1
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Foglierini M, Nortier P, Schelling R, Winiger RR, Jacquet P, O'Dell S, Demurtas D, Mpina M, Lweno O, Muller YD, Petrovas C, Daubenberger C, Perreau M, Doria-Rose NA, Gottardo R, Perez L. RAIN: machine learning-based identification for HIV-1 bNAbs. Nat Commun 2024; 15:5339. [PMID: 38914562 PMCID: PMC11196741 DOI: 10.1038/s41467-024-49676-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infections. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoires is still lacking. Here, we develop a straightforward computational method for the Rapid Automatic Identification of bNAbs (RAIN) based on machine learning methods. In contrast to other approaches, which use one-hot encoding amino acid sequences or structural alignment for prediction, RAIN uses a combination of selected sequence-based features for the accurate prediction of HIV-1 bNAbs. We demonstrate the performance of our approach on non-biased, experimentally obtained and sequenced BCR repertoires from HIV-1 immune donors. RAIN processing leads to the successful identification of distinct HIV-1 bNAbs targeting the CD4-binding site of the envelope glycoprotein. In addition, we validate the identified bNAbs using an in vitro neutralization assay and we solve the structure of one of them in complex with the soluble native-like heterotrimeric envelope glycoprotein by single-particle cryo-electron microscopy (cryo-EM). Overall, we propose a method to facilitate and accelerate HIV-1 bNAbs discovery from non-selected immune repertoires.
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Affiliation(s)
- Mathilde Foglierini
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Centre for Human Immunology, Lausanne, Switzerland
- Biomedical Data Science Centre, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pauline Nortier
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Centre for Human Immunology, Lausanne, Switzerland
| | - Rachel Schelling
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Centre for Human Immunology, Lausanne, Switzerland
| | - Rahel R Winiger
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Centre for Human Immunology, Lausanne, Switzerland
| | - Philippe Jacquet
- Scientific Computing and Research Support Unit, University of Lausanne, Lausanne, Switzerland
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Davide Demurtas
- Interdisciplinary center of electron microscopy, CIME, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Omar Lweno
- Ifakara Health Institute, Bagamoyo, United Republic of Tanzania
| | - Yannick D Muller
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Centre for Human Immunology, Lausanne, Switzerland
| | - Constantinos Petrovas
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Matthieu Perreau
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raphael Gottardo
- Biomedical Data Science Centre, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurent Perez
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
- Centre for Human Immunology, Lausanne, Switzerland.
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2
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Perez L, Foglierini M. RAIN: a Machine Learning-based identification for HIV-1 bNAbs. RESEARCH SQUARE 2024:rs.3.rs-4023897. [PMID: 38903123 PMCID: PMC11188109 DOI: 10.21203/rs.3.rs-4023897/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infection. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoire is still lacking. Here, we developed a straightforward computational method for Rapid Automatic Identification of bNAbs (RAIN) based on Machine Learning methods. In contrast to other approaches using one-hot encoding amino acid sequences or structural alignment for prediction, RAIN uses a combination of selected sequence-based features for accurate prediction of HIV-1 bNAbs. We demonstrate the performance of our approach on non-biased, experimentally obtained sequenced BCR repertoires from HIV-1 immune donors. RAIN processing leads to the successful identification of novel HIV-1 bNAbs targeting the CD4-binding site of the envelope glycoprotein. In addition, we validate the identified bNAbs using in vitro neutralization assay and we solve the structure of one of them in complex with the soluble native-like heterotrimeric envelope glycoprotein by single-particle cryo-electron microscopy (cryo-EM). Overall, we propose a method to facilitate and accelerate HIV-1 bNAbs discovery from non-selected immune repertoires.
