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Kisakov DN, Antonets DV, Shaburova EV, Kisakova LA, Tigeeva EV, Yakovlev VA, Starostina EV, Borgoyakova MB, Protopopova EV, Svyatchenko VA, Loktev VB, Rudometov AP, Ilyichev AA, Nepomnyashchikh TS, Karpenko LI. DNA Vaccine Encoding the Artificial T-Cell Polyepitope Immunogen of Tick-Borne Encephalitis Virus. Bull Exp Biol Med 2023; 176:72-76. [PMID: 38091143 DOI: 10.1007/s10517-023-05970-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Indexed: 12/19/2023]
Abstract
A promising approach to the development of new means for preventing infection caused by tick-borne encephalitis virus can be DNA vaccines encoding polyepitope T-cell immunogens. A DNA vaccine pVAX-AG4-ub encoding an artificial polyepitope immunogen that includes cytotoxic and T-helper epitopes from the NS1, NS3, NS5, and E proteins of the tick-borne encephalitis virus has been obtained. The developed construct ensured the synthesis of the corresponding mRNAs in transfected eukaryotic cells. Immunization of mice with pVAX-AG4-ub induced the formation of a virus-specific T-cell response providing 50% protection from lethal infection with the virus.
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Affiliation(s)
- D N Kisakov
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia.
| | - D V Antonets
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - E V Shaburova
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - L A Kisakova
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - E V Tigeeva
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - V A Yakovlev
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - E V Starostina
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - M B Borgoyakova
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - E V Protopopova
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - V A Svyatchenko
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - V B Loktev
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - A P Rudometov
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - A A Ilyichev
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - T S Nepomnyashchikh
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - L I Karpenko
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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3
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Karpenko LI, Apartsin EK, Dudko SG, Starostina EV, Kaplina ON, Antonets DV, Volosnikova EA, Zaitsev BN, Bakulina AY, Venyaminova AG, Ilyichev AA, Bazhan SI. Cationic Polymers for the Delivery of the Ebola DNA Vaccine Encoding Artificial T-Cell Immunogen. Vaccines (Basel) 2020; 8:vaccines8040718. [PMID: 33271964 PMCID: PMC7760684 DOI: 10.3390/vaccines8040718] [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: 11/02/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 11/16/2022] Open
Abstract
Background: According to current data, an effective Ebola virus vaccine should induce both humoral and T-cell immunity. In this work, we focused our efforts on methods for delivering artificial T-cell immunogen in the form of a DNA vaccine, using generation 4 polyamidoamine dendrimers (PAMAM G4) and a polyglucin:spermidine conjugate (PG). Methods: Optimal conditions were selected for obtaining complexes of previously developed DNA vaccines with cationic polymers. The sizes, mobility and surface charge of the complexes with PG and PAMAM 4G have been determined. The immunogenicity of the obtained vaccine constructs was investigated in BALB/c mice. Results: It was shown that packaging of DNA vaccine constructs both in the PG envelope and the PAMAM 4G envelope results in an increase in their immunogenicity as compared with the group of mice immunized with the of vector plasmid pcDNA3.1 (a negative control). The highest T-cell responses were shown in mice immunized with complexes of DNA vaccines with PG and these responses significantly exceeded those in the groups of animals immunized with both the combination of naked DNAs and the combination DNAs coated with PAMAM 4G. In the group of animals immunized with complexes of the DNA vaccines with PAMAM 4G, no statistical differences were found in the ability to induce T-cell responses, as compared with the group of mice immunized with the combination of naked DNAs. Conclusions: The PG conjugate can be considered as a promising and safe means to deliver DNA-based vaccines. The use of PAMAM requires further optimization.
