1
|
Heidarnejad F, Namvar A, Sadat SM, Pordanjani PM, Rezaei F, Namdari H, Arjmand S, Bolhassani A. In silico designing of novel epitope-based peptide vaccines against HIV-1. Biotechnol Lett 2024; 46:315-354. [PMID: 38403788 DOI: 10.1007/s10529-023-03464-x] [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: 04/20/2023] [Revised: 11/16/2023] [Accepted: 12/21/2023] [Indexed: 02/27/2024]
Abstract
The HIV-1 virus has been regarded as a catastrophe for human well-being. The global incidence of HIV-1-infected individuals is increasing. Hence, development of effective immunostimulatory molecules has recently attracted an increasing attention in the field of vaccine design against HIV-1 infection. In this study, we explored the impacts of CD40L and IFN-γ as immunostimulatory adjuvants for our candidate HIV-1 Nef vaccine in human and mouse using immunoinformatics analyses. Overall, 18 IFN-γ-based vaccine constructs (9 constructs in human and 9 constructs in mouse), and 18 CD40L-based vaccine constructs (9 constructs in human and 9 constructs in mouse) were designed. To find immunogenic epitopes, important characteristics of each component (e.g., MHC-I and MHC-II binding, and peptide-MHC-I/MHC-II molecular docking) were determined. Then, the selected epitopes were applied to create multiepitope constructs. Finally, the physicochemical properties, linear and discontinuous B cell epitopes, and molecular interaction between the 3D structure of each construct and CD40, IFN-γ receptor or toll-like receptors (TLRs) were predicted. Our data showed that the full-length CD40L and IFN-γ linked to the N-terminal region of Nef were capable of inducing more effective immune response than multiepitope vaccine constructs. Moreover, molecular docking of the non-allergenic full-length- and epitope-based CD40L and IFN-γ constructs to their cognate receptors, CD40 and IFN-γ receptors, and TLRs 4 and 5 in mouse were more potent than in human. Generally, these findings suggest that the full forms of these adjuvants could be more efficient for improvement of HIV-1 Nef vaccine candidate compared to the designed multiepitope-based constructs.
Collapse
Affiliation(s)
| | - Ali Namvar
- Iranian Comprehensive Hemophilia Care Center, Tehran, Iran
| | - Seyed Mehdi Sadat
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Rezaei
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Haideh Namdari
- Iranian Tissue Bank Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sina Arjmand
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
2
|
Kaur A, Vaccari M. Exploring HIV Vaccine Progress in the Pre-Clinical and Clinical Setting: From History to Future Prospects. Viruses 2024; 16:368. [PMID: 38543734 PMCID: PMC10974975 DOI: 10.3390/v16030368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 04/01/2024] Open
Abstract
The human immunodeficiency virus (HIV) continues to pose a significant global health challenge, with millions of people affected and new cases emerging each year. While various treatment and prevention methods exist, including antiretroviral therapy and non-vaccine approaches, developing an effective vaccine remains the most crucial and cost-effective solution to combating the HIV epidemic. Despite significant advancements in HIV research, the HIV vaccine field has faced numerous challenges, and only one clinical trial has demonstrated a modest level of efficacy. This review delves into the history of HIV vaccines and the current efforts in HIV prevention, emphasizing pre-clinical vaccine development using the non-human primate model (NHP) of HIV infection. NHP models offer valuable insights into potential preventive strategies for combating HIV, and they play a vital role in informing and guiding the development of novel vaccine candidates before they can proceed to human clinical trials.
Collapse
Affiliation(s)
- Amitinder Kaur
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA;
- School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Monica Vaccari
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA;
- School of Medicine, Tulane University, New Orleans, LA 70112, USA
| |
Collapse
|
3
|
Heidarnejad F, Bolhassani A, Ajdary S, Milani A, Sadeghi SA. Investigation of Immunostimulatory Effects of IFN-γ Cytokine and CD40 Ligand Costimulatory Molecule for Development of HIV-1 Therapeutic Vaccine Candidate. Adv Biol (Weinh) 2024; 8:e2300402. [PMID: 37840398 DOI: 10.1002/adbi.202300402] [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: 08/03/2023] [Revised: 09/22/2023] [Indexed: 10/17/2023]
Abstract
The most crucial disadvantage of DNA-based vaccines is their low immunogenicity; therefore, finding an effectual adjuvant is essential for their development. Herein, immunostimulatory effects of IFNγ cytokine and a CD40 ligand (CD40L) costimulatory molecule are evaluated as combined with an antigen, and also linked to an antigen in mice. For this purpose, after preparation of the HIV-1 Nef, IFNγ, and CD40L DNA constructs, and also their recombinant protein in an Escherichia coli expression system, nine groups of female BALB/c mice are immunized with different regimens of DNA constructs. About 3 weeks and also 3 months after the last injection, humoral and cellular immune responses are assessed in mice sera and splenocytes. Additionally, mice splenocytes are exposed to single-cycle replicable (SCR) HIV-1 virions for evaluating their potency in the secretion of cytokines in vitro. The data indicate that the linkage of IFNγ and CD40L to Nef antigen can significantly induce the Th-1 pathway and activate cytotoxic T lymphocytes compared to other regimens. Moreover, groups receiving the IFNγ-Nef and CD40L-Nef fusion DNA constructs show higher secretion of IFNγ and TNF-α from virion-infected lymphocytes than other groups. Therefore, the IFNγ-Nef and CD40L-Nef fusion DNA constructs are suggested to be a potential option for development of an efficient HIV-1 vaccine.