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Affiliation(s)
- Laurent Perez
- Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathilde Foglierini
- Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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3
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Bale S, Yang L, Alirezaei M, Wilson R, Ota T, Doyle ED, Cottrell C, Guenaga J, Tran K, Li W, Stamatatos L, Nemazee D, Ward AB, Wyatt RT. Fusion of the molecular adjuvant C3d to cleavage-independent native-like HIV-1 Env trimers improves the elicited antibody response. Front Immunol 2023; 14:1180959. [PMID: 37283743 PMCID: PMC10239957 DOI: 10.3389/fimmu.2023.1180959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/27/2023] [Indexed: 06/08/2023] Open
Abstract
An effective HIV vaccine likely requires the elicitation of neutralizing antibodies (NAbs) against multiple HIV-1 clades. The recently developed cleavage-independent native flexibly linked (NFL) envelope (Env) trimers exhibit well-ordered conformation and elicit autologous tier 2 NAbs in multiple animal models. Here, we investigated whether the fusion of molecular adjuvant C3d to the Env trimers can improve B- cell germinal center (GC) formation and antibody responses. To generate Env-C3d trimers, we performed a glycine-serine- based (G4S) flexible peptide linker screening and identified a linker range that allowed native folding. A 30-60- amino- acid- long linker facilitates Env-to-C3d association and achieves the secretion of well-ordered trimers and the structural integrity and functional integrity of Env and C3d. The fusion of C3d did not dramatically affect the antigenicity of the Env trimers and enhanced the ability of the Env trimers to engage and activate B cells in vitro. In mice, the fusion of C3d enhanced germinal center formation, the magnitude of Env-specific binding antibodies, and the avidity of the antibodies in the presence of an adjuvant. The Sigma Adjuvant System (SAS) did not affect the trimer integrity in vitro but contributed to altered immunogenicity in vivo, resulting in increased tier 1 neutralization, likely by increased exposure of variable region 3 (V3). Taken together, the results indicate that the fusion of the molecular adjuvant, C3d, to the Env trimers improves antibody responses and could be useful for Env-based vaccines against HIV.
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Affiliation(s)
- Shridhar Bale
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Lifei Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Mehrdad Alirezaei
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Richard Wilson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Takayuki Ota
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Esmeralda D. Doyle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Christopher A. Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Javier Guenaga
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Karen Tran
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Wenjuan Li
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Leonidas Stamatatos
- Vaccines and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Andrew B. Ward
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, United States
| | - Richard T. Wyatt
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, United States
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4
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Thébault P, Cailhier JF, Lapointe R. Blood Sample Processing and Banking for Functional and Molecular Analyses. Methods Mol Biol 2023; 2614:37-46. [PMID: 36587117 DOI: 10.1007/978-1-0716-2914-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Immune monitoring of circulating immune cells in the blood provides insight into a patient's own immune response over the course of a treatment or disease progression. Information such as whether immune cells are functional or non-functional and what specific proteins they express or secrete can be essential to understand if (and how) a treatment is working or a disease is progressing. To do so, it requires careful handling and storage of precious biological samples with the goals of obtaining a large amount of information from limited samples and minimizing future research costs by the use of banked samples. Many factors, including blood sample types, time of collection, containers used, preservatives and other additives, transport means, and length of transit time, all affect the quality of the samples and the stability of biomarkers and must be considered at the initial collection stage. An efficient study design includes provisions for further processing of the original samples, such as cryopreservation of isolated cells, purification of DNA and RNA, and preparation of specimens for genomic, immunological, and biochemical analyses. Development of standard operating procedures and quality control plans is a safeguard of the samples' quality and of the validity of the results. Here, we focus on the collection and processing of blood suitable for plasma and peripheral blood mononuclear cell (PBMC) banking, including collection, processing, and storage of samples, based on our experience.
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Affiliation(s)
- Paméla Thébault
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Institut du cancer de Montréal, Montréal, QC, Canada
| | - Jean-François Cailhier
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Institut du cancer de Montréal, Montréal, QC, Canada.,Faculté de Médecine, Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Réjean Lapointe
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada. .,Institut du cancer de Montréal, Montréal, QC, Canada. .,Faculté de Médecine, Département de Médecine, Université de Montréal, Montréal, QC, Canada.
