1
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Patel A, Rosenke K, Parzych EM, Feldmann F, Bharti S, Griffin AJ, Schouest B, Lewis M, Choi J, Chokkalingam N, Machado V, Smith BJ, Frase D, Ali AR, Lovaglio J, Nguyen B, Hanley PW, Walker SN, Gary EN, Kulkarni A, Generotti A, Francica JR, Rosenthal K, Kulp DW, Esser MT, Smith TRF, Shaia C, Weiner DB, Feldmann H. In vivo delivery of engineered synthetic DNA-encoded SARS-CoV-2 monoclonal antibodies for pre-exposure prophylaxis in non-human primates. Emerg Microbes Infect 2024; 13:2294860. [PMID: 38165394 PMCID: PMC10903752 DOI: 10.1080/22221751.2023.2294860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
COVID-19 remains a major public health concern. Monoclonal antibodies have received emergency use authorization (EUA) for pre-exposure prophylaxis against COVID-19 among high-risk groups for treatment of mild to moderate COVID-19. In addition to recombinant biologics, engineered synthetic DNA-encoded antibodies (DMAb) are an important strategy for direct in vivo delivery of protective mAb. A DMAb cocktail was synthetically engineered to encode the immunoglobulin heavy and light chains of two different two different Fc-engineered anti-SARS-CoV-2 antibodies. The DMAbs were designed to enhance in vivo expression and delivered intramuscularly to cynomolgus and rhesus macaques with a modified in vivo delivery regimen. Serum levels were detected in macaques, along with specific binding to SARS-CoV-2 spike receptor binding domain protein and neutralization of multiple SARS-CoV-2 variants of concern in pseudovirus and authentic live virus assays. Prophylactic administration was protective in rhesus macaques against signs of SARS-CoV-2 (USA-WA1/2020) associated disease in the lungs. Overall, the data support further study of DNA-encoded antibodies as an additional delivery mode for prevention of COVID-19 severe disease. These data have implications for human translation of gene-encoded mAbs for emerging infectious diseases and low dose mAb delivery against COVID-19.
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Affiliation(s)
- Ami Patel
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | - Kyle Rosenke
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Elizabeth M. Parzych
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | - Friederike Feldmann
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Suman Bharti
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | - Amanda J. Griffin
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | | | - Matt Lewis
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jihae Choi
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | - Neethu Chokkalingam
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | | | - Brian J. Smith
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Drew Frase
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | - Ali R. Ali
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | - Jamie Lovaglio
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Brian Nguyen
- Inovio Pharmaceuticals, Plymouth Meeting, PA, USA
| | - Patrick W. Hanley
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Susanne N. Walker
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | - Ebony N. Gary
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | - Abhijeet Kulkarni
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | | | - Joseph R. Francica
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Kim Rosenthal
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Daniel W. Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | - Mark T. Esser
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Carl Shaia
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - David B. Weiner
- Vaccine and Immunotherapy Center, The Wistar Institute of Anatomy and Biology, Philadelphia, PA, USA
| | - Heinz Feldmann
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
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2
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Andrade VM, Maricic I, Kalia R, Jachimowicz L, Bedoya O, Kulp DW, Humeau L, Smith TRF. Delineation of DNA and mRNA COVID-19 vaccine-induced immune responses in preclinical animal models. Hum Vaccin Immunother 2023; 19:2281733. [PMID: 38012018 PMCID: PMC10760386 DOI: 10.1080/21645515.2023.2281733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023] Open
Abstract
Nucleic acid vaccines are designed based on genetic sequences (DNA or mRNA) of a target antigen to be expressed in vivo to drive a host immune response. In response to the COVID-19 pandemic, mRNA and DNA vaccines based on the SARS-CoV-2 Spike antigen were developed. Surprisingly, head-to-head characterizations of the immune responses elicited by each vaccine type has not been performed to date. Here, we have employed a range of preclinical animal models including the hamster, guinea pig, rabbit, and mouse to compare and delineate the immune response raised by DNA, administered intradermally (ID) with electroporation (EP) and mRNA vaccines (BNT162b2 or mRNA-1273), administered intramuscularly (IM), expressing the SARS-CoV-2 WT spike antigen. The results revealed clear differences in the quality and magnitude of the immune response between the two vaccine platforms. The DNA vaccine immune response was characterized by strong T cell responses, while the mRNA vaccine elicited robust humoral responses. The results may assist in guiding the disease target each vaccine type may be best matched against and suggest mechanisms to further enhance the breadth of each platform's immune response.
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Affiliation(s)
| | - Igor Maricic
- Preclinical R&D, Inovio Pharmaceuticals Inc, San Diego, CA, USA
| | - Richa Kalia
- Preclinical R&D, Inovio Pharmaceuticals Inc, San Diego, CA, USA
| | | | - Olivia Bedoya
- Preclinical R&D, Inovio Pharmaceuticals Inc, San Diego, CA, USA
| | - Daniel W. Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Laurent Humeau
- Preclinical R&D, Inovio Pharmaceuticals Inc, San Diego, CA, USA
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3
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Tursi NJ, Xu Z, Kulp DW, Weiner DB. Gene-encoded nanoparticle vaccine platforms for in vivo assembly of multimeric antigen to promote adaptive immunity. Wiley Interdiscip Rev Nanomed Nanobiotechnol 2023; 15:e1880. [PMID: 36807845 PMCID: PMC10665986 DOI: 10.1002/wnan.1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 02/23/2023]
Abstract
Nanoparticle vaccines are a diverse category of vaccines for the prophylaxis or treatment of various diseases. Several strategies have been employed for their optimization, especially to enhance vaccine immunogenicity and generate potent B-cell responses. Two major modalities utilized for particulate antigen vaccines include using nanoscale structures for antigen delivery and nanoparticles that are themselves vaccines due to antigen display or scaffolding-the latter of which we will define as "nanovaccines." Multimeric antigen display has a variety of immunological benefits compared to monomeric vaccines mediated through potentiating antigen-presenting cell presentation and enhancing antigen-specific B-cell responses through B-cell activation. The majority of nanovaccine assembly is done in vitro using cell lines. However, in vivo assembly of scaffolded vaccines potentiated using nucleic acids or viral vectors is a burgeoning modality of nanovaccine delivery. Several advantages to in vivo assembly exist, including lower costs of production, fewer production barriers, as well as more rapid development of novel vaccine candidates for emerging diseases such as SARS-CoV-2. This review will characterize the methods for de novo assembly of nanovaccines in the host using methods of gene delivery including nucleic acid and viral vectored vaccines. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Nicholas J. Tursi
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ziyang Xu
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel W. Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - David B. Weiner
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
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4
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Tursi NJ, Xu Z, Helble M, Walker S, Liaw K, Chokkalingam N, Kannan T, Wu Y, Tello-Ruiz E, Park DH, Zhu X, Wise MC, Smith TRF, Majumdar S, Kossenkov A, Kulp DW, Weiner DB. Engineered antibody cytokine chimera synergizes with DNA-launched nanoparticle vaccines to potentiate melanoma suppression in vivo. Front Immunol 2023; 14:1072810. [PMID: 36911698 PMCID: PMC9997082 DOI: 10.3389/fimmu.2023.1072810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
Cancer immunotherapy has demonstrated great promise with several checkpoint inhibitors being approved as the first-line therapy for some types of cancer, and new engineered cytokines such as Neo2/15 now being evaluated in many studies. In this work, we designed antibody-cytokine chimera (ACC) scaffolding cytokine mimetics on a full-length tumor-specific antibody. We characterized the pharmacokinetic (PK) and pharmacodynamic (PD) properties of first-generation ACC TA99-Neo2/15, which synergized with DLnano-vaccines to suppress in vivo melanoma proliferation and induced significant systemic cytokine activation. A novel second-generation ACC TA99-HL2-KOA1, with retained IL-2Rβ/γ binding and attenuated but preserved IL-2Rα binding, induced lower systemic cytokine activation with non-inferior protection in murine tumor studies. Transcriptomic analyses demonstrated an upregulation of Type I interferon responsive genes, particularly ISG15, in dendritic cells, macrophages and monocytes following TA99-HL2-KOA1 treatment. Characterization of additional ACCs in combination with cancer vaccines will likely be an important area of research for treating melanoma and other types of cancer.
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Affiliation(s)
- Nicholas J Tursi
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ziyang Xu
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michaela Helble
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Susanne Walker
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - Kevin Liaw
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - Neethu Chokkalingam
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - Toshitha Kannan
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - Yuanhan Wu
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - Edgar Tello-Ruiz
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - Daniel H Park
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - Xizhou Zhu
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - Megan C Wise
- Inovio Pharmaceuticals, Bluebell, PA, United States
| | | | - Sonali Majumdar
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - Andrew Kossenkov
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - Daniel W Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
| | - David B Weiner
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, United States
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5
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Bordoloi D, Bhojnagarwala PS, Perales-Puchalt A, Kulkarni AJ, Zhu X, Liaw K, O’Connell RP, Park DH, Kulp DW, Zhang R, Weiner DB. A mAb against surface-expressed FSHR engineered to engage adaptive immunity for ovarian cancer immunotherapy. JCI Insight 2022; 7:162553. [PMID: 36509287 PMCID: PMC9746812 DOI: 10.1172/jci.insight.162553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022] Open
Abstract
Despite advances in ovarian cancer (OC) therapy, recurrent OC remains a poor-prognosis disease. Because of the close interaction between OC cells and the tumor microenvironment (TME), it is important to develop strategies that target tumor cells and engage components of the TME. A major obstacle in the development of OC therapies is the identification of targets with expression limited to tumor surface to avoid off-target interactions. The follicle-stimulating hormone receptor (FSHR) has selective expression on ovarian granulosa cells and is expressed on 50%-70% of serous OCs. We generated mAbs targeting the external domain of FSHR using in vivo-expressed FSHR vector. By high-throughput flow analysis, we identified multiple clones and downselected D2AP11, a potent FSHR surface-targeted mAb. D2AP11 identifies important OC cell lines derived from tumors with different mutations, including BRCA1/2, and lines resistant to a wide range of therapies. We used D2AP11 to develop a bispecific T cell engager. In vitro addition of PBMCs and T cells to D2AP11-TCE induced specific and potent killing of different genetic and immune escape OC lines, with EC50s in the ng/ml range, and attenuated tumor burden in OC-challenged mouse models. These studies demonstrate the potential utility of biologics targeting FSHR for OC and perhaps other FSHR-positive cancers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Rugang Zhang
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, Pennsylvania, USA
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6
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Gary EN, Tursi NJ, Warner B, Parzych EM, Ali AR, Frase D, Moffat E, Embury-Hyatt C, Smith TRF, Broderick KE, Humeau L, Kobasa D, Patel A, Kulp DW, Weiner DB. Mucosal chemokine adjuvant enhances synDNA vaccine-mediated responses to SARS-CoV-2 and provides heterologous protection in vivo. Cell Rep Med 2022; 3:100693. [PMID: 35839767 PMCID: PMC9237025 DOI: 10.1016/j.xcrm.2022.100693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/16/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022]
Abstract
The global coronavirus disease 2019 (COVID-19) pandemic has claimed more than 5 million lives. Emerging variants of concern (VOCs) continually challenge viral control. Directing vaccine-induced humoral and cell-mediated responses to mucosal surfaces may enhance vaccine efficacy. Here we investigate the immunogenicity and protective efficacy of optimized synthetic DNA plasmids encoding wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (pS) co-formulated with the plasmid-encoded mucosal chemokine cutaneous T cell-attracting chemokine (pCTACK; CCL27). pCTACK-co-immunized animals exhibit increased spike-specific antibodies at the mucosal surface and increased frequencies of interferon gamma (IFNγ)+ CD8+ T cells in the respiratory mucosa. pCTACK co-immunization confers 100% protection from heterologous Delta VOC challenge. This study shows that mucosal chemokine adjuvants can direct vaccine-induced responses to specific immunological sites and have significant effects on heterologous challenge. Further study of this unique chemokine-adjuvanted vaccine approach in the context of SARS-CoV-2 vaccines is likely important.
