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Hung HC, Tan BF, Lin WS, Wu SC. Glycan masking of NTD loops with a chimeric RBD of the spike protein as a vaccine design strategy against emerging SARS-CoV-2 Omicron variants. J Med Virol 2024; 96:e29893. [PMID: 39192804 DOI: 10.1002/jmv.29893] [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: 01/17/2024] [Revised: 07/12/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
The N-terminal domain (NTD) of the SARS-CoV-2 S protein comprises five exposed protruding loops. Deletions, insertions, and substitutions within these NTD loops play a significant role in viral evolution and contribute to immune evasion. We reported previously that introducing the glycan masking mutation R158N/Y160T in the NTD loop led to increased titers of neutralizing antibodies against the SARS-CoV-2 Wuhan-Hu-01 strain, as well as the Alpha, Beta, and Delta variants. In this study, we conducted further investigations on 10 additional glycan-masking sites in the NTD loops. Our findings indicate that the introduction of glycan masking mutations, specifically N87/G89T, H146N/N148T, N185/K187T, and V213N/D215T significantly enhanced neutralizing antibody titers against the Delta variant. The combination of dual glycan-masking mutations R158N/Y160T+V213N/D215T and R158N/Y160T+G219N results in a shift toward the Omicron BA.1. Furthermore, the introduction of the Omicron receptor binding domain (RBD) alongside these two dual glycan masking mutations of Wuhan-Hu-1 and XBB.1 NTD sequences resulted in a noticeable shift in antigenic distances, aligning with the Omicron BA.4/5, BA.2.75.2, BQ.1.1, and XBB.1 subvariants on the antigenic map. This strategic combination, which involves the dual glycan masking mutations R158N/Y160T+V213N/D215T and R158N/Y160T+G219N in the NTD loops, along with the domain swap incorporating the Omicron RBD, emerges as a promising vaccine design strategy for the continuous development of next-generation SARS-CoV-2 vaccines.
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Affiliation(s)
- Hao-Chan Hung
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Boon-Fatt Tan
- Department of Pediatrics, National Taiwan University Hospital, Hsin-Chu Branch, Hsinchu, Taiwan
| | - Wei-Shuo Lin
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Suh-Chin Wu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
- Adimmune Corporation, Taichung, Taiwan
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2
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Xu D, Powell AE, Utz A, Sanyal M, Do J, Patten JJ, Moliva JI, Sullivan NJ, Davey RA, Kim PS. Design of universal Ebola virus vaccine candidates via immunofocusing. Proc Natl Acad Sci U S A 2024; 121:e2316960121. [PMID: 38319964 PMCID: PMC10873634 DOI: 10.1073/pnas.2316960121] [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: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024] Open
Abstract
The Ebola virus causes hemorrhagic fever in humans and poses a significant threat to global public health. Although two viral vector vaccines have been approved to prevent Ebola virus disease, they are distributed in the limited ring vaccination setting and only indicated for prevention of infection from orthoebolavirus zairense (EBOV)-one of three orthoebolavirus species that have caused previous outbreaks. Ebola virus glycoprotein GP mediates viral infection and serves as the primary target of neutralizing antibodies. Here, we describe a universal Ebola virus vaccine approach using a structure-guided design of candidates with hyperglycosylation that aims to direct antibody responses away from variable regions and toward conserved epitopes of GP. We first determined the hyperglycosylation landscape on Ebola virus GP and used that to generate hyperglycosylated GP variants with two to four additional glycosylation sites to mask the highly variable glycan cap region. We then created vaccine candidates by displaying wild-type or hyperglycosylated GP variants on ferritin nanoparticles (Fer). Immunization with these antigens elicited potent neutralizing antisera against EBOV in mice. Importantly, we observed consistent cross-neutralizing activity against Bundibugyo virus and Sudan virus from hyperglycosylated GP-Fer with two or three additional glycans. In comparison, elicitation of cross-neutralizing antisera was rare in mice immunized with wild-type GP-Fer. These results demonstrate a potential strategy to develop universal Ebola virus vaccines that confer cross-protective immunity against existing and emerging filovirus species.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Abigail E. Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA94305
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA94305
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Jonathan Do
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - J. J. Patten
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Juan I. Moliva
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Nancy J. Sullivan
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
- Department of Biology, Boston University, Boston, MA02118
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Chan Zuckerberg Biohub, San Francisco, CA94158
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3
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Zhang Q, Yang Y, Lan J, Wang Z, Gao Y, Li X, Mao W, Xie J, Mi LZ, Zhang X, Wang X, Mu X, Mei K. Inducing enhanced neutralizing antibodies against broad SARS-CoV-2 variants through glycan-shielding multiple non-neutralizing epitopes of RBD. Front Immunol 2023; 14:1259386. [PMID: 38149245 PMCID: PMC10750354 DOI: 10.3389/fimmu.2023.1259386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction Since the outbreak of SARS-CoV-2, vaccines have demonstrated their effectiveness in resisting virus infection, reducing severity, and lowering the mortality rate in infected individuals. However, due to the rapid and ongoing mutations of SARS-CoV-2, the protective ability of many available vaccines has been challenged. Therefore, there is an urgent need for vaccines capable of eliciting potent broadly neutralizing antibodies against various SARS-CoV-2 variants. Methods In this study, we developed a novel subunit vaccine candidate for SARS-CoV-2 by introducing a series of shielding glycans to the Fc-fused receptor-binding domain (RBD) of the prototypic spike protein. This approach aims to mask non-neutralizing epitopes and focus the immune response on crucial neutralizing epitopes. Results All modified sites were confirmed to be highly glycosylated through mass spectrometry analysis. The binding affinity of the glycan-shielded RBD (gsRBD) to the human ACE2 receptor was comparable to that of the wildtype RBD (wtRBD). Immunizing mice with gsRBD when combined with either Freund's adjuvant or aluminum adjuvant demonstrated that the introduction of the glycan shield did not compromise the antibody-inducing ability of RBD. Importantly, the gsRBD significantly enhanced the generation of neutralizing antibodies against SARS-CoV-2 pseudoviruses compared to the wtRBD. Notably, it exhibited remarkable protective activity against Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529), approximately 3-fold, 7- fold, and 17-fold higher than wtRBD, respectively. Discussion Our data proved this multiple-epitope masking strategy as an effective approach for highly active vaccine production.
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Affiliation(s)
- Qingyun Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yi Yang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Jun Lan
- School of Life Sciences, Tsinghua University, Beijing, China
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Ziyi Wang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xiao Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Weidong Mao
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Jing Xie
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Li-Zhi Mi
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xinquan Wang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin Mu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
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4
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Hulbert SW, Desai P, Jewett MC, DeLisa MP, Williams AJ. Glycovaccinology: The design and engineering of carbohydrate-based vaccine components. Biotechnol Adv 2023; 68:108234. [PMID: 37558188 DOI: 10.1016/j.biotechadv.2023.108234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/12/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
Vaccines remain one of the most important pillars in preventative medicine, providing protection against a wide array of diseases by inducing humoral and/or cellular immunity. Of the many possible candidate antigens for subunit vaccine development, carbohydrates are particularly appealing because of their ubiquitous presence on the surface of all living cells, viruses, and parasites as well as their known interactions with both innate and adaptive immune cells. Indeed, several licensed vaccines leverage bacterial cell-surface carbohydrates as antigens for inducing antigen-specific plasma cells secreting protective antibodies and the development of memory T and B cells. Carbohydrates have also garnered attention in other aspects of vaccine development, for example, as adjuvants that enhance the immune response by either activating innate immune responses or targeting specific immune cells. Additionally, carbohydrates can function as immunomodulators that dampen undesired humoral immune responses to entire protein antigens or specific, conserved regions on antigenic proteins. In this review, we highlight how the interplay between carbohydrates and the adaptive and innate arms of the immune response is guiding the development of glycans as vaccine components that act as antigens, adjuvants, and immunomodulators. We also discuss how advances in the field of synthetic glycobiology are enabling the design, engineering, and production of this new generation of carbohydrate-containing vaccine formulations with the potential to prevent infectious diseases, malignancies, and complex immune disorders.
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Affiliation(s)
- Sophia W Hulbert
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Primit Desai
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Matthew P DeLisa
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA; Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Cornell Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
| | - Asher J Williams
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
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5
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Xu D, Powell AE, Utz A, Sanyal M, Do J, Patten J, Moliva JI, Sullivan NJ, Davey RA, Kim PS. Design of universal Ebola virus vaccine candidates via immunofocusing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.14.562364. [PMID: 37904982 PMCID: PMC10614775 DOI: 10.1101/2023.10.14.562364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ebola virus causes hemorrhagic fever in humans and poses a significant threat to global public health. Although two viral vector vaccines have been approved to prevent Ebola virus disease, they are distributed in the limited ring vaccination setting and only indicated for prevention of infection from orthoebolavirus zairense (EBOV) - one of three orthoebolavirus species that have caused previous outbreaks. Ebola virus glycoprotein GP mediates viral infection and serves as the primary target of neutralizing antibodies. Here we describe a universal Ebola virus vaccine approach using structure-guided design of candidates with hyperglycosylation that aims to direct antibody responses away from variable regions and toward conserved epitopes of GP. We first determined the hyperglycosylation landscape on Ebola virus GP and used that to generate hyperglycosylated GP variants with two to four additional glycosylation sites to mask the highly variable glycan cap region. We then created vaccine candidates by displaying wild-type or hyperglycosylated GP variants on ferritin nanoparticles (Fer). Immunization with these antigens elicited potent neutralizing antisera against EBOV in mice. Importantly, we observed consistent cross-neutralizing activity against Bundibugyo virus and Sudan virus from hyperglycosylated GP-Fer with two or three additional glycans. In comparison, elicitation of cross-neutralizing antisera was rare in mice immunized with wild-type GP-Fer. These results demonstrate a potential strategy to develop universal Ebola virus vaccines that confer cross-protective immunity against existing and emerging filovirus species.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Abigail E. Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Do
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - J.J. Patten
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Juan I. Moliva
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nancy J. Sullivan
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Biology, Boston University, Boston, MA 02118, USA
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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6
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Olia AS, Cheng C, Zhou T, Biju A, Harris DR, Changela A, Duan H, Ivleva VB, Kong WP, Ou L, Rawi R, Tsybovsky Y, Van Wazer DJ, Corrigan AR, Gonelli CA, Lee M, McKee K, Narpala S, O’Dell S, Parchment DK, Stancofski ESD, Stephens T, Tan I, Teng IT, Wang S, Wei Q, Yang Y, Yang Z, Zhang B, Novak J, Renfrow MB, Doria-Rose NA, Koup RA, McDermott AB, Gall JG, Lei QP, Mascola JR, Kwong PD. Soluble prefusion-closed HIV-envelope trimers with glycan-covered bases. iScience 2023; 26:107403. [PMID: 37554450 PMCID: PMC10404741 DOI: 10.1016/j.isci.2023.107403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/23/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023] Open
Abstract
Soluble HIV-1-envelope (Env) trimers elicit immune responses that target their solvent-exposed protein bases, the result of removing these trimers from their native membrane-bound context. To assess whether glycosylation could limit these base responses, we introduced sequons encoding potential N-linked glycosylation sites (PNGSs) into base-proximal regions. Expression and antigenic analyses indicated trimers bearing six-introduced PNGSs to have reduced base recognition. Cryo-EM analysis revealed trimers with introduced PNGSs to be prone to disassembly and introduced PNGS to be disordered. Protein-base and glycan-base trimers induced reciprocally symmetric ELISA responses, in which only a small fraction of the antibody response to glycan-base trimers recognized protein-base trimers and vice versa. EM polyclonal epitope mapping revealed glycan-base trimers -even those that were stable biochemically- to elicit antibodies that recognized disassembled trimers. Introduced glycans can thus mask the protein base but their introduction may yield neo-epitopes that dominate the immune response.