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5
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Kaduk M, Corcoran M, Karlsson Hedestam GB. Addressing IGHV Gene Structural Diversity Enhances Immunoglobulin Repertoire Analysis: Lessons From Rhesus Macaque. Front Immunol 2022; 13:818440. [PMID: 35419009 PMCID: PMC8995469 DOI: 10.3389/fimmu.2022.818440] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
The accurate germline gene assignment and assessment of somatic hypermutation in antibodies induced by immunization or infection are important in immunological studies. Here, we illustrate issues specific to the construction of comprehensive immunoglobulin (IG) germline gene reference databases for outbred animal species using rhesus macaques, a frequently used non-human primate model, as a model test case. We demonstrate that the genotypic variation found in macaque germline inference studies is reflected in similar levels of gene diversity in genomic assemblies. We show that the high frequency of IG heavy chain V (IGHV) region structural and gene copy number variation between subjects means that individual animals lack genes that are present in other animals. Therefore, gene databases compiled from a single or too few animals will inevitably result in inaccurate gene assignment and erroneous SHM level assessment for those genes it lacks. We demonstrate this by assigning a test macaque IgG library to the KIMDB, a database compiled of germline IGHV sequences from 27 rhesus macaques, and, alternatively, to the IMGT rhesus macaque database, based on IGHV genes inferred primarily from the genomic sequence of the rheMac10 reference assembly, supplemented with 10 genes from the Mmul_051212 assembly. We found that the use of a gene-restricted database led to overestimations of SHM by up to 5% due to misassignments. The principles described in the current study provide a model for the creation of comprehensive immunoglobulin reference databases from outbred species to ensure accurate gene assignment, lineage tracing and SHM calculations.
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Affiliation(s)
- Mateusz Kaduk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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6
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Aljedani SS, Liban TJ, Tran K, Phad G, Singh S, Dubrovskaya V, Pushparaj P, Martinez-Murillo P, Rodarte J, Mileant A, Mangala Prasad V, Kinzelman R, O’Dell S, Mascola JR, Lee KK, Karlsson Hedestam GB, Wyatt RT, Pancera M. Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization. PLoS Pathog 2021; 17:e1009543. [PMID: 34559844 PMCID: PMC8494329 DOI: 10.1371/journal.ppat.1009543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 10/06/2021] [Accepted: 09/01/2021] [Indexed: 12/31/2022] Open
Abstract
Understanding the molecular mechanisms by which antibodies target and neutralize the HIV-1 envelope glycoprotein (Env) is critical in guiding immunogen design and vaccine development aimed at eliciting cross-reactive neutralizing antibodies (NAbs). Here, we analyzed monoclonal antibodies (mAbs) isolated from non-human primates (NHPs) immunized with variants of a native flexibly linked (NFL) HIV-1 Env stabilized trimer derived from the tier 2 clade C 16055 strain. The antibodies displayed neutralizing activity against the autologous virus with potencies ranging from 0.005 to 3.68 μg/ml (IC50). Structural characterization using negative-stain EM and X-ray crystallography identified the variable region 2 (V2) of the 16055 NFL trimer to be the common epitope for these antibodies. The crystal structures revealed that the V2 segment adopts a β-hairpin motif identical to that observed in the 16055 NFL crystal structure. These results depict how vaccine-induced antibodies derived from different clonal lineages penetrate through the glycan shield to recognize a hypervariable region within V2 (residues 184-186) that is unique to the 16055 strain. They also provide potential explanations for the potent autologous neutralization of these antibodies, confirming the immunodominance of this site and revealing that multiple angles of approach are permissible for affinity/avidity that results in potent neutralizing capacity. The structural analysis reveals that the most negatively charged paratope correlated with the potency of the mAbs. The atomic level information is of interest to both define the means of autologous neutralization elicited by different tier 2-based immunogens and facilitate trimer redesign to better target more conserved regions of V2 to potentially elicit cross-neutralizing HIV-1 antibodies.