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Affiliation(s)
- Ebony N Gary
- The Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Nicholas J Tursi
- The Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bryce Warner
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Elizabeth M Parzych
- The Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Ali R Ali
- The Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Drew Frase
- The Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Estella Moffat
- National Center for Foreign Animal Disease (NCFAD), Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Carissa Embury-Hyatt
- National Center for Foreign Animal Disease (NCFAD), Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | | | | | | | - Darwyn Kobasa
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Ami Patel
- The Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Daniel W Kulp
- The Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - David B Weiner
- The Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA.
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7
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Xu Z, Walker S, Wise MC, Chokkalingam N, Purwar M, Moore A, Tello-Ruiz E, Wu Y, Majumdar S, Konrath KM, Kulkarni A, Tursi NJ, Zaidi FI, Reuschel EL, Patel I, Obeirne A, Du J, Schultheis K, Gites L, Smith T, Mendoza J, Broderick KE, Humeau L, Pallesen J, Weiner DB, Kulp DW. Induction of tier-2 neutralizing antibodies in mice with a DNA-encoded HIV envelope native like trimer. Nat Commun 2022; 13:695. [PMID: 35121758 PMCID: PMC8816947 DOI: 10.1038/s41467-022-28363-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 01/11/2022] [Indexed: 12/30/2022] Open
Abstract
HIV Envelope (Env) is the main vaccine target for induction of neutralizing antibodies. Stabilizing Env into native-like trimer (NLT) conformations is required for recombinant protein immunogens to induce autologous neutralizing antibodies(nAbs) against difficult to neutralize HIV strains (tier-2) in rabbits and non-human primates. Immunizations of mice with NLTs have generally failed to induce tier-2 nAbs. Here, we show that DNA-encoded NLTs fold properly in vivo and induce autologous tier-2 nAbs in mice. DNA-encoded NLTs also uniquely induce both CD4 + and CD8 + T-cell responses as compared to corresponding protein immunizations. Murine neutralizing antibodies are identified with an advanced sequencing technology. The structure of an Env-Ab (C05) complex, as determined by cryo-EM, identifies a previously undescribed neutralizing Env C3/V5 epitope. Beyond potential functional immunity gains, DNA vaccines permit in vivo folding of structured antigens and provide significant cost and speed advantages for enabling rapid evaluation of new HIV vaccines.
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Affiliation(s)
- Ziyang Xu
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Susanne Walker
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Megan C Wise
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | - Neethu Chokkalingam
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Mansi Purwar
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Alan Moore
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Edgar Tello-Ruiz
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Yuanhan Wu
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Sonali Majumdar
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Kylie M Konrath
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Abhijeet Kulkarni
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Nicholas J Tursi
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Faraz I Zaidi
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Emma L Reuschel
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Ishaan Patel
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - April Obeirne
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Jianqiu Du
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | | | - Lauren Gites
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | - Trevor Smith
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | - Janess Mendoza
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | | | - Laurent Humeau
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | - Jesper Pallesen
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - David B Weiner
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Daniel W Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA.
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8
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Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, Wu Y, Willis J, Kulp DW, Das R, Dunbrack RL, Schief W, Kuhlman B, Siegel JB, Gray JJ. PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Biophysicist (Rockv) 2021; 2:108-122. [PMID: 35128343 DOI: 10.35459/tbp.2019.000147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Biomolecular structure drives function, and computational capabilities have progressed such that the prediction and computational design of biomolecular structures is increasingly feasible. Because computational biophysics attracts students from many different backgrounds and with different levels of resources, teaching the subject can be challenging. One strategy to teach diverse learners is with interactive multimedia material that promotes self-paced, active learning. We have created a hands-on education strategy with a set of sixteen modules that teach topics in biomolecular structure and design, from fundamentals of conformational sampling and energy evaluation to applications like protein docking, antibody design, and RNA structure prediction. Our modules are based on PyRosetta, a Python library that encapsulates all computational modules and methods in the Rosetta software package. The workshop-style modules are implemented as Jupyter Notebooks that can be executed in the Google Colaboratory, allowing learners access with just a web browser. The digital format of Jupyter Notebooks allows us to embed images, molecular visualization movies, and interactive coding exercises. This multimodal approach may better reach students from different disciplines and experience levels as well as attract more researchers from smaller labs and cognate backgrounds to leverage PyRosetta in their science and engineering research. All materials are freely available at https://github.com/RosettaCommons/PyRosetta.notebooks.
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Affiliation(s)
- Kathy H Le
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States
| | - Jason C Klima
- Institute for Protein Design, University of Washington, Seattle, Washington, United States.,Department of Biochemistry, University of Washington, Seattle, Washington, United States.,Lyell Immunopharma, Inc., Seattle, Washington, United States
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | - Jason Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States.,Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania, United States
| | - Steven Bertolani
- Department of Chemistry, Department of Biochemistry and Molecular Medicine, Genome Center, University of California, Davis, Davis, California, United States
| | - Shourya S Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | - Andrew Leaver-Fay
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Brian Weitzner
- Institute for Protein Design, University of Washington, Seattle, Washington, United States.,Department of Biochemistry, University of Washington, Seattle, Washington, United States.,Lyell Immunopharma, Inc., Seattle, Washington, United States
| | - Jack Maguire
- Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Ramya Rangan
- Program in Biophysics, Stanford University, Stanford, California, United States
| | - Matt A Adrianowycz
- Program in Biophysics, Stanford University, Stanford, California, United States
| | - Rebecca F Alford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | - Aleexsan Adal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | - Morgan L Nance
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, United States
| | - Yuanhan Wu
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, United States
| | - Jordan Willis
- RubrYc Therapeutics, San Ramon, California, United States
| | - Daniel W Kulp
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, United States
| | - Rhiju Das
- Program in Biophysics, Stanford University, Stanford, California, United States
| | | | - William Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States
| | - Brian Kuhlman
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States.,Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Justin B Siegel
- Department of Chemistry, Department of Biochemistry and Molecular Medicine, Genome Center, University of California, Davis, Davis, California, United States
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, United States
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9
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Xu Z, Patel A, Tursi NJ, Zhu X, Muthumani K, Kulp DW, Weiner DB. Harnessing Recent Advances in Synthetic DNA and Electroporation Technologies for Rapid Vaccine Development Against COVID-19 and Other Emerging Infectious Diseases. Front Med Technol 2020; 2:571030. [PMID: 35047878 PMCID: PMC8757735 DOI: 10.3389/fmedt.2020.571030] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/08/2020] [Indexed: 12/30/2022] Open
Abstract
DNA vaccines are considered as a third-generation vaccination approach in which antigenic materials are encoded as DNA plasmids for direct in vivo production to elicit adaptive immunity. As compared to other platforms, DNA vaccination is considered to have a strong safety profile, as DNA plasmids neither replicate nor elicit vector-directed immune responses in hosts. While earlier work found the immune responses induced by DNA vaccines to be sub-optimal in larger mammals and humans, recent developments in key synthetic DNA and electroporation delivery technologies have now allowed DNA vaccines to elicit significantly more potent and consistent responses in several clinical studies. This paper will review findings from the recent clinical and preclinical studies on DNA vaccines targeting emerging infectious diseases (EID) including COVID-19 caused by the SARS-CoV-2 virus, and the technological advancements pivotal to the improved responses-including the use of the advanced delivery technology, DNA-encoded cytokine/mucosal adjuvants, and innovative concepts in immunogen design. With continuous advancement over the past three decades, the DNA approach is now poised to develop vaccines against COVID-19, as well as other EIDs.
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Affiliation(s)
- Ziyang Xu
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA, United States
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ami Patel
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA, United States
| | - Nicholas J Tursi
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA, United States
| | - Xizhou Zhu
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA, United States
| | - Kar Muthumani
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA, United States
| | - Daniel W Kulp
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA, United States
| | - David B Weiner
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA, United States
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10
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Walker SN, Chokkalingam N, Reuschel EL, Purwar M, Xu Z, Gary EN, Kim KY, Helble M, Schultheis K, Walters J, Ramos S, Muthumani K, Smith TRF, Broderick KE, Tebas P, Patel A, Weiner DB, Kulp DW. SARS-CoV-2 Assays To Detect Functional Antibody Responses That Block ACE2 Recognition in Vaccinated Animals and Infected Patients. J Clin Microbiol 2020; 58:e01533-20. [PMID: 32855181 PMCID: PMC7587116 DOI: 10.1128/jcm.01533-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of COVID-19, resulting in cases of mild to severe respiratory distress and significant mortality. The global outbreak of this novel coronavirus has now infected >20 million people worldwide, with >5 million cases in the United States (11 August 2020). The development of diagnostic and research tools to determine infection and vaccine efficacy is critically needed. We have developed multiple serologic assays using newly designed SARS-CoV-2 reagents for detecting the presence of receptor-binding antibodies in sera. The first assay is surface plasmon resonance (SPR) based and can quantitate both antibody binding to the SARS-CoV-2 spike protein and blocking to the Angiotensin-converting enzyme 2 (ACE2) receptor in a single experiment. The second assay is enzyme-linked immunosorbent assay (ELISA) based and can measure competition and blocking of the ACE2 receptor to the SARS-CoV-2 spike protein with antispike antibodies. The assay is highly versatile, and we demonstrate the broad utility of the assay by measuring antibody functionality of sera from small animals and nonhuman primates immunized with an experimental SARS-CoV-2 vaccine. In addition, we employ the assay to measure receptor blocking of sera from SARS-CoV-2-infected patients. The assay is shown to correlate with pseudovirus neutralization titers. This type of rapid, surrogate neutralization diagnostic can be employed widely to help study SARS-CoV-2 infection and assess the efficacy of vaccines.
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Affiliation(s)
- Susanne N Walker
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Neethu Chokkalingam
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Emma L Reuschel
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Mansi Purwar
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Ziyang Xu
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Ebony N Gary
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Kevin Y Kim
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Michaela Helble
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | - Jewell Walters
- Inovio Pharmaceuticals, Plymouth Meeting, Pennsylvania, USA
| | | | - Kar Muthumani
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | | | - Pablo Tebas
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ami Patel
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - David B Weiner
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Daniel W Kulp
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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11
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Wise MC, Xu Z, Tello-Ruiz E, Beck C, Trautz A, Patel A, Elliott ST, Chokkalingam N, Kim S, Kerkau MG, Muthumani K, Jiang J, Fisher PD, Ramos SJ, Smith TR, Mendoza J, Broderick KE, Montefiori DC, Ferrari G, Kulp DW, Humeau LM, Weiner DB. In vivo delivery of synthetic DNA-encoded antibodies induces broad HIV-1-neutralizing activity. J Clin Invest 2020; 130:827-837. [PMID: 31697648 DOI: 10.1172/jci132779] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/24/2019] [Indexed: 02/06/2023] Open
Abstract
Interventions to prevent HIV-1 infection and alternative tools in HIV cure therapy remain pressing goals. Recently, numerous broadly neutralizing HIV-1 monoclonal antibodies (bNAbs) have been developed that possess the characteristics necessary for potential prophylactic or therapeutic approaches. However, formulation complexities, especially for multiantibody deliveries, long infusion times, and production issues could limit the use of these bNAbs when deployed, globally affecting their potential application. Here, we describe an approach utilizing synthetic DNA-encoded monoclonal antibodies (dmAbs) for direct in vivo production of prespecified neutralizing activity. We designed 16 different bNAbs as dmAb cassettes and studied their activity in small and large animals. Sera from animals administered dmAbs neutralized multiple HIV-1 isolates with activity similar to that of their parental recombinant mAbs. Delivery of multiple dmAbs to a single animal led to increased neutralization breadth. Two dmAbs, PGDM1400 and PGT121, were advanced into nonhuman primates for study. High peak-circulating levels (between 6 and 34 μg/ml) of these dmAbs were measured, and the sera of all animals displayed broad neutralizing activity. The dmAb approach provides an important local delivery platform for the in vivo generation of HIV-1 bNAbs and for other infectious disease antibodies.