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Affiliation(s)
- Larisa I. Karpenko
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
- Correspondence: (L.I.K.); (S.I.B.); Tel.: +7-383-363-47-00 (ext. 2001) (L.I.K. & S.I.B.)
| | - Evgeny K. Apartsin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.K.A.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Laboratoire de Chimie de Coordination, CNRS, 31077 Toulouse, France
| | - Sergei G. Dudko
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Ekaterina V. Starostina
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Olga N. Kaplina
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Denis V. Antonets
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Ekaterina A. Volosnikova
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Boris N. Zaitsev
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Anastasiya Yu. Bakulina
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aliya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.K.A.); (A.G.V.)
| | - Alexander A. Ilyichev
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Sergei I. Bazhan
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
- Correspondence: (L.I.K.); (S.I.B.); Tel.: +7-383-363-47-00 (ext. 2001) (L.I.K. & S.I.B.)
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Bazhan SI, Antonets DV, Starostina EV, Ilyicheva TN, Kaplina ON, Marchenko VY, Volkova OY, Bakulina AY, Karpenko LI. In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice. J Biomol Struct Dyn 2020; 40:3196-3212. [PMID: 33222632 DOI: 10.1080/07391102.2020.1845978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The polyepitope strategy is promising approach for successfully creating a broadly protective flu vaccine, which targets T-lymphocytes (both CD4+ and CD8+) to recognise the most conserved epitopes of viral proteins. In this study, we employed a computer-aided approach to develop several artificial antigens potentially capable of evoking immune responses to different virus subtypes. These antigens included conservative T-cell epitopes of different influenza A virus proteins. To design epitope-based antigens we used experimentally verified information regarding influenza virus T-cell epitopes from the Immune Epitope Database (IEDB) (http://www.iedb.org). We constructed two "human" and two "murine" variants of polyepitope antigens. Amino acid sequences of target polyepitope antigens were designed using our original TEpredict/PolyCTLDesigner software. Immunogenic and protective features of DNA constructs encoding "murine" target T-cell immunogens were studied in BALB/c mice. We showed that mice groups immunised with a combination of computer-generated "murine" DNA immunogens had a 37.5% survival rate after receiving a lethal dose of either A/California/4/2009 (H1N1) virus or A/Aichi/2/68 (H3N2) virus, while immunisation with live flu H1N1 and H3N2 vaccine strains provided protection against homologous viruses and failed to protect against heterologous viruses. These results demonstrate that mechanisms of cross-protective immunity may be associated with the stimulation of specific T-cell responses. This study demonstrates that our computer-aided approach may be successfully used for rational designing artificial polyepitope antigens capable of inducing virus-specific T-lymphocyte responses and providing partial protection against two different influenza virus subtypes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sergei I Bazhan
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Denis V Antonets
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Ekaterina V Starostina
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Tatyana N Ilyicheva
- Department of zoonotic infections and Influenza, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Olga N Kaplina
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Vasiliy Yu Marchenko
- Department of zoonotic infections and Influenza, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Olga Yu Volkova
- Immunogenetics laboratory, Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya Yu Bakulina
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia.,Laboratory of structural bioinformatics and molecular modeling, Novosibirsk State University, Novosibirsk, Russia
| | - Larisa I Karpenko
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
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Ortega-Tirado D, Arvizu-Flores AA, Velazquez C, Garibay-Escobar A. The role of immunoinformatics in the development of T-cell peptide-based vaccines against Mycobacterium tuberculosis. Expert Rev Vaccines 2020; 19:831-841. [PMID: 32945209 DOI: 10.1080/14760584.2020.1825950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Tuberculosis (TB) is a major health problem worldwide. The BCG, the only authorized vaccine to fight TB, shows a variable protection in the adult population highlighting the need of a new vaccine. Immunoinformatics offers a variety of tools that can predict immunogenic T-cell peptides of Mycobacterium tuberculosis (Mtb) that can be used to create a new vaccine. Immunoinformatics has made possible the identification of immunogenic T-cell peptides of Mtb that have been tested in vitro showing a potential for using these molecules as part of a new TB vaccine. AREAS COVERED This review summarizes the most common immunoinformatics tools to identify immunogenic T-cell peptides and presents a compilation about research studies that have identified T-cell peptides of Mtb by using immunoinformatics. Also, it is provided a summary of the TB vaccines undergoing clinical trials. EXPERT OPINION In the next few years, the field of peptide-based vaccines will keep growing along with the development of more efficient and sophisticated immunoinformatic tools to identify immunogenic peptides with a greater accuracy.
