study, different immunoinformatics and computational vaccinology approaches were employed to design an efficient multi-epitope oral vaccine against H. pylori. Our multi-epitope vaccine is composed of heat labile enterotoxin IIc B (LT-IIc) that is used as a mucosal adjuvant to enhance vaccine immunogenicity for oral immunization, cartilage oligomeric matrix protein (COMP) to increase vaccine stability in acidic pH of gut, one experimentally protective antigen, OipA, and two hypothetical protective antigens, HP0487 and HP0906, and "CTGKSC" peptide motif that target epithelial microfold cells (M cells) to enhance vaccine uptake from the gut barrier. All the aforesaid segments were joined to each other by proper linkers. The vaccine construct was modeled, validated, and refined by different programs to achieve a high-quality 3D structure. The resulting high-quality model was applied for conformational B-cell epitopes selection and docking analyses with a toll-like receptor 2 (TLR2). Moreover, molecular dynamics studies demonstrated that the protein-TLR2 docked model was stable during simulation time. We believe that our vaccine candidate can induce mucosal sIgA and IgG antibodies, and Th1/Th2/Th17-mediated protective immunity that are crucial for eradicating H. pylori infection. In sum, the computational results suggest that our newly designed vaccine could serve as a promising anti-H. pylori vaccine candidate.
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Affiliation(s)
- Navid Nezafat
- Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Mahboobeh Eslami
- Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran and Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Mohammad Reza Rahbar
- Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran and Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Younes Ghasemi
- Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran and Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran. and Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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67
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A humanized mouse model identifies key amino acids for low immunogenicity of H7N9 vaccines. Sci Rep 2017; 7:1283. [PMID: 28455520 PMCID: PMC5430863 DOI: 10.1038/s41598-017-01372-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/29/2017] [Indexed: 11/30/2022] Open
Abstract
Influenza vaccines of H7N9 subtype are consistently less immunogenic in humans than vaccines developed for other subtypes. Although prior immunoinformatic analysis identified T-cell epitopes in H7 hemagglutinin (HA) which potentially enhance regulatory T cell response due to conservation with the human genome, the links between the T-cell epitopes and low immunogenicity of H7 HA remains unknown due to the lack of animal models reproducing the response observed in humans. Here, we utilized a humanized mouse model to recapitulate the low immunogenicity of H7 HA. Our analysis demonstrated that modification of a single H7 epitope by changing 3 amino acids so that it is homologous with a known H3 immunogenic epitope sequence significantly improved the immunogenicity of the H7 HA in the humanized mouse model, leading to a greater than 4-fold increase in HA-binding IgG responses. Thus, we provide experimental evidence for the important contribution of this H7-specific T cell epitope in determining the immunogenicity of an influenza vaccine. Furthermore, this study delineates strategies that can be used for screening and selecting vaccine strains using immunoinformatics tools and a humanized mouse model.