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Affiliation(s)
- Megan C Wise
- Inovio Pharmaceuticals, Plymouth Meeting, Pennsylvania, USA
| | - Ziyang Xu
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edgar Tello-Ruiz
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | - Aspen Trautz
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Ami Patel
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Sarah Tc Elliott
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Neethu Chokkalingam
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Sophie Kim
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | - Kar Muthumani
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Jingjing Jiang
- Inovio Pharmaceuticals, Plymouth Meeting, Pennsylvania, USA
| | - Paul D Fisher
- Inovio Pharmaceuticals, Plymouth Meeting, Pennsylvania, USA
| | | | | | - Janess Mendoza
- Inovio Pharmaceuticals, Plymouth Meeting, Pennsylvania, USA
| | | | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Daniel W Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | - David B Weiner
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
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12
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Xu Z, Chokkalingam N, Tello-Ruiz E, Wise MC, Bah MA, Walker S, Tursi NJ, Fisher PD, Schultheis K, Broderick KE, Humeau L, Kulp DW, Weiner DB. A DNA-Launched Nanoparticle Vaccine Elicits CD8 + T-cell Immunity to Promote In Vivo Tumor Control. Cancer Immunol Res 2020; 8:1354-1364. [PMID: 32913042 DOI: 10.1158/2326-6066.cir-20-0061] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/10/2020] [Accepted: 08/14/2020] [Indexed: 02/02/2023]
Abstract
Cytolytic T cells (CTL) play a pivotal role in surveillance against tumors. Induction of CTL responses by vaccination may be challenging, as it requires direct transduction of target cells or special adjuvants to promote cross-presentation. Here, we observed induction of robust CTL responses through electroporation-facilitated, DNA-launched nanoparticle vaccination (DLnano-vaccines). Electroporation was observed to mediate transient tissue apoptosis and macrophage infiltration, which were deemed essential to the induction of CTLs by DLnano-vaccines through a systemic macrophage depletion study. Bolus delivery of protein nano-vaccines followed by electroporation, however, failed to induce CTLs, suggesting direct in vivo production of nano-vaccines may be required. Following these observations, new DLnano-vaccines scaffolding immunodominant melanoma Gp100 and Trp2 epitopes were designed and shown to induce more potent and consistent epitope-specific CTL responses than the corresponding DNA monomeric vaccines or CpG-adjuvanted peptide vaccines. DNA, but not recombinant protein, nano-vaccinations induced CTL responses to these epitopes and suppressed melanoma tumor growth in mouse models in a CD8+ T-cell-dependent fashion. Further studies to explore the use of DLnano-vaccines against other cancer targets and the biology with which they induce CTLs are important.
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Affiliation(s)
- Ziyang Xu
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia Pennsylvania
| | - Neethu Chokkalingam
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Edgar Tello-Ruiz
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Megan C Wise
- Inovio Pharmaceuticals, Plymouth Meeting, Pennsylvania
| | - Mamadou A Bah
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Susanne Walker
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Nicholas J Tursi
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Paul D Fisher
- Inovio Pharmaceuticals, Plymouth Meeting, Pennsylvania
| | | | | | | | - Daniel W Kulp
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania.
| | - David B Weiner
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, Pennsylvania.
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13
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Xu Z, Chokkalingam N, Tello-Ruiz E, Walker S, Kulp DW, Weiner DB. Incorporation of a Novel CD4+ Helper Epitope Identified from Aquifex aeolicus Enhances Humoral Responses Induced by DNA and Protein Vaccinations. iScience 2020; 23:101399. [PMID: 32763137 PMCID: PMC7409978 DOI: 10.1016/j.isci.2020.101399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/25/2020] [Accepted: 07/20/2020] [Indexed: 01/12/2023] Open
Abstract
CD4+ T cells play an important role in the maturation of the antibody responses. Conjugation of identified CD4+ T cell helper epitope to the target antigen has been developed as a strategy to enhance vaccine-induced humoral immunity. In this work, we reported the identification of a novel HLA-IAb helper epitope LS-3 from Aquifex aeolicus. In silico analysis predicted this epitope to have high binding affinity to common human HLA alleles and have complementary binding coverage to the established PADRE epitope. Introduction of HLA-IAb knockout mutations to the LS-3 epitope significantly attenuated humoral responses induced by a vaccine containing this epitope. Finally, engineered fusion of the epitope to a model antigen, influenza hemagglutinin, significantly improved both binding and hemagglutination inhibition antibody responses in mice receiving DNA or protein vaccines. In summary, LS-3 and additional identified CD4+ helper epitopes may be further explored to improve vaccine responses in translational studies. Identification of a novel CD4+ helper epitope, LS-3, from Aquifex aeolicus In silico analysis predicts high binding affinity of LS-3 to human HLA-DR alleles Fusing LS-3 to antigen enhances humoral response by vaccinations
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Affiliation(s)
- Ziyang Xu
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA; Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Neethu Chokkalingam
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Edgar Tello-Ruiz
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Susanne Walker
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Daniel W Kulp
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA.
| | - David B Weiner
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA.
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14
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Smith TRF, Patel A, Ramos S, Elwood D, Zhu X, Yan J, Gary EN, Walker SN, Schultheis K, Purwar M, Xu Z, Walters J, Bhojnagarwala P, Yang M, Chokkalingam N, Pezzoli P, Parzych E, Reuschel EL, Doan A, Tursi N, Vasquez M, Choi J, Tello-Ruiz E, Maricic I, Bah MA, Wu Y, Amante D, Park DH, Dia Y, Ali AR, Zaidi FI, Generotti A, Kim KY, Herring TA, Reeder S, Andrade VM, Buttigieg K, Zhao G, Wu JM, Li D, Bao L, Liu J, Deng W, Qin C, Brown AS, Khoshnejad M, Wang N, Chu J, Wrapp D, McLellan JS, Muthumani K, Wang B, Carroll MW, Kim JJ, Boyer J, Kulp DW, Humeau LMPF, Weiner DB, Broderick KE. Immunogenicity of a DNA vaccine candidate for COVID-19. Nat Commun 2020; 11:2601. [PMID: 32433465 PMCID: PMC7239918 DOI: 10.1038/s41467-020-16505-0] [Citation(s) in RCA: 412] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/08/2020] [Indexed: 01/07/2023] Open
Abstract
The coronavirus family member, SARS-CoV-2 has been identified as the causal agent for the pandemic viral pneumonia disease, COVID-19. At this time, no vaccine is available to control further dissemination of the disease. We have previously engineered a synthetic DNA vaccine targeting the MERS coronavirus Spike (S) protein, the major surface antigen of coronaviruses, which is currently in clinical study. Here we build on this prior experience to generate a synthetic DNA-based vaccine candidate targeting SARS-CoV-2 S protein. The engineered construct, INO-4800, results in robust expression of the S protein in vitro. Following immunization of mice and guinea pigs with INO-4800 we measure antigen-specific T cell responses, functional antibodies which neutralize the SARS-CoV-2 infection and block Spike protein binding to the ACE2 receptor, and biodistribution of SARS-CoV-2 targeting antibodies to the lungs. This preliminary dataset identifies INO-4800 as a potential COVID-19 vaccine candidate, supporting further translational study.
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Affiliation(s)
- Trevor R. F. Smith
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Ami Patel
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Stephanie Ramos
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Dustin Elwood
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Xizhou Zhu
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Jian Yan
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Ebony N. Gary
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Susanne N. Walker
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Katherine Schultheis
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Mansi Purwar
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Ziyang Xu
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Jewell Walters
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Pratik Bhojnagarwala
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Maria Yang
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Neethu Chokkalingam
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Patrick Pezzoli
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Elizabeth Parzych
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Emma L. Reuschel
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Arthur Doan
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Nicholas Tursi
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Miguel Vasquez
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Jihae Choi
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Edgar Tello-Ruiz
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Igor Maricic
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Mamadou A. Bah
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Yuanhan Wu
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Dinah Amante
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Daniel H. Park
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Yaya Dia
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Ali Raza Ali
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Faraz I. Zaidi
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Alison Generotti
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Kevin Y. Kim
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Timothy A. Herring
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Sophia Reeder
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Viviane M. Andrade
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Karen Buttigieg
- 0000 0004 5909 016Xgrid.271308.fNational Infection Service, Public Health England, Porton Down, Wiltshire, UK
| | - Gan Zhao
- Advaccine (Suzhou) Biopharmaceuticals Co., Ltd, Suzhou, China
| | - Jiun-Ming Wu
- Advaccine (Suzhou) Biopharmaceuticals Co., Ltd, Suzhou, China
| | - Dan Li
- 0000 0001 0125 2443grid.8547.eKey Laboratory of Medical Molecular Virology of MOH and MOE and Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Linlin Bao
- 0000 0001 0125 2443grid.8547.eKey Laboratory of Medical Molecular Virology of MOH and MOE and Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jiangning Liu
- 0000 0001 0125 2443grid.8547.eKey Laboratory of Medical Molecular Virology of MOH and MOE and Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei Deng
- 0000 0001 0125 2443grid.8547.eKey Laboratory of Medical Molecular Virology of MOH and MOE and Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chuan Qin
- 0000 0001 0125 2443grid.8547.eKey Laboratory of Medical Molecular Virology of MOH and MOE and Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ami Shah Brown
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Makan Khoshnejad
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Nianshuang Wang
- 0000 0004 1936 9924grid.89336.37Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712 USA
| | - Jacqueline Chu
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Daniel Wrapp
- 0000 0004 1936 9924grid.89336.37Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712 USA
| | - Jason S. McLellan
- 0000 0004 1936 9924grid.89336.37Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712 USA
| | - Kar Muthumani
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Bin Wang
- 0000 0001 0125 2443grid.8547.eKey Laboratory of Medical Molecular Virology of MOH and MOE and Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Miles W. Carroll
- 0000 0004 5909 016Xgrid.271308.fNational Infection Service, Public Health England, Porton Down, Wiltshire, UK
| | - J. Joseph Kim
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Jean Boyer
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - Daniel W. Kulp
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Laurent M. P. F. Humeau
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
| | - David B. Weiner
- 0000 0001 1956 6678grid.251075.4Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104 USA
| | - Kate E. Broderick
- 0000 0004 0417 098Xgrid.421774.3Inovio Pharmaceuticals, Plymouth Meeting, Philadelphia, PA 19462 USA
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15
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Moyer TJ, Kato Y, Abraham W, Chang JYH, Kulp DW, Watson N, Turner HL, Menis S, Abbott RK, Bhiman JN, Melo MB, Simon HA, Herrera-De la Mata S, Liang S, Seumois G, Agarwal Y, Li N, Burton DR, Ward AB, Schief WR, Crotty S, Irvine DJ. Author Correction: A Engineered immunogen binding to alum adjuvant enhances humoral immunity. Nat Med 2020; 26:804. [PMID: 32405059 PMCID: PMC7223225 DOI: 10.1038/s41591-020-0861-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Tyson J Moyer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Yu Kato
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Wuhbet Abraham
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jason Y H Chang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel W Kulp
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Nicki Watson
- Whitehead Institute of Biomedical Research, Cambridge, MA, USA
| | - Hannah L Turner
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sergey Menis
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert K Abbott
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jinal N Bhiman
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Mariane B Melo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Hayley A Simon
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Shu Liang
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Gregory Seumois
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Yash Agarwal
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Na Li
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dennis R Burton
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Andrew B Ward
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - William R Schief
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shane Crotty
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA. .,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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16
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Xu Z, Wise MC, Chokkalingam N, Walker S, Tello‐Ruiz E, Elliott STC, Perales‐Puchalt A, Xiao P, Zhu X, Pumroy RA, Fisher PD, Schultheis K, Schade E, Menis S, Guzman S, Andersen H, Broderick KE, Humeau LM, Muthumani K, Moiseenkova‐Bell V, Schief WR, Weiner DB, Kulp DW. In Vivo Assembly of Nanoparticles Achieved through Synergy of Structure-Based Protein Engineering and Synthetic DNA Generates Enhanced Adaptive Immunity. Adv Sci (Weinh) 2020; 7:1902802. [PMID: 32328416 PMCID: PMC7175333 DOI: 10.1002/advs.201902802] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/28/2019] [Indexed: 05/25/2023]
Abstract
Nanotechnologies are considered to be of growing importance to the vaccine field. Through decoration of immunogens on multivalent nanoparticles, designed nanovaccines can elicit improved humoral immunity. However, significant practical and monetary challenges in large-scale production of nanovaccines have impeded their widespread clinical translation. Here, an alternative approach is illustrated integrating computational protein modeling and adaptive electroporation-mediated synthetic DNA delivery, thus enabling direct in vivo production of nanovaccines. DNA-launched nanoparticles are demonstrated displaying an HIV immunogen spontaneously self-assembled in vivo. DNA-launched nanovaccines induce stronger humoral responses than their monomeric counterparts in both mice and guinea pigs, and uniquely elicit CD8+ effector T-cell immunity as compared to recombinant protein nanovaccines. Improvements in vaccine responses recapitulate when DNA-launched nanovaccines with alternative scaffolds and decorated antigen are designed and evaluated. Finally, evaluation of functional immune responses induced by DLnanovaccines demonstrates that, in comparison to control mice or mice immunized with DNA-encoded hemagglutinin monomer, mice immunized with a DNA-launched hemagglutinin nanoparticle vaccine fully survive a lethal influenza challenge, and have substantially lower viral load, weight loss, and influenza-induced lung pathology. Additional study of these next-generation in vivo-produced nanovaccines may offer advantages for immunization against multiple disease targets.