Collapse
Affiliation(s)
- Fatemeh Heidarnejad
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, 1316943551, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, 1316943551, Iran
| | - Soheila Ajdary
- Department of Immunology, Pasteur Institute of Iran, Tehran, 1316943551, Iran
| | - Alireza Milani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, 1316943551, Iran
- Iranian Comprehensive Hemophilia Care Center, Tehran, 1415863675, Iran
| | - Seyed Amir Sadeghi
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, 1316943551, Iran
| |
Collapse
|
4
|
Falqui M, Perdiguero B, Coloma R, Albert M, Marcos-Villar L, McGrail JP, Sorzano CÓS, Esteban M, Gómez CE, Guerra S. An MVA-based vector expressing cell-free ISG15 increases IFN-I production and improves HIV-1-specific CD8 T cell immune responses. Front Cell Infect Microbiol 2023; 13:1187193. [PMID: 37313341 PMCID: PMC10258332 DOI: 10.3389/fcimb.2023.1187193] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 06/15/2023] Open
Abstract
The human immunodeficiency virus (HIV), responsible of the Acquired Immune Deficiency Syndrome (AIDS), continues to be a major global public health issue with any cure or vaccine available. The Interferon-stimulated gene 15 (ISG15) encodes a ubiquitin-like protein that is induced by interferons and plays a critical role in the immune response. ISG15 is a modifier protein that covalently binds to its targets via a reversible bond, a process known as ISGylation, which is the best-characterized activity of this protein to date. However, ISG15 can also interact with intracellular proteins via non-covalent binding or act as a cytokine in the extracellular space after secretion. In previous studies we proved the adjuvant effect of ISG15 when delivered by a DNA-vector in heterologous prime-boost combination with a Modified Vaccinia virus Ankara (MVA)-based recombinant virus expressing HIV-1 antigens Env/Gag-Pol-Nef (MVA-B). Here we extended these results evaluating the adjuvant effect of ISG15 when expressed by an MVA vector. For this, we generated and characterized two novel MVA recombinants expressing different forms of ISG15, the wild-type ISG15GG (able to perform ISGylation) or the mutated ISG15AA (unable to perform ISGylation). In mice immunized with the heterologous DNA prime/MVA boost regimen, the expression of the mutant ISG15AA from MVA-Δ3-ISG15AA vector in combination with MVA-B induced an increase in the magnitude and quality of HIV-1-specific CD8 T cells as well as in the levels of IFN-I released, providing a better immunostimulatory activity than the wild-type ISG15GG. Our results confirm the importance of ISG15 as an immune adjuvant in the vaccine field and highlights its role as a potential relevant component in HIV-1 immunization protocols.
Collapse
Affiliation(s)
- Michela Falqui
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rocio Coloma
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Manuel Albert
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Laura Marcos-Villar
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Joseph Patrick McGrail
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlos Óscar S. Sorzano
- Biocomputing Unit and Computational Genomics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| |
Collapse
|
5
|
Zhu W, Lévy-Leduc C, Ternès N. Identification of prognostic and predictive biomarkers in high-dimensional data with PPLasso. BMC Bioinformatics 2023; 24:25. [PMID: 36690931 PMCID: PMC9869528 DOI: 10.1186/s12859-023-05143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
In clinical trials, identification of prognostic and predictive biomarkers has became essential to precision medicine. Prognostic biomarkers can be useful for the prevention of the occurrence of the disease, and predictive biomarkers can be used to identify patients with potential benefit from the treatment. Previous researches were mainly focused on clinical characteristics, and the use of genomic data in such an area is hardly studied. A new method is required to simultaneously select prognostic and predictive biomarkers in high dimensional genomic data where biomarkers are highly correlated. We propose a novel approach called PPLasso, that integrates prognostic and predictive effects into one statistical model. PPLasso also takes into account the correlations between biomarkers that can alter the biomarker selection accuracy. Our method consists in transforming the design matrix to remove the correlations between the biomarkers before applying the generalized Lasso. In a comprehensive numerical evaluation, we show that PPLasso outperforms the traditional Lasso and other extensions on both prognostic and predictive biomarker identification in various scenarios. Finally, our method is applied to publicly available transcriptomic and proteomic data.
