1
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Sahoo A, Jones AT, Cheedarla N, Gangadhara S, Roy V, Styles TM, Shiferaw A, Walter KL, Williams LD, Shen X, Ozorowski G, Lee WH, Burton S, Yi L, Song X, Qin ZS, Derdeyn CA, Ward AB, Clements JD, Varadarajan R, Tomaras GD, Kozlowski PA, Alter G, Amara RR. A clade C HIV-1 vaccine protects against heterologous SHIV infection by modulating IgG glycosylation and T helper response in macaques. Sci Immunol 2022; 7:eabl4102. [PMID: 35867800 PMCID: PMC9410801 DOI: 10.1126/sciimmunol.abl4102] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The rising global HIV-1 burden urgently requires vaccines capable of providing heterologous protection. Here, we developed a clade C HIV-1 vaccine consisting of priming with modified vaccinia Ankara (MVA) and boosting with cyclically permuted trimeric gp120 (CycP-gp120) protein, delivered either orally using a needle-free injector or through parenteral injection. We tested protective efficacy of the vaccine against intrarectal challenges with a pathogenic heterologous clade C SHIV infection in rhesus macaques. Both routes of vaccination induced a strong envelope-specific IgG in serum and rectal secretions directed against V1V2 scaffolds from a global panel of viruses with polyfunctional activities. Envelope-specific IgG showed lower fucosylation compared with total IgG at baseline, and most of the vaccine-induced proliferating blood CD4+ T cells did not express CCR5 and α4β7, markers associated with HIV target cells. After SHIV challenge, both routes of vaccination conferred significant and equivalent protection, with 40% of animals remaining uninfected at the end of six weekly repeated challenges with an estimated efficacy of 68% per exposure. Induction of envelope-specific IgG correlated positively with G1FB glycosylation, and G2S2F glycosylation correlated negatively with protection. Vaccine-induced TNF-α+ IFN-γ+ CD8+ T cells and TNF-α+ CD4+ T cells expressing low levels of CCR5 in the rectum at prechallenge were associated with decreased risk of SHIV acquisition. These results demonstrate that the clade C MVA/CycP-gp120 vaccine provides heterologous protection against a tier2 SHIV rectal challenge by inducing a polyfunctional antibody response with distinct Fc glycosylation profile, as well as cytotoxic CD8 T cell response and CCR5-negative T helper response in the rectum.
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Affiliation(s)
- Anusmita Sahoo
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Andrew T Jones
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sailaja Gangadhara
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Vicky Roy
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Tiffany M Styles
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ayalnesh Shiferaw
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Korey L Walter
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - LaTonya D Williams
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, San Diego, CA 92121, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, San Diego, CA 92121, USA
| | - Samantha Burton
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Lasanajak Yi
- Department of Biochemistry, Emory Glycomics and Molecular Interactions Core (EGMIC), School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xuezheng Song
- Department of Biochemistry, Emory Glycomics and Molecular Interactions Core (EGMIC), School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Cynthia A Derdeyn
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, San Diego, CA 92121, USA
| | - John D Clements
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 8638, USA
| | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, Karnataka 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560012, India
| | - Georgia D Tomaras
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Rama Rao Amara
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
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2
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Malladi S, Patel UR, Rajmani RS, Singh R, Pandey S, Kumar S, Khaleeq S, van Vuren PJ, Riddell S, Goldie S, Gayathri S, Chakraborty D, Kalita P, Pramanick I, Agarwal N, Reddy P, Girish N, Upadhyaya A, Khan MS, Kanjo K, Bhat M, Mani S, Bhattacharyya S, Siddiqui S, Tyagi A, Jha S, Pandey R, Tripathi S, Dutta S, McAuley AJ, Singanallur N, Vasan SS, Ringe RP, Varadarajan R. Immunogenicity and Protective Efficacy of a Highly Thermotolerant, Trimeric SARS-CoV-2 Receptor Binding Domain Derivative. ACS Infect Dis 2021; 7:2546-2564. [PMID: 34260218 PMCID: PMC8996237 DOI: 10.1021/acsinfecdis.1c00276] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 02/07/2023]
Abstract