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Affiliation(s)
- Ziyang Xu
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
- Department of PharmacologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Megan C. Wise
- Inovio PharmaceuticalsPlymouth MeetingPhiladelphiaPA19422USA
| | - Neethu Chokkalingam
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
| | - Susanne Walker
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
| | - Edgar Tello‐Ruiz
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
| | - Sarah T. C. Elliott
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
| | | | - Peng Xiao
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
| | - Xizhou Zhu
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
| | - Ruth A. Pumroy
- Department of PharmacologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Paul D. Fisher
- Inovio PharmaceuticalsPlymouth MeetingPhiladelphiaPA19422USA
| | | | - Eric Schade
- Inovio PharmaceuticalsPlymouth MeetingPhiladelphiaPA19422USA
| | - Sergey Menis
- Department of Immunology and MicrobiologyThe Scripps Research InstituteLa JollaCA92037USA
- IAVI Neutralizing Antibody CenterThe Scripps Research InstituteLa JollaCA92037USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen DiscoveryThe Scripps Research InstituteLa JollaCA92037USA
| | - Stacy Guzman
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
| | | | | | | | - Kar Muthumani
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
| | - Vera Moiseenkova‐Bell
- Department of PharmacologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - William R. Schief
- Department of Immunology and MicrobiologyThe Scripps Research InstituteLa JollaCA92037USA
- IAVI Neutralizing Antibody CenterThe Scripps Research InstituteLa JollaCA92037USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen DiscoveryThe Scripps Research InstituteLa JollaCA92037USA
- Ragon Institute of MGHMIT and HarvardCambridgeMA02139USA
| | - David B. Weiner
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
| | - Daniel W. Kulp
- The Vaccine and Immunotherapy CenterThe Wistar InstitutePhiladelphiaPA19104USA
- Department of MicrobiologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
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17
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Cirelli KM, Carnathan DG, Nogal B, Martin JT, Rodriguez OL, Upadhyay AA, Enemuo CA, Gebru EH, Choe Y, Viviano F, Nakao C, Pauthner MG, Reiss S, Cottrell CA, Smith ML, Bastidas R, Gibson W, Wolabaugh AN, Melo MB, Cossette B, Kumar V, Patel NB, Tokatlian T, Menis S, Kulp DW, Burton DR, Murrell B, Schief WR, Bosinger SE, Ward AB, Watson CT, Silvestri G, Irvine DJ, Crotty S. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. Cell 2020; 180:206. [PMID: 31923396 PMCID: PMC7009795 DOI: 10.1016/j.cell.2019.12.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Steichen JM, Lin YC, Havenar-Daughton C, Pecetta S, Ozorowski G, Willis JR, Toy L, Sok D, Liguori A, Kratochvil S, Torres JL, Kalyuzhniy O, Melzi E, Kulp DW, Raemisch S, Hu X, Bernard SM, Georgeson E, Phelps N, Adachi Y, Kubitz M, Landais E, Umotoy J, Robinson A, Briney B, Wilson IA, Burton DR, Ward AB, Crotty S, Batista FD, Schief WR. A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses. Science 2019; 366:eaax4380. [PMID: 31672916 PMCID: PMC7092357 DOI: 10.1126/science.aax4380] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/17/2019] [Indexed: 12/11/2022]
Abstract
Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity-determining region 3 (HCDR3) is a major barrier. Exploiting ultradeep human antibody sequencing data, we identified a diverse set of potential antibody precursors for a bnAb with dominant HCDR3 contacts. We then developed HIV envelope trimer-based immunogens that primed responses from rare bnAb-precursor B cells in a mouse model and bound a range of potential bnAb-precursor human naïve B cells in ex vivo screens. Our repertoire-guided germline-targeting approach provides a framework for priming the induction of many HIV bnAbs and could be applied to most HCDR3-dominant antibodies from other pathogens.
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Affiliation(s)
- Jon M Steichen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ying-Cing Lin
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Colin Havenar-Daughton
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Simone Pecetta
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jordan R Willis
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Laura Toy
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sven Kratochvil
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Jonathan L Torres
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eleonora Melzi
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Daniel W Kulp
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Vaccine and Immune Therapy Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Sebastian Raemisch
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steffen M Bernard
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicole Phelps
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Umotoy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amanda Robinson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shane Crotty
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA.
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Facundo D Batista
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
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19
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Havenar-Daughton C, Sarkar A, Kulp DW, Toy L, Hu X, Deresa I, Kalyuzhniy O, Kaushik K, Upadhyay AA, Menis S, Landais E, Cao L, Diedrich JK, Kumar S, Schiffner T, Reiss SM, Seumois G, Yates JR, Paulson JC, Bosinger SE, Wilson IA, Schief WR, Crotty S. The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen. Sci Transl Med 2019; 10:10/448/eaat0381. [PMID: 29973404 DOI: 10.1126/scitranslmed.aat0381] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/30/2018] [Indexed: 12/12/2022]
Abstract
Traditional vaccine development to prevent some of the worst current pandemic diseases has been unsuccessful so far. Germline-targeting immunogens have potential to prime protective antibodies (Abs) via more targeted immune responses. Success of germline-targeting vaccines in humans will depend on the composition of the human naive B cell repertoire, including the frequencies and affinities of epitope-specific B cells. However, the human naive B cell repertoire remains largely undefined. Assessment of antigen-specific human naive B cells among hundreds of millions of B cells from multiple donors may be used as pre-phase 1 ex vivo human testing to potentially forecast B cell and Ab responses to new vaccine designs. VRC01 is an HIV broadly neutralizing Ab (bnAb) against the envelope CD4-binding site (CD4bs). We characterized naive human B cells recognizing eOD-GT8, a germline-targeting HIV-1 vaccine candidate immunogen designed to prime VRC01-class Abs. Several distinct subclasses of VRC01-class naive B cells were identified, sharing sequence characteristics with inferred precursors of known bnAbs VRC01, VRC23, PCIN63, and N6. Multiple naive B cell clones exactly matched mature VRC01-class bnAb L-CDR3 sequences. Non-VRC01-class B cells were also characterized, revealing recurrent public light chain sequences. Unexpectedly, we also identified naive B cells related to the IOMA-class CD4bs bnAb. These different subclasses within the human repertoire had strong initial affinities (KD) to the immunogen, up to 13 nM, and represent encouraging indications that multiple independent pathways may exist for vaccine-elicited VRC01-class bnAb development in most individuals. The frequencies of these distinct eOD-GT8 B cell specificities give insights into antigen-specific compositional features of the human naive B cell repertoire and provide actionable information for vaccine design and advancement.
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Affiliation(s)
- Colin Havenar-Daughton
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anita Sarkar
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.,Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Laura Toy
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Isaiah Deresa
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kirti Kaushik
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amit A Upadhyay
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Sergey Menis
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elise Landais
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Liwei Cao
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sonu Kumar
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Torben Schiffner
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Samantha M Reiss
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Grégory Seumois
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C Paulson
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven E Bosinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Ian A Wilson
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
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20
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Cirelli KM, Carnathan DG, Nogal B, Martin JT, Rodriguez OL, Upadhyay AA, Enemuo CA, Gebru EH, Choe Y, Viviano F, Nakao C, Pauthner MG, Reiss S, Cottrell CA, Smith ML, Bastidas R, Gibson W, Wolabaugh AN, Melo MB, Cossette B, Kumar V, Patel NB, Tokatlian T, Menis S, Kulp DW, Burton DR, Murrell B, Schief WR, Bosinger SE, Ward AB, Watson CT, Silvestri G, Irvine DJ, Crotty S. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. Cell 2019; 177:1153-1171.e28. [PMID: 31080066 PMCID: PMC6619430 DOI: 10.1016/j.cell.2019.04.012] [Citation(s) in RCA: 230] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/26/2019] [Accepted: 04/05/2019] [Indexed: 12/14/2022]
Abstract
Conventional immunization strategies will likely be insufficient for the development of a broadly neutralizing antibody (bnAb) vaccine for HIV or other difficult pathogens because of the immunological hurdles posed, including B cell immunodominance and germinal center (GC) quantity and quality. We found that two independent methods of slow delivery immunization of rhesus monkeys (RMs) resulted in more robust T follicular helper (TFH) cell responses and GC B cells with improved Env-binding, tracked by longitudinal fine needle aspirates. Improved GCs correlated with the development of >20-fold higher titers of autologous nAbs. Using a new RM genomic immunoglobulin locus reference, we identified differential IgV gene use between immunization modalities. Ab mapping demonstrated targeting of immunodominant non-neutralizing epitopes by conventional bolus-immunized animals, whereas slow delivery-immunized animals targeted a more diverse set of epitopes. Thus, alternative immunization strategies can enhance nAb development by altering GCs and modulating the immunodominance of non-neutralizing epitopes.
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Affiliation(s)
- Kimberly M Cirelli
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Diane G Carnathan
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bartek Nogal
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jacob T Martin
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Oscar L Rodriguez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amit A Upadhyay
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Chiamaka A Enemuo
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Etse H Gebru
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury Choe
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Federico Viviano
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Catherine Nakao
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Matthias G Pauthner
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Samantha Reiss
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A Cottrell
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raiza Bastidas
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Amber N Wolabaugh
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Mariane B Melo
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benjamin Cossette
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Venkatesh Kumar
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Nirav B Patel
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Talar Tokatlian
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergey Menis
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Dennis R Burton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - William R Schief
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Steven E Bosinger
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Andrew B Ward
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Guido Silvestri
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Darrell J Irvine
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA; Departments of Biological Engineering and Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
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21
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Xu Z, Kulp DW. Protein engineering and particulate display of B-cell epitopes to facilitate development of novel vaccines. Curr Opin Immunol 2019; 59:49-56. [PMID: 31029909 DOI: 10.1016/j.coi.2019.03.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/08/2019] [Accepted: 03/18/2019] [Indexed: 12/11/2022]
Abstract
Induction of antigen-specific humoral immunity is a correlate of protection for many diseases and remains a primary vaccine goal. Pathogens can evade such responses by limiting epitope access, by diversifying surface residues, or by keeping antigens in metastable conformations. B cells can target diverse epitopes on an antigen, but only a subset of which produce functional antibodies. Structure-based immunogen engineering can help overcome these hurdles by using structural information for targeted induction of particular antibodies while improving the overall vaccine immunogenicity. This review will cover recent progress in vaccine design, specifically focusing on strategies to stabilize antigens for optimal B-cell epitope exposure, engineer synthetic B-cell epitopes to induce antibodies with specific features and enhancement of vaccine potency through antigen presentation on multivalent particles.
