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Mandal S, Ghosh JS, Lohani SC, Zhao M, Cheng Y, Burrack R, Luo M, Li Q. A long-term stable cold-chain-friendly HIV mRNA vaccine encoding multi-epitope viral protease cleavage site immunogens inducing immunogen-specific protective T cell immunity. Emerg Microbes Infect 2024; 13:2377606. [PMID: 38979723 PMCID: PMC11259082 DOI: 10.1080/22221751.2024.2377606] [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: 01/04/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024]
Abstract
The lack of success in clinical trials for HIV vaccines highlights the need to explore novel strategies for vaccine development. Research on highly exposed seronegative (HESN) HIV-resistant Kenyan female sex workers revealed naturally protective immunity is correlated with a focused immune response mediated by virus-specific CD8 T cells. Further studies indicated that the immune response is unconventionally focused on highly conserved sequences around HIV viral protease cleavage sites (VPCS). Thus, taking an unconventional approach to HIV vaccine development, we designed lipid nanoparticles loaded with mRNA that encodes multi-epitopes of VPCS (MEVPCS-mRNA LNP), a strategic design to boost antigen presentation by dendritic cells, promoting effective cellular immunity. Furthermore, we developed a novel cold-chain compatible mRNA LNP formulation, ensuring long-term stability and compatibility with cold-chain storage/transport, widening accessibility of mRNA LNP vaccine in low-income countries. The in-vivo mouse study demonstrated that the vaccinated group generated VPCS-specific CD8 memory T cells, both systemically and at mucosal sites of viral entry. The MEVPCS-mRNA LNP vaccine-induced CD8 T cell immunity closely resembled that of the HESN group and displayed a polyfunctional profile. Notably, it induced minimal to no activation of CD4 T cells. This proof-of-concept study underscores the potential of the MEVPCS-mRNA LNP vaccine in eliciting CD8 T cell memory specific to the highly conserved multiple VPCS, consequently having a broad coverage in human populations and limiting viral escape mutation. The MEVPCS-mRNA LNP vaccine holds promise as a candidate for an effective prophylactic HIV vaccine.
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Affiliation(s)
- Subhra Mandal
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jayadri Sekhar Ghosh
- Nebraska Center for Virology, Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Saroj Chandra Lohani
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Miaoyun Zhao
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Yilun Cheng
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rachel Burrack
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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2
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Natural Immunity against HIV-1: Progression of Understanding after Association Studies. Viruses 2022; 14:v14061243. [PMID: 35746714 PMCID: PMC9227919 DOI: 10.3390/v14061243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022] Open
Abstract
Natural immunity against HIV has been observed in many individuals in the world. Among them, a group of female sex workers enrolled in the Pumwani sex worker cohort remained HIV uninfected for more than 30 years despite high-risk sex work. Many studies have been carried out to understand this natural immunity to HIV in the hope to develop effective vaccines and preventions. This review focuses on two such examples. These studies started from identifying immunogenetic or genetic associations with resistance to HIV acquisition, and followed up with an in-depth investigation to understand the biological relevance of the correlations of protection, and to develop and test novel vaccines and preventions.
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3
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Durán-Lobato M, López-Estévez AM, Cordeiro AS, Dacoba TG, Crecente-Campo J, Torres D, Alonso MJ. Nanotechnologies for the delivery of biologicals: Historical perspective and current landscape. Adv Drug Deliv Rev 2021; 176:113899. [PMID: 34314784 DOI: 10.1016/j.addr.2021.113899] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/05/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022]
Abstract
Biological macromolecule-based therapeutics irrupted in the pharmaceutical scene generating a great hope due to their outstanding specificity and potency. However, given their susceptibility to degradation and limited capacity to overcome biological barriers new delivery technologies had to be developed for them to reach their targets. This review aims at analyzing the historical seminal advances that shaped the development of the protein/peptide delivery field, along with the emerging technologies on the lead of the current landscape. Particularly, focus is made on technologies with a potential for transmucosal systemic delivery of protein/peptide drugs, followed by approaches for the delivery of antigens as new vaccination strategies, and formulations of biological drugs in oncology, with special emphasis on mAbs. Finally, a discussion of the key challenges the field is facing, along with an overview of prospective advances are provided.