The receptor binding domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We designed a trimeric, highly thermotolerant glycan engineered RBD by fusion to a heterologous, poorly immunogenic disulfide linked trimerization domain derived from cartilage matrix protein. The protein expressed at a yield of ∼80-100 mg/L in transiently transfected Expi293 cells, as well as CHO and HEK293 stable cell lines and formed homogeneous disulfide-linked trimers. When lyophilized, these possessed remarkable functional stability to transient thermal stress of up to 100 °C and were stable to long-term storage of over 4 weeks at 37 °C unlike an alternative RBD-trimer with a different trimerization domain. Two intramuscular immunizations with a human-compatible SWE adjuvanted formulation elicited antibodies with pseudoviral neutralizing titers in guinea pigs and mice that were 25-250 fold higher than corresponding values in human convalescent sera. Against the beta (B.1.351) variant of concern (VOC), pseudoviral neutralization titers for RBD trimer were ∼3-fold lower than against wildtype B.1 virus. RBD was also displayed on a designed ferritin-like Msdps2 nanoparticle. This showed decreased yield and immunogenicity relative to trimeric RBD. Replicative virus neutralization assays using mouse sera demonstrated that antibodies induced by the trimers neutralized all four VOC to date, namely B.1.1.7, B.1.351, P.1, and B.1.617.2 without significant differences. Trimeric RBD immunized hamsters were protected from viral challenge. The excellent immunogenicity, thermotolerance, and high yield of these immunogens suggest that they are a promising modality to combat COVID-19, including all SARS-CoV-2 VOC to date.
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Affiliation(s)
- Sameer
Kumar Malladi
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Unnatiben Rajeshbhai Patel
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Raju S. Rajmani
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Randhir Singh
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Suman Pandey
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Sahil Kumar
- Virology
Unit, Institute of Microbial Technology,
Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160036, India
| | - Sara Khaleeq
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Petrus Jansen van Vuren
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Shane Riddell
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Sarah Goldie
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Savitha Gayathri
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Debajyoti Chakraborty
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Parismita Kalita
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Ishika Pramanick
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Nupur Agarwal
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Poorvi Reddy
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Nidhi Girish
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Aditya Upadhyaya
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Mohammad Suhail Khan
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Kawkab Kanjo
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Madhuraj Bhat
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Shailendra Mani
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Gurugram-Faridabad
Expressway, Faridabad 121001, India
| | - Sankar Bhattacharyya
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Gurugram-Faridabad
Expressway, Faridabad 121001, India
| | - Samreen Siddiqui
- Max Super
Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 1100017, India
| | - Akansha Tyagi
- Max Super
Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 1100017, India
| | - Sujeet Jha
- Max Super
Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 1100017, India
| | - Rajesh Pandey
- Integrative
Genomics of Host-Pathogen (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Shashank Tripathi
- Department
of Microbiology & Cell Biology, Indian
Institute of Science, Bengaluru 560012, India
- Centre
for Infectious Disease Research, Indian
Institute of Science, Bengaluru 560012, India
| | - Somnath Dutta
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Alexander J. McAuley
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Nagendrakumar
Balasubramanian Singanallur
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Seshadri S. Vasan
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
- Department
of Health Sciences, University of York, York YO10 5DD, United Kingdom
| | - Rajesh P. Ringe
- Virology
Unit, Institute of Microbial Technology,
Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160036, India
| | - Raghavan Varadarajan
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
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3
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Malladi SK, Singh R, Pandey S, Gayathri S, Kanjo K, Ahmed S, Khan MS, Kalita P, Girish N, Upadhyaya A, Reddy P, Pramanick I, Bhasin M, Mani S, Bhattacharyya S, Joseph J, Thankamani K, Raj VS, Dutta S, Singh R, Nadig G, Varadarajan R. Design of a highly thermotolerant, immunogenic SARS-CoV-2 spike fragment. J Biol Chem 2021; 296:100025. [PMID: 33154165 PMCID: PMC7832000 DOI: 10.1074/jbc.ra120.016284] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