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Affiliation(s)
- Ziyang Xu
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Daniel W Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104, United States.
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22
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Tokatlian T, Read BJ, Jones CA, Kulp DW, Menis S, Chang JYH, Steichen JM, Kumari S, Allen JD, Dane EL, Liguori A, Sangesland M, Lingwood D, Crispin M, Schief WR, Irvine DJ. Innate immune recognition of glycans targets HIV nanoparticle immunogens to germinal centers. Science 2019. [PMID: 30573546 DOI: 10.1126/science:aat9120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
In vaccine design, antigens are often arrayed in a multivalent nanoparticle form, but in vivo mechanisms underlying the enhanced immunity elicited by such vaccines remain poorly understood. We compared the fates of two different heavily glycosylated HIV antigens, a gp120-derived mini-protein and a large, stabilized envelope trimer, in protein nanoparticle or "free" forms after primary immunization. Unlike monomeric antigens, nanoparticles were rapidly shuttled to the follicular dendritic cell (FDC) network and then concentrated in germinal centers in a complement-, mannose-binding lectin (MBL)-, and immunogen glycan-dependent manner. Loss of FDC localization in MBL-deficient mice or via immunogen deglycosylation significantly affected antibody responses. These findings identify an innate immune-mediated recognition pathway promoting antibody responses to particulate antigens, with broad implications for humoral immunity and vaccine design.
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Affiliation(s)
- Talar Tokatlian
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benjamin J Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Health Sciences and Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Jones
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel W Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jason Y H Chang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jon M Steichen
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sudha Kumari
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joel D Allen
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Eric L Dane
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alessia Liguori
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Max Crispin
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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23
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Tokatlian T, Read BJ, Jones CA, Kulp DW, Menis S, Chang JYH, Steichen JM, Kumari S, Allen JD, Dane EL, Liguori A, Sangesland M, Lingwood D, Crispin M, Schief WR, Irvine DJ. Innate immune recognition of glycans targets HIV nanoparticle immunogens to germinal centers. Science 2018; 363:649-654. [PMID: 30573546 DOI: 10.1126/science.aat9120] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
In vaccine design, antigens are often arrayed in a multivalent nanoparticle form, but in vivo mechanisms underlying the enhanced immunity elicited by such vaccines remain poorly understood. We compared the fates of two different heavily glycosylated HIV antigens, a gp120-derived mini-protein and a large, stabilized envelope trimer, in protein nanoparticle or "free" forms after primary immunization. Unlike monomeric antigens, nanoparticles were rapidly shuttled to the follicular dendritic cell (FDC) network and then concentrated in germinal centers in a complement-, mannose-binding lectin (MBL)-, and immunogen glycan-dependent manner. Loss of FDC localization in MBL-deficient mice or via immunogen deglycosylation significantly affected antibody responses. These findings identify an innate immune-mediated recognition pathway promoting antibody responses to particulate antigens, with broad implications for humoral immunity and vaccine design.
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Affiliation(s)
- Talar Tokatlian
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benjamin J Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Health Sciences and Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Jones
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel W Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jason Y H Chang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jon M Steichen
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sudha Kumari
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joel D Allen
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Eric L Dane
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alessia Liguori
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Max Crispin
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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24
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Tokatlian T, Kulp DW, Mutafyan AA, Jones CA, Menis S, Georgeson E, Kubitz M, Zhang MH, Melo MB, Silva M, Yun DS, Schief WR, Irvine DJ. Enhancing Humoral Responses Against HIV Envelope Trimers via Nanoparticle Delivery with Stabilized Synthetic Liposomes. Sci Rep 2018; 8:16527. [PMID: 30410003 PMCID: PMC6224390 DOI: 10.1038/s41598-018-34853-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/27/2018] [Indexed: 02/05/2023] Open
Abstract
An HIV vaccine capable of eliciting durable neutralizing antibody responses continues to be an important unmet need. Multivalent nanoparticles displaying a high density of envelope trimers may be promising immunogen forms to elicit strong and durable humoral responses to HIV, but critical particle design criteria remain to be fully defined. To this end, we developed strategies to covalently anchor a stabilized gp140 trimer, BG505 MD39, on the surfaces of synthetic liposomes to study the effects of trimer density and vesicle stability on vaccine-elicited humoral responses in mice. CryoEM imaging revealed homogeneously distributed and oriented MD39 on the surface of liposomes irrespective of particle size, lipid composition, and conjugation strategy. Immunization with covalent MD39-coupled liposomes led to increased germinal center and antigen-specific T follicular helper cell responses and significantly higher avidity serum MD39-specific IgG responses compared to immunization with soluble MD39 trimers. A priming immunization with liposomal-MD39 was important for elicitation of high avidity antibody responses, regardless of whether booster immunizations were administered with either soluble or particulate trimers. The stability of trimer anchoring to liposomes was critical for these effects, as germinal center and output antibody responses were further increased by liposome compositions incorporating sphingomyelin that exhibited high in vitro stability in the presence of serum. Together these data highlight key liposome design features for optimizing humoral immunity to lipid nanoparticle immunogens.
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Affiliation(s)
| | - Daniel W Kulp
- International AIDS Vaccine Initiative, New York, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, California, USA.,Vaccine and Immunotherapy Center, The Wistar Institute, Pennsylvania, USA
| | | | | | - Sergey Menis
- International AIDS Vaccine Initiative, New York, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, California, USA
| | - Erik Georgeson
- International AIDS Vaccine Initiative, New York, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, California, USA
| | - Mike Kubitz
- International AIDS Vaccine Initiative, New York, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, California, USA
| | | | | | | | | | - William R Schief
- International AIDS Vaccine Initiative, New York, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, California, USA.,Immunology and Microbial Science, TSRI, California, USA.,Ragon Institute of MGH, MIT, and Harvard, Massachusetts, USA
| | - Darrell J Irvine
- Koch Institute, MIT, Massachusetts, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, California, USA. .,Department of Biological Engineering and Materials Science & Engineering, MIT, Massachusetts, USA. .,Ragon Institute of MGH, MIT, and Harvard, Massachusetts, USA. .,Howard Hughes Medical Institute, Maryland, USA.
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25
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Abbott RK, Lee JH, Menis S, Skog P, Rossi M, Ota T, Kulp DW, Bhullar D, Kalyuzhniy O, Havenar-Daughton C, Schief WR, Nemazee D, Crotty S. Precursor Frequency and Affinity Determine B Cell Competitive Fitness in Germinal Centers, Tested with Germline-Targeting HIV Vaccine Immunogens. Immunity 2017; 48:133-146.e6. [PMID: 29287996 DOI: 10.1016/j.immuni.2017.11.023] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/12/2017] [Accepted: 11/28/2017] [Indexed: 01/28/2023]
Abstract
How precursor frequencies and antigen affinities impact interclonal B cell competition is a particularly relevant issue for candidate germline-targeting HIV vaccine designs because of the in vivo rarity of naive B cells that recognize broadly neutralizing epitopes. Knowing the frequencies and affinities of HIV-specific VRC01-class naive human B cells, we transferred B cells with germline VRC01 B cell receptors into congenic recipients to elucidate the roles of precursor frequency, antigen affinity, and avidity on B cell responses following immunization. All three factors were interdependently limiting for competitive success of VRC01-class B cells. In physiological high-affinity conditions using a multivalent immunogen, rare VRC01-class B cells successfully competed in germinal centers (GC), underwent extensive somatic hypermutation, and differentiated into memory B cells. The data reveal dominant influences of precursor frequency, affinity, and avidity for interclonal GC competition and indicate that germline-targeting immunogens can overcome these challenges with high-affinity multimeric designs.
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Affiliation(s)
- Robert K Abbott
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeong Hyun Lee
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patrick Skog
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meghan Rossi
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Takayuki Ota
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Vaccine and Immune Therapy Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Deepika Bhullar
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Colin Havenar-Daughton
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA.
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
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26
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Kulp DW, Steichen JM, Pauthner M, Hu X, Schiffner T, Liguori A, Cottrell CA, Havenar-Daughton C, Ozorowski G, Georgeson E, Kalyuzhniy O, Willis JR, Kubitz M, Adachi Y, Reiss SM, Shin M, de Val N, Ward AB, Crotty S, Burton DR, Schief WR. Structure-based design of native-like HIV-1 envelope trimers to silence non-neutralizing epitopes and eliminate CD4 binding. Nat Commun 2017; 8:1655. [PMID: 29162799 PMCID: PMC5698488 DOI: 10.1038/s41467-017-01549-6] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/26/2017] [Indexed: 12/12/2022] Open
Abstract
Elicitation of broadly neutralizing antibodies (bnAbs) is a primary HIV vaccine goal. Native-like trimers mimicking virion-associated spikes present nearly all bnAb epitopes and are therefore promising vaccine antigens. However, first generation native-like trimers expose epitopes for non-neutralizing antibodies (non-nAbs), which may hinder bnAb induction. We here employ computational and structure-guided design to develop improved native-like trimers that reduce exposure of non-nAb epitopes in the V3-loop and trimer base, minimize both CD4 reactivity and CD4-induced non-nAb epitope exposure, and increase thermal stability while maintaining bnAb antigenicity. In rabbit immunizations with native-like trimers of the 327c isolate, improved trimers suppress elicitation of V3-directed and tier-1 neutralizing antibodies and induce robust autologous tier-2 neutralization, unlike a first-generation trimer. The improved native-like trimers from diverse HIV isolates, and the design methods, have promise to assist in the development of a HIV vaccine. Eliciting broadly neutralizing antibodies (bnAbs) is a primary HIV vaccine goal, but available immunogens expose epitopes for development of non-nAbs. Here, the authors use computational and structure-guided design to develop improved native-like envelope trimers and analyze Ab response in animal models.
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Affiliation(s)
- Daniel W Kulp
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Vaccine and Immune Therapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Jon M Steichen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Matthias Pauthner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Christopher A Cottrell
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Colin Havenar-Daughton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jordan R Willis
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Samantha M Reiss
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Mia Shin
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Natalia de Val
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA.,Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA.,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA. .,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, 92037, USA. .,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA.
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27
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Pauthner M, Havenar-Daughton C, Sok D, Nkolola JP, Bastidas R, Boopathy AV, Carnathan DG, Chandrashekar A, Cirelli KM, Cottrell CA, Eroshkin AM, Guenaga J, Kaushik K, Kulp DW, Liu J, McCoy LE, Oom AL, Ozorowski G, Post KW, Sharma SK, Steichen JM, de Taeye SW, Tokatlian T, Torrents de la Peña A, Butera ST, LaBranche CC, Montefiori DC, Silvestri G, Wilson IA, Irvine DJ, Sanders RW, Schief WR, Ward AB, Wyatt RT, Barouch DH, Crotty S, Burton DR. Elicitation of Robust Tier 2 Neutralizing Antibody Responses in Nonhuman Primates by HIV Envelope Trimer Immunization Using Optimized Approaches. Immunity 2017. [PMID: 28636956 PMCID: PMC5483234 DOI: 10.1016/j.immuni.2017.05.007] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The development of stabilized recombinant HIV envelope trimers that mimic the virion surface molecule has increased enthusiasm for a neutralizing antibody (nAb)-based HIV vaccine. However, there is limited experience with recombinant trimers as immunogens in nonhuman primates, which are typically used as a model for humans. Here, we tested multiple immunogens and immunization strategies head-to-head to determine their impact on the quantity, quality, and kinetics of autologous tier 2 nAb development. A bilateral, adjuvanted, subcutaneous immunization protocol induced reproducible tier 2 nAb responses after only two immunizations 8 weeks apart, and these were further enhanced by a third immunization with BG505 SOSIP trimer. We identified immunogens that minimized non-neutralizing V3 responses and demonstrated that continuous immunogen delivery could enhance nAb responses. nAb responses were strongly associated with germinal center reactions, as assessed by lymph node fine needle aspiration. This study provides a framework for preclinical and clinical vaccine studies targeting nAb elicitation.