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Affiliation(s)
- Adam S. Olia
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea Biju
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darcy R. Harris
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anita Changela
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongying Duan
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vera B. Ivleva
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wing-Pui Kong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - David J. Van Wazer
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angela R. Corrigan
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Myungjin Lee
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O’Dell
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ivy Tan
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qing Wei
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yongping Yang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhengrong Yang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew B. Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Richard A. Koup
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason G. Gall
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Q. Paula Lei
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R. Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Yang L, Caradonna TM, Schmidt AG, Chakraborty AK. Mechanisms that promote the evolution of cross-reactive antibodies upon vaccination with designed influenza immunogens. Cell Rep 2023; 42:112160. [PMID: 36867533 PMCID: PMC10184763 DOI: 10.1016/j.celrep.2023.112160] [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: 02/15/2022] [Revised: 07/18/2022] [Accepted: 02/09/2023] [Indexed: 03/04/2023] Open
Abstract
Immunogens that elicit broadly neutralizing antibodies targeting the conserved receptor-binding site (RBS) on influenza hemagglutinin may serve as candidates for a universal influenza vaccine. Here, we develop a computational model to interrogate antibody evolution by affinity maturation after immunization with two types of immunogens: a heterotrimeric "chimera" hemagglutinin that is enriched for the RBS epitope relative to other B cell epitopes and a cocktail composed of three non-epitope-enriched homotrimers of the monomers that comprise the chimera. Experiments in mice find that the chimera outperforms the cocktail for eliciting RBS-directed antibodies. We show that this result follows from an interplay between how B cells engage these antigens and interact with diverse helper T cells and requires T cell-mediated selection of germinal center B cells to be a stringent constraint. Our results shed light on antibody evolution and highlight how immunogen design and T cells modulate vaccination outcomes.
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Affiliation(s)
- Leerang Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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8
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Martina CE, Crowe JE, Meiler J. Glycan masking in vaccine design: Targets, immunogens and applications. Front Immunol 2023; 14:1126034. [PMID: 37033915 PMCID: PMC10076883 DOI: 10.3389/fimmu.2023.1126034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023] Open
Abstract
Glycan masking is a novel technique in reverse vaccinology in which sugar chains (glycans) are added on the surface of immunogen candidates to hide regions of low interest and thus focus the immune system on highly therapeutic epitopes. This shielding strategy is inspired by viruses such as influenza and HIV, which are able to escape the immune system by incorporating additional glycosylation and preventing the binding of therapeutic antibodies. Interestingly, the glycan masking technique is mainly used in vaccine design to fight the same viruses that naturally use glycans to evade the immune system. In this review we report the major successes obtained with the glycan masking technique in epitope-focused vaccine design. We focus on the choice of the target antigen, the strategy for immunogen design and the relevance of the carrier vector to induce a strong immune response. Moreover, we will elucidate the different applications that can be accomplished with glycan masking, such as shifting the immune response from hyper-variable epitopes to more conserved ones, focusing the response on known therapeutic epitopes, broadening the response to different viral strains/sub-types and altering the antigen immunogenicity to elicit higher or lower immune response, as desired.
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Affiliation(s)
- Cristina E. Martina
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
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9
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Kraft JC, Pham MN, Shehata L, Brinkkemper M, Boyoglu-Barnum S, Sprouse KR, Walls AC, Cheng S, Murphy M, Pettie D, Ahlrichs M, Sydeman C, Johnson M, Blackstone A, Ellis D, Ravichandran R, Fiala B, Wrenn S, Miranda M, Sliepen K, Brouwer PJM, Antanasijevic A, Veesler D, Ward AB, Kanekiyo M, Pepper M, Sanders RW, King NP. Antigen- and scaffold-specific antibody responses to protein nanoparticle immunogens. Cell Rep Med 2022; 3:100780. [PMID: 36206752 PMCID: PMC9589121 DOI: 10.1016/j.xcrm.2022.100780] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/27/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022]
Abstract
Protein nanoparticle scaffolds are increasingly used in next-generation vaccine designs, and several have established records of clinical safety and efficacy. Yet the rules for how immune responses specific to nanoparticle scaffolds affect the immunogenicity of displayed antigens have not been established. Here we define relationships between anti-scaffold and antigen-specific antibody responses elicited by protein nanoparticle immunogens. We report that dampening anti-scaffold responses by physical masking does not enhance antigen-specific antibody responses. In a series of immunogens that all use the same nanoparticle scaffold but display four different antigens, only HIV-1 envelope glycoprotein (Env) is subdominant to the scaffold. However, we also demonstrate that scaffold-specific antibody responses can competitively inhibit antigen-specific responses when the scaffold is provided in excess. Overall, our results suggest that anti-scaffold antibody responses are unlikely to suppress antigen-specific antibody responses for protein nanoparticle immunogens in which the antigen is immunodominant over the scaffold.
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Affiliation(s)
- John C Kraft
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Laila Shehata
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Mitch Brinkkemper
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Suna Cheng
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Mike Murphy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Blackstone
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Samuel Wrenn
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Marcos Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marion Pepper
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105 AZ Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
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10
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Lin WS, Chen IC, Chen HC, Lee YC, Wu SC. Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Front Immunol 2021; 12:795741. [PMID: 34925381 PMCID: PMC8674692 DOI: 10.3389/fimmu.2021.795741] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
Glycan-masking the vaccine antigen by mutating the undesired antigenic sites with an additional N-linked glycosylation motif can refocus B-cell responses to desired epitopes, without affecting the antigen's overall-folded structure. This study examined the impact of glycan-masking mutants of the N-terminal domain (NTD) and receptor-binding domain (RBD) of SARS-CoV-2, and found that the antigenic design of the S protein increases the neutralizing antibody titers against the Wuhan-Hu-1 ancestral strain and the recently emerged SARS-CoV-2 variants Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). Our results demonstrated that the use of glycan-masking Ad-S-R158N/Y160T in the NTD elicited a 2.8-fold, 6.5-fold, and 4.6-fold increase in the IC-50 NT titer against the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2) variants, respectively. Glycan-masking of Ad-S-D428N in the RBD resulted in a 3.0-fold and 2.0-fold increase in the IC-50 neutralization titer against the Alpha (B.1.1.7) and Beta (B.1.351) variants, respectively. The use of glycan-masking in Ad-S-R158N/Y160T and Ad-S-D428N antigen design may help develop universal COVID-19 vaccines against current and future emerging SARS-CoV-2 variants.
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Affiliation(s)
- Wei-Shuo Lin
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - I-Chen Chen
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Hui-Chen Chen
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Chien Lee
- Department of Infectious Diseases, Fu Jen Catholic University Hospital, New Taipei City, Taiwan
| | - Suh-Chin Wu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan.,Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
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11
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Shalash AO, Hussein WM, Skwarczynski M, Toth I. Key Considerations for the Development of Safe and Effective SARS-CoV-2 Subunit Vaccine: A Peptide-Based Vaccine Alternative. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100985. [PMID: 34176237 PMCID: PMC8373118 DOI: 10.1002/advs.202100985] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/18/2021] [Indexed: 05/14/2023]
Abstract
COVID-19 is disastrous to global health and the economy. SARS-CoV-2 infection exhibits similar clinical symptoms and immunopathological sequelae to SARS-CoV infection. Therefore, much of the developmental progress on SARS-CoV vaccines can be utilized for the development of SARS-CoV-2 vaccines. Careful antigen selection during development is always of utmost importance for the production of effective vaccines that do not compromise recipient safety. This holds especially true for SARS-CoV vaccines, as several immunopathological disorders are associated with the activity of structural and nonstructural proteins encoded in the virus's genetic material. Whole viral protein and RNA-encoding full-length proteins contain both protective and "dangerous" sequences, unless pathological fragments are deleted. In light of recent advances, peptide vaccines may present a very safe and effective alternative. Peptide vaccines can avoid immunopathological pro-inflammatory sequences, focus immune responses on neutralizing immunogenic epitopes, avoid off-target antigen loss, combine antigens with different protective roles or mechanisms, even from different viral proteins, and avoid mutant escape by employing highly conserved cryptic epitopes. In this review, an attempt is made to exploit the similarities between SARS-CoV and SARS-CoV-2 in vaccine antigen screening, with particular attention to the pathological and immunogenic properties of SARS proteins.
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Affiliation(s)
- Ahmed O. Shalash
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt. LuciaQLD4072Australia
| | - Waleed M. Hussein
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt. LuciaQLD4072Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt. LuciaQLD4072Australia
| | - Istvan Toth
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt. LuciaQLD4072Australia
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQLD4072Australia
- School of PharmacyThe University of QueenslandWoolloongabbaQLD4102Australia
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12
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LeBlanc EV, Kim Y, Capicciotti CJ, Colpitts CC. Hepatitis C Virus Glycan-Dependent Interactions and the Potential for Novel Preventative Strategies. Pathogens 2021; 10:pathogens10060685. [PMID: 34205894 PMCID: PMC8230238 DOI: 10.3390/pathogens10060685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infections continue to be a major contributor to liver disease worldwide. HCV treatment has become highly effective, yet there are still no vaccines or prophylactic strategies available to prevent infection and allow effective management of the global HCV burden. Glycan-dependent interactions are crucial to many aspects of the highly complex HCV entry process, and also modulate immune evasion. This review provides an overview of the roles of viral and cellular glycans in HCV infection and highlights glycan-focused advances in the development of entry inhibitors and vaccines to effectively prevent HCV infection.
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Affiliation(s)
- Emmanuelle V. LeBlanc
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada; (E.V.L.); (Y.K.); (C.J.C.)
| | - Youjin Kim
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada; (E.V.L.); (Y.K.); (C.J.C.)
| | - Chantelle J. Capicciotti
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada; (E.V.L.); (Y.K.); (C.J.C.)
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
- Department of Surgery, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Che C. Colpitts
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada; (E.V.L.); (Y.K.); (C.J.C.)
- Correspondence:
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13
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Zhang B, Chao CW, Tsybovsky Y, Abiona OM, Hutchinson GB, Moliva JI, Olia AS, Pegu A, Phung E, Stewart-Jones GBE, Verardi R, Wang L, Wang S, Werner A, Yang ES, Yap C, Zhou T, Mascola JR, Sullivan NJ, Graham BS, Corbett KS, Kwong PD. A platform incorporating trimeric antigens into self-assembling nanoparticles reveals SARS-CoV-2-spike nanoparticles to elicit substantially higher neutralizing responses than spike alone. Sci Rep 2020; 10:18149. [PMID: 33097791 PMCID: PMC7584627 DOI: 10.1038/s41598-020-74949-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022] Open
Abstract
Antigens displayed on self-assembling nanoparticles can stimulate strong immune responses and have been playing an increasingly prominent role in structure-based vaccines. However, the development of such immunogens is often complicated by inefficiencies in their production. To alleviate this issue, we developed a plug-and-play platform using the spontaneous isopeptide-bond formation of the SpyTag:SpyCatcher system to display trimeric antigens on self-assembling nanoparticles, including the 60-subunit Aquifex aeolicus lumazine synthase (LuS) and the 24-subunit Helicobacter pylori ferritin. LuS and ferritin coupled to SpyTag expressed well in a mammalian expression system when an N-linked glycan was added to the nanoparticle surface. The respiratory syncytial virus fusion (F) glycoprotein trimer-stabilized in the prefusion conformation and fused with SpyCatcher-could be efficiently conjugated to LuS-SpyTag or ferritin-SpyTag, enabling multivalent display of F trimers with prefusion antigenicity. Similarly, F-glycoprotein trimers from human parainfluenza virus-type 3 and spike-glycoprotein trimers from SARS-CoV-2 could be displayed on LuS nanoparticles with decent yield and antigenicity. Notably, murine vaccination with 0.08 µg of SARS-CoV-2 spike-LuS nanoparticle elicited similar neutralizing responses as 2.0 µg of spike, which was ~ 25-fold higher on a weight-per-weight basis. The versatile platform described here thus allows for multivalent plug-and-play presentation on self-assembling nanoparticles of trimeric viral antigens, with SARS-CoV-2 spike-LuS nanoparticles inducing particularly potent neutralizing responses.