Virtually all SARS-CoV-2 vaccines currently in clinical testing are stored in a refrigerated or frozen state prior to use. This is a major impediment to deployment in resource-poor settings. Furthermore, several of them use viral vectors or mRNA. In contrast to protein subunit vaccines, there is limited manufacturing expertise for these nucleic-acid-based modalities, especially in the developing world. Neutralizing antibodies, the clearest known correlate of protection against SARS-CoV-2, are primarily directed against the receptor-binding domain (RBD) of the viral spike protein, suggesting that a suitable RBD construct might serve as a more accessible vaccine ingredient. We describe a monomeric, glycan-engineered RBD protein fragment that is expressed at a purified yield of 214 mg/l in unoptimized, mammalian cell culture and, in contrast to a stabilized spike ectodomain, is tolerant of exposure to temperatures as high as 100 °C when lyophilized, up to 70 °C in solution and stable for over 4 weeks at 37 °C. In prime:boost guinea pig immunizations, when formulated with the MF59-like adjuvant AddaVax, the RBD derivative elicited neutralizing antibodies with an endpoint geometric mean titer of ∼415 against replicative virus, comparing favorably with several vaccine formulations currently in the clinic. These features of high yield, extreme thermotolerance, and satisfactory immunogenicity suggest that such RBD subunit vaccine formulations hold great promise to combat COVID-19.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Animals
- Antibodies, Neutralizing/biosynthesis
- Antibodies, Viral/biosynthesis
- Binding Sites
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/biosynthesis
- COVID-19 Vaccines/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Female
- Guinea Pigs
- HEK293 Cells
- Hot Temperature
- Humans
- Immunogenicity, Vaccine
- Models, Molecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Domains
- Protein Interaction Domains and Motifs
- Protein Stability
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- SARS-CoV-2/chemistry
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vaccination
- Vaccine Potency
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Affiliation(s)
| | - Randhir Singh
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Suman Pandey
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Savitha Gayathri
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Kawkab Kanjo
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Shahbaz Ahmed
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | | | - Parismita Kalita
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Nidhi Girish
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Aditya Upadhyaya
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Poorvi Reddy
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Ishika Pramanick
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Munmun Bhasin
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Shailendra Mani
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Jeswin Joseph
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Kerala, India
| | - Karthika Thankamani
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Kerala, India
| | - V Stalin Raj
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Kerala, India
| | - Somnath Dutta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Gautham Nadig
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India.
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4
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A facile method of mapping HIV-1 neutralizing epitopes using chemically masked cysteines and deep sequencing. Proc Natl Acad Sci U S A 2020; 117:29584-29594. [PMID: 33168755 DOI: 10.1073/pnas.2010256117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Identification of specific epitopes targeted by neutralizing antibodies is essential to advance epitope-based vaccine design strategies. We report a facile methodology for rapid epitope mapping of neutralizing antibodies (NAbs) against HIV-1 Envelope (Env) at single-residue resolution, using Cys labeling, viral neutralization assays, and deep sequencing. This was achieved by the generation of a library of Cys mutations in Env glycoprotein on the viral surface, covalent labeling of the Cys residues using a Cys-reactive label that masks epitope residues, followed by infection of the labeled mutant virions in mammalian cells in the presence of NAbs. Env gene sequencing from NAb-resistant viruses was used to accurately delineate epitopes for the NAbs VRC01, PGT128, and PGT151. These agreed well with corresponding experimentally determined structural epitopes previously inferred from NAb:Env structures. HIV-1 infection is associated with complex and polyclonal antibody responses, typically composed of multiple antibody specificities. Deconvoluting the epitope specificities in a polyclonal response is a challenging task. We therefore extended our methodology to map multiple specificities of epitopes targeted in polyclonal sera, elicited in immunized animals as well as in an HIV-1-infected elite neutralizer capable of neutralizing tier 3 pseudoviruses with high titers. The method can be readily extended to other viruses for which convenient reverse genetics or lentiviral surface display systems are available.