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Affiliation(s)
- Matthias Pauthner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Colin Havenar-Daughton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Joseph P Nkolola
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Raiza Bastidas
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Archana V Boopathy
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Diane G Carnathan
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kimberly M Cirelli
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Christopher A Cottrell
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexey M Eroshkin
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Bioinformatics Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Javier Guenaga
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kirti Kaushik
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jinyan Liu
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Laura E McCoy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Infection & Immunity, University College London, London WC1E 6BT, UK
| | - Aaron L Oom
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; University of California, San Diego, La Jolla, CA 92093, USA
| | - Gabriel Ozorowski
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kai W Post
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Bioinformatics Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Shailendra K Sharma
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jon M Steichen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven W de Taeye
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Talar Tokatlian
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alba Torrents de la Peña
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Salvatore T Butera
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Celia C LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Guido Silvestri
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ian A Wilson
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Darrell J Irvine
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Departments of Biological Engineering and Materials Science & Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rogier W Sanders
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA; Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Andrew B Ward
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Richard T Wyatt
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dan H Barouch
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA.
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28
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Crooks ET, Osawa K, Tong T, Grimley SL, Dai YD, Whalen RG, Kulp DW, Menis S, Schief WR, Binley JM. Effects of partially dismantling the CD4 binding site glycan fence of HIV-1 Envelope glycoprotein trimers on neutralizing antibody induction. Virology 2017; 505:193-209. [PMID: 28279830 DOI: 10.1016/j.virol.2017.02.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 12/31/2022]
Abstract
Previously, VLPs bearing JR-FL strain HIV-1 Envelope trimers elicited potent neutralizing antibodies (nAbs) in 2/8 rabbits (PLoS Pathog 11(5): e1004932) by taking advantage of a naturally absent glycan at position 197 that borders the CD4 binding site (CD4bs). In new immunizations, we attempted to improve nAb responses by removing the N362 glycan that also lines the CD4bs. All 4 rabbits developed nAbs. One targeted the N197 glycan hole like our previous sera. Two sera depended on the N463 glycan, again suggesting CD4bs overlap. Heterologous boosts appeared to reduce nAb clashes with the N362 glycan. The fourth serum targeted a N362 glycan-sensitive epitope. VLP manufacture challenges prevented us from immunizing larger rabbit numbers to empower a robust statistical analysis. Nevertheless, trends suggest that targeted glycan removal may improve nAb induction by exposing new epitopes and that it may be possible to modify nAb specificity using rational heterologous boosts.
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Affiliation(s)
- Ema T Crooks
- San Diego Biomedical Research Institute, 10865 Road to the Cure, San Diego, CA 92121, USA
| | - Keiko Osawa
- San Diego Biomedical Research Institute, 10865 Road to the Cure, San Diego, CA 92121, USA
| | - Tommy Tong
- San Diego Biomedical Research Institute, 10865 Road to the Cure, San Diego, CA 92121, USA
| | - Samantha L Grimley
- San Diego Biomedical Research Institute, 10865 Road to the Cure, San Diego, CA 92121, USA
| | - Yang D Dai
- The Scripps Research Institute, Department of Immunology and Microbial Science, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Robert G Whalen
- Altravax, Inc., 725 San Aleso Avenue, Suite 2, Sunnyvale, CA 94085, USA
| | - Daniel W Kulp
- IAVI Neutralizing Antibody Center at The Scripps Research Institute, Department of Immunology and Microbial Science, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sergey Menis
- IAVI Neutralizing Antibody Center at The Scripps Research Institute, Department of Immunology and Microbial Science, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - William R Schief
- IAVI Neutralizing Antibody Center at The Scripps Research Institute, Department of Immunology and Microbial Science, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - James M Binley
- San Diego Biomedical Research Institute, 10865 Road to the Cure, San Diego, CA 92121, USA.
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29
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Escolano A, Steichen JM, Dosenovic P, Kulp DW, Golijanin J, Sok D, Freund NT, Gitlin AD, Oliveira T, Araki T, Lowe S, Chen ST, Heinemann J, Yao KH, Georgeson E, Saye-Francisco KL, Gazumyan A, Adachi Y, Kubitz M, Burton DR, Schief WR, Nussenzweig MC. Sequential Immunization Elicits Broadly Neutralizing Anti-HIV-1 Antibodies in Ig Knockin Mice. Cell 2016; 166:1445-1458.e12. [PMID: 27610569 DOI: 10.1016/j.cell.2016.07.030] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/05/2016] [Accepted: 07/20/2016] [Indexed: 12/14/2022]
Abstract
A vaccine that elicits broadly neutralizing antibodies (bNAbs) against HIV-1 is likely to be protective, but this has not been achieved. To explore immunization regimens that might elicit bNAbs, we produced and immunized mice expressing the predicted germline PGT121, a bNAb specific for the V3-loop and surrounding glycans on the HIV-1 spike. Priming with an epitope-modified immunogen designed to activate germline antibody-expressing B cells, followed by ELISA-guided boosting with a sequence of directional immunogens, native-like trimers with decreasing epitope modification, elicited heterologous tier-2-neutralizing responses. In contrast, repeated immunization with the priming immunogen did not. Antibody cloning confirmed elicitation of high levels of somatic mutation and tier-2-neutralizing antibodies resembling the authentic human bNAb. Our data establish that sequential immunization with specifically designed immunogens can induce high levels of somatic mutation and shepherd antibody maturation to produce bNAbs from their inferred germline precursors.
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Affiliation(s)
- Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Jon M Steichen
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pia Dosenovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Daniel W Kulp
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Devin Sok
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Natalia T Freund
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Alexander D Gitlin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Thiago Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Tatsuya Araki
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Sarina Lowe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Spencer T Chen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Jennifer Heinemann
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Erik Georgeson
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karen L Saye-Francisco
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Yumiko Adachi
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - William R Schief
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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30
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Briney B, Sok D, Jardine JG, Kulp DW, Skog P, Menis S, Jacak R, Kalyuzhniy O, de Val N, Sesterhenn F, Le KM, Ramos A, Jones M, Saye-Francisco KL, Blane TR, Spencer S, Georgeson E, Hu X, Ozorowski G, Adachi Y, Kubitz M, Sarkar A, Wilson IA, Ward AB, Nemazee D, Burton DR, Schief WR. Tailored Immunogens Direct Affinity Maturation toward HIV Neutralizing Antibodies. Cell 2016; 166:1459-1470.e11. [PMID: 27610570 PMCID: PMC5018249 DOI: 10.1016/j.cell.2016.08.005] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/20/2016] [Accepted: 08/02/2016] [Indexed: 11/24/2022]
Abstract
Induction of broadly neutralizing antibodies (bnAbs) is a primary goal of HIV vaccine development. VRC01-class bnAbs are important vaccine leads because their precursor B cells targeted by an engineered priming immunogen are relatively common among humans. This priming immunogen has demonstrated the ability to initiate a bnAb response in animal models, but recall and maturation toward bnAb development has not been shown. Here, we report the development of boosting immunogens designed to guide the genetic and functional maturation of previously primed VRC01-class precursors. Boosting a transgenic mouse model expressing germline VRC01 heavy chains produced broad neutralization of near-native isolates (N276A) and weak neutralization of fully native HIV. Functional and genetic characteristics indicate that the boosted mAbs are consistent with partially mature VRC01-class antibodies and place them on a maturation trajectory that leads toward mature VRC01-class bnAbs. The results show how reductionist sequential immunization can guide maturation of HIV bnAb responses. Designed boosting immunogens to follow a VRC01-class germline-targeting prime Boosted Abs selectively incorporate VRC01-class somatic mutations Sequential boosts elicit VRC01-class mAbs with broad neutralization of N276A viruses Vaccine-elicited VRC01-class mAbs neutralize one fully native HIV isolate
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Affiliation(s)
- Bryan Briney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph G Jardine
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patrick Skog
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ronald Jacak
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Natalia de Val
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fabian Sesterhenn
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Khoa M Le
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alejandra Ramos
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meaghan Jones
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karen L Saye-Francisco
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tanya R Blane
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Skye Spencer
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yumiko Adachi
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anita Sarkar
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02129, USA.
| | - William R Schief
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02129, USA.
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31
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Steichen JM, Kulp DW, Tokatlian T, Escolano A, Dosenovic P, Stanfield RL, McCoy LE, Ozorowski G, Hu X, Kalyuzhniy O, Briney B, Schiffner T, Garces F, Freund NT, Gitlin AD, Menis S, Georgeson E, Kubitz M, Adachi Y, Jones M, Mutafyan AA, Yun DS, Mayer CT, Ward AB, Burton DR, Wilson IA, Irvine DJ, Nussenzweig MC, Schief WR. HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies. Immunity 2016; 45:483-496. [PMID: 27617678 PMCID: PMC5040827 DOI: 10.1016/j.immuni.2016.08.016] [Citation(s) in RCA: 260] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/28/2016] [Accepted: 08/25/2016] [Indexed: 11/24/2022]
Abstract
Broadly neutralizing antibodies (bnAbs) against the N332 supersite of the HIV envelope (Env) trimer are the most common bnAbs induced during infection, making them promising leads for vaccine design. Wild-type Env glycoproteins lack detectable affinity for supersite-bnAb germline precursors and are therefore unsuitable immunogens to prime supersite-bnAb responses. We employed mammalian cell surface display to design stabilized Env trimers with affinity for germline-reverted precursors of PGT121-class supersite bnAbs. The trimers maintained native-like antigenicity and structure, activated PGT121 inferred-germline B cells ex vivo when multimerized on liposomes, and primed PGT121-like responses in PGT121 inferred-germline knockin mice. Design intermediates have levels of epitope modification between wild-type and germline-targeting trimers; their mutation gradient suggests sequential immunization to induce bnAbs, in which the germline-targeting prime is followed by progressively less-mutated design intermediates and, lastly, with native trimers. The vaccine design strategies described could be utilized to target other epitopes on HIV or other pathogens.
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Affiliation(s)
- Jon M Steichen
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Talar Tokatlian
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Pia Dosenovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Robyn L Stanfield
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Laura E McCoy
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Torben Schiffner
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fernando Garces
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Natalia T Freund
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Alexander D Gitlin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Sergey Menis
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yumiko Adachi
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meaghan Jones
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew A Mutafyan
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Dong Soo Yun
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Christian T Mayer
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Departments of Biological Engineering and Materials Science & Engineering, MIT, Cambridge, MA 02139, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - William R Schief
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.
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32
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Sok D, Briney B, Jardine JG, Kulp DW, Menis S, Pauthner M, Wood A, Lee EC, Le KM, Jones M, Ramos A, Kalyuzhniy O, Adachi Y, Kubitz M, MacPherson S, Bradley A, Friedrich GA, Schief WR, Burton DR. Priming HIV-1 broadly neutralizing antibody precursors in human Ig loci transgenic mice. Science 2016; 353:1557-1560. [PMID: 27608668 DOI: 10.1126/science.aah3945] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
Abstract
A major obstacle to a broadly neutralizing antibody (bnAb)-based HIV vaccine is the activation of appropriate B cell precursors. Germline-targeting immunogens must be capable of priming rare bnAb precursors in the physiological setting. We tested the ability of the VRC01-class bnAb germline-targeting immunogen eOD-GT8 60mer (60-subunit self-assembling nanoparticle) to activate appropriate precursors in mice transgenic for human immunoglobulin (Ig) loci. Despite an average frequency of, at most, about one VRC01-class precursor per mouse, we found that at least 29% of singly immunized mice produced a VRC01-class memory response, suggesting that priming generally succeeded when at least one precursor was present. The results demonstrate the feasibility of using germline targeting to prime specific and exceedingly rare bnAb-precursor B cells within a humanlike repertoire.
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Affiliation(s)
- Devin Sok
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph G Jardine
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthias Pauthner
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew Wood
- Kymab Ltd, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - E-Chiang Lee
- Kymab Ltd, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Khoa M Le
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meaghan Jones
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alejandra Ramos
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yumiko Adachi
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Skye MacPherson
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Allan Bradley
- Kymab Ltd, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK. Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Glenn A Friedrich
- Kymab Ltd, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - William R Schief
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of Massachusetts General Hospital (MGH), MIT, and Harvard, Cambridge, MA 02129, USA.