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4
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Sherry D, Worth R, Sayed Y. Elasticity-Associated Functionality and Inhibition of the HIV Protease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1371:79-108. [PMID: 34351572 DOI: 10.1007/5584_2021_655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV protease plays a critical role in the life cycle of the virus through the generation of mature and infectious virions. Detailed knowledge of the structure of the enzyme and its substrate has led to the development of protease inhibitors. However, the development of resistance to all currently available protease inhibitors has contributed greatly to the decreased success of antiretroviral therapy. When therapy failure occurs, multiple mutations are found within the protease sequence starting with primary mutations, which directly impact inhibitor binding, which can also negatively impact viral fitness and replicative capacity by decreasing the binding affinity of the natural substrates to the protease. As such, secondary mutations which are located outside of the active site region accumulate to compensate for the recurrently deleterious effects of primary mutations. However, the resistance mechanism of these secondary mutations is not well understood, but what is known is that these secondary mutations contribute to resistance in one of two ways, either through increasing the energetic penalty associated with bringing the protease into the closed conformation, or, through decreasing the stability of the protein/drug complex in a manner that increases the dissociation rate of the drug, leading to diminished inhibition. As a result, the elasticity of the enzyme-substrate complex has been implicated in the successful recognition and catalysis of the substrates which may be inferred to suggest that the elasticity of the enzyme/drug complex plays a role in resistance. A realistic representation of the dynamic nature of the protease may provide a more powerful tool in structure-based drug design algorithms.
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Affiliation(s)
- Dean Sherry
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Roland Worth
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
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5
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Dacoba TG, Ruiz-Gatón L, Benito A, Klein M, Dupin D, Luo M, Menta M, Teijeiro-Osorio D, Loinaz I, Alonso MJ, Crecente-Campo J. Technological challenges in the preclinical development of an HIV nanovaccine candidate. Drug Deliv Transl Res 2021; 10:621-634. [PMID: 32040775 DOI: 10.1007/s13346-020-00721-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite a very active research in the field of nanomedicine, only a few nano-based drug delivery systems have reached the market. The "death valley" between research and commercialization has been partially attributed to the limited characterization and reproducibility of the nanoformulations. Our group has previously reported the potential of a peptide-based nanovaccine candidate for the prevention of SIV infection in macaques. This vaccine candidate is composed of chitosan/dextran sulfate nanoparticles containing twelve SIV peptide antigens. The aim of this work was to rigorously characterize one of these nanoformulations containing a specific peptide, following a quality-by-design approach. The evaluation of the different quality attributes was performed by several complementary techniques, such as dynamic light scattering, nanoparticle tracking analysis, and electron microscopy for particle size characterization. The inter-batch reproducibility was validated by three independent laboratories. Finally, the long-term stability and scalability of the manufacturing technique were assessed. Overall, these data, together with the in vivo efficacy results obtained in macaques, underline the promise this new vaccine holds with regard to its translation to clinical trials. Graphical abstract.
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Affiliation(s)
- Tamara G Dacoba
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), IDIS Research Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.,Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Pharmacy, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Luisa Ruiz-Gatón
- CIDETEC, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Gipuzkoa, 20014, Donostia-San Sebastián, Spain
| | - Ana Benito
- CIDETEC, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Gipuzkoa, 20014, Donostia-San Sebastián, Spain
| | - Marlène Klein
- Ultra Trace Analyses Aquitaine (UT2A/ADERA), Technopôle Hélioparc Pau-Pyrénées, 64053, Pau Cedex 9, France
| | - Damien Dupin
- CIDETEC, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Gipuzkoa, 20014, Donostia-San Sebastián, Spain
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mathieu Menta
- Ultra Trace Analyses Aquitaine (UT2A/ADERA), Technopôle Hélioparc Pau-Pyrénées, 64053, Pau Cedex 9, France
| | - Desirée Teijeiro-Osorio
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), IDIS Research Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.,Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Pharmacy, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Iraida Loinaz