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Affiliation(s)
- Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cara W Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Olubukola M Abiona
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Geoffrey B Hutchinson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Juan I Moliva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emily Phung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Institute for Biomedical Sciences, George Washington University, Washington, DC, USA
| | - Guillaume B E Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anne Werner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christina Yap
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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14
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Zhang B, Chao CW, Tsybovsky Y, Abiona OM, Hutchinson GB, Moliva JI, Olia AS, Pegu A, Phung E, Stewart-Jones G, Verardi R, Wang L, Wang S, Werner A, Yang ES, Yap C, Zhou T, Mascola JR, Sullivan NJ, Graham BS, Corbett KS, Kwong PD. A Platform Incorporating Trimeric Antigens into Self-Assembling Nanoparticles Reveals SARS-CoV-2-Spike Nanoparticles to Elicit Substantially Higher Neutralizing Responses than Spike Alone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.11.147496. [PMID: 32676596 PMCID: PMC7359518 DOI: 10.1101/2020.06.11.147496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Antigens displayed on self-assembling nanoparticles can stimulate strong immune responses and have been playing an increasingly prominent role in structure-based vaccines. However, the development of such immunogens is often complicated by inefficiencies in their production. To alleviate this issue, we developed a plug-and-play platform using the spontaneous isopeptide-bond formation of the SpyTag:SpyCatcher system to display trimeric antigens on self-assembling nanoparticles, including the 60-subunit Aquifex aeolicus lumazine synthase (LuS) and the 24-subunit Helicobacter pylori ferritin. LuS and ferritin coupled to SpyTag expressed well in a mammalian expression system when an N-linked glycan was added to the nanoparticle surface. The respiratory syncytial virus fusion (F) glycoprotein trimer - stabilized in the prefusion conformation and fused with SpyCatcher - could be efficiently conjugated to LuS-SpyTag or ferritin-SpyTag, enabling multivalent display of F trimers with prefusion antigenicity. Similarly, F-glycoprotein trimers from human parainfluenza virus-type 3 and spike-glycoprotein trimers from SARS-CoV-2 could be displayed on LuS nanoparticles with decent yield and antigenicity. Notably, murine vaccination with the SARS-CoV-2 spike-LuS nanoparticles elicited ~25-fold higher neutralizing responses, weight-per-weight relative to spike alone. The versatile platform described here thus allows for multivalent plug-and-play presentation on self-assembling nanoparticles of trimeric viral antigens, with SARS-CoV-2 spike-LuS nanoparticles inducing particularly potent neutralizing responses.
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Affiliation(s)
- Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Cara W. Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Olubukola M. Abiona
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Geoffrey B. Hutchinson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Juan I. Moliva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Adam S. Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Emily Phung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Institute for Biomedical Sciences, George Washington University, Washington, DC, USA
| | - Guillaume Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Anne Werner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Christina Yap
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kizzmekia S. Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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15
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Antibody Responses Elicited by Immunization with BG505 Trimer Immune Complexes. J Virol 2019; 93:JVI.01188-19. [PMID: 31375582 DOI: 10.1128/jvi.01188-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 11/20/2022] Open
Abstract
Immune complex (IC) vaccines have been successfully used to increase immune responses against various pathogens, including HIV-1. Additionally, IC vaccines can induce qualitatively different antibody responses, with distinct antigenic specificities compared to the same antigens used alone. Here we measured the HIV-1-specific antibody responses in female New Zealand White rabbits after immunization with ICs made from BG505 SOSIP.664 trimers (BG505 trimers) and three rabbit monoclonal antibodies (MAbs) with different neutralization profiles. Two of the MAbs were specific for a hole in the glycan shield of the BG505 trimer, while the third, which bound less avidly, was specific for determinants at the gp41-gp120 interface. We found that immunization with one of the glycan-hole-specific ICs resulted in lower levels of trimer-binding antibodies compared to vaccination with the uncomplexed trimer, and that ICs made using either of the glycan-hole-specific MAbs resulted in lower rates of anti-trimer antibody decay. We concluded that ICs based on MAbs that bound to the immunodominant glycan hole epitope likely diverted antibody responses, to some extent, away from this site and to other regions of the trimer. However, this outcome was not accompanied by a widening of the breadth or an increase in the potency of neutralizing antibody responses compared with uncomplexed trimers.IMPORTANCE Immunodominant epitopes may suppress immune responses to more desirable determinants, such as those that elicit potentially protective neutralizing antibody responses. To overcome this problem, we attempted to mask immunodominant glycan holes by immunizing rabbits with ICs consisting of the BG505 SOSIP.664 gp140 trimer and MAbs that targeted the glycan holes. We found that IC vaccination likely diverted antibody responses, to some extent, away from the glycan holes and toward other regions of the trimer. IC vaccination resulted in slower decay of HIV-1-specific antibodies than did immunization with uncomplexed trimer. We did not observe a widening of the breadth or an increase in the potency of neutralizing antibody responses compared to uncomplexed trimers. Our results suggest that selective epitope dampening of BG505 trimers by ICs is rather ineffective. However, IC vaccination may represent a novel means of increasing the duration of vaccine-induced antibody responses.
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16
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Protect, modify, deprotect (PMD): A strategy for creating vaccines to elicit antibodies targeting a specific epitope. Proc Natl Acad Sci U S A 2019; 116:9947-9952. [PMID: 31028143 PMCID: PMC6525525 DOI: 10.1073/pnas.1822062116] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The discovery of broadly neutralizing Abs (bnAbs) against infectious agents such as influenza virus and HIV-1 has sparked interest in creating vaccines that focus an Ab response toward a particular epitope of a protein. These “immunofocusing” strategies have shown promise but are also burdened with inherent limitations. We introduce an immunofocusing method called protect, modify, deprotect (PMD) that uses a bnAb as a molecular stencil to create vaccine candidates that direct the immune response toward the epitope of the bnAb. PMD has the potential to provide epitope-specific immunofocusing, in a generalizable manner. In creating vaccines against infectious agents, there is often a desire to direct an immune response toward a particular conformational epitope on an antigen. We present a method, called protect, modify, deprotect (PMD), to generate immunogenic proteins aimed to direct a vaccine-induced antibody (Ab) response toward an epitope defined by a specific monoclonal Ab (mAb). The mAb is used to protect the target epitope on the protein. Then the remaining exposed surfaces of the protein are modified to render them nonimmunogenic. Finally, the epitope is deprotected by removal of the mAb. The resultant protein is modified at surfaces other than the target epitope. We validate PMD using a well-characterized antigen, hen egg white lysozyme, then demonstrate the utility of PMD using influenza virus hemagglutinin (HA). We use an mAb to protect a highly conserved epitope on the stem domain of HA. Exposed surface amines are then modified with short polyethylene glycol chains. The resultant antigen shows markedly reduced binding to mAbs that target the head region of HA, while maintaining binding to mAbs at the epitope of interest. This antigenic preference is also observed with yeast cells displaying Ab fragments. Antisera from guinea pigs immunized with the PMD-modified HA show increased cross-reactivity with HAs from other influenza strains, compared with antisera obtained with unmodified HA trimers. PMD has the potential to direct an Ab response at high resolution and could be used in combination with other such strategies. There are many attractive targets for the application of PMD.
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17
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Urbanowicz RA, Wang R, Schiel JE, Keck ZY, Kerzic MC, Lau P, Rangarajan S, Garagusi KJ, Tan L, Guest JD, Ball JK, Pierce BG, Mariuzza RA, Foung SKH, Fuerst TR. Antigenicity and Immunogenicity of Differentially Glycosylated Hepatitis C Virus E2 Envelope Proteins Expressed in Mammalian and Insect Cells. J Virol 2019; 93:e01403-18. [PMID: 30651366 PMCID: PMC6430559 DOI: 10.1128/jvi.01403-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023] Open
Abstract
The development of a prophylactic vaccine for hepatitis C virus (HCV) remains a global health challenge. Cumulative evidence supports the importance of antibodies targeting the HCV E2 envelope glycoprotein to facilitate viral clearance. However, a significant challenge for a B cell-based vaccine is focusing the immune response on conserved E2 epitopes capable of eliciting neutralizing antibodies not associated with viral escape. We hypothesized that glycosylation might influence the antigenicity and immunogenicity of E2. Accordingly, we performed head-to-head molecular, antigenic, and immunogenic comparisons of soluble E2 (sE2) produced in (i) mammalian (HEK293) cells, which confer mostly complex- and high-mannose-type glycans; and (ii) insect (Sf9) cells, which impart mainly paucimannose-type glycans. Mass spectrometry demonstrated that all 11 predicted N-glycosylation sites were utilized in both HEK293- and Sf9-derived sE2, but that N-glycans in insect sE2 were on average smaller and less complex. Both proteins bound CD81 and were recognized by conformation-dependent antibodies. Mouse immunogenicity studies revealed that similar polyclonal antibody responses were generated against antigenic domains A to E of E2. Although neutralizing antibody titers showed that Sf9-derived sE2 induced moderately stronger responses than did HEK293-derived sE2 against the homologous HCV H77c isolate, the two proteins elicited comparable neutralization titers against heterologous isolates. Given that global alteration of HCV E2 glycosylation by expression in different hosts did not appreciably affect antigenicity or overall immunogenicity, a more productive approach to increasing the antibody response to neutralizing epitopes may be complete deletion, rather than just modification, of specific N-glycans proximal to these epitopes.IMPORTANCE The development of a vaccine for hepatitis C virus (HCV) remains a global health challenge. A major challenge for vaccine development is focusing the immune response on conserved regions of the HCV envelope protein, E2, capable of eliciting neutralizing antibodies. Modification of E2 by glycosylation might influence the immunogenicity of E2. Accordingly, we performed molecular and immunogenic comparisons of E2 produced in mammalian and insect cells. Mass spectrometry demonstrated that the predicted glycosylation sites were utilized in both mammalian and insect cell E2, although the glycan types in insect cell E2 were smaller and less complex. Mouse immunogenicity studies revealed similar polyclonal antibody responses. However, insect cell E2 induced stronger neutralizing antibody responses against the homologous isolate used in the vaccine, albeit the two proteins elicited comparable neutralization titers against heterologous isolates. A more productive approach for vaccine development may be complete deletion of specific glycans in the E2 protein.
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Affiliation(s)
- Richard A Urbanowicz
- School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and The University of Nottingham, Nottingham, United Kingdom
| | - Ruixue Wang
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - John E Schiel
- University of Maryland Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, Maryland, USA
| | - Zhen-Yong Keck
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Melissa C Kerzic
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Patrick Lau
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Sneha Rangarajan
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Kyle J Garagusi
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Lei Tan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Johnathan D Guest
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Jonathan K Ball
- School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and The University of Nottingham, Nottingham, United Kingdom
| | - Brian G Pierce
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Roy A Mariuzza
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Steven K H Foung
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas R Fuerst
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
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18
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Chen TH, Liu WC, Lin CY, Liu CC, Jan JT, Spearman M, Butler M, Wu SC. Glycan-masking hemagglutinin antigens from stable CHO cell clones for H5N1 avian influenza vaccine development. Biotechnol Bioeng 2018; 116:598-609. [PMID: 30080931 DOI: 10.1002/bit.26810] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/06/2018] [Accepted: 08/02/2018] [Indexed: 12/29/2022]
Abstract
Refocusing of B-cell responses can be achieved by preserving the overall fold of the antigen structure but selectively mutating the undesired antigenic sites with additional N-linked glycosylation motifs for glycan masking the vaccine antigen. We previously reported that glycan-masking recombinant H5 hemagglutinin (rH5HA) antigens on residues 83, 127, and 138 (g127 + g138 or g83 + g127 + 138 rH5HA) elicited broader neutralizing antibodies and protection against heterologous clades/subclades of high pathogenic avian influenza H5N1 viruses. In this study, we engineered the stably expressing Chinese hamster ovary (CHO) cell clones for producing the glycan-masking g127 + g138 and g83 + g127 + g138 rH5HA antigens. All of these glycan-masking rH5HA antigens produced in stable CHO cell clones were found to be mostly oligomeric structures. Only the immunization with the glycan-masking g127 + g138 but not g83 + g127 + g138 rH5HA antigens elicited more potent neutralizing antibody titers against four out of five heterologous clades/subclades of H5N1 viral strains. The increased neutralizing antibody titers against these heterologous viral strains were correlated with the increased amounts of stem-binding antibodies, only the glycan-masking g127 + g138 rH5HA antigens can translate into more protection against live viral challenges. The stable CHO cell line-produced glycan-masking g127 + g138 rH5HA can be used for H5N1 subunit vaccine development.