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of Massachusetts General Hospital (MGH), MIT, and Harvard, Cambridge, MA 02129, USA.
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McCoy LE, van Gils MJ, Ozorowski G, Messmer T, Briney B, Voss JE, Kulp DW, Macauley MS, Sok D, Pauthner M, Menis S, Cottrell CA, Torres JL, Hsueh J, Schief WR, Wilson IA, Ward AB, Sanders RW, Burton DR. Holes in the Glycan Shield of the Native HIV Envelope Are a Target of Trimer-Elicited Neutralizing Antibodies. Cell Rep 2016; 16:2327-38. [PMID: 27545891 DOI: 10.1016/j.celrep.2016.07.074] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/25/2016] [Accepted: 07/27/2016] [Indexed: 10/21/2022] Open
Abstract
A major advance in the search for an HIV vaccine has been the development of a near-native Envelope trimer (BG505 SOSIP.664) that can induce robust autologous Tier 2 neutralization. Here, potently neutralizing monoclonal antibodies (nAbs) from rabbits immunized with BG505 SOSIP.664 are shown to recognize an immunodominant region of gp120 centered on residue 241. Residue 241 occupies a hole in the glycan defenses of the BG505 isolate, with fewer than 3% of global isolates lacking a glycan site at this position. However, at least one conserved glycan site is missing in 89% of viruses, suggesting the presence of glycan holes in most HIV isolates. Serum evidence is consistent with targeting of holes in natural infection. The immunogenic nature of breaches in the glycan shield has been under-appreciated in previous attempts to understand autologous neutralizing antibody responses and has important potential consequences for HIV vaccine design.
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Affiliation(s)
- Laura E McCoy
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Infection & Immunity, University College London, London WC1E 6BT, UK
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Gabriel Ozorowski
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Terrence Messmer
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James E Voss
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthew S Macauley
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthias Pauthner
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A Cottrell
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Torres
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica Hsueh
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Ian A Wilson
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; Weill Medical College of Cornell University, New York, NY 10065, USA.
| | - Dennis R Burton
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.
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34
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Jardine JG, Kulp DW, Havenar-Daughton C, Sarkar A, Briney B, Sok D, Sesterhenn F, Ereño-Orbea J, Kalyuzhniy O, Deresa I, Hu X, Spencer S, Jones M, Georgeson E, Adachi Y, Kubitz M, deCamp AC, Julien JP, Wilson IA, Burton DR, Crotty S, Schief WR. HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen. Science 2016; 351:1458-63. [PMID: 27013733 DOI: 10.1126/science.aad9195] [Citation(s) in RCA: 314] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 02/24/2016] [Indexed: 12/13/2022]
Abstract
Induction of broadly neutralizing antibodies (bnAbs) is a major HIV vaccine goal. Germline-targeting immunogens aim to initiate bnAb induction by activating bnAb germline precursor B cells. Critical unmet challenges are to determine whether bnAb precursor naïve B cells bind germline-targeting immunogens and occur at sufficient frequency in humans for reliable vaccine responses. Using deep mutational scanning and multitarget optimization, we developed a germline-targeting immunogen (eOD-GT8) for diverse VRC01-class bnAbs. We then used the immunogen to isolate VRC01-class precursor naïve B cells from HIV-uninfected donors. Frequencies of true VRC01-class precursors, their structures, and their eOD-GT8 affinities support this immunogen as a candidate human vaccine prime. These methods could be applied to germline targeting for other classes of HIV bnAbs and for Abs to other pathogens.
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Affiliation(s)
- Joseph G Jardine
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Colin Havenar-Daughton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Anita Sarkar
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fabian Sesterhenn
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - June Ereño-Orbea
- Program in Molecular Structure and Function, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Isaiah Deresa
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Skye Spencer
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meaghan Jones
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yumiko Adachi
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Allan C deCamp
- Vaccine and Infectious Disease Division, Statistical Center for HIV/AIDS Research and Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jean-Philippe Julien
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Program in Molecular Structure and Function, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada. Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
| | - William R Schief
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA.
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35
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Dosenovic P, von Boehmer L, Escolano A, Jardine J, Freund NT, Gitlin AD, McGuire AT, Kulp DW, Oliveira T, Scharf L, Pietzsch J, Gray MD, Cupo A, van Gils MJ, Yao KH, Liu C, Gazumyan A, Seaman MS, Björkman PJ, Sanders RW, Moore JP, Stamatatos L, Schief WR, Nussenzweig MC. Immunization for HIV-1 Broadly Neutralizing Antibodies in Human Ig Knockin Mice. Cell 2015; 161:1505-15. [PMID: 26091035 DOI: 10.1016/j.cell.2015.06.003] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 05/29/2015] [Accepted: 05/29/2015] [Indexed: 12/11/2022]
Abstract
A subset of individuals infected with HIV-1 develops broadly neutralizing antibodies (bNAbs) that can prevent infection, but it has not yet been possible to elicit these antibodies by immunization. To systematically explore how immunization might be tailored to produce them, we generated mice expressing the predicted germline or mature heavy chains of a potent bNAb to the CD4 binding site (CD4bs) on the HIV-1 envelope glycoprotein (Env). Immunogens specifically designed to activate B cells bearing germline antibodies are required to initiate immune responses, but they do not elicit bNAbs. In contrast, native-like Env trimers fail to activate B cells expressing germline antibodies but elicit bNAbs by selecting for a restricted group of light chains bearing specific somatic mutations that enhance neutralizing activity. The data suggest that vaccination to elicit anti-HIV-1 antibodies will require immunization with a succession of related immunogens.
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Affiliation(s)
- Pia Dosenovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Lotta von Boehmer
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Joseph Jardine
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Natalia T Freund
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Alexander D Gitlin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thiago Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Louise Scharf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John Pietzsch
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Matthew D Gray
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Cassie Liu
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Pamela J Björkman
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rogier W Sanders
- Department of Microbiology and Immunology, Weill Medical College, Cornell University, New York, NY 10065, USA; Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98109, USA
| | - William R Schief
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute.
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Pritchard LK, Spencer DIR, Royle L, Bonomelli C, Seabright GE, Behrens AJ, Kulp DW, Menis S, Krumm SA, Dunlop DC, Crispin DJ, Bowden TA, Scanlan CN, Ward AB, Schief WR, Doores KJ, Crispin M. Glycan clustering stabilizes the mannose patch of HIV-1 and preserves vulnerability to broadly neutralizing antibodies. Nat Commun 2015; 6:7479. [PMID: 26105115 PMCID: PMC4500839 DOI: 10.1038/ncomms8479] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 05/13/2015] [Indexed: 12/22/2022] Open
Abstract
The envelope spike of HIV-1 employs a ‘glycan shield’ to protect itself from antibody-mediated neutralization. Paradoxically, however, potent broadly neutralizing antibodies (bnAbs) have been isolated which target this shield. The unusually high glycan density on the gp120 subunit limits processing during biosynthesis, leaving a region of under-processed oligomannose-type structures which is a primary target of these bnAbs. Here we investigate the contribution of individual glycosylation sites to formation of this so-called intrinsic mannose patch. Deletion of individual sites has a limited effect on the overall size of the intrinsic mannose patch but leads to changes in the processing of neighboring glycans. These structural changes are largely tolerated by a panel of glycan-dependent bnAbs targeting these regions, indicating a degree of plasticity in their recognition. These results support the intrinsic mannose patch as a stable target for vaccine design.
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Affiliation(s)
- Laura K Pritchard
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Louise Royle
- Ludger Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14 3EB, UK
| | - Camille Bonomelli
- 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
| | - Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Daniel W Kulp
- 1] Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA [2] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Sergey Menis
- 1] Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA [2] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Stefanie A Krumm
- King's College London School of Medicine at Guy's, King's and St Thomas' Hospitals, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - D Cameron Dunlop
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Daniel J Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher N Scanlan
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, IAVI Neutralizing Antibody Center, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - William R Schief
- 1] Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA [2] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA [3] Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Katie J Doores
- King's College London School of Medicine at Guy's, King's and St Thomas' Hospitals, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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37
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Jardine JG, Ota T, Sok D, Pauthner M, Kulp DW, Kalyuzhniy O, Skog PD, Thinnes TC, Bhullar D, Briney B, Menis S, Jones M, Kubitz M, Spencer S, Adachi Y, Burton DR, Schief WR, Nemazee D. HIV-1 VACCINES. Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen. Science 2015; 349:156-61. [PMID: 26089355 DOI: 10.1126/science.aac5894] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 06/11/2015] [Indexed: 12/19/2022]
Abstract
A major goal of HIV-1 vaccine research is the design of immunogens capable of inducing broadly neutralizing antibodies (bnAbs) that bind to the viral envelope glycoprotein (Env). Poor binding of Env to unmutated precursors of bnAbs, including those of the VRC01 class, appears to be a major problem for bnAb induction. We engineered an immunogen that binds to VRC01-class bnAb precursors and immunized knock-in mice expressing germline-reverted VRC01 heavy chains. Induced antibodies showed characteristics of VRC01-class bnAbs, including a short CDRL3 (light-chain complementarity-determining region 3) and mutations that favored binding to near-native HIV-1 gp120 constructs. In contrast, native-like immunogens failed to activate VRC01-class precursors. The results suggest that rational epitope design can prime rare B cell precursors for affinity maturation to desired targets.
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Affiliation(s)
- Joseph G Jardine
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Takayuki Ota
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthias Pauthner
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patrick D Skog
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Theresa C Thinnes
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deepika Bhullar
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meaghan Jones
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mike Kubitz
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Skye Spencer
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yumiko Adachi
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA.
| | - William R Schief
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA.
| | - David Nemazee
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Sok D, Doores KJ, Briney B, Le KM, Saye-Francisco KL, Ramos A, Kulp DW, Julien JP, Menis S, Wickramasinghe L, Seaman MS, Schief WR, Wilson IA, Poignard P, Burton DR. Promiscuous glycan site recognition by antibodies to the high-mannose patch of gp120 broadens neutralization of HIV. Sci Transl Med 2014; 6:236ra63. [PMID: 24828077 DOI: 10.1126/scitranslmed.3008104] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Broadly neutralizing monoclonal antibodies (bnmAbs) that target the high-mannose patch centered around the glycan at position 332 on HIV Env are promising vaccine leads and therapeutic candidates because they effectively protect against mucosal SHIV challenge and strongly suppress SHIV viremia in established infection in macaque models. However, these antibodies demonstrate varying degrees of dependency on the N332 glycan site, and the origins of their neutralization breadth are not always obvious. By measuring neutralization on an extended range of glycan site viral variants, we found that some bnmAbs can use alternate N-linked glycans in the absence of the N332 glycan site and therefore neutralize a substantial number of viruses lacking the site. Furthermore, many of the antibodies can neutralize viruses in which the N332 glycan site is shifted to the 334 position. Finally, we found that a combination of three antibody families that target the high-mannose patch can lead to 99% neutralization coverage of a large panel of viruses containing the N332/N334 glycan site and up to 66% coverage for viruses that lack the N332/N334 glycan site. The results indicate that a diverse response against the high-mannose patch may provide near-equivalent coverage as a combination of bnmAbs targeting multiple epitopes. Additionally, the ability of some bnmAbs to use other N-linked glycan sites can help counter neutralization escape mediated by shifting of glycosylation sites. Overall, this work highlights the importance of promiscuous glycan binding properties in bnmAbs to the high-mannose patch for optimal antiviral activity in either protective or therapeutic modalities.
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Affiliation(s)
- Devin Sok
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katie J Doores
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK.
| | - Bryan Briney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Khoa M Le
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karen L Saye-Francisco
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alejandra Ramos
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, New York, NY 10038, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, New York, NY 10038, USA
| | - Jean-Philippe Julien
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, New York, NY 10038, USA
| | - Lalinda Wickramasinghe
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, New York, NY 10038, USA
| | | | - William R Schief
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, New York, NY 10038, USA. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02142, USA
| | - Ian A Wilson
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pascal Poignard
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, New York, NY 10038, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02142, USA.