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Affiliation(s)
- Safia S. Aljedani
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Tyler J. Liban
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Karen Tran
- The Scripps Research Institute, IAVI Neutralizing Antibody Center, La Jolla, California, United States of America
| | - Ganesh Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Suruchi Singh
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Viktoriya Dubrovskaya
- The Scripps Research Institute, IAVI Neutralizing Antibody Center, La Jolla, California, United States of America
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Paola Martinez-Murillo
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Justas Rodarte
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Alex Mileant
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Vidya Mangala Prasad
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Rachel Kinzelman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | | | - Richard T. Wyatt
- The Scripps Research Institute, IAVI Neutralizing Antibody Center, La Jolla, California, United States of America
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
- * E-mail:
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7
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Dubrovskaya V, Tran K, Ozorowski G, Guenaga J, Wilson R, Bale S, Cottrell CA, Turner HL, Seabright G, O'Dell S, Torres JL, Yang L, Feng Y, Leaman DP, Vázquez Bernat N, Liban T, Louder M, McKee K, Bailer RT, Movsesyan A, Doria-Rose NA, Pancera M, Karlsson Hedestam GB, Zwick MB, Crispin M, Mascola JR, Ward AB, Wyatt RT. Vaccination with Glycan-Modified HIV NFL Envelope Trimer-Liposomes Elicits Broadly Neutralizing Antibodies to Multiple Sites of Vulnerability. Immunity 2019; 51:915-929.e7. [PMID: 31732167 PMCID: PMC6891888 DOI: 10.1016/j.immuni.2019.10.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/04/2019] [Accepted: 10/22/2019] [Indexed: 01/31/2023]
Abstract
The elicitation of broadly neutralizing antibodies (bNAbs) against the HIV-1 envelope glycoprotein (Env) trimer remains a major vaccine challenge. Most cross-conserved protein determinants are occluded by self-N-glycan shielding, limiting B cell recognition of the underlying polypeptide surface. The exceptions to the contiguous glycan shield include the conserved receptor CD4 binding site (CD4bs) and glycoprotein (gp)41 elements proximal to the furin cleavage site. Accordingly, we performed heterologous trimer-liposome prime:boosting in rabbits to drive B cells specific for cross-conserved sites. To preferentially expose the CD4bs to B cells, we eliminated proximal N-glycans while maintaining the native-like state of the cleavage-independent NFL trimers, followed by gradual N-glycan restoration coupled with heterologous boosting. This approach successfully elicited CD4bs-directed, cross-neutralizing Abs, including one targeting a unique glycan-protein epitope and a bNAb (87% breadth) directed to the gp120:gp41 interface, both resolved by high-resolution cryoelectron microscopy. This study provides proof-of-principle immunogenicity toward eliciting bNAbs by vaccination.
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Affiliation(s)
- Viktoriya Dubrovskaya
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karen Tran
- International AIDS Vaccine Initiative, Neutralizing Antibody Center at The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Javier Guenaga
- International AIDS Vaccine Initiative, Neutralizing Antibody Center at The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Richard Wilson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shridhar Bale
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gemma Seabright
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lifei Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Feng
- International AIDS Vaccine Initiative, Neutralizing Antibody Center at The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel P Leaman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Néstor Vázquez Bernat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Tyler Liban
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mark Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Arlette Movsesyan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Andrew B Ward
- International AIDS Vaccine Initiative, Neutralizing Antibody Center at 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; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, 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; International AIDS Vaccine Initiative, Neutralizing Antibody Center at 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.