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Affiliation(s)
- Ting-Hsuan Chen
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Wen-Chun Liu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chia-Ying Lin
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chia-Chyi Liu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Jia-Tsrong Jan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Maureen Spearman
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael Butler
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Suh-Chin Wu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan.,Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
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19
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Duan H, Chen X, Boyington JC, Cheng C, Zhang Y, Jafari AJ, Stephens T, Tsybovsky Y, Kalyuzhniy O, Zhao P, Menis S, Nason MC, Normandin E, Mukhamedova M, DeKosky BJ, Wells L, Schief WR, Tian M, Alt FW, Kwong PD, Mascola JR. Glycan Masking Focuses Immune Responses to the HIV-1 CD4-Binding Site and Enhances Elicitation of VRC01-Class Precursor Antibodies. Immunity 2018; 49:301-311.e5. [PMID: 30076101 PMCID: PMC6896779 DOI: 10.1016/j.immuni.2018.07.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/11/2018] [Accepted: 07/09/2018] [Indexed: 11/18/2022]
Abstract
An important class of HIV-1 broadly neutralizing antibodies, termed the VRC01 class, targets the conserved CD4-binding site (CD4bs) of the envelope glycoprotein (Env). An engineered Env outer domain (OD) eOD-GT8 60-mer nanoparticle has been developed as a priming immunogen for eliciting VRC01-class precursors and is planned for clinical trials. However, a substantial portion of eOD-GT8-elicited antibodies target non-CD4bs epitopes, potentially limiting its efficacy. We introduced N-linked glycans into non-CD4bs surfaces of eOD-GT8 to mask irrelevant epitopes and evaluated these mutants in a mouse model that expressed diverse immunoglobulin heavy chains containing human IGHV1-2∗02, the germline VRC01 VH segment. Compared to the parental eOD-GT8, a mutant with five added glycans stimulated significantly higher proportions of CD4bs-specific serum responses and CD4bs-specific immunoglobulin G+ B cells including VRC01-class precursors. These results demonstrate that glycan masking can limit elicitation of off-target antibodies and focus immune responses to the CD4bs, a major target of HIV-1 vaccine design.
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Affiliation(s)
- Hongying Duan
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Xuejun Chen
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Cheng Cheng
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Oleksandr Kalyuzhniy
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Sergey Menis
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Martha C Nason
- Biostatistics Research Branch, Division of Clinical Research, NIAID, NIH, Bethesda, MD 20852, USA
| | - Erica Normandin
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Brandon J DeKosky
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Department of Chemical & Petroleum Engineering, The University of Kansas, Lawrence, KS 66045, USA; Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - William R Schief
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ming Tian
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Frederick W Alt
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Peter D Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA.
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20
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HIV-1 Vaccines Based on Antibody Identification, B Cell Ontogeny, and Epitope Structure. Immunity 2018; 48:855-871. [DOI: 10.1016/j.immuni.2018.04.029] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 12/12/2022]
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21
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Yu WH, Zhao P, Draghi M, Arevalo C, Karsten CB, Suscovich TJ, Gunn B, Streeck H, Brass AL, Tiemeyer M, Seaman M, Mascola JR, Wells L, Lauffenburger DA, Alter G. Exploiting glycan topography for computational design of Env glycoprotein antigenicity. PLoS Comput Biol 2018; 14:e1006093. [PMID: 29677181 PMCID: PMC5931682 DOI: 10.1371/journal.pcbi.1006093] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 05/02/2018] [Accepted: 03/16/2018] [Indexed: 11/20/2022] Open
Abstract
Mounting evidence suggests that glycans, rather than merely serving as a “shield”, contribute critically to antigenicity of the HIV envelope (Env) glycoprotein, representing critical antigenic determinants for many broadly neutralizing antibodies (bNAbs). While many studies have focused on defining the role of individual glycans or groups of proximal glycans in bNAb binding, little is known about the effects of changes in the overall glycan landscape in modulating antibody access and Env antigenicity. Here we developed a systems glycobiology approach to reverse engineer the complexity of HIV glycan heterogeneity to guide antigenicity-based de novo glycoprotein design. bNAb binding was assessed against a panel of 94 recombinant gp120 monomers exhibiting defined glycan site occupancies. Using a Bayesian machine learning algorithm, bNAb-specific glycan footprints were identified and used to design antigens that selectively alter bNAb antigenicity as a proof-of concept. Our approach provides a new design strategy to predictively modulate antigenicity via the alteration of glycan topography, thereby focusing the humoral immune response on sites of viral vulnerability for HIV. Carbohydrates on the HIV Env glycoprotein, previously often considered as a “shield” permitting immune evasion, can themselves represent targets for broadly neutralizing antibody (bNAb) recognition. Efforts to define the impact of individual glycans on bNAb recognition have clearly illustrated the critical nature of individual or groups of glycans on bNAb binding. However, glycans represent half the mass of the HIV envelope glycoprotein, representing a lattice of interacting sugars that shape the topographical landscape that alters antibody accessiblity to the underlying protein. However, whether alterations in individual glycans alter the broader interactions among glycans, proximal and distal, has not been heretofore rigorously examined, nor how this lattice may be actively exploited to improve antigenicity. To address this challenge, we describe here a systems glycobiology approach to reverse engineer the complex relationship between bNAb binding and glycan landscape effects on Env proteins spanning across various clades and tiers. Glycan occupancy was interrogated across every potential N-glycan site in 94 recombinant gp120 recombinant antigens. Sequences, glycan occupancy, as well as bNAb binding profiles were integrated across each of the 94-atngeins to generate a machine learning computational model enabling the identification of the glycan site determinants involved in binding to any given bNAb. Moreover, this model was used to generate a panel of novel gp120 variants with augmented selective bNAb binding profiles, further validating the contributions of glycans in Env antigen design. Whether glycan-optimization will additionally influence immunogenicity, particularly on emerging stabilized trimers, is unknown, but this study provides a proof of concept for selectively and agnostically exploiting both proximal and distal viral protein glycosylation in a principled manner to improve target Ab binding profiles.
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Affiliation(s)
- Wen-Han Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Peng Zhao
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia, United States of America
| | - Monia Draghi
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America
| | - Claudia Arevalo
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America
| | - Christina B Karsten
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America
| | - Todd J Suscovich
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America
| | - Bronwyn Gunn
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America
| | - Hendrik Streeck
- Institute for HIV Research, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Abraham L Brass
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia, United States of America
| | - Michael Seaman
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Lance Wells
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia, United States of America
| | - Douglas A Lauffenburger
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America
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22
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Behrens AJ, Seabright GE, Crispin M. Targeting Glycans of HIV Envelope Glycoproteins for Vaccine Design. CHEMICAL BIOLOGY OF GLYCOPROTEINS 2017. [DOI: 10.1039/9781782623823-00300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The surface of the envelope spike of the human immunodeficiency virus (HIV) is covered with a dense array of glycans, which is sufficient to impede the host antibody response while maintaining a window for receptor recognition. The glycan density significantly exceeds that typically observed on self glycoproteins and is sufficiently high to disrupt the maturation process of glycans, from oligomannose- to complex-type glycosylation, that normally occurs during glycoprotein transit through the secretory system. It is notable that this generates a degree of homogeneity not seen in the highly mutated protein moiety. The conserved, close glycan packing and divergences from default glycan processing give a window for immune recognition. Encouragingly, in a subset of individuals, broadly neutralizing antibodies (bNAbs) have been isolated that recognize these features and are protective in passive-transfer models. Here, we review the recent advances in our understanding of the glycan shield of HIV and outline the strategies that are being pursued to elicit glycan-binding bNAbs by vaccination.
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Affiliation(s)
- Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
| | - Gemma E. Seabright
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
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23
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Liu Q, Acharya P, Dolan MA, Zhang P, Guzzo C, Lu J, Kwon A, Gururani D, Miao H, Bylund T, Chuang GY, Druz A, Zhou T, Rice WJ, Wigge C, Carragher B, Potter CS, Kwong PD, Lusso P. Quaternary contact in the initial interaction of CD4 with the HIV-1 envelope trimer. Nat Struct Mol Biol 2017; 24:370-378. [PMID: 28218750 DOI: 10.1038/nsmb.3382] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/25/2017] [Indexed: 12/19/2022]
Abstract
Binding of the gp120 envelope (Env) glycoprotein to the CD4 receptor is the first step in the HIV-1 infectious cycle. Although the CD4-binding site has been extensively characterized, the initial receptor interaction has been difficult to study because of major CD4-induced structural rearrangements. Here we used cryogenic electron microscopy (cryo-EM) to visualize the initial contact of CD4 with the HIV-1 Env trimer at 6.8-Å resolution. A single CD4 molecule is embraced by a quaternary HIV-1-Env surface formed by coalescence of the previously defined CD4-contact region with a second CD4-binding site (CD4-BS2) in the inner domain of a neighboring gp120 protomer. Disruption of CD4-BS2 destabilized CD4-trimer interaction and abrogated HIV-1 infectivity by preventing the acquisition of coreceptor-binding competence. A corresponding reduction in HIV-1 infectivity occurred after the mutation of CD4 residues that interact with CD4-BS2. Our results document the critical role of quaternary interactions in the initial HIV-Env-receptor contact, with implications for treatment and vaccine design.
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Affiliation(s)
- Qingbo Liu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Priyamvada Acharya
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA
| | - Michael A Dolan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Peng Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Christina Guzzo
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Jacky Lu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Alice Kwon
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Deepali Gururani
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Huiyi Miao
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - William J Rice
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA
| | - Christoph Wigge
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Paolo Lusso
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
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24
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O'Connell RJ, Excler JL, Polonis VR, Ratto-Kim S, Cox J, Jagodzinski LL, Liu M, Wieczorek L, McNeil JG, El-Habib R, Michael NL, Gilliam BL, Paris R, VanCott TC, Tomaras GD, Birx DL, Robb ML, Kim JH. Safety and Immunogenicity of a Randomized Phase 1 Prime-Boost Trial With ALVAC-HIV (vCP205) and Oligomeric Glycoprotein 160 From HIV-1 Strains MN and LAI-2 Adjuvanted in Alum or Polyphosphazene. J Infect Dis 2016; 213:1946-54. [PMID: 26908741 DOI: 10.1093/infdis/jiw059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 02/03/2016] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Prime-boost regimens comprising ALVAC-HIV (prime) and human immunodeficiency virus type 1 (HIV) Env (boost) induce HIV-specific neutralizing antibody and cell-mediated immune responses, but the impact of boost schedule and adjuvant requires further definition. METHODS A phase 1 trial was conducted. In part A (open label), 19 volunteers received oligomeric glycoprotein 160 from HIV strains MN and LAI-2 (ogp160 MN/LAI-2) with dose escalation (25, 50, 100 μg) and either polyphosphazene (pP) or alum adjuvant. In part B, 72 volunteers received either placebo (n=12) or recombinant canarypox virus expressing HIV antigens (ALVAC-HIV [vCP205]) with different doses and schedules of ogp160 MN/LAI-2 in pP or alum (n = 60). RESULTS The vaccines were safe and well tolerated, with no vaccine-related serious adverse events. Anti-gp70 V1V2 antibody responses were detected in 17 of 19 part A volunteers (89%) and 10%-100% of part B volunteers. Use of a peripheral blood mononuclear cell-based assay revealed that US-1 primary isolate neutralization was induced in 2 of 19 recipients of ogp160 protein alone (10.5%) and 5 of 49 prime-boost volunteers (10.2%). Among ogp160 recipients, those who received pP were more likely than those who received alum to have serum that neutralized tier 2 viruses (12% vs 0%; P = .015). CONCLUSIONS Administration of ogp160 with pP induces primary isolate tier 2 neutralizing antibody responses in a small percentage of volunteers, demonstrating proof of concept and underscoring the importance of further optimization of prime-boost strategies for HIV infection prevention. CLINICAL TRIALS REGISTRATION NCT00004579.