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68
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Stephen-Victor E, Bosschem I, Haesebrouck F, Bayry J. The Yin and Yang of regulatory T cells in infectious diseases and avenues to target them. Cell Microbiol 2017; 19. [DOI: 10.1111/cmi.12746] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Emmanuel Stephen-Victor
- Institut National de la Santé et de la Recherche Médicale; Paris France
- Centre de Recherche des Cordeliers; Equipe-Immunopathologie et Immunointervention Thérapeutique; Paris France
- Sorbonne Universités; Université Pierre et Marie Curie; Paris France
| | - Iris Bosschem
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine; Ghent University; Merelbeke Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine; Ghent University; Merelbeke Belgium
| | - Jagadeesh Bayry
- Institut National de la Santé et de la Recherche Médicale; Paris France
- Centre de Recherche des Cordeliers; Equipe-Immunopathologie et Immunointervention Thérapeutique; Paris France
- Sorbonne Universités; Université Pierre et Marie Curie; Paris France
- Université Paris Descartes; Sorbonne Paris Cité; Paris France
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69
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Heinson AI, Gunawardana Y, Moesker B, Hume CCD, Vataga E, Hall Y, Stylianou E, McShane H, Williams A, Niranjan M, Woelk CH. Enhancing the Biological Relevance of Machine Learning Classifiers for Reverse Vaccinology. Int J Mol Sci 2017; 18:ijms18020312. [PMID: 28157153 PMCID: PMC5343848 DOI: 10.3390/ijms18020312] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/17/2017] [Indexed: 12/11/2022] Open
Abstract
Reverse vaccinology (RV) is a bioinformatics approach that can predict antigens with protective potential from the protein coding genomes of bacterial pathogens for subunit vaccine design. RV has become firmly established following the development of the BEXSERO® vaccine against Neisseria meningitidis serogroup B. RV studies have begun to incorporate machine learning (ML) techniques to distinguish bacterial protective antigens (BPAs) from non-BPAs. This research contributes significantly to the RV field by using permutation analysis to demonstrate that a signal for protective antigens can be curated from published data. Furthermore, the effects of the following on an ML approach to RV were also assessed: nested cross-validation, balancing selection of non-BPAs for subcellular localization, increasing the training data, and incorporating greater numbers of protein annotation tools for feature generation. These enhancements yielded a support vector machine (SVM) classifier that could discriminate BPAs (n = 200) from non-BPAs (n = 200) with an area under the curve (AUC) of 0.787. In addition, hierarchical clustering of BPAs revealed that intracellular BPAs clustered separately from extracellular BPAs. However, no immediate benefit was derived when training SVM classifiers on data sets exclusively containing intra- or extracellular BPAs. In conclusion, this work demonstrates that ML classifiers have great utility in RV approaches and will lead to new subunit vaccines in the future.
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Affiliation(s)
- Ashley I Heinson
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK.
| | | | - Bastiaan Moesker
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK.
| | - Carmen C Denman Hume
- London School of Hygiene and Tropical Medicine (LSHTM), Department of Pathogen Molecular BiologyLondon WC1E 7HT, UK.
| | - Elena Vataga
- Solutions, University of Southampton, Southampton SO17 1BJ, UK.
| | - Yper Hall
- Public Health England, National Infection Service, Porton Down Salisbury, SP4 0JG, UK.
| | - Elena Stylianou
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK.
| | - Helen McShane
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK.
| | - Ann Williams
- Public Health England, National Infection Service, Porton Down Salisbury, SP4 0JG, UK.
| | - Mahesan Niranjan
- Department of Electronics and Computer Science, University of Southampton, Southampton SO17 1BJ, UK.
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70
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Ahmad TA, Eweida AE, El-Sayed LH. T-cell epitope mapping for the design of powerful vaccines. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.vacrep.2016.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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71
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De Groot AS, Moise L, Olive D, Einck L, Martin W. Agility in adversity: Vaccines on Demand. Expert Rev Vaccines 2016; 15:1087-91. [PMID: 27389971 DOI: 10.1080/14760584.2016.1205951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Is the US ready for a biological attack using Ebola virus or Anthrax? Will vaccine developers be able to produce a Zika virus vaccine, before the epidemic spreads around the world? A recent report by The Blue Ribbon Study Panel on Biodefense argues that the US is not ready for these challenges, however, technologies and capabilities that could address these deficiencies are within reach. Vaccine technologies have advanced and readiness has improved in recent years, due to advances in sequencing technology and computational power making the 'vaccines on demand' concept a reality. Building a robust strategy to design effective biodefense vaccines from genome sequences harvested by real-time biosurveillance will benefit from technologies that are being brought to bear on the cancer cure 'moonshot'. When combined with flexible vaccine production platforms, vaccines on demand will relegate expensive and, in some cases, insufficiently effective vaccine stockpiles to the dust heap of history.