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8
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Dosenovic P, Pettersson AK, Wall A, Thientosapol ES, Feng J, Weidle C, Bhullar K, Kara EE, Hartweger H, Pai JA, Gray MD, Parks KR, Taylor JJ, Pancera M, Stamatatos L, Nussenzweig MC, McGuire AT. Anti-idiotypic antibodies elicit anti-HIV-1-specific B cell responses. J Exp Med 2019; 216:2316-2330. [PMID: 31345931 PMCID: PMC6780999 DOI: 10.1084/jem.20190446] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/29/2019] [Accepted: 06/24/2019] [Indexed: 12/23/2022] Open
Abstract
Human anti-HIV-1 broadly neutralizing antibodies (bNAbs) protect against infection in animal models. However, bNAbs have not been elicited by vaccination in diverse wild-type animals or humans, in part because B cells expressing the precursors of these antibodies do not recognize most HIV-1 envelopes (Envs). Immunogens have been designed that activate these B cell precursors in vivo, but they also activate competing off-target responses. Here we report on a complementary approach to expand specific B cells using an anti-idiotypic antibody, iv8, that selects for naive human B cells expressing immunoglobulin light chains with 5-amino acid complementarity determining region 3s, a key feature of anti-CD4 binding site (CD4bs)-specific VRC01-class antibodies. In mice, iv8 induced target cells to expand and mature in the context of a polyclonal immune system and produced serologic responses targeting the CD4bs on Env. In summary, the results demonstrate that an anti-idiotypic antibody can specifically recognize and expand rare B cells that express VRC01-class antibodies against HIV-1.
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Affiliation(s)
- Pia Dosenovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | | | - Abigail Wall
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Eddy S Thientosapol
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Junli Feng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Connor Weidle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Komal Bhullar
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Ervin E Kara
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Harald Hartweger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Joy A Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Matthew D Gray
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - K Rachael Parks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.,University of Washington University of Washington, Department of Global Health, Seattle, WA
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.,University of Washington University of Washington, Department of Global Health, Seattle, WA.,University of Washington University of Washington, Department of Immunology, Seattle, WA
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA .,University of Washington University of Washington, Department of Global Health, Seattle, WA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY .,Howard Hughes Medical Institute, Chevy Chase, MD
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA .,University of Washington University of Washington, Department of Global Health, Seattle, WA
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9
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Wong J, Choi SYC, Liu R, Xu E, Killam J, Gout PW, Wang Y. Potential Therapies for Infectious Diseases Based on Targeting Immune Evasion Mechanisms That Pathogens Have in Common With Cancer Cells. Front Cell Infect Microbiol 2019; 9:25. [PMID: 30809511 PMCID: PMC6379255 DOI: 10.3389/fcimb.2019.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/24/2019] [Indexed: 12/18/2022] Open
Abstract
Many global infectious diseases are not well-controlled, underlining a critical need for new, more effective therapies. Pathogens and pathogen-infected host cells, like cancer cells, evade immune surveillance via immune evasion mechanisms. The present study indicates that pathogenic bacteria, endoparasites, and virus-infected host cells can have immune evasion mechanisms in common with cancers. These include entry into dormancy and metabolic reprogramming to aerobic glycolysis leading to excessive secretion of lactic acid and immobilization of local host immunity. The latter evasion tactic provides a therapeutic target for cancer, as shown by our recent finding that patient-derived cancer xenografts can be growth-arrested, without major host toxicity, by inhibiting their lactic acid secretion (as mediated by the MCT4 transporter)-with evidence of host immunity restoration. Accordingly, the multiplication of bacteria, endoparasites, and viruses that primarily depend on metabolic reprogramming to aerobic glycolysis for survival may be arrested using cancer treatment strategies that inhibit their lactic acid secretion. Immune evasion mechanisms shared by pathogens and cancer cells likely represent fundamental, evolutionarily-conserved mechanisms that may be particularly critical to their welfare. As such, their targeting may lead to novel therapies for infectious diseases.