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Affiliation(s)
- Robert J O'Connell
- Department of Retrovirology, US Army Medical Directorate, Armed Forces Institute of Medical Sciences, Bangkok, Thailand
| | - Jean-Louis Excler
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda US Military HIV Research Program
| | | | | | - Josephine Cox
- International AIDS Vaccine Initiative, New York, New York
| | | | - Michelle Liu
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda US Military HIV Research Program
| | | | | | | | | | - Bruce L Gilliam
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore
| | - Robert Paris
- US Military Malaria Research Program, Walter Reed Army Institute of Research, Silver Spring
| | | | | | | | - Merlin L Robb
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda US Military HIV Research Program
| | - Jerome H Kim
- US Military HIV Research Program International Vaccine Institute, Seoul, Republic of Korea
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25
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Sliepen K, Sanders RW. HIV-1 envelope glycoprotein immunogens to induce broadly neutralizing antibodies. Expert Rev Vaccines 2016; 15:349-65. [PMID: 26654478 DOI: 10.1586/14760584.2016.1129905] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The long pursuit for a vaccine against human immunodeficiency virus 1 (HIV-1) has recently been boosted by a number of exciting developments. An HIV-1 subunit vaccine ideally should elicit potent broadly neutralizing antibodies (bNAbs), but raising bNAbs by vaccination has proved extremely difficult because of the characteristics of the HIV-1 envelope glycoprotein complex (Env). However, the isolation of bNAbs from HIV-1-infected patients demonstrates that the human humoral immune system is capable of making such antibodies. Therefore, a focus of HIV-1 vaccinology is the elicitation of bNAbs by engineered immunogens and by using vaccination strategies aimed at mimicking the bNAb maturation pathways in HIV-infected patients. Important clues can also be taken from the successful subunit vaccines against hepatitis B virus and human papillomavirus. Here, we review the different types of HIV-1 immunogens and vaccination strategies that are being explored in the search for an HIV-1 vaccine that induces bNAbs.
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Affiliation(s)
- Kwinten Sliepen
- a Department of Medical Microbiology, Academic Medical Center , University of Amsterdam , Amsterdam , The Netherlands
| | - Rogier W Sanders
- a Department of Medical Microbiology, Academic Medical Center , University of Amsterdam , Amsterdam , The Netherlands.,b Department of Microbiology and Immunology , Weill Medical College of Cornell University , New York , NY , USA
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Yang Z, Li J, Liu Q, Yuan T, Zhang Y, Chen LQ, Lou Q, Sun Z, Ying H, Xu J, Dimitrov DS, Zhang MY. Identification of Non-HIV Immunogens That Bind to Germline b12 Predecessors and Prime for Elicitation of Cross-clade Neutralizing HIV-1 Antibodies. PLoS One 2015; 10:e0126428. [PMID: 26010511 PMCID: PMC4444298 DOI: 10.1371/journal.pone.0126428] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/02/2015] [Indexed: 12/19/2022] Open
Abstract
A fundamental challenge for developing an effective and safe HIV-1 vaccine is to identify vaccine immunogens that can initiate and maintain immune responses leading to elicitation of broadly neutralizing HIV-1 antibodies (bnAbs) through complex maturation pathways. We have previously found that HIV-1 envelope glycoproteins (Env) lack measurable binding to putative germline predecessors of known bnAbs and proposed to search for non-HIV immunogens that could initiate their somatic maturation. Using bnAb b12 as a model bnAb and yeast display technology, we isolated five (poly)peptides from plant leaves, insects, E. coli strains, and sea water microbes that bind to b12 putative germline and intermediate antibodies. Rabbit immunization with the (poly)peptides alone induced high titers of cross-reactive antibodies that neutralized HIV-1 isolates SF162 and JRFL. Priming rabbits with the (poly)peptides followed by boosts with trimeric gp140SF162 and then resurfaced Env (RSC3) induced antibodies that competed with mature b12 and neutralized tier 1 and 2 viruses from clade B, C and E, while control rabbits without (poly)peptide priming induced antibodies that did not compete with mature b12 and neutralized fewer isolates. The degree of competition with mature b12 for binding to gp140SF162 correlated with the neutralizing activity of the rabbit IgG. Reversing the order of the two boosting immunogens significantly affected the binding profile and neutralization potency of the rabbit IgG. Our study is the first to provide evidence that appears to support the concept that non-HIV immunogens may initiate immune responses leading to elicitation of cross-clade neutralizing antibodies.
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Affiliation(s)
- Zheng Yang
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Jingjing Li
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Qingsheng Liu
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Tingting Yuan
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Yanyu Zhang
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Li-Qing Chen
- Center of Laboratory Animals, Zhejiang Academy of Medical Sciences, Zhejiang, China
| | - Qi Lou
- Center of Laboratory Animals, Zhejiang Academy of Medical Sciences, Zhejiang, China
| | - Zehua Sun
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Huazhong Ying
- Center of Laboratory Animals, Zhejiang Academy of Medical Sciences, Zhejiang, China
| | - Jianqing Xu
- Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Dimiter S. Dimitrov
- Protein Interactions group, Laboratory of Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
| | - Mei-Yun Zhang
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
- Liver Disease Institute, Shenzhen Third People’s Hospital, Shenzhen, 518112, China
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Wang S, Mata-Fink J, Kriegsman B, Hanson M, Irvine DJ, Eisen HN, Burton DR, Wittrup KD, Kardar M, Chakraborty AK. Manipulating the selection forces during affinity maturation to generate cross-reactive HIV antibodies. Cell 2015; 160:785-797. [PMID: 25662010 PMCID: PMC4357364 DOI: 10.1016/j.cell.2015.01.027] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/03/2014] [Accepted: 12/19/2014] [Indexed: 01/16/2023]
Abstract
Generation of potent antibodies by a mutation-selection process called affinity maturation is a key component of effective immune responses. Antibodies that protect against highly mutable pathogens must neutralize diverse strains. Developing effective immunization strategies to drive their evolution requires understanding how affinity maturation happens in an environment where variants of the same antigen are present. We present an in silico model of affinity maturation driven by antigen variants which reveals that induction of cross-reactive antibodies often occurs with low probability because conflicting selection forces, imposed by different antigen variants, can frustrate affinity maturation. We describe how variables such as temporal pattern of antigen administration influence the outcome of this frustrated evolutionary process. Our calculations predict, and experiments in mice with variant gp120 constructs of the HIV envelope protein confirm, that sequential immunization with antigen variants is preferred over a cocktail for induction of cross-reactive antibodies focused on the shared CD4 binding site epitope.
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Affiliation(s)
- Shenshen Wang
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jordi Mata-Fink
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Barry Kriegsman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Melissa Hanson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Darrell J Irvine
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Herman N Eisen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Dennis R Burton
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - K Dane Wittrup
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Arup K Chakraborty
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139.
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28
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Boes A, Spiegel H, Edgue G, Kapelski S, Scheuermayer M, Fendel R, Remarque E, Altmann F, Maresch D, Reimann A, Pradel G, Schillberg S, Fischer R. Detailed functional characterization of glycosylated and nonglycosylated variants of malaria vaccine candidate PfAMA1 produced in Nicotiana benthamiana and analysis of growth inhibitory responses in rabbits. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:222-34. [PMID: 25236489 DOI: 10.1111/pbi.12255] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 08/07/2014] [Accepted: 08/10/2014] [Indexed: 06/03/2023]
Abstract
One of the most promising malaria vaccine candidate antigens is the Plasmodium falciparum apical membrane antigen 1 (PfAMA1). Several studies have shown that this blood-stage antigen can induce strong parasite growth inhibitory antibody responses. PfAMA1 contains up to six recognition sites for N-linked glycosylation, a post-translational modification that is absent in P. falciparum. To prevent any potential negative impact of N-glycosylation, the recognition sites have been knocked out in most PfAMA1 variants expressed in eukaryotic hosts. However, N-linked glycosylation may increase efficacy by improving immunogenicity and/or focusing the response towards relevant epitopes by glycan masking. We describe the production of glycosylated and nonglycosylated PfAMA1 in Nicotiana benthamiana and its detailed characterization in terms of yield, integrity and protective efficacy. Both PfAMA1 variants accumulated to high levels (>510 μg/g fresh leaf weight) after transient expression, and high-mannose-type N-glycans were confirmed for the glycosylated variant. No significant differences between the N. benthamiana and Pichia pastoris PfAMA1 variants were detected in conformation-sensitive ligand-binding studies. Specific titres of >2 × 10(6) were induced in rabbits, and strong reactivity with P. falciparum schizonts was observed in immunofluorescence assays, as well as up to 100% parasite growth inhibition for both variants, with IC₅₀ values of ~35 μg/mL. Competition assays indicated that a number of epitopes were shielded from immune recognition by N-glycans, warranting further studies to determine how glycosylation can be used for the directed targeting of immune responses. These results highlight the potential of plant transient expression systems as a production platform for vaccine candidates.
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Affiliation(s)
- Alexander Boes
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
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29
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Toukach PV, Egorova KS. Bacterial, plant, and fungal carbohydrate structure databases: daily usage. Methods Mol Biol 2015; 1273:55-85. [PMID: 25753703 DOI: 10.1007/978-1-4939-2343-4_5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Natural carbohydrates play important roles in living systems and therefore are used as diagnostic and therapeutic targets. The main goal of glycomics is systematization of carbohydrates and elucidation of their role in human health and disease. The amount of information on natural carbohydrates accumulates rapidly, but scientists still lack databases and computer-assisted tools needed for orientation in the glycomic information space. Therefore, freely available, regularly updated, and cross-linked databases are demanded. Bacterial Carbohydrate Structure Database (Bacterial CSDB) was developed for provision of structural, bibliographic, taxonomic, NMR spectroscopic, and other related information on bacterial and archaeal carbohydrate structures. Its main features are (1) coverage above 90%, (2) high data consistence (above 90% of error-free records), and (3) presence of manually verified bibliographic, NMR spectroscopic, and taxonomic annotations. Recently, CSDB has been expanded to cover carbohydrates of plant and fungal origin. The achievement of full coverage in the plant and fungal domains is expected in the future. CSDB is freely available on the Internet as a web service at http://csdb.glycoscience.ru. This chapter aims at showing how to use CSDB in your daily scientific practice.
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Affiliation(s)
- Philip V Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow, 119991, Russia,
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30
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Bowles EJ, Schiffner T, Rosario M, Needham GA, Ramaswamy M, McGouran J, Kessler B, LaBranche C, McMichael AJ, Montefiori D, Sattentau QJ, Hanke T, Stewart-Jones GBE. Comparison of neutralizing antibody responses elicited from highly diverse polyvalent heterotrimeric HIV-1 gp140 cocktail immunogens versus a monovalent counterpart in rhesus macaques. PLoS One 2014; 9:e114709. [PMID: 25490553 PMCID: PMC4260879 DOI: 10.1371/journal.pone.0114709] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 11/12/2014] [Indexed: 12/22/2022] Open
Abstract
Eliciting neutralizing antibodies capable of inactivating a broad spectrum of HIV-1 strains is a major goal of HIV-1 vaccine design. The challenge is that envelopes (Envs) of circulating viruses are almost certainly different from any Env used in a vaccine. A novel immunogen composed of a highly diverse set of gp140 Envs including subtypes A, B, C, D and F was developed to stimulate a more cross-neutralizing antibody response. Env heterotrimers composed of up to 54 different gp140s were produced with the aim of focusing the response to the conserved regions of Env while reducing the dominance of any individual hypervariable region. Heterotrimeric gp140 Envs of inter- and intra-subtype combinations were shown to bind CD4 and a panel of neutralizing monoclonal antibodies with similar affinity to monovalent UG37 gp140. Macaques immunized with six groups of heterotrimer mixtures showed slightly more potent neutralizing antibody responses in TZM-BL tier 1 and A3R5 tier 2 pseudovirus assays than macaques immunized with monovalent Env gp140, and exhibited a marginally greater focus on the CD4-binding site. Carbopol enhanced neutralization when used as an adjuvant instead of RIBI in combination with UG37 gp140. These data indicate that cross-subtype heterotrimeric gp140 Envs may elicit some improvement of the neutralizing antibody response in macaques compared to monovalent gp140 Env.