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5
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Probing the Structure of the HIV-1 Envelope Trimer Using Aspartate Scanning Mutagenesis. J Virol 2020; 94:JVI.01426-20. [PMID: 32817217 DOI: 10.1128/jvi.01426-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/11/2020] [Indexed: 12/20/2022] Open
Abstract
HIV-1 envelope (Env) glycoprotein gp160 exists as a trimer of heterodimers on the viral surface. In most structures of the soluble ectodomain of trimeric HIV-1 envelope glycoprotein, the regions from 512 to 517 of the fusion peptide and from 547 to 568 of the N-heptad repeat are disordered. We used aspartate scanning mutagenesis of subtype B strain JRFL Env as an alternate method to probe residue burial in the context of cleaved, cell surface-expressed Env, as buried residues should be intolerant to substitution with Asp. The data are inconsistent with a fully disordered 547 to 568 stretch, as residues 548, 549, 550, 555, 556, 559, 562, and 566 to 569 are all sensitive to Asp substitution. In the fusion peptide region, residues 513 and 515 were also sensitive to Asp substitution, suggesting that the fusion peptide may not be fully exposed in native Env. gp41 is metastable in the context of native trimer. Introduction of Asp at residues that are exposed in the prefusion state but buried in the postfusion state is expected to destabilize the postfusion state and any intermediate states where the residue is buried. We therefore performed soluble CD4 (sCD4)-induced gp120 shedding experiments to identify Asp mutants at residues 551, 554 to 559, 561 to 567, and 569 that could prevent gp120 shedding. We also observed similar mutational effects on shedding for equivalent mutants in the context of clade C Env from isolate 4-2J.41. These substitutions can potentially be used to stabilize native-like trimer derivatives that are used as HIV-1 vaccine immunogens.IMPORTANCE In most crystal structures of the soluble ectodomain of the HIV-1 Env trimer, some residues in the fusion and N-heptad repeat regions are disordered. Whether this is true in the context of native, functional Env on the virion surface is not known. This knowledge may be useful for stabilizing Env in its prefusion conformation and will also help to improve understanding of the viral entry process. Burial of the charged residue Asp in a protein structure is highly destabilizing. We therefore used Asp scanning mutagenesis to probe the burial of apparently disordered residues in native Env and to examine the effect of mutations in these regions on Env stability and conformation as probed by antibody binding to cell surface-expressed Env, CD4-induced shedding of HIV-1 gp120, and viral infectivity studies. Mutations that prevent shedding can potentially be used to stabilize native-like Env constructs for use as vaccine immunogens.
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6
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Sharma A, Chattopadhyay G, Chopra P, Bhasin M, Thakur C, Agarwal S, Ahmed S, Chandra N, Varadarajan R, Singh R. VapC21 Toxin Contributes to Drug-Tolerance and Interacts With Non-cognate VapB32 Antitoxin in Mycobacterium tuberculosis. Front Microbiol 2020; 11:2037. [PMID: 33042034 PMCID: PMC7517352 DOI: 10.3389/fmicb.2020.02037] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
The prokaryotic ubiquitous Toxin-antitoxin (TA) modules encodes for a stable toxin and an unstable antitoxin. VapBC subfamily is the most abundant Type II TA system in M. tuberculosis genome. However, the exact physiological role for most of these Type II TA systems are still unknown. Here, we have comprehensively characterized the VapBC21 TA locus from M. tuberculosis. The overexpression of VapC21 inhibited mycobacterial growth in a bacteriostatic manner and as expected, growth inhibition was abrogated upon co-expression of the cognate antitoxin, VapB21. We observed that the deletion of vapC21 had no noticeable influence on the in vitro and in vivo growth of M. tuberculosis. Using co-expression and biophysical studies, we observed that in addition to VapB21, VapC21 is also able to interact with non-cognate antitoxin, VapB32. The strength of interaction varied between the cognate and non-cognate TA pairs. The overexpression of VapC21 resulted in differential expression of approximately 435 transcripts in M. tuberculosis. The transcriptional profiles obtained upon ectopic expression of VapC21 was similar to those reported in M. tuberculosis upon exposure to stress conditions such as nutrient starvation and enduring hypoxic response. Further, VapC21 overexpression also led to increased expression of WhiB7 regulon and bacterial tolerance to aminoglycosides and ethambutol. Taken together, these results indicate that a complex network of interactions exists between non-cognate TA pairs and VapC21 contributes to drug tolerance in vitro.