- CIDETEC, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Gipuzkoa, 20014, Donostia-San Sebastián, Spain
| | - María J Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), IDIS Research Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain. .,Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Pharmacy, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
| | - José Crecente-Campo
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), IDIS Research Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain. .,Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Pharmacy, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
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6
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Daniel M, Liang B, Luo M. Assessment of the population coverage of an HIV-1 vaccine targeting sequences surrounding the viral protease cleavage sites in Gag, Pol, or all 12 protease cleavage sites. Vaccine 2021; 39:2676-2683. [PMID: 33863573 DOI: 10.1016/j.vaccine.2021.03.068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 01/06/2023]
Abstract
Development of an effective HIV-1 vaccine has been a great challenge faced by the research community. Recently a novel strategy targeting the viral protease cleavage sites (PCSs) has been tested and shown promising results. This T cell-based vaccine strategy depends on individuals expressing certain HLA class I molecules and since each population has unique distributions of HLA class I alleles, population coverage analysis is required to assess feasibility. Utilizing the validated CD8 T cell epitope data from previous studies we conducted coverage analysis of an HIV-1 vaccine targeting the sequences surrounding all 12-PCSs, Gag-PCSs, and Pol-PCSs. The population coverage, average epitope hit, and minimum number of epitopes recognized by 90% of the population (PC90) was compiled for 66 countries and 16 geographical regions using the web tool provided by "Immune Epitope Database and Analysis Resource". Our analysis shows that the coverage for an HIV-1 vaccine targeting sequences surrounding all 12 PCSs, 5 PCSs in Gag or 6 PCSs in Pol can cover ~ 70% to ~ 100% of the populations analyzed. There was no statistical difference in population coverages for the majority of populations examined when comparing the CD8 T cell epitope sets (12-PCSs, Gag-PCSs, and Pol-PCSs). As expected, vaccines targeting more sequences will have more CD8 T cell epitopes, as the mean average epitope hit for the 12-PCSs, Gag-PCSs, and Pol-PCSs across all countries studied was 9.45, 4.76, and 4.74, respectively, and across all geographical regions was 9.76, 4.99, and 4.92, respectively. The average PC90 for the 12-PCSs, Gag-PCSs, and Pol-PCSs across all countries studied was 2.53, 1.31, and 1.41, respectively, and across all geographical regions was 2.24, 1.23, and 1.29, respectively. Thus, vaccines targeting sequences surrounding the HIV-1 PCSs can cover broad populations; however, whether targeting a subset of the PCSs is sufficient to prevent acquisition requires further preclinical investigation.
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Affiliation(s)
- Mathew Daniel
- Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Binhua Liang
- Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada; National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Ma Luo
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada; Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
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7
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Li H, Omange RW, Liang B, Toledo N, Hai Y, Liu LR, Schalk D, Crecente-Campo J, Dacoba TG, Lambe AB, Lim SY, Li L, Kashem MA, Wan Y, Correia-Pinto JF, Seaman MS, Liu XQ, Balshaw RF, Li Q, Schultz-Darken N, Alonso MJ, Plummer FA, Whitney JB, Luo M. Vaccine targeting SIVmac251 protease cleavage sites protects macaques against vaginal infection. J Clin Invest 2021; 130:6429-6442. [PMID: 32853182 DOI: 10.1172/jci138728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/20/2020] [Indexed: 01/03/2023] Open
Abstract
After over 3 decades of research, an effective anti-HIV vaccine remains elusive. The recently halted HVTN702 clinical trial not only further stresses the challenge to develop an effective HIV vaccine but also emphasizes that unconventional and novel vaccine strategies are urgently needed. Here, we report that a vaccine focusing the immune response on the sequences surrounding the 12 viral protease cleavage sites (PCSs) provided greater than 80% protection to Mauritian cynomolgus macaques against repeated intravaginal SIVmac251 challenges. The PCS-specific T cell responses correlated with vaccine efficacy. The PCS vaccine did not induce immune activation or inflammation known to be associated with increased susceptibility to HIV infection. Machine learning analyses revealed that the immune microenvironment generated by the PCS vaccine was predictive of vaccine efficacy. Our study demonstrates, for the first time to our knowledge, that a vaccine which targets only viral maturation, but lacks full-length Env and Gag immunogens, can prevent intravaginal infection in a stringent macaque/SIV challenge model. Targeting HIV maturation thus offers a potentially novel approach to developing an effective HIV vaccine.