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Affiliation(s)
- David Ortega-Tirado
- Departamento De Ciencias Químico Biológicas Universidad De Sonora , Hermosillo, Sonora, México
| | - Aldo A Arvizu-Flores
- Departamento De Ciencias Químico Biológicas Universidad De Sonora , Hermosillo, Sonora, México
| | - Carlos Velazquez
- Departamento De Ciencias Químico Biológicas Universidad De Sonora , Hermosillo, Sonora, México
| | - Adriana Garibay-Escobar
- Departamento De Ciencias Químico Biológicas Universidad De Sonora , Hermosillo, Sonora, México
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In silico Designed Ebola Virus T-Cell Multi-Epitope DNA Vaccine Constructions Are Immunogenic in Mice. Vaccines (Basel) 2019; 7:vaccines7020034. [PMID: 30934980 PMCID: PMC6630745 DOI: 10.3390/vaccines7020034] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/16/2022] Open
Abstract
Background: The lack of effective vaccines against Ebola virus initiates a search for new approaches to overcoming this problem. The aim of the study was to design artificial polyepitope T-cell immunogens⁻⁻candidate DNA vaccines against Ebola virus and to evaluate their capacity to induce a specific immune response in a laboratory animal model. Method: Design of two artificial polyepitope T-cell immunogens, one of which (EV.CTL) includes cytotoxic and the other (EV.Th)⁻⁻T-helper epitopes of Ebola virus proteins was carried out using original TEpredict/PolyCTLDesigner software. Synthesized genes were cloned in pcDNA3.1 plasmid vector. Target gene expression was estimated by synthesis of specific mRNAs and proteins in cells transfected with recombinant plasmids. Immunogenicity of obtained DNA vaccine constructs was evaluated according to their capacity to induce T-cell response in BALB/c mice using IFNγ ELISpot and ICS. Results: We show that recombinant plasmids pEV.CTL and pEV.Th encoding artificial antigens provide synthesis of corresponding mRNAs and proteins in transfected cells, as well as induce specific responses both to CD4+ and CD8+ T-lymphocytes in immunized animals. Conclusions: The obtained recombinant plasmids can be regarded as promising DNA vaccine candidates in future studies of their capacity to induce cytotoxic and protective responses against Ebola virus.
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Kar P, Ruiz-Perez L, Arooj M, Mancera RL. Current methods for the prediction of T-cell epitopes. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Prattusha Kar
- School of Pharmacy and Biomedical Sciences; Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University; Perth Western Australia 6845 Australia
| | - Lanie Ruiz-Perez
- School of Pharmacy and Biomedical Sciences; Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University; Perth Western Australia 6845 Australia
| | - Mahreen Arooj
- School of Pharmacy and Biomedical Sciences; Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University; Perth Western Australia 6845 Australia
| | - Ricardo L. Mancera
- School of Pharmacy and Biomedical Sciences; Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University; Perth Western Australia 6845 Australia
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8
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Identification and evaluation of the novel immunodominant antigen Rv2351c from Mycobacterium tuberculosis. Emerg Microbes Infect 2017; 6:e48. [PMID: 28588287 PMCID: PMC5520311 DOI: 10.1038/emi.2017.34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 03/06/2017] [Accepted: 04/09/2017] [Indexed: 11/19/2022]
Abstract