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Affiliation(s)
- Arun Sharma
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | | | - Pankaj Chopra
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Munmun Bhasin
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Sakshi Agarwal
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
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7
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Jones AT, Shen X, Walter KL, LaBranche CC, Wyatt LS, Tomaras GD, Montefiori DC, Moss B, Barouch DH, Clements JD, Kozlowski PA, Varadarajan R, Amara RR. HIV-1 vaccination by needle-free oral injection induces strong mucosal immunity and protects against SHIV challenge. Nat Commun 2019; 10:798. [PMID: 30778066 PMCID: PMC6379385 DOI: 10.1038/s41467-019-08739-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/25/2019] [Indexed: 02/08/2023] Open
Abstract
The oral mucosa is an attractive site for mucosal vaccination, however the thick squamous epithelium limits antigen uptake. Here we utilize a modified needle-free injector to deliver immunizations to the sublingual and buccal (SL/B) tissue of rhesus macaques. Needle-free SL/B vaccination with modified vaccinia Ankara (MVA) and a recombinant trimeric gp120 protein generates strong vaccine-specific IgG responses in serum as well as vaginal, rectal and salivary secretions. Vaccine-induced IgG responses show a remarkable breadth against gp70-V1V2 sequences from multiple clades of HIV-1. In contrast, topical SL/B immunizations generates minimal IgG responses. Following six intrarectal pathogenic SHIV-SF162P3 challenges, needle-free but not topical immunization results in a significant delay of acquisition of infection. Delay of infection correlates with non-neutralizing antibody effector function, Env-specific CD4+ T-cell responses, and gp120 V2 loop specific antibodies. These results demonstrate needle-free MVA/gp120 oral vaccination as a practical and effective route to induce protective immunity against HIV-1.
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Affiliation(s)
- Andrew T Jones
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, Georgia, 30329, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Korey L Walter
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Celia C LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Linda S Wyatt
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - John D Clements
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, 8638, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Rama Rao Amara
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30329, USA.
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, Georgia, 30329, USA.
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8
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Design, display and immunogenicity of HIV1 gp120 fragment immunogens on virus-like particles. Vaccine 2018; 36:6345-6353. [PMID: 30220462 DOI: 10.1016/j.vaccine.2018.07.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/26/2018] [Accepted: 07/16/2018] [Indexed: 12/17/2022]
Abstract
The broadly neutralizing antibody against HIV-1, b12, binds to the CD4 binding site (CD4bs) on the outer domain (OD) of the gp120 subunit of HIV-1 Env. We have previously reported the design of an E. coli expressed fragment of HIV-1 gp120, b122a, containing about 70% of the b12 epitope with the idea of focusing the immune response to this structure. Since the b122a structure was found to be only partially folded, as assessed by circular dichroism and protease resistance, we attempted to stabilize it by the introduction of additional disulfide bonds. One such mutant, b122a1-b showed increased stability and bound b12 with 30-fold greater affinity as compared to b122a. Various b122a and OD fragment proteins were displayed on the surface of Qβ virus-like particles. Sera raised against these particles in six-month long rabbit immunization studies could neutralize Tier1 viruses across different subtypes with the best results observed with b122a1-b displayed particles. Significantly higher amounts of antibodies directed towards the CD4bs were also elicited by particles displaying b122a1-b. This study highlights the ability of fragment immunogens to focus the antibody response to the conserved CD4bs of HIV-1.