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Affiliation(s)
- Emma J. Bowles
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
- * E-mail: (EJB); (GSJ)
| | - Torben Schiffner
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Maximillian Rosario
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
| | - Gemma A. Needham
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Meghna Ramaswamy
- Division of Retrovirology, Centre for AIDS Reagents, National Institute of Biological Standards and Control, South Mimms, Potters Bar, Herts, United Kingdom
| | - Joanna McGouran
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt Kessler
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Celia LaBranche
- Division of Surgical Sciences, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Andrew J. McMichael
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
| | - David Montefiori
- Division of Surgical Sciences, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Quentin J. Sattentau
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Tomáš Hanke
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, United Kingdom
| | - Guillaume B. E. Stewart-Jones
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
- * E-mail: (EJB); (GSJ)
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31
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Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries. PLoS One 2014; 9:e114159. [PMID: 25473968 PMCID: PMC4256389 DOI: 10.1371/journal.pone.0114159] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/04/2014] [Indexed: 12/22/2022] Open
Abstract
There is a need for techniques capable of identifying the antigenic epitopes targeted by polyclonal antibody responses during deliberate or natural immunization. Although successful, traditional phage library screening is laborious and can map only some of the epitopes. To accelerate and improve epitope identification, we have employed massive sequencing of phage-displayed antigen-specific libraries using the Illumina MiSeq platform. This enabled us to precisely identify the regions of a model antigen, the meningococcal NadA virulence factor, targeted by serum antibodies in vaccinated individuals and to rank hundreds of antigenic fragments according to their immunoreactivity. We found that next generation sequencing can significantly empower the analysis of antigen-specific libraries by allowing simultaneous processing of dozens of library/serum combinations in less than two days, including the time required for antibody-mediated library selection. Moreover, compared with traditional plaque picking, the new technology (named Phage-based Representation OF Immuno-Ligand Epitope Repertoire or PROFILER) provides superior resolution in epitope identification. PROFILER seems ideally suited to streamline and guide rational antigen design, adjuvant selection, and quality control of newly produced vaccines. Furthermore, this method is also susceptible to find important applications in other fields covered by traditional quantitative serology.
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32
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Hyperglycosylated stable core immunogens designed to present the CD4 binding site are preferentially recognized by broadly neutralizing antibodies. J Virol 2014; 88:14002-16. [PMID: 25253346 DOI: 10.1128/jvi.02614-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED The HIV-1 surface envelope glycoprotein (Env) trimer mediates entry into CD4(+) CCR5(+) host cells. Env possesses conserved antigenic determinants, such as the gp120 primary receptor CD4 binding site (CD4bs), a known neutralization target. Env also contains variable regions and protein surfaces occluded within the trimer that elicit nonneutralizing antibodies. Here we engineered additional N-linked glycans onto a cysteine-stabilized gp120 core (0G) deleted of its major variable regions to preferentially expose the conformationally fixed CD4bs. Three, 6, 7, and 10 new NXT/S glycan (G) motifs were engineered into 0G to encode 3G, 6G, 7G, and 10G cores. Following purification, most glycoproteins, except for 10G, were recognized by broadly neutralizing CD4bs-directed antibodies. Gel and glycan mass spectrometry confirmed that additional N-glycans were posttranslationally added to the redesigned cores. Binding kinetics revealed high-affinity recognition by seven broadly neutralizing CD4bs-directed antibodies and low to no binding by non-broadly neutralizing CD4bs-directed antibodies. Rabbits inoculated with the hyperglycosylated cores elicited IgM and IgG responses to each given protein that were similar in their neutralization characteristics to those elicited by parental 0G. Site-specific glycan masking effects were detected in the elicited sera, and the antisera competed with b12 for CD4bs-directed binding specificity. However, the core-elicited sera showed limited neutralization activity. Trimer priming or boosting of the core immunogens elicited tier 1-level neutralization that mapped to both the CD4bs and V3 and appeared to be trimer dependent. Fine mapping at the CD4bs indicated that conformational stabilization of the cores and addition of N-glycans altered the molecular surface of Env sites of vulnerability to neutralizing antibody, suggesting an explanation for why the elicited neutralization was not improved by this rational design strategy. IMPORTANCE Major obstacles to developing an effective HIV-1 vaccine include the variability of the envelope surface glycoproteins and its high-density glycan shield, generated by incorporation of host (human) glycosylation. HIV-1 does harbor highly conserved sites on the exposed envelope protein surface of gp120, one of which is the virus receptor (CD4) binding site. Several broadly neutralizing antibodies elicited from HIV patients do target this gp120 CD4 binding site (CD4bs); however, gp120 immunogens do not elicit broadly neutralizing antibodies. In this study, we targeted the CD4bs by conformational stabilization and additional glycan masking. We used the atomic-level structure to reengineer gp120 cores to preferentially present the cysteine-stabilized CD4bs and to mask (by glycan) nonneutralizing determinants. Importantly, glycan masking did successfully focus antibody responses to the CD4bs; however, the elicited CD4bs-directed antibodies did not neutralize HIV or bind to unmodified gp120, presumably due to the structure-guided modifications of the modified gp120 core.
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Ball JK, Tarr AW, McKeating JA. The past, present and future of neutralizing antibodies for hepatitis C virus. Antiviral Res 2014; 105:100-11. [PMID: 24583033 PMCID: PMC4034163 DOI: 10.1016/j.antiviral.2014.02.013] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/08/2014] [Accepted: 02/13/2014] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus (HCV) is a major cause of liver disease and hepatocellular carcinoma worldwide. HCV establishes a chronic infection in the majority of cases. However, some individuals clear the virus, demonstrating a protective role for the host immune response. Although new all-oral drug combinations may soon replace traditional ribavirin-interferon therapy, the emerging drug cocktails will be expensive and associated with side-effects and resistance, making a global vaccine an urgent priority. T cells are widely accepted to play an essential role in clearing acute HCV infection, whereas the role antibodies play in resolution and disease pathogenesis is less well understood. Recent studies have provided an insight into viral neutralizing determinants and the protective role of antibodies during infection. This review provides a historical perspective of the role neutralizing antibodies play in HCV infection and discusses the therapeutic benefits of antibody-based therapies. This article forms part of a symposium in Antiviral Research on "Hepatitis C: next steps toward global eradication."
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Affiliation(s)
- Jonathan K Ball
- School of Life Sciences and The Nottingham Digestive Diseases Centre Biomedical Research Unit, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Alexander W Tarr
- School of Life Sciences and The Nottingham Digestive Diseases Centre Biomedical Research Unit, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Jane A McKeating
- Viral Hepatitis Research Group and Centre for Human Virology, Institute for Biomedical Research, University of Birmingham, Birmingham B15 2TT, United Kingdom.
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Abstract
The development of an effective vaccine has been hindered by the enormous diversity of human immunodeficiency virus-1 (HIV-1) and its ability to escape a myriad of host immune responses. In addition, conserved vulnerable regions on the HIV-1 envelope glycoprotein are often poorly immunogenic and elicit broadly neutralizing antibody responses (BNAbs) in a minority of HIV-1-infected individuals and only after several years of infection. All of the known BNAbs demonstrate high levels of somatic mutations and often display other unusual traits, such as a long heavy chain complementarity determining region 3 (CDRH3) and autoreactivity that can be limited by host tolerance controls. Nonetheless, the demonstration that HIV-1-infected individuals can make potent BNAbs is encouraging, and recent progress in isolating such antibodies and mapping their immune pathways of development is providing new strategies for vaccination.
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Affiliation(s)
- John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
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35
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Sampath S, Carrico C, Janes J, Gurumoorthy S, Gibson C, Melcher M, Chitnis CE, Wang R, Schief WR, Smith JD. Glycan masking of Plasmodium vivax Duffy Binding Protein for probing protein binding function and vaccine development. PLoS Pathog 2013; 9:e1003420. [PMID: 23853575 PMCID: PMC3681752 DOI: 10.1371/journal.ppat.1003420] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 04/30/2013] [Indexed: 11/19/2022] Open
Abstract
Glycan masking is an emerging vaccine design strategy to focus antibody responses to specific epitopes, but it has mostly been evaluated on the already heavily glycosylated HIV gp120 envelope glycoprotein. Here this approach was used to investigate the binding interaction of Plasmodium vivax Duffy Binding Protein (PvDBP) and the Duffy Antigen Receptor for Chemokines (DARC) and to evaluate if glycan-masked PvDBPII immunogens would focus the antibody response on key interaction surfaces. Four variants of PVDBPII were generated and probed for function and immunogenicity. Whereas two PvDBPII glycosylation variants with increased glycan surface coverage distant from predicted interaction sites had equivalent binding activity to wild-type protein, one of them elicited slightly better DARC-binding-inhibitory activity than wild-type immunogen. Conversely, the addition of an N-glycosylation site adjacent to a predicted PvDBP interaction site both abolished its interaction with DARC and resulted in weaker inhibitory antibody responses. PvDBP is composed of three subdomains and is thought to function as a dimer; a meta-analysis of published PvDBP mutants and the new DBPII glycosylation variants indicates that critical DARC binding residues are concentrated at the dimer interface and along a relatively flat surface spanning portions of two subdomains. Our findings suggest that DARC-binding-inhibitory antibody epitope(s) lie close to the predicted DARC interaction site, and that addition of N-glycan sites distant from this site may augment inhibitory antibodies. Thus, glycan resurfacing is an attractive and feasible tool to investigate protein structure-function, and glycan-masked PvDBPII immunogens might contribute to P. vivax vaccine development. An important goal of many vaccine efforts is to inhibit pathogen invasion of host cells, but few approaches exist to target vaccine antibodies on invasion blocking epitopes. Glycan masking is a vaccine design strategy to hide protein surfaces with carbohydrates and focus antibodies on exposed surfaces. This approach has mostly been evaluated on the heavily glycosylated HIV envelope glycoprotein, but it has never been tested on eukaryotic pathogens, such as Plasmodium, which have limited N-glycosylation machinery and therefore may provide a better platform to explore this strategy. Here, we used glycan masking to investigate the binding interaction between Plasmodium vivax Duffy binding protein (PvDBP) and the Duffy Antigen Receptor for Chemokines (DARC). This study showed that addition of an N-glycan site in a predicted host interaction surface abolished binding and potentially covered up an inhibitory antibody epitope. In contrast, addition of multiple N-glycan sites distant from predicted interaction surfaces did not inhibit binding but did slightly enhance elicitation of inhibitory antibodies. This analysis shows that glycan resurfacing offers an integrated approach to characterize protein function and immunogenicity and that glycan resurfacing of PvDBPII immunogens may have utility in P. vivax-malaria vaccine development.
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Affiliation(s)
- Sowmya Sampath
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Chris Carrico
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Joel Janes
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Sairam Gurumoorthy
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Claire Gibson
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Martin Melcher
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Chetan E. Chitnis
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Ruobing Wang
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - William R. Schief
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (WRS); (JDS)
| | - Joseph D. Smith
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Pathobiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (WRS); (JDS)
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36
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Bhattacharyya S, Singh P, Rathore U, Purwar M, Wagner D, Arendt H, DeStefano J, LaBranche CC, Montefiori DC, Phogat S, Varadarajan R. Design of an Escherichia coli expressed HIV-1 gp120 fragment immunogen that binds to b12 and induces broad and potent neutralizing antibodies. J Biol Chem 2013; 288:9815-9825. [PMID: 23430741 DOI: 10.1074/jbc.m112.425959] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
b12, one of the few broadly neutralizing antibodies against HIV-1, binds to the CD4 binding site (CD4bs) on the gp120 subunit of HIV-1 Env. Two small fragments of HIV-1 gp120, b121a and b122a, which display about 70% of the b12 epitope and include solubility-enhancing mutations, were designed. Bacterially expressed b121a/b122a were partially folded and could bind b12 but not the CD4bs-directed non-neutralizing antibody b6. Sera from rabbits primed with b121a or b122a protein fragments and boosted with full-length gp120 showed broad neutralizing activity in a TZM-bl assay against a 16-virus panel that included nine Tier 2 and 3 viruses as well as in a five-virus panel previously designed to screen for broad neutralization. Using a mean IC50 cut-off of 50, sera from control rabbits immunized with gp120 alone neutralized only one virus of the 14 non-Tier 1 viruses tested (7%), whereas sera from b121a- and b122a-immunized rabbits neutralized seven (50%) and twelve (86%) viruses, respectively. Serum depletion studies confirmed that neutralization was gp120-directed and that sera from animals immunized with gp120 contained lower amounts of CD4bs-directed antibodies than corresponding sera from animals immunized with b121a/b122a. Competition binding assays with b12 also showed that b121a/2a sera contained significantly higher amounts of antibodies directed toward the CD4 binding site than the gp120 sera. The data demonstrate that it is possible to elicit broadly neutralizing sera against HIV-1 in small animals.