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Affiliation(s)
- Hongzhao Li
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Robert W Omange
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Binhua Liang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nikki Toledo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Yan Hai
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Lewis R Liu
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Dane Schalk
- Scientific Protocol Implementation Unit, Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Jose Crecente-Campo
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus Vida, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Tamara G Dacoba
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus Vida, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - So-Yon Lim
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Lin Li
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Mohammad Abul Kashem
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Yanmin Wan
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jorge F Correia-Pinto
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus Vida, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiao Qing Liu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Robert F Balshaw
- Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Nancy Schultz-Darken
- Scientific Protocol Implementation Unit, Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Maria J Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus Vida, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - James B Whitney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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8
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Toledo NPL, Li H, Omange RW, Dacoba TG, Crecente-Campo J, Schalk D, Kashem MA, Rakasz E, Schultz-Darken N, Li Q, Whitney JB, Alonso MJ, Plummer FA, Luo M. Cervico-Vaginal Inflammatory Cytokine and Chemokine Responses to Two Different SIV Immunogens. Front Immunol 2020; 11:1935. [PMID: 32983121 PMCID: PMC7477078 DOI: 10.3389/fimmu.2020.01935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/17/2020] [Indexed: 12/26/2022] Open
Abstract
Studies have shown that vaccine vectors and route of immunization can differentially activate different arms of the immune system. However, the effects of different HIV vaccine immunogens on mucosal inflammation have not yet been studied. Because mucosal sites are the primary route of HIV infection, we evaluated the cervico-vaginal inflammatory cytokine and chemokine levels of Mauritian cynomolgus macaques following immunization and boost using two different SIV vaccine immunogens. The PCS vaccine delivers 12 20-amino acid peptides overlapping the 12 protease cleavage sites, and the Gag/Env vaccine delivers the full Gag and full Env proteins of simian immunodeficiency virus. We showed that the PCS vaccine prime and boosts induced short-lived, lower level increases of a few pro-inflammatory/chemotactic cytokines. In the PCS-vaccine group only the levels of MCP-1 were significantly increased above the baseline (P = 0.0078, Week 6; P = 0.0078, Week 17; P = 0.0234; Week 51) following multiple boosts. In contrast, immunizations with the Gag/Env vaccine persistently increased the levels of multiple cytokines/chemokines. In the Gag/Env group, higher than baseline levels were consistently observed for IL-8 (P = 0.0078, Week 16; P = 0.0078, Week 17; P = 0.0156, Week 52), IL-1β (P = 0.0234, Week 16; P = 0.0156, Week 17; P = 0.0156, Week 52), and MIP-1α (P = 0.0313, Week 16; P = 0.0156, Week 17; P = 0.0313, Week 52). Over time, repeated boosts altered the relative levels of these cytokines between the Gag/Env and PCS vaccine group. 18 weeks after final boost with a higher dosage, IP-10 levels (P = 0.0313) in the Gag/Env group remained higher than baseline. Thus, the influence of vaccine immunogens on mucosal inflammation needs to be considered when developing and evaluating candidate HIV vaccines.
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Affiliation(s)
- Nikki P L Toledo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Hongzhao Li
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Robert W Omange
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Tamara G Dacoba
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus Vida, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jose Crecente-Campo
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus Vida, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Dane Schalk
- Scientific Protocol Implementation Unit, Wisconsin National Primate Research Center, Madison, WI, United States
| | - Mohammad A Kashem
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Eva Rakasz
- Scientific Protocol Implementation Unit, Wisconsin National Primate Research Center, Madison, WI, United States
| | - Nancy Schultz-Darken
- Scientific Protocol Implementation Unit, Wisconsin National Primate Research Center, Madison, WI, United States
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - James B Whitney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Maria J Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus Vida, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
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9
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Hernandez-Sanchez PG, Guerra-Palomares SE, Arguello JR, Noyola DE, Garcia-Sepulveda CA. Diversity of Mexican HIV-1 Protease Sequences. AIDS Res Hum Retroviruses 2020; 36:457-458. [PMID: 31931590 DOI: 10.1089/aid.2019.0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Pedro G. Hernandez-Sanchez
- Laboratorio de Genómica Viral y Humana, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Sandra E. Guerra-Palomares
- Laboratorio de Genómica Viral y Humana, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - J. Rafael Arguello
- Departamento de Inmunobiología Molecular, Centro de Investigación Biomédica, Universidad Autónoma de Coahuila, Torreón, México
| | - Daniel E. Noyola
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Christian A. Garcia-Sepulveda
- Laboratorio de Genómica Viral y Humana, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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10
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Singh D, Sisodia DS, Singh P. Compositional framework for multitask learning in the identification of cleavage sites of HIV-1 protease. J Biomed Inform 2020; 102:103376. [PMID: 31935461 DOI: 10.1016/j.jbi.2020.103376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 11/18/2022]
Abstract
Inadequate patient samples and costly annotated data generations result into the smaller dataset in the biomedical domain. Due to which the predictions with a trained model that usually reveal a single small dataset association are fail to derive robust insights. To cope with the data sparsity, a promising strategy of combining data from the different related tasks is exercised in various application. Motivated by, successful work in the various bioinformatics application, we propose a multitask learning model based on multi-kernel that exploits the dependencies among various related tasks. This work aims to combine the knowledge from experimental studies of the different dataset to build stronger predictive models for HIV-1 protease cleavage sites prediction. In this study, a set of peptide data from one source is referred as 'task' and to integrate interactions from multiple tasks; our method exploits the common features and parameters sharing across the data source. The proposed framework uses feature integration, feature selection, multi-kernel and multifactorial evolutionary algorithm to model multitask learning. The framework considered seven different feature descriptors and four different kernel variants of support vector machines to form the optimal multi-kernel learning model. To validate the effectiveness of the model, the performance parameters such as average accuracy, and area under curve have been evaluated on the suggested model. We also carried out Friedman and post hoc statistical test to substantiate the significant improvement achieved by the proposed framework. The result obtained following the extensive experiment confirms the belief that multitask learning in cleavage site identification can improve the performance.