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9
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Rathore U, Purwar M, Vignesh VS, Das R, Kumar AA, Bhattacharyya S, Arendt H, DeStefano J, Wilson A, Parks C, La Branche CC, Montefiori DC, Varadarajan R. Bacterially expressed HIV-1 gp120 outer-domain fragment immunogens with improved stability and affinity for CD4-binding site neutralizing antibodies. J Biol Chem 2018; 293:15002-15020. [PMID: 30093409 DOI: 10.1074/jbc.ra118.005006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
Protein minimization is an attractive approach for designing vaccines against rapidly evolving pathogens such as human immunodeficiency virus, type 1 (HIV-1), because it can help in focusing the immune response toward conserved conformational epitopes present on complex targets. The outer domain (OD) of HIV-1 gp120 contains epitopes for a large number of neutralizing antibodies and therefore is a primary target for structure-based vaccine design. We have previously designed a bacterially expressed outer-domain immunogen (ODEC) that bound CD4-binding site (CD4bs) ligands with 3-12 μm affinity and elicited a modest neutralizing antibody response in rabbits. In this study, we have optimized ODEC using consensus sequence design, cyclic permutation, and structure-guided mutations to generate a number of variants with improved yields, biophysical properties, stabilities, and affinities (KD of 10-50 nm) for various CD4bs targeting broadly neutralizing antibodies, including the germline-reverted version of the broadly neutralizing antibody VRC01. In contrast to ODEC, the optimized immunogens elicited high anti-gp120 titers in rabbits as early as 6 weeks post-immunization, before any gp120 boost was given. Following two gp120 boosts, sera collected at week 22 showed cross-clade neutralization of tier 1 HIV-1 viruses. Using a number of different prime/boost combinations, we have identified a cyclically permuted OD fragment as the best priming immunogen, and a trimeric, cyclically permuted gp120 as the most suitable boosting molecule among the tested immunogens. This study also provides insights into some of the biophysical correlates of improved immunogenicity.
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Affiliation(s)
- Ujjwal Rathore
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Mansi Purwar
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | | | - Raksha Das
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Aditya Arun Kumar
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Sanchari Bhattacharyya
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Heather Arendt
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Joanne DeStefano
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Aaron Wilson
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Christopher Parks
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Celia C La Branche
- the Department of Surgery, Duke University Medical Center, Durham, North Carolina 27707
| | - David C Montefiori
- the Department of Surgery, Duke University Medical Center, Durham, North Carolina 27707
| | - Raghavan Varadarajan
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012,
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10
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A Trimeric HIV-1 Envelope gp120 Immunogen Induces Potent and Broad Anti-V1V2 Loop Antibodies against HIV-1 in Rabbits and Rhesus Macaques. J Virol 2018; 92:JVI.01796-17. [PMID: 29237847 PMCID: PMC5809733 DOI: 10.1128/jvi.01796-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/02/2017] [Indexed: 02/04/2023] Open
Abstract
Trimeric HIV-1 envelope (Env) immunogens are attractive due to their ability to display quaternary epitopes targeted by broadly neutralizing antibodies (bNAbs) while obscuring unfavorable epitopes. Results from the RV144 trial highlighted the importance of vaccine-induced HIV-1 Env V1V2-directed antibodies, with key regions of the V2 loop as targets for vaccine-mediated protection. We recently reported that a trimeric JRFL-gp120 immunogen, generated by inserting an N-terminal trimerization domain in the V1 loop region of a cyclically permuted gp120 (cycP-gp120), induces neutralizing activity against multiple tier-2 HIV-1 isolates in guinea pigs in a DNA prime/protein boost approach. Here, we tested the immunogenicity of cycP-gp120 in a protein prime/boost approach in rabbits and as a booster immunization to DNA/modified