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Affiliation(s)
| | - Pranveer Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ujjwal Rathore
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Mansi Purwar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Denise Wagner
- AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative, New York, New York 11220
| | - Heather Arendt
- AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative, New York, New York 11220
| | - Joanne DeStefano
- AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative, New York, New York 11220
| | - Celia C LaBranche
- Department of Surgery, Duke University, Durham, North Carolina 27705
| | | | - Sanjay Phogat
- AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative, New York, New York 11220.
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064, India; AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative, New York, New York 11220.
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37
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Hoot S, McGuire AT, Cohen KW, Strong RK, Hangartner L, Klein F, Diskin R, Scheid JF, Sather DN, Burton DR, Stamatatos L. Recombinant HIV envelope proteins fail to engage germline versions of anti-CD4bs bNAbs. PLoS Pathog 2013; 9:e1003106. [PMID: 23300456 PMCID: PMC3536657 DOI: 10.1371/journal.ppat.1003106] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/10/2012] [Indexed: 12/16/2022] Open
Abstract
Vaccine candidates for HIV-1 so far have not been able to elicit broadly neutralizing antibodies (bNAbs) although they express the epitopes recognized by bNAbs to the HIV envelope glycoprotein (Env). To understand whether and how Env immunogens interact with the predicted germline versions of known bNAbs, we screened a large panel (N:56) of recombinant Envs (from clades A, B and C) for binding to the germline predecessors of the broadly neutralizing anti-CD4 binding site antibodies b12, NIH45-46 and 3BNC60. Although the mature antibodies reacted with diverse Envs, the corresponding germline antibodies did not display Env-reactivity. Experiments conducted with engineered chimeric antibodies combining the mature and germline heavy and light chains, respectively and vice-versa, revealed that both antibody chains are important for the known cross-reactivity of these antibodies. Our results also indicate that in order for b12 to display its broad cross-reactivity, multiple somatic mutations within its VH region are required. A consequence of the failure of the germline b12 to bind recombinant soluble Env is that Env-induced B-cell activation through the germline b12 BCR does not take place. Our study provides a new explanation for the difficulties in eliciting bNAbs with recombinant soluble Env immunogens. Our study also highlights the need for intense efforts to identify rare naturally occurring or engineered Envs that may engage the germline BCR versions of bNAbs. Recombinant HIV Envelope glycoproteins (Env), the sole target of anti-HIV neutralizing antibodies, have, so far, not been able to elicit broadly neutralizing antibodies (bNAbs) although they express the corresponding epitopes. Such constructs elicit neutralizing antibodies of very narrow neutralizing breadth; antibodies whose epitopes are primarily located within variable domains of Env. Diverse approaches that have been evaluated over the past two decades to overcome this limitation were met with limited success. The exact reasons for the lack of elicitation of bNAbs during immunization with Env are not well understood. Here we show that recombinant Env proteins are inefficient in engaging the predicted germline BCRs of known bnAbs. Thus, our study provides new insights as to why recombinant Env immunogens have failed to elicit bNAbs. Our results indicate that, as a first step in eliciting bNAbs by immunization, Env immunogens should be designed that would engage the germline BCR versions of bNAbs.
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Affiliation(s)
- Sam Hoot
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Andrew T. McGuire
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Kristen W. Cohen
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- University of Washington, Department of Global Health, Seattle, Washington, United States of America
| | - Roland K. Strong
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lars Hangartner
- Department of Immunology, IAVI Neutralizing Antibody Center and Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America
| | - Florian Klein
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - Ron Diskin
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Johannes F. Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - D. Noah Sather
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Dennis R. Burton
- Department of Immunology, IAVI Neutralizing Antibody Center and Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - Leonidas Stamatatos
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- University of Washington, Department of Global Health, Seattle, Washington, United States of America
- * E-mail:
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38
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Mata-Fink J, Kriegsman B, Yu HX, Zhu H, Hanson MC, Irvine DJ, Wittrup KD. Rapid conformational epitope mapping of anti-gp120 antibodies with a designed mutant panel displayed on yeast. J Mol Biol 2012; 425:444-56. [PMID: 23159556 PMCID: PMC3785227 DOI: 10.1016/j.jmb.2012.11.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 11/16/2022]
Abstract
gp120 is a substrate for protein engineering both for human immunodeficiency virus (HIV) immunogen design and as a bait for isolating anti-HIV antibodies from patient samples. In this work, we describe the display of a stripped core gp120 on the yeast cell surface. Validation against a panel of neutralizing antibodies confirms that yeast-displayed gp120 presents the CD4 binding site in the correct conformation. We map the epitope of the broadly neutralizing anti-gp120 antibody VRC01 using both a random mutagenesis library and a defined mutant panel and find that the resultant epitope maps are consistent with one another and with the crystallographically identified contact residues. Mapping the VRC01-competitive antibodies b12 and b13 reveals energetic differences in their epitopes that are not obvious from existing crystal structures. These data suggest mutation sets that abrogate binding to broadly neutralizing antibodies with greater specificity than the canonical mutation D368R, useful in rapidly assessing the nature of a vaccine response.
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Affiliation(s)
- Jordi Mata-Fink
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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39
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Affiliation(s)
- K. S. Egorova
- N.D. Zelinsky Institute of Organic Chemistry, Leninsky prospekt 47, 119991 Moscow,
Russian Federation
| | - Ph. V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Leninsky prospekt 47, 119991 Moscow,
Russian Federation
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40
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Abstract
Although vaccines have proven life saving against a myriad of infectious diseases, various pathogens have remained refractory to prophylaxis of their host by active immunization. New insights in the three dimensional (3D) structure, domain organization and dynamics of viral and bacterial surface proteins can guide the design of effective vaccines in several ways. In this review we highlight recent developments in structure-based vaccine design that are aimed at stabilization of native conformations and focusing immune response to conserved epitopes. Detailed 3D structures of pathogen surface proteins provide knowledge on how to minimize complex antigens or how to redesign the surface of an immunogen in order to induce only relevant neutralizing antibodies against a broad range of serotypes. Structure - based vaccines with reduced complexity and broad efficacy could greatly enhance the number of people that might benefit from the therapies that are developed.
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Affiliation(s)
- Jaap W Back
- Pepscan Therapeutics, Lelystad, The Netherlands
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41
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Chuang GY, Boyington JC, Joyce MG, Zhu J, Nabel GJ, Kwong PD, Georgiev I. Computational prediction of N-linked glycosylation incorporating structural properties and patterns. ACTA ACUST UNITED AC 2012; 28:2249-55. [PMID: 22782545 DOI: 10.1093/bioinformatics/bts426] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION N-linked glycosylation occurs predominantly at the N-X-T/S motif, where X is any amino acid except proline. Not all N-X-T/S sequons are glycosylated, and a number of web servers for predicting N-linked glycan occupancy using sequence and/or residue pattern information have been developed. None of the currently available servers, however, utilizes protein structural information for the prediction of N-glycan occupancy. RESULTS Here, we describe a novel classifier algorithm, NGlycPred, for the prediction of glycan occupancy at the N-X-T/S sequons. The algorithm utilizes both structural as well as residue pattern information and was trained on a set of glycosylated protein structures using the Random Forest algorithm. The best predictor achieved a balanced accuracy of 0.687 under 10-fold cross-validation on a curated dataset of 479 N-X-T/S sequons and outperformed sequence-based predictors when evaluated on the same dataset. The incorporation of structural information, including local contact order, surface accessibility/composition and secondary structure thus improves the prediction accuracy of glycan occupancy at the N-X-T/S consensus sequon. AVAILABILITY AND IMPLEMENTATION NGlycPred is freely available to non-commercial users as a web-based server at http://exon.niaid.nih.gov/nglycpred/.
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Affiliation(s)
- Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA 20892, USA
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42
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Van Regenmortel MHV. Basic research in HIV vaccinology is hampered by reductionist thinking. Front Immunol 2012; 3:194. [PMID: 22787464 PMCID: PMC3391733 DOI: 10.3389/fimmu.2012.00194] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/21/2012] [Indexed: 01/05/2023] Open
Abstract
This review describes the structure-based reverse vaccinology approach aimed at developing vaccine immunogens capable of inducing antibodies that broadly neutralize HIV-1. Some basic principles of protein immunochemistry are reviewed and the implications of the extensive polyspecificity of antibodies for vaccine development are underlined. Although it is natural for investigators to want to know the cause of an effective immunological intervention, the classic notion of causality is shown to have little explanatory value for a system as complex as the immune system, where any observed effect always results from many interactions between a large number of components. Causal explanations are reductive because a single factor is singled out for attention and given undue explanatory weight on its own. Other examples of the negative impact of reductionist thinking on HIV vaccine development are discussed. These include (1) the failure to distinguish between the chemical nature of antigenicity and the biological nature of immunogenicity, (2) the belief that when an HIV-1 epitope is reconstructed by rational design to better fit a neutralizing monoclonal antibody (nMab), this will produce an immunogen able to elicit Abs with the same neutralizing capacity as the Ab used as template for designing the antigen, and (3) the belief that protection against infection can be analyzed at the level of individual molecular interactions although it has meaning only at the level of an entire organism. The numerous unsuccessful strategies that have been used to design HIV-1 vaccine immunogens are described and it is suggested that the convergence of so many negative experimental results justifies the conclusion that reverse vaccinology is unlikely to lead to the development of a preventive HIV-1 vaccine. Immune correlates of protection in vaccines have not yet been identified because this will become feasible only retrospectively once an effective vaccine exists. The finding that extensive antibody affinity maturation is needed to obtain mature anti-HIV-1 Abs endowed with a broad neutralizing capacity explains why antigens designed to fit matured Mabs are not effective vaccine immunogens since these are administered to naive recipients who possess only B-cell receptors corresponding to the germline version of the matured Abs.
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Affiliation(s)
- Marc H. V. Van Regenmortel
- Stellenbosch Institute of Advanced Study, Wallenberg Research Center at Stellenbosch University,Stellenbosch, South Africa
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43
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Broader neutralizing antibodies against H5N1 viruses using prime-boost immunization of hyperglycosylated hemagglutinin DNA and virus-like particles. PLoS One 2012; 7:e39075. [PMID: 22720032 PMCID: PMC3374787 DOI: 10.1371/journal.pone.0039075] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/17/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Highly pathogenic avian influenza (HPAI) H5N1 viruses and their transmission capability from birds to humans have raised global concerns about a potential human pandemic. The inherent nature of antigenic changes in influenza viruses has not been sufficiently taken into account in immunogen designs for broadly protective HPAI H5N1 vaccines. METHODS We designed a hyperglycosylated HA vaccine using N-linked glycan masking on highly variable sequences in the HA1 globular head. Immunization of these hyperglycosylated HA DNA vaccines followed by a flagellin-containing virus-like particle booster in mice was conducted to evaluate neutralizing antibody responses against various clades of HPAI H5N1 viruses. RESULTS We introduced nine N-X-S/T motifs in five HA1 regions: 83NNT, 86NNT, 94NFT, 127NSS, 138NRT, 156NTT, 161NRS, 182NDT, and 252NAT according to sequence alignment analyses from 163 HPAI H5N1 human isolates. Although no significant differences of anti-HA total IgG titers were found with these hyperglycosyalted HA compared to the wild-type control, the 83NNT and 127NSS mutants elicited significantly potent cross-clade neutralizing antibodies against HPAI H5N1 viruses. CONCLUSIONS This finding may have value in terms of novel immunogen design for developing cross-protective H5N1 vaccines.