Collapse
Affiliation(s)
- Wencan Zhu
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120, Palaiseau, France.
- Biostatistics and Programming Department, Sanofi R&D, 91380, Chilly Mazarin, France.
| | - Céline Lévy-Leduc
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120, Palaiseau, France
| | - Nils Ternès
- Biostatistics and Programming Department, Sanofi R&D, 91380, Chilly Mazarin, France
| |
Collapse
|
6
|
Sobia P, Archary D. Preventive HIV Vaccines-Leveraging on Lessons from the Past to Pave the Way Forward. Vaccines (Basel) 2021; 9:vaccines9091001. [PMID: 34579238 PMCID: PMC8472969 DOI: 10.3390/vaccines9091001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Almost four decades on, since the 1980’s, with hundreds of HIV vaccine candidates tested in both non-human primates and humans, and several HIV vaccines trials later, an efficacious HIV vaccine continues to evade us. The enormous worldwide genetic diversity of HIV, combined with HIV’s inherent recombination and high mutation rates, has hampered the development of an effective vaccine. Despite the advent of antiretrovirals as pre-exposure prophylaxis and preventative treatment, which have shown to be effective, HIV infections continue to proliferate, highlighting the great need for a vaccine. Here, we provide a brief history for the HIV vaccine field, with the most recent disappointments and advancements. We also provide an update on current passive immunity trials, testing proof of the concept of the most clinically advanced broadly neutralizing monoclonal antibodies for HIV prevention. Finally, we include mucosal immunity, the importance of vaccine-elicited immune responses and the challenges thereof in the most vulnerable environment–the female genital tract and the rectal surfaces of the gastrointestinal tract for heterosexual and men who have sex with men transmissions, respectively.
Collapse
Affiliation(s)
- Parveen Sobia
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4001, South Africa
- Correspondence: ; Tel.: +27-(0)-31-655-0540
| |
Collapse
|
7
|
Enhancement of HIV-1 Env-Specific CD8 T Cell Responses Using Interferon-Stimulated Gene 15 as an Immune Adjuvant. J Virol 2020; 95:JVI.01155-20. [PMID: 33115866 DOI: 10.1128/jvi.01155-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/21/2020] [Indexed: 12/22/2022] Open
Abstract
Induction of the endogenous innate immune system by interferon (IFN) triggers the expression of many proteins that serve like alarm bells in the body, activating an immune response. After a viral infection, one of the genes activated by IFN induction is the IFN-stimulated gene 15 (ISG15), which encodes a ubiquitin-like protein that undergoes a reversible posttranslational modification (ISGylation). ISG15 protein can also act unconjugated, intracellularly and secreted, acting as a cytokine. Although ISG15 has an essential role in host defense responses to microbial infection, its role as an immunomodulator in the vaccine field remains to be defined. In this investigation, we showed that ISG15 exerts an immunomodulatory role in human immunodeficiency virus (HIV) vaccines. In mice, after priming with a DNA-ISG15 vector mixed with a DNA expressing HIV-1 gp120 (DNA-gp120), followed by a booster with a modified vaccinia virus Ankara (MVA) vector expressing HIV-1 antigens, both wild-type ISG15-conjugated (ISG15-wt) and mutant unconjugated (ISG15-mut) proteins act as immune adjuvants by increasing the magnitude and quality of HIV-1-specific CD8 T cells, with ISG15-wt providing better immunostimulatory activity than ISG15-mut. The HIV-1 Env-specific CD8 T cell responses showed a predominant T effector memory (TEM) phenotype in all groups. Moreover, the amount of DNA-gp120 used to immunize mice could be reduced 5-fold after mixing with DNA-ISG15 without affecting the potency and the quality of the HIV-1 Env-specific immune responses. Our study clearly highlights the potential use of the IFN-induced ISG15 protein as immune adjuvant to enhance immune responses to HIV antigens, suggesting that this molecule might be exploitable for prophylactic and therapeutic vaccine approaches against pathogens.IMPORTANCE Our study described the potential role of ISG15 as an immunomodulatory molecule in the optimization of HIV/AIDS vaccine candidates. Using a DNA prime-MVA boost immunization protocol, our results indicated an increase in the potency and the quality of the HIV-1 Env-specific CD8 T cell response. These results highlight the adjuvant potency of ISG15 to elicit improved viral antigen presentation to the immune system, resulting in an enhanced HIV-1 vaccine immune response. The DNA-ISG15 vector could find applicability in the vaccine field in combination with other nucleic acid-based vector vaccines.