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Affiliation(s)
- Deepak Singh
- Department of Computer Science and Engineering, National Institute of Technology, Raipur, C.G, India.
| | - Dilip Singh Sisodia
- Department of Computer Science and Engineering, National Institute of Technology, Raipur, C.G, India.
| | - Pradeep Singh
- Department of Computer Science and Engineering, National Institute of Technology, Raipur, C.G, India.
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11
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Cognitive Framework for HIV-1 Protease Cleavage Site Classification Using Evolutionary Algorithm. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2019. [DOI: 10.1007/s13369-019-03871-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Cervera L, Gòdia F, Tarrés-Freixas F, Aguilar-Gurrieri C, Carrillo J, Blanco J, Gutiérrez-Granados S. Production of HIV-1-based virus-like particles for vaccination: achievements and limits. Appl Microbiol Biotechnol 2019; 103:7367-7384. [DOI: 10.1007/s00253-019-10038-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/20/2022]
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Dacoba T, Omange RW, Li H, Crecente-Campo J, Luo M, Alonso MJ. Polysaccharide Nanoparticles Can Efficiently Modulate the Immune Response against an HIV Peptide Antigen. ACS NANO 2019; 13:4947-4959. [PMID: 30964270 PMCID: PMC6607401 DOI: 10.1021/acsnano.8b07662] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/08/2019] [Indexed: 05/30/2023]
Abstract
The development of an effective HIV vaccine continues to be a major health challenge since, so far, only the RV144 trial has demonstrated a modest clinical efficacy. Recently, the targeting of the 12 highly conserved protease cleavage sites (PCS1-12) has been presented as a strategy seeking to hamper the maturation and infectivity of HIV. To pursue this line of research, and because peptide antigens have low immunogenicity, we have included these peptides in engineered nanoparticles, aiming at overcoming this limitation. More specifically, we investigated whether the covalent attachment of a PCS peptide (PCS5) to polysaccharide-based nanoparticles, and their coadministration with polyinosinic:polycytidylic acid (poly(I:C)), improved the generated immune response. To this end, PCS5 was first conjugated to two different polysaccharides (chitosan and hyaluronic acid) through either a stable or a cleavable bond and then associated with an oppositely charged polymer (dextran sulfate and chitosan) and poly(I:C) to form the nanoparticles. Nanoparticles associating PCS5 by ionic interactions were used in this study as the control formulation. In vivo, all nanosystems elicited high anti-PCS5 antibodies. Nanoparticles containing PCS5 conjugated and poly(I:C) seemed to induce the strongest activation of antigen-presenting cells. Interestingly, T cell activation presented different kinetics depending on the prototype. These findings show that both the nanoparticle composition and the conjugation of the HIV peptide antigen may play an important role in the generation of humoral and cellular responses.