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44
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Kong L, Sattentau QJ. Antigenicity and Immunogenicity in HIV-1 Antibody-Based Vaccine Design. JOURNAL OF AIDS & CLINICAL RESEARCH 2012; S8:3. [PMID: 23227445 PMCID: PMC3515071 DOI: 10.4172/2155-6113] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Neutralizing antibodies can protect from infection by immunodeficiency viruses. However, the induction by active vaccination of antibodies that can potently neutralize a broad range of circulating virus strains is a goal not yet achieved, despite more than 2 decades of research. Here we review progress made in the field, from early empirical studies to today's rational structure-based vaccine antigen design. We discuss the existence of broadly neutralizing antibodies, their implications for epitope discovery and recent progress made in antigen design. Finally, we consider the relationship between antigenicity and immunogenicity for B cell recognition and antibody production, a major hurdle for rational vaccine design to overcome.
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Affiliation(s)
- Leopold Kong
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Quentin J Sattentau
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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45
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Dey AK, Burke B, Sun Y, Sirokman K, Nandi A, Hartog K, Lian Y, Geonnotti AR, Montefiori D, Franti M, Martin G, Carfi A, Kessler P, Martin L, Srivastava IK, Barnett SW. Elicitation of neutralizing antibodies directed against CD4-induced epitope(s) using a CD4 mimetic cross-linked to a HIV-1 envelope glycoprotein. PLoS One 2012; 7:e30233. [PMID: 22291921 PMCID: PMC3265465 DOI: 10.1371/journal.pone.0030233] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 12/12/2011] [Indexed: 11/19/2022] Open
Abstract
The identification of HIV-1 envelope glycoprotein (Env) structures that can generate broadly neutralizing antibodies (BNAbs) is pivotal to the development of a successful vaccine against HIV-1 aimed at eliciting effective humoral immune responses. To that end, the production of novel Env structure(s) that might induce BNAbs by presentation of conserved epitopes, which are otherwise occluded, is critical. Here, we focus on a structure that stabilizes Env in a conformation representative of its primary (CD4) receptor-bound state, thereby exposing highly conserved "CD4 induced" (CD4i) epitope(s) known to be important for co-receptor binding and subsequent virus infection. A CD4-mimetic miniprotein, miniCD4 (M64U1-SH), was produced and covalently complexed to recombinant, trimeric gp140 envelope glycoprotein (gp140) using site-specific disulfide linkages. The resulting gp140-miniCD4 (gp140-S-S-M64U1) complex was recognized by CD4i antibodies and the HIV-1 co-receptor, CCR5. The gp140-miniCD4 complex elicited the highest titers of CD4i binding antibodies as well as enhanced neutralizing antibodies against Tier 1 viruses as compared to gp140 protein alone following immunization of rabbits. Neutralization against HIV-2(7312/V434M) and additional serum mapping confirm the specific elicitation of antibodies directed to the CD4i epitope(s). These results demonstrate the utility of structure-based approach in improving immunogenic response against specific region, such as the CD4i epitope(s) here, and its potential role in vaccine application.
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Affiliation(s)
- Antu K. Dey
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
| | - Brian Burke
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
| | - Yide Sun
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
| | - Klara Sirokman
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
| | - Avishek Nandi
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
| | - Karin Hartog
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
| | - Ying Lian
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
| | - Anthony R. Geonnotti
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael Franti
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
| | - Grégoire Martin
- CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, Gif sur Yvette, France
| | - Andrea Carfi
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
| | - Pascal Kessler
- CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, Gif sur Yvette, France
| | - Loïc Martin
- CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, Gif sur Yvette, France
| | - Indresh K. Srivastava
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
| | - Susan W. Barnett
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts, United States of America
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46
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Ahmed FK, Clark BE, Burton DR, Pantophlet R. An engineered mutant of HIV-1 gp120 formulated with adjuvant Quil A promotes elicitation of antibody responses overlapping the CD4-binding site. Vaccine 2012; 30:922-30. [PMID: 22142583 PMCID: PMC3733221 DOI: 10.1016/j.vaccine.2011.11.089] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/20/2011] [Accepted: 11/22/2011] [Indexed: 01/08/2023]
Abstract
A major priority in HIV vaccine research is the development of an immunogen to elicit broadly neutralizing antibodies (NAbs). Monoclonal antibody (mAb) b12 is one of now several broadly neutralizing mAbs that bind epitopes overlapping the CD4-binding site (CD4bs) on HIV-1 gp120 and that serve as templates to engineer effective immunogens. We are exploring a strategy whereby extra glycans are incorporated onto gp120 to occlude the epitopes of non-neutralizing mAbs while maintaining exposure of the b12 site. Immunizing with these so-called hyperglycosylated gp120s is hypothesized to preferentially elicit b12-like NAbs. Here, the effects of two adjuvants, monophosphoryl lipid A (MPL) and Quil A, on eliciting b12-like responses when formulated with a new hyperglycosylated mutant, ΔN2mCHO(Q105N), is presented. Sera from ΔN2mCHO(Q105N)_MPL immunized animals bound the homologous antigen ΔN2mCHO(Q105N) with greater preference than sera from ΔN2mCHO(Q105N)_QuilA immunized animals, demonstrating the modulation of antibody fine specificity by these two adjuvants. We also found that sera from ΔN2mCHO(Q105N)_QuilA immunized animals bound best to a resurfaced HIV gp120 core protein on which non-CD4bs epitopes are substituted with non-HIV residues, suggesting that these sera contain a relatively larger fraction of CD4bs-specific antibodies. Consistent with these data, inhibition assays revealed epitope overlap with the binding sites of the CD4bs-specific antibodies b12, b13 and VRC03. Unexpectedly, these sera did not exhibit significant neutralizing activity against a set of HIV-1 primary strains. Our results show that although formulating mutant ΔN2mCHO(Q105N) with Quil A promotes the elicitation of CD4bs-directed antibodies relative to wild-type gp120, tweaking of the immunization regimen is needed to yield robust, CD4bs-focused NAbs.
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Affiliation(s)
- Fatima K. Ahmed
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A1S6, Canada
| | - Brenda E. Clark
- Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A1S6, Canada
| | - Dennis R. Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02129, USA
| | - Ralph Pantophlet
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A1S6, Canada
- Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A1S6, Canada
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47
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Abstract
The genetic diversity of pathogens presents a challenge to the development of broadly effective vaccines. In this issue, Scarselli et al. combine atomic-level structural information with genomics and classical vaccinology to design a single immunogen that elicits protective immunity against more than 300 natural variants of the bacterial pathogen meningococcus B. This accomplishment provides a glimpse of the power of structure-based vaccine design to create immunogens capable of eliciting protective responses against genetically diverse pathogens.
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Affiliation(s)
- Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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48
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Stanfield RL, Julien JP, Pejchal R, Gach JS, Zwick MB, Wilson IA. Structure-based design of a protein immunogen that displays an HIV-1 gp41 neutralizing epitope. J Mol Biol 2011; 414:460-76. [PMID: 22033480 PMCID: PMC3245871 DOI: 10.1016/j.jmb.2011.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 10/03/2011] [Accepted: 10/10/2011] [Indexed: 01/21/2023]
Abstract
Antibody Z13e1 is a relatively broadly neutralizing anti-human immunodeficiency virus type 1 antibody that recognizes the membrane-proximal external region (MPER) of the human immunodeficiency virus type 1 envelope glycoprotein gp41. Based on the crystal structure of an MPER epitope peptide in complex with Z13e1 Fab, we identified an unrelated protein, interleukin (IL)-22, with a surface-exposed region that is structurally homologous in its backbone to the gp41 Z13e1 epitope. By grafting the gp41 Z13e1 epitope sequence onto the structurally homologous region in IL-22, we engineered a novel protein (Z13-IL22-2) that contains the MPER epitope sequence for use as a potential immunogen and as a reagent for the detection of Z13e1-like antibodies. The Z13-IL22-2 protein binds Fab Z13e1 with a K(d) of 73 nM. The crystal structure of Z13-IL22-2 in complex with Fab Z13e1 shows that the epitope region is faithfully replicated in the Fab-bound scaffold protein; however, isothermal calorimetry studies indicate that Fab binding to Z13-IL22-2 is not a lock-and-key event, leaving open the question of whether conformational changes upon binding occur in the Fab, in Z13-IL-22, or in both.
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Affiliation(s)
- Robyn L Stanfield
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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49
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Engineering, expression, purification, and characterization of stable clade A/B recombinant soluble heterotrimeric gp140 proteins. J Virol 2011; 86:128-42. [PMID: 22031951 DOI: 10.1128/jvi.06363-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The envelope glycoprotein (Env) of human immunodeficiency virus type 1 (HIV-1) is composed of two noncovalently associated subunits: an extracellular subunit (gp120) and a transmembrane subunit (gp41). The functional unit of Env on the surface of infectious virions is a trimer of gp120/gp41 heterodimers. Env is the target of anti-HIV neutralizing antibodies. A considerable effort has been invested in the engineering of recombinant soluble forms of the virion-associated Env trimer as vaccine candidates to elicit anti-HIV neutralizing antibody responses. These soluble constructs contain three gp120 subunits and the extracellular segments of the corresponding gp41 subunits. The individual gp120/gp41 protomers on these soluble trimers are identical in amino acid sequence (homotrimers). Here, we engineered novel soluble trimeric gp140 proteins that are formed by the association of gp140 protomers that differ in amino acid sequence and glycosylation patterns (heterotrimers). Specifically, we engineered soluble heterotrimeric proteins composed of clade A and clade B Env protomers. The clade A gp140 protomers were derived from viruses isolated during acute infection (Q168a2, Q259d2.17, and Q461e2), whereas the clade B gp140 protomers were derived from a virus isolated during chronic infection (SF162). The amino acid sequence divergence between the clade A and the clade B Envs is approximately 24%. Neutralization epitopes in the CD4 binding sites and coreceptor binding sites, as well as the membrane-proximal external region (MPER), were differentially expressed on the heterotrimeric and homotrimeric proteins. The heterotrimeric gp140s elicited broader anti-tier 1 isolate neutralizing antibody responses than did the homotrimeric gp140s.
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Henry KA, Murira A, van Houten NE, Scott JK. Developing strategies to enhance and focus humoral immune responses using filamentous phage as a model antigen. Bioeng Bugs 2011; 2:275-83. [PMID: 22008640 DOI: 10.4161/bbug.2.5.16559] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Filamentous bacteriophage are commonly used as immunogenic carriers for peptides and proteins displayed on the phage surface. Previously, we showed that immunization with phage to which peptides had been chemically conjugated can elicit a focused anti-peptide antibody response compared with traditional carrier molecules bearing the same peptide, perhaps due to the low surface complexity of the phage. The regularity of its surface also gives the phage other advantages as a carrier, including immunological simplicity and thousands of well-defined sites for chemical conjugation. More recently, we showed that focusing of antibody responses against 'target' peptides was enhanced when the phage's molecular surface was simplified by removal of immunodominant B-cell epitopes present on the minor coat protein, pIII. The pIII-truncated variant elicits an antibody response that is largely restricted to the exposed N-terminus of the major coat protein, pVIII, and to phage-associated bacterial lipopolysaccharide, and a significant fraction of this response cross-reacts with a 12-residue peptide covering the surface-exposed region of pVIII. This allows one to track antibody responses against the phage (and any associated haptens) as they develop over time, and characterize them using a combination of serological, flow cytometric, cellular and immunogenetic assays. The filamentous phage thus provides an excellent model system for studying various aspects of the antibody response, all with the goal of targeting antibody production against weakly immunogenic peptides, proteins and carbohydrates.
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Affiliation(s)
- Kevin A Henry
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A1S6, Canada
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