vaccinia Ankara (MVA)-vaccinated rabbits and rhesus macaques. In rabbits, two cycP-gp120 protein immunizations induced 100-fold higher titers of high-avidity gp120-specific IgG than two gp120 immunizations, with four total gp120 immunizations being required to induce comparable titers. cycP-gp120 also induced markedly enhanced neutralizing activity against tier-1A and -1B HIV-1 isolates, substantially higher binding and breadth to gp70-V1V2 scaffolds derived from a multiclade panel of global HIV-1 isolates, and antibodies targeting key regions of the V2-loop region associated with reduced risk of infection in RV144. Similarly, boosting MVA- or DNA/MVA-primed rabbits or rhesus macaques with cycP-gp120 showed a robust expansion of gp70-V1V2-specific IgG, neutralization breadth to tier-1B HIV-1 isolates, and antibody-dependent cellular cytotoxicity activity. These results demonstrate that cycP-gp120 serves as a robust HIV Env immunogen that induces broad anti-V1V2 antibodies and promotes neutralization breadth against HIV-1. IMPORTANCE Recent focus in HIV-1 vaccine development has been the design of trimeric HIV-1 Env immunogens that closely resemble native HIV-1 Env, with a major goal being the induction of bNAbs. While the generation of bNAbs is considered a gold standard in vaccine-induced antibody responses, results from the RV144 trial showed that nonneutralizing antibodies directed toward the V1V2 loop of HIV-1 gp120, specifically the V2 loop region, were associated with decreased risk of infection, demonstrating the need for the development of Env immunogens that induce a broad anti-V1V2 antibody response. In this study, we show that a novel trimeric gp120 protein, cycP-gp120, generates high titers of high-avidity and broadly cross-reactive anti-V1V2 antibodies, a result not found in animals immunized with monomeric gp120. These results reveal the potential of cycP-gp120 as a vaccine candidate to induce antibodies associated with reduced risk of HIV-1 infection in humans.
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11
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Liu ZJ, Bai J, Liu FL, Zhang XY, Wang JZ. Focus on the therapeutic efficacy of 3BNC117 against HIV-1: In vitro studies, in vivo studies, clinical trials and challenges. Int Immunopharmacol 2017; 52:44-50. [PMID: 28858725 DOI: 10.1016/j.intimp.2017.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/11/2017] [Accepted: 08/21/2017] [Indexed: 11/29/2022]
Abstract
3BNC117, which was discovered in 2011, is a broadly neutralizing antibody (bNAb) and specifically neutralizes the human immunodeficiency virus type-1 (HIV-1) by targeting the CD4-binding site. This is the first comprehensive review that focuses on the role of 3BNC117 in the prevention of HIV-1 and acquired immune deficiency syndrome (AIDS). Briefly, 3BNC117 neutralizes many HIV/SHIV strains in vitro, blocks HIV-1 acquisition in animal models via a pre-exposure prophylaxis, alleviates HIV-1-associated viremia via a post-exposure therapeutic effect, prevents the establishment of latent HIV-1 reservoirs, and induces both humoral and cellular anti-HIV immune responses in vivo. The outcomes of Phase I and Phase IIa clinical trials in 2015 and 2016 showed the safety, tolerability, and therapeutic efficacy of 3BNC117 in HIV-1-infected human individuals. Nevertheless, anti-3BNC117 antibodies and HIV-1 strains resistant to 3BNC117 pose clinical challenges to immunotherapy with 3BNC117, so potential strategies for optimizing the potency of 3BNC117 are suggested here. Predictably, HIV-1 prevention and AIDS treatment will benefit from combinational immunotherapies with 3BNC117 and other pharmaceuticals (bNAbs, antiretroviral medicines, viral inducers, etc.) in the near future.
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Affiliation(s)
- Zhi-Jun Liu
- Hebei University of Engineering, Affiliated Hospital, College of Medicine, Handan 056002, PR China
| | - Jing Bai
- Hebei University of Engineering, Affiliated Hospital, College of Medicine, Handan 056002, PR China
| | - Feng-Li Liu
- Hebei University of Engineering, Affiliated Hospital, College of Medicine, Handan 056002, PR China
| | - Xiang-Yang Zhang
- Hebei University of Engineering, Affiliated Hospital, College of Medicine, Handan 056002, PR China
| | - Jing-Zhang Wang
- Hebei University of Engineering, Affiliated Hospital, College of Medicine, Handan 056002, PR China.
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