Collapse
|
8
|
Dos Reis EC, Leal VNC, Soares JLDS, Fernandes FP, Souza de Lima D, de Alencar BC, Pontillo A. Flagellin/NLRC4 Pathway Rescues NLRP3-Inflammasome Defect in Dendritic Cells From HIV-Infected Patients: Perspective for New Adjuvant in Immunocompromised Individuals. Front Immunol 2019; 10:1291. [PMID: 31244842 PMCID: PMC6579915 DOI: 10.3389/fimmu.2019.01291] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 05/21/2019] [Indexed: 12/27/2022] Open
Abstract
Introduction: NLRP3 inflammasome plays a key role in dendritic cells (DC) activation in response to vaccine adjuvants, however we previously showed that it is not properly activated in DC from HIV-infected patients (HIV-DC), explaining, at least in part, the poor response to immunization of these patients. Taking in account that several cytoplasmic receptors are able to activate inflammasome, and that bacterial components are considered as a novel and efficient adjuvant, we postulated that bacterial flagellin (FLG), a natural ligand of NAIP/NLRC4 inflammasome, could rescue the activation of the complex in HIV-DC. Objective: Demonstrate that FLG is able to activate monocyte-derived dendritic cells from HIV-infected individuals better than LPS, and to what extent the entity of inflammasome activation differs between DC from HIV-infected patients and healthy donors. Methods: Monocyte-derived dendritic cells from HIV-infected patients (HIV-DC) and healthy donors (HD-DC) were stimulated with FLG, and inflammasome as well as DC activation (phenotypic profile, cytokine production, autologous lymphocytes activation) were compared. Chemical and genetic inhibitors were used to depict the relative contribution of NLRC4 and NLRP3 in HIV/HD-DC response to FLG. Results: FLG properly activates HD-DC and HIV-DC. FLG induces higher inflammasome activation than LPS in HIV-DC. FLG acts through NLRC4 and NLRP3 in HD-DC, but at a lesser extent in HIV-DC due to intrinsic NLRP3 defect. Conclusions: FLG by-passes NLRP3 defect in HIV-DC, through the activation of NAIP/NLRC4 inflammasome, indicating possible future use of the bacterial component as an efficient adjuvant in immunocompromised individuals.
Collapse
Affiliation(s)
- Edione Cristina Dos Reis
- Laboratory of Immunogenetics, Department of Immunology, Institute of Biomedical Sciences/ICB, University of São Paulo/USP, São Paulo, Brazil
| | - Vinícius Nunes Cordeiro Leal
- Laboratory of Immunogenetics, Department of Immunology, Institute of Biomedical Sciences/ICB, University of São Paulo/USP, São Paulo, Brazil
| | - Jaíne Lima da Silva Soares
- Laboratory of Immunogenetics, Department of Immunology, Institute of Biomedical Sciences/ICB, University of São Paulo/USP, São Paulo, Brazil
| | - Fernanda Pereira Fernandes
- Laboratory of Immunogenetics, Department of Immunology, Institute of Biomedical Sciences/ICB, University of São Paulo/USP, São Paulo, Brazil
| | - Dhêmerson Souza de Lima
- Laboratory of Immunogenetics, Department of Immunology, Institute of Biomedical Sciences/ICB, University of São Paulo/USP, São Paulo, Brazil
| | - Bruna Cunha de Alencar
- Laboratory of Immune System Cell Biology, Department of Immunology, Institute of Biomedical Sciences/ICB, University of São Paulo/USP, São Paulo, Brazil
| | - Alessandra Pontillo
- Laboratory of Immunogenetics, Department of Immunology, Institute of Biomedical Sciences/ICB, University of São Paulo/USP, São Paulo, Brazil
| |
Collapse
|
9
|
Shattock R. HIV vaccine research in Canada. AIDS Res Ther 2017; 14:54. [PMID: 28893293 PMCID: PMC5594529 DOI: 10.1186/s12981-017-0181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 08/25/2017] [Indexed: 11/24/2022] Open
|