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Affiliation(s)
- Anne S De Groot
- a EpiVax, Inc. , Providence , RI , USA.,b Institute for Immunology and Informatics , University of Rhode Island , Providence , RI , USA
| | - Leonard Moise
- a EpiVax, Inc. , Providence , RI , USA.,b Institute for Immunology and Informatics , University of Rhode Island , Providence , RI , USA
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72
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Host-directed therapies for antimicrobial resistant respiratory tract infections. Curr Opin Pulm Med 2016; 22:203-11. [DOI: 10.1097/mcp.0000000000000271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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73
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Kumar S, Thangakani AM, Nagarajan R, Singh SK, Velmurugan D, Gromiha MM. Autoimmune Responses to Soluble Aggregates of Amyloidogenic Proteins Involved in Neurodegenerative Diseases: Overlapping Aggregation Prone and Autoimmunogenic regions. Sci Rep 2016; 6:22258. [PMID: 26924748 PMCID: PMC4770294 DOI: 10.1038/srep22258] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/10/2016] [Indexed: 12/21/2022] Open
Abstract
Why do patients suffering from neurodegenerative diseases generate autoantibodies that selectively bind soluble aggregates of amyloidogenic proteins? Presently, molecular basis of interactions between the soluble aggregates and human immune system is unknown. By analyzing sequences of experimentally validated T-cell autoimmune epitopes, aggregating peptides, amyloidogenic proteins and randomly generated peptides, here we report overlapping regions that likely drive aggregation as well as generate autoantibodies against the aggregates. Sequence features, that make short peptides susceptible to aggregation, increase their incidence in human T-cell autoimmune epitopes by 4–6 times. Many epitopes are predicted to be significantly aggregation prone (aggregation propensities ≥10%) and the ones containing experimentally validated aggregating regions are enriched in hydrophobicity by 10–20%. Aggregate morphologies also influence Human Leukocyte Antigen (HLA) - types recognized by the aggregating regions containing epitopes. Most (88%) epitopes that contain amyloid fibril forming regions bind HLA-DR, while majority (63%) of those containing amorphous β-aggregating regions bind HLA-DQ. More than two-thirds (70%) of human amyloidogenic proteins contain overlapping regions that are simultaneously aggregation prone and auto-immunogenic. Such regions help clear soluble aggregates by generating selective autoantibodies against them. This can be harnessed for early diagnosis of proteinopathies and for drug/vaccine design against them.
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Affiliation(s)
- Sandeep Kumar
- Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield MO 63017, USA
| | - A Mary Thangakani
- Center for Advanced Studies in Crystallography and Biophysics and Bioinformatics Infrastructure Facility, University of Madras, Chennai 600025, India
| | - R Nagarajan
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Satish K Singh
- Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield MO 63017, USA
| | - D Velmurugan
- Center for Advanced Studies in Crystallography and Biophysics and Bioinformatics Infrastructure Facility, University of Madras, Chennai 600025, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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Moise L, Beseme S, Tassone R, Liu R, Kibria F, Terry F, Martin W, De Groot AS. T cell epitope redundancy: cross-conservation of the TCR face between pathogens and self and its implications for vaccines and autoimmunity. Expert Rev Vaccines 2016; 15:607-17. [PMID: 26588466 DOI: 10.1586/14760584.2016.1123098] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
T cells are extensively trained on 'self' in the thymus and then move to the periphery, where they seek out and destroy infections and regulate immune response to self-antigens. T cell receptors (TCRs) on T cells' surface recognize T cell epitopes, short linear strings of amino acids presented by antigen-presenting cells. Some of these epitopes activate T effectors, while others activate regulatory T cells. It was recently discovered that T cell epitopes that are highly conserved on their TCR face with human genome sequences are often associated with T cells that regulate immune response. These TCR-cross-conserved or 'redundant epitopes' are more common in proteins found in pathogens that have co-evolved with humans than in other non-commensal pathogens. Epitope redundancy might be the link between pathogens and autoimmune disease. This article reviews recently published data and addresses epitope redundancy, the "elephant in the room" for vaccine developers and T cell immunologists.