There is an urgent need for new immunodominant antigens to improve the diagnosis of tuberculosis (TB) and the efficacy of the TB vaccine to control the disease worldwide. In this study, we evaluated the diagnostic potential of a novel Mycobacterium tuberculosis (MTB)-specific antigen, Rv2351c, from region of difference (RD) 7 of the MTB genome, and investigated the potency of the vaccine by identifying its immunological function in human and animal immunological experiments. Twenty T-cell epitopes were identified using TEpredict and prediction tools from the Immune Epitope Database and Analysis Resource. A total of 159 subjects, including 61 patients with pulmonary TB, 38 patients with no TB and 55 healthy donors, were recruited and analyzed with an enzyme-linked immunospot (ELISpot) assay. The ELISpot assay using Rv2351c to detect TB infection, as compared with bacteriological tests as the gold standard, had a sensitivity and specificity of 61.4% (35/57) and 91.4% (85/93), respectively. The ELISpot assay using Rv2351c had a good conformance (κ=0.554) as compared with the bacteriological test. Rv2351c also elicited a potent cellular immune response with a high expression of cytokines (IFN-γ (4978±596.7 μg/mL) and IL-4 (68.3±15.5 μg/mL)) and a potent humoral immune response with a high concentration of IgG (1:2.2 × 106), IgG1 (1:4.5 × 105) and IgG2a (1:1.6 × 106) in immunized BALB/c mice. In addition, the ratio of IgG2a/IgG1 indicated that Rv2351c induced cellular immunity in the mice. The results of this study indicated that Rv2351c is an antigen with good immunogenicity that may potentially be used to develop diagnostic techniques and new TB vaccines.
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9
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Reguzova A, Antonets D, Karpenko L, Ilyichev A, Maksyutov R, Bazhan S. Design and evaluation of optimized artificial HIV-1 poly-T cell-epitope immunogens. PLoS One 2015; 10:e0116412. [PMID: 25786238 PMCID: PMC4364888 DOI: 10.1371/journal.pone.0116412] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 12/09/2014] [Indexed: 11/18/2022] Open
Abstract
A successful HIV vaccine in addition to induction of antibody responses should elicit effective T cell responses. Here we described possible strategies for rational design of T-cell vaccine capable to induce high levels of both CD4+ and CD8+ T- cell responses. We developed artificial HIV-1 polyepitope T-cell immunogens based on the conserved natural CD8+ and CD4+ T cell epitopes from different HIV-1 strains and restricted by the most frequent major human leukocyte antigen (HLA) alleles. Designed immunogens contain optimized core polyepitope sequence and additional "signal" sequences which increase epitope processing and presentation to CD8+ and CD4+ T-lymphocytes: N-terminal ubiquitin, N-terminal signal peptide and C-terminal tyrosine motif of LAMP-1 protein. As a result we engineered three T cell immunogens - TCI-N, TCI-N2, and TCI-N3, with different combinations of signal sequences. All designed immunogens were able to elicit HIV-specific CD4+ and CD8+ T cell responses following immunization. Attachment of either ubiquitin or ER-signal/LAMP-1 sequences increased both CD4+ and CD8+ mediated HIV-specific T cell responses in comparison with polyepitope immunogen without any additional signal sequences. Moreover, TCI-N3 polyepitope immunogen with ubiquitin generated highest magnitude of HIV-specific CD4+ and CD8+ T cell responses in our study. Obtained data suggests that attachment of signal sequences targeting polyepitope immunogens to either MHC class I or MHC class II presentation pathways may improve immunogenicity of T-cell vaccines. These results support the strategy of the rational T cell immunogen design and contribute to the development of effective HIV-1 vaccine.