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Bates JT, Keefer CJ, Slaughter JC, Kulp DW, Schief WR, Crowe JE. Escape from neutralization by the respiratory syncytial virus-specific neutralizing monoclonal antibody palivizumab is driven by changes in on-rate of binding to the fusion protein. Virology 2014; 454-455:139-44. [PMID: 24725940 DOI: 10.1016/j.virol.2014.02.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 02/09/2014] [Accepted: 02/10/2014] [Indexed: 01/14/2023]
Abstract
The role of binding kinetics in determining neutralizing potency for antiviral antibodies is poorly understood. While it is believed that increased steady-state affinity correlates positively with increased virus-neutralizing activity, the relationship between association or dissociation rate and neutralization potency is unclear. We investigated the effect of naturally-occurring antibody resistance mutations in the RSV F protein on the kinetics of binding to palivizumab. Escape from palivizumab-mediated neutralization of RSV occurred with reduced association rate (Kon) for binding to RSV F protein, while alteration of dissociation rate (Koff) did not significantly affect neutralizing activity. Interestingly, linkage of reduced Kon with reduced potency mirrored the effect of increased Kon found in a high-affinity enhanced potency palivizumab variant (motavizumab). These data suggest that association rate is the dominant factor driving neutralization potency for antibodies to RSV F protein antigenic site A and determines the potency of antibody somatic variants or efficiency of escape of viral glycoprotein variants.
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Affiliation(s)
- John T Bates
- The Vanderbilt Vaccine Center, Departments of Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United states
| | - Christopher J Keefer
- The Vanderbilt Vaccine Center, Departments of Pediatrics, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United states
| | - James C Slaughter
- The Vanderbilt Vaccine Center, Departments of Biostatistics and Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United states
| | - Daniel W Kulp
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United states
| | - William R Schief
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United states; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United states
| | - James E Crowe
- The Vanderbilt Vaccine Center, Departments of Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United states; The Vanderbilt Vaccine Center, Departments of Pediatrics, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United states.
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40
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Abstract
Despite the tremendous successes of current vaccines, infectious diseases still take a heavy toll on the global population, and that provides strong rationale for broadening our vaccine development repertoire. Structural vaccinology, in which protein structure information is utilized to design immunogens, has promise to provide new vaccines against traditionally difficult targets. Crystal structures of antigens containing one or more protection epitopes, especially when in complex with a protective antibody, are the launching point for immunogen design. Integrating structure and sequence information for families of broadly neutralizing antibodies (bNAbs) has recently enabled the creation of germline-targeting immunogens that bind and activate germline B-cells in order to initiate the elicitation of such antibodies. The contacts between antigen and neutralizing antibody define a structural epitope, and methods have been developed to transplant epitopes to scaffold proteins for structural stabilization, and to design minimized antigens that retain one or more key epitopes while eliminating other potentially distracting or unnecessary features. To develop vaccines that protect against antigenically variable pathogens, pioneering structure-based work demonstrated that multiple strain-specific epitopes could be engineered onto a single immunogen. We review these recent structural vaccinology efforts to engineer germline-targeting, epitope-specific, and/or broad coverage immunogens.
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Affiliation(s)
- Daniel W Kulp
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
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41
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Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Szyperski TG, Solomon EI, DeGrado WF. Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins. Nat Chem 2012; 4:900-6. [PMID: 23089864 PMCID: PMC3568993 DOI: 10.1038/nchem.1454] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 08/09/2012] [Indexed: 12/18/2022]
Abstract
De novo proteins provide a unique opportunity for investigating the structure-function relationships of metalloproteins in a minimal, well-defined, and controlled scaffold. Herein, we describe the rational programming of function in a de novo designed di-iron carboxylate protein from the due ferri family. Originally created to catalyze O2-dependent, two-electron oxidation of hydroquinones, the protein was reprogrammed to catalyze the selective N-hydroxylation of arylamines by remodeling the substrate access cavity and introducing a critical third His ligand to the metal binding cavity. Additional second-and third-shell modifications were required to stabilize the His ligand in the core of the protein. These changes resulted in at least a 106 –fold increase in the relative rates of the two reactions. This result highlights the potential for using de novo proteins as scaffolds for future investigations of geometric and electronic factors that influence the catalytic tuning of di-iron active sites.
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Affiliation(s)
- Amanda J Reig
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). J Comput Chem 2012; 33:1645-61. [PMID: 22565567 PMCID: PMC3432414 DOI: 10.1002/jcc.22968] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 02/16/2012] [Accepted: 03/02/2012] [Indexed: 01/22/2023]
Abstract
We present the Molecular Software Library (MSL), a C++ library for molecular modeling. MSL is a set of tools that supports a large variety of algorithms for the design, modeling, and analysis of macromolecules. Among the main features supported by the library are methods for applying geometric transformations and alignments, the implementation of a rich set of energy functions, side chain optimization, backbone manipulation, calculation of solvent accessible surface area, and other tools. MSL has a number of unique features, such as the ability of storing alternative atomic coordinates (for modeling) and multiple amino acid identities at the same backbone position (for design). It has a straightforward mechanism for extending its energy functions and can work with any type of molecules. Although the code base is large, MSL was created with ease of developing in mind. It allows the rapid implementation of simple tasks while fully supporting the creation of complex applications. Some of the potentialities of the software are demonstrated here with examples that show how to program complex and essential modeling tasks with few lines of code. MSL is an ongoing and evolving project, with new features and improvements being introduced regularly, but it is mature and suitable for production and has been used in numerous protein modeling and design projects. MSL is open-source software, freely downloadable at http://msl-libraries.org. We propose it as a common platform for the development of new molecular algorithms and to promote the distribution, sharing, and reutilization of computational methods.
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Affiliation(s)
| | | | | | - Brett T. Hannigan
- U. of Pennsylvania, Genomics and Computational Biology Graduate Group
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Gront D, Kulp DW, Vernon RM, Strauss CEM, Baker D. Generalized fragment picking in Rosetta: design, protocols and applications. PLoS One 2011; 6:e23294. [PMID: 21887241 PMCID: PMC3160850 DOI: 10.1371/journal.pone.0023294] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 07/12/2011] [Indexed: 11/21/2022] Open
Abstract
The Rosetta de novo structure prediction and loop modeling protocols begin with coarse grained Monte Carlo searches in which the moves are based on short fragments extracted from a database of known structures. Here we describe a new object oriented program for picking fragments that greatly extends the functionality of the previous program (nnmake) and opens the door for new approaches to structure modeling. We provide a detailed description of the code design and architecture, highlighting its modularity, and new features such as extensibility, total control over the fragment picking workflow and scoring system customization. We demonstrate that the program provides at least as good building blocks for ab-initio structure prediction as the previous program, and provide examples of the wide range of applications that are now accessible.
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Affiliation(s)
- Dominik Gront
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
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Donald JE, Kulp DW, DeGrado WF. Salt bridges: geometrically specific, designable interactions. Proteins 2011; 79:898-915. [PMID: 21287621 DOI: 10.1002/prot.22927] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 10/04/2010] [Accepted: 10/22/2010] [Indexed: 12/19/2022]
Abstract
Salt bridges occur frequently in proteins, providing conformational specificity and contributing to molecular recognition and catalysis. We present a comprehensive analysis of these interactions in protein structures by surveying a large database of protein structures. Salt bridges between Asp or Glu and His, Arg, or Lys display extremely well-defined geometric preferences. Several previously observed preferences are confirmed, and others that were previously unrecognized are discovered. Salt bridges are explored for their preferences for different separations in sequence and in space, geometric preferences within proteins and at protein-protein interfaces, co-operativity in networked salt bridges, inclusion within metal-binding sites, preference for acidic electrons, apparent conformational side chain entropy reduction on formation, and degree of burial. Salt bridges occur far more frequently between residues at close than distant sequence separations, but, at close distances, there remain strong preferences for salt bridges at specific separations. Specific types of complex salt bridges, involving three or more members, are also discovered. As we observe a strong relationship between the propensity to form a salt bridge and the placement of salt-bridging residues in protein sequences, we discuss the role that salt bridges might play in kinetically influencing protein folding and thermodynamically stabilizing the native conformation. We also develop a quantitative method to select appropriate crystal structure resolution and B-factor cutoffs. Detailed knowledge of these geometric and sequence dependences should aid de novo design and prediction algorithms.
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Affiliation(s)
- Jason E Donald
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
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Zhang Y, Kulp DW, Lear JD, DeGrado WF. Experimental and Computational Evaluation of Forces Directing the Association of Transmembrane Helices. J Am Chem Soc 2009; 131:11341-3. [DOI: 10.1021/ja904625b] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yao Zhang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, and Department of Biochemistry and Biophysics, University of Pennsylvania, 1009 Stellar Chance Laboratories, 36th and Hamilton Walk, Philadelphia, Pennsylvania 19104
| | - Daniel W. Kulp
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, and Department of Biochemistry and Biophysics, University of Pennsylvania, 1009 Stellar Chance Laboratories, 36th and Hamilton Walk, Philadelphia, Pennsylvania 19104
| | - James D. Lear
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, and Department of Biochemistry and Biophysics, University of Pennsylvania, 1009 Stellar Chance Laboratories, 36th and Hamilton Walk, Philadelphia, Pennsylvania 19104
| | - William F. DeGrado
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, and Department of Biochemistry and Biophysics, University of Pennsylvania, 1009 Stellar Chance Laboratories, 36th and Hamilton Walk, Philadelphia, Pennsylvania 19104
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Cegelski L, Steuber D, Mehta AK, Kulp DW, Axelsen PH, Schaefer J. Conformational and quantitative characterization of oritavancin-peptidoglycan complexes in whole cells of Staphylococcus aureus by in vivo 13C and 15N labeling. J Mol Biol 2006; 357:1253-62. [PMID: 16483598 DOI: 10.1016/j.jmb.2006.01.040] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 12/24/2005] [Accepted: 01/06/2006] [Indexed: 11/27/2022]
Abstract
Solid-state NMR has been used to examine the cell walls of intact whole cells of Staphyloccus aureus grown on media containing D-[1-(13)C]alanine, [(15)N]glycine, and the alanine racemase inhibitor, alaphosphin. The results of in situ site-selective, four-frequency NMR experiments show directly for the first time that (i) 54% of the cell-wall peptidoglycan stems have D-alanine termini and 46%, D-alanine-D-alanine termini; (ii) the molar ratio of stems ending in D-alanine to esterified alditol repeats of cell-wall teichoic and lipoteichoic acids is 3:2; and (iii) 50% of the mature cell-wall binding sites for a fluorinated oritavancin analogue consist of two nearest-neighbor peptide stems of different glycan strands. The drug is bound to the D-Ala-D-Ala terminus of one stem and is proximate to the bridging pentaglycyl segment that cross-links the two stems. Structural details of the binding site are revealed in a model of the glycopeptide-peptidoglycan interaction produced by molecular dynamics simulations with internuclear distance restraints determined by NMR.
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Affiliation(s)
- Lynette Cegelski
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
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McLaughlin WA, Kulp DW, de la Cruz J, Lu XJ, Lawson CL, Berman HM. A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction. ACTA ACUST UNITED AC 2005; 5:255-65. [PMID: 15704013 DOI: 10.1007/s10969-005-4902-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Accepted: 11/17/2004] [Indexed: 01/11/2023]
Abstract
A classification model of a DNA-binding protein chain was created based on identification of alpha helices within the chain likely to bind to DNA. Using the model, all chains in the Protein Data Bank were classified. For many of the chains classified with high confidence, previous documentation for DNA-binding was found, yet no sequence homology to the structures used to train the model was detected. The result indicates that the chain model can be used to supplement sequence based methods for annotating the function of DNA-binding. Four new candidates for DNA-binding were found, including two structures solved through structural genomics efforts. For each of the candidate structures, possible sites of DNA-binding are indicated by listing the residue ranges of alpha helices likely to interact with DNA.
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Affiliation(s)
- William A McLaughlin
- Department of Chemistry and Chemical Biology, Rutgers-The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
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