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Affiliation(s)
- Leonard Moise
- a EpiVax, Inc ., Providence , RI , USA.,b Institute for Immunology and Informatics , University of Rhode Island , Providence , RI , USA
| | | | - Ryan Tassone
- b Institute for Immunology and Informatics , University of Rhode Island , Providence , RI , USA
| | - Rui Liu
- b Institute for Immunology and Informatics , University of Rhode Island , Providence , RI , USA
| | | | | | | | - Anne S De Groot
- a EpiVax, Inc ., Providence , RI , USA.,b Institute for Immunology and Informatics , University of Rhode Island , Providence , RI , USA
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Valdivia-Olarte H, Requena D, Ramirez M, Saravia LE, Izquierdo R, Falconi-Agapito F, Zavaleta M, Best I, Fernández-Díaz M, Zimic M. Design of a predicted MHC restricted short peptide immunodiagnostic and vaccine candidate for Fowl adenovirus C in chicken infection. Bioinformation 2015; 11:460-5. [PMID: 26664030 PMCID: PMC4658644 DOI: 10.6026/97320630011460] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/18/2015] [Indexed: 11/23/2022] Open
Abstract
Fowl adenoviruses (FAdVs) are the ethiologic agents of multiple pathologies in chicken. There are five different species of FAdVs grouped as FAdV-A, FAdV-B, FAdV-C, FAdV-D, and FAdV-E. It is of interest to develop immunodiagnostics and vaccine candidate for Peruvian FAdV-C in chicken infection using MHC restricted short peptide candidates. We sequenced the complete genome of one FAdV strain isolated from a chicken of a local farm. A total of 44 protein coding genes were identified in each genome. We sequenced twelve Cobb chicken MHC alleles from animals of different farms in the central coast of Peru, and subsequently determined three optimal human MHC-I and four optimal human MHC-II substitute alleles for MHC-peptide prediction. The potential MHC restricted short peptide epitope-like candidates were predicted using human specific (with determined suitable chicken substitutes) NetMHC MHC-peptide prediction model with web server features from all the FAdV genomes available. FAdV specific peptides with calculated binding values to known substituted chicken MHC-I and MHC-II were further filtered for diagnostics and potential vaccine epitopes. Promiscuity to the 3/4 optimal human MHC-I/II alleles and conservation among the available FAdV genomes was considered in this analysis. The localization on the surface of the protein was considered for class II predicted peptides. Thus, a set of class I and class II specific peptides from FAdV were reported in this study. Hence, a multiepitopic protein was built with these peptides, and subsequently tested to confirm the production of specific antibodies in chicken.
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Affiliation(s)
- Hugo Valdivia-Olarte
- Farvet s.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta. Ica – Peru
- Laboratorio de Bioinformática y Biologáa
Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofáa, Universidad Peruana Cayetano Heredia,
Av. Honorio Delgado 430, San Martin de Porres. Lima – Peru
| | - David Requena
- Farvet s.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta. Ica – Peru
- Laboratorio de Bioinformática y Biologáa
Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofáa, Universidad Peruana Cayetano Heredia,
Av. Honorio Delgado 430, San Martin de Porres. Lima – Peru
| | - Manuel Ramirez
- Farvet s.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta. Ica – Peru
- Laboratorio de Bioinformática y Biologáa
Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofáa, Universidad Peruana Cayetano Heredia,
Av. Honorio Delgado 430, San Martin de Porres. Lima – Peru
| | - Luis E Saravia
- Farvet s.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta. Ica – Peru
| | - Ray Izquierdo
- Farvet s.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta. Ica – Peru
| | | | - Milagros Zavaleta
- Farvet s.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta. Ica – Peru
| | - Iván Best
- Farvet s.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta. Ica – Peru
| | | | - Mirko Zimic
- Farvet s.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta. Ica – Peru
- Laboratorio de Bioinformática y Biologáa
Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofáa, Universidad Peruana Cayetano Heredia,
Av. Honorio Delgado 430, San Martin de Porres. Lima – Peru
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