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Affiliation(s)
- Alena Reguzova
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk region, 630559, Russia
| | - Denis Antonets
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk region, 630559, Russia
| | - Larisa Karpenko
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk region, 630559, Russia
| | - Alexander Ilyichev
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk region, 630559, Russia
| | - Rinat Maksyutov
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk region, 630559, Russia
| | - Sergei Bazhan
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk region, 630559, Russia
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10
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Karpenko LI, Bazhan SI, Antonets DV, Belyakov IM. Novel approaches in polyepitope T-cell vaccine development against HIV-1. Expert Rev Vaccines 2013; 13:155-73. [PMID: 24308576 DOI: 10.1586/14760584.2014.861748] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
RV144 clinical trial was modestly effective in preventing HIV infection. New alternative approaches are needed to design improved HIV-1 vaccines and their delivery strategies. One of these approaches is construction of synthetic polyepitope HIV-1 immunogen using protective T- and B-cell epitopes that can induce broadly neutralizing antibodies and responses of cytotoxic (CD8(+) CTL) and helpers (CD4(+) Th) T-lymphocytes. This approach seems to be promising for designing of new generation of vaccines against HIV-1, enables in theory to cope with HIV-1 antigenic variability, focuses immune responses on protective determinants and enables to exclude from the vaccine compound that can induce autoantibodies or antibodies enhancing HIV-1 infectivity. Herein, the authors will focus on construction and rational design of polyepitope T-cell HIV-1 immunogens and their delivery, including: advantages and disadvantages of existing T-cell epitope prediction methods; features of organization of polyepitope immunogens, which can generate high-level CD8(+) and CD4(+) T-lymphocyte responses; the strategies to optimize efficient processing, presentation and immunogenicity of polyepitope constructs; original software to design polyepitope immunogens; and delivery vectors as well as mucosal strategies of vaccination. This new knowledge may bring us a one step closer to developing an effective T-cell vaccine against HIV-1, other chronic viral infections and cancer.
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Affiliation(s)
- Larisa I Karpenko
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region, 630559, Russia
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Antonets DV, Bazhan SI. PolyCTLDesigner: a computational tool for constructing polyepitope T-cell antigens. BMC Res Notes 2013; 6:407. [PMID: 24107711 PMCID: PMC3853014 DOI: 10.1186/1756-0500-6-407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 09/24/2013] [Indexed: 11/10/2022] Open
Abstract
Background Construction of artificial polyepitope antigens is one of the most promising strategies for developing more efficient and safer vaccines evoking T-cell immune responses. Epitope rearrangements and utilization of certain spacer sequences have been proven to greatly influence the immunogenicity of polyepitope constructs. However, despite numerous efforts towards constructing and evaluating artificial polyepitope immunogens as well as despite numerous computational methods elaborated to date for predicting T-cell epitopes, peptides binding to TAP and for antigen processing prediction, only a few computational tools were currently developed for rational design of polyepitope antigens. Findings Here we present a PolyCTLDesigner program that is intended for constructing polyepitope immunogens. Given a set of either known or predicted T-cell epitopes the program selects N-terminal flanking sequences for each epitope to optimize its binding to TAP (if necessary) and joins resulting oligopeptides into a polyepitope in a way providing efficient liberation of potential epitopes by proteasomal and/or immunoproteasomal processing. And it also tries to minimize the number of non-target junctional epitopes resulting from artificial juxtaposition of target epitopes within the polyepitope. For constructing polyepitopes, PolyCTLDesigner utilizes known amino acid patterns of TAP-binding and proteasomal/immunoproteasomal cleavage specificity together with genetic algorithm and graph theory approaches. The program was implemented using Python programming language and it can be used either interactively or through scripting, which allows users familiar with Python to create custom pipelines. Conclusions The developed software realizes a rational approach to designing poly-CTL-epitope antigens and can be used to develop new candidate polyepitope vaccines. The current version of PolyCTLDesigner is integrated with our TEpredict program for predicting T-cell epitopes, and thus it can be used not only for constructing the polyepitope antigens based on preselected sets of T-cell epitopes, but also for predicting cytotoxic and helper T-cell epitopes within selected protein antigens. PolyCTLDesigner is freely available from the project’s web site: http://tepredict.sourceforge.net/PolyCTLDesigner.html.
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Affiliation(s)
- Denis V Antonets
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russian Federation.
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