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Affiliation(s)
- Tamara
G. Dacoba
- Center
for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus
Vida, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
- Department
of Pharmacology, Pharmacy and Pharmaceutical Technology, School of
Pharmacy, Campus Vida, Universidade de Santiago
de Compostela, Santiago de Compostela 15782, Spain
| | - Robert W. Omange
- Department
of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Hongzhao Li
- Department
of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - José Crecente-Campo
- Center
for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus
Vida, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
- Department
of Pharmacology, Pharmacy and Pharmaceutical Technology, School of
Pharmacy, Campus Vida, Universidade de Santiago
de Compostela, Santiago de Compostela 15782, Spain
| | - Ma Luo
- Department
of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- National
Microbiology Laboratory, Public Health Agency
of Canada, Winnipeg, MB R3E 3L5, Canada
| | - Maria Jose Alonso
- Center
for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus
Vida, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
- Department
of Pharmacology, Pharmacy and Pharmaceutical Technology, School of
Pharmacy, Campus Vida, Universidade de Santiago
de Compostela, Santiago de Compostela 15782, Spain
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14
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Li H, Hai Y, Lim SY, Toledo N, Crecente-Campo J, Schalk D, Li L, Omange RW, Dacoba TG, Liu LR, Kashem MA, Wan Y, Liang B, Li Q, Rakasz E, Schultz-Darken N, Alonso MJ, Plummer FA, Whitney JB, Luo M. Mucosal antibody responses to vaccines targeting SIV protease cleavage sites or full-length Gag and Env proteins in Mauritian cynomolgus macaques. PLoS One 2018; 13:e0202997. [PMID: 30153293 PMCID: PMC6112674 DOI: 10.1371/journal.pone.0202997] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023] Open
Abstract
HIV mutates rapidly and infects CD4+ T cells, especially when they are activated. A vaccine targeting conserved, essential viral elements while limiting CD4+ T cell activation could be effective. Learning from natural immunity observed in a group of highly HIV-1 exposed seronegative Kenyan female sex workers, we are testing a novel candidate HIV vaccine targeting the 12 viral protease cleavage sites (PCSs) (the PCS vaccine), in comparison with a vaccine targeting full-length Gag and Env (the Gag/Env vaccine) in a Mauritian cynomolgus macaque/SIV model. In this study we evaluated these vaccines for induction of mucosal antibodies to SIV immunogens at the female genital tract. Bio-Plex and Western blot analyses of cervicovaginal lavage samples showed that both the PCS and Gag/Env vaccines can elicit mucosal IgG antibody responses to SIV immunogens. Significantly higher increase of anti-PCS antibodies was induced by the PCS vaccine than by the Gag/Env vaccine (p<0.0001). The effect of the mucosal antibody responses in protection from repeated low dose pathogenic SIVmac251 challenges is being evaluated.
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Affiliation(s)
- Hongzhao Li
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Yan Hai
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - So-Yon Lim
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States of America
| | - Nikki Toledo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Jose Crecente-Campo
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus Vida, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Dane Schalk
- Scientific Protocol Implementation Unit, Wisconsin National Primate Research Center, Madison, WI, United States of America
| | - Lin Li
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Robert W Omange
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Tamara G Dacoba
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus Vida, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Lewis R Liu
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mohammad Abul Kashem
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Yanmin Wan
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Binhua Liang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Eva Rakasz
- Immunology Services Unit, Wisconsin National Primate Research Center, Madison, WI, United States of America
| | - Nancy Schultz-Darken
- Scientific Protocol Implementation Unit, Wisconsin National Primate Research Center, Madison, WI, United States of America
| | - Maria J Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Campus Vida, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - James B Whitney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States of America.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States of America
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
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15
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Li H, Li L, Liu LR, Omange RW, Toledo N, Kashem MA, Hai Y, Liang B, Plummer FA, Luo M. Hypothetical endogenous SIV-like antigens in Mauritian cynomolgus macaques. Bioinformation 2018; 14:48-52. [PMID: 29618899 PMCID: PMC5879946 DOI: 10.6026/97320630014048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 01/24/2023] Open
Abstract
Simian immunodeficiency virus (SIV) infection of Mauritian cynomolgus macaques (MCMs) is an increasingly important nonhuman primate model for HIV vaccine research. We previously reported that in MCMs anti-SIV antibodies can be naturally developed without exogenous infection or vaccination, and that a vaccine targeting SIV protease cleavage sites (PCS) can cross-induce antibodies to non-PCS SIV antigens. We speculate that this is potentially caused by the existence of endogenous SIV-like antigens. External stimuli (such as environmental factors and vaccination) may induce expression of endogenous SIV-like antigens to elicit these antibodies. Database and mass spectrometry analyses were conducted to search for such antigens. We identified endogenous SIV-like DNA sequences in cynomolgus macaque genome and non-PCS peptide homologous to SIV Env protein in PBMCs of a PCS-vaccinated monkey. Our preliminary insights suggest that endogenous SIV-like antigens may be one of the possible reasons for the natural and cross-inducible SIV antibodies in MCMs.
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Affiliation(s)
- Hongzhao Li
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Lin Li
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
| | - Lewis R Liu
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Robert W Omange
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Nikki Toledo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Mohammad Abul Kashem
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Yan Hai
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Binhua Liang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 3N4, Canada
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
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16
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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
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