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Affiliation(s)
- Jodi Wong
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Stephen Yiu Chuen Choi
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada.,Vancouver Prostate Centre, Vancouver, BC, Canada.,Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Rongrong Liu
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Eddie Xu
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada.,Vancouver Prostate Centre, Vancouver, BC, Canada.,Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - James Killam
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Peter W Gout
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada.,Vancouver Prostate Centre, Vancouver, BC, Canada.,Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
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10
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Shah HB, Smith K, Wren JD, Webb CF, Ballard JD, Bourn RL, James JA, Lang ML. Insights From Analysis of Human Antigen-Specific Memory B Cell Repertoires. Front Immunol 2019; 9:3064. [PMID: 30697210 PMCID: PMC6340933 DOI: 10.3389/fimmu.2018.03064] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/11/2018] [Indexed: 12/17/2022] Open
Abstract
Memory B cells that are generated during an infection or following vaccination act as sentinels to guard against future infections. Upon repeat antigen exposure memory B cells differentiate into new antibody-secreting plasma cells to provide rapid and sustained protection. Some pathogens evade or suppress the humoral immune system, or induce memory B cells with a diminished ability to differentiate into new plasma cells. This leaves the host vulnerable to chronic or recurrent infections. Single cell approaches coupled with next generation antibody gene sequencing facilitate a detailed analysis of the pathogen-specific memory B cell repertoire. Monoclonal antibodies that are generated from antibody gene sequences allow a functional analysis of the repertoire. This review discusses what has been learned thus far from analysis of diverse pathogen-specific memory B cell compartments and describes major differences in their repertoires. Such information may illuminate ways to advance the goal of improving vaccine and therapeutic antibody design.
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Affiliation(s)
- Hemangi B Shah
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Kenneth Smith
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Jonathan D Wren
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Department of Biochemistry and Molecular Biology and Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Carol F Webb
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Division of Rheumatology, Immunology and Allergy, Department of Cell Biology and Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Jimmy D Ballard
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Rebecka L Bourn
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Judith A James
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Department of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Mark L Lang
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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11
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Zhou JO, Ton T, Morriss JW, Nguyen D, Fera D. Structural Insights from HIV-Antibody Coevolution and Related Immunization Studies. AIDS Res Hum Retroviruses 2018; 34:760-768. [PMID: 29984587 DOI: 10.1089/aid.2018.0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is a rapidly evolving pathogen that causes acquired immunodeficiency syndrome (AIDS) in humans. There are ∼30-35 million people infected with HIV around the world, and ∼25 million have died since the first reported cases in 1981. In addition, each year 2-3 million people become newly infected, and >1 million die of AIDS. An HIV-1 vaccine would help halt an AIDS pandemic, and efforts to develop a vaccine have focused on targeting the HIV-1 envelope, Env, found on the surface of the virus. A number of chronically infected individuals have been shown to produce antibodies, called broadly neutralizing antibodies (bnAbs), that target many strains of HIV-1 by binding to Env, thus suggesting promise for HIV-1 vaccine development. BnAbs take years to develop, and have a number of traits that inhibit their production; thus, a number of researchers are trying to understand the pathways that result in bnAb production, so that they can be elicited more rapidly by vaccination. This review discusses results and implications from two HIV-1-infected individuals studied longitudinally who produced bnAbs against two different sites on HIV-1 Env, and immunization studies that used Envs derived from those individuals.
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Affiliation(s)
- Jeffrey O. Zhou
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania
| | - Therese Ton
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Julia W. Morriss
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Diep Nguyen
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania
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12
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Targeting the HIV-1 Spike and Coreceptor with Bi- and Trispecific Antibodies for Single-Component Broad Inhibition of Entry. J Virol 2018; 92:JVI.00384-18. [PMID: 29976677 DOI: 10.1128/jvi.00384-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/29/2018] [Indexed: 12/15/2022] Open
Abstract
Protection against acquiring human immunodeficiency virus (HIV) infection may not require a vaccine in the conventional sense, because broadly neutralizing antibodies (bNAbs) alone prevent HIV infection in relevant animal challenge models. Additionally, bNAbs as therapeutics can effectively suppress HIV replication in infected humans and in animal models. Combinations of bNAbs are generally even more effective, and bNAb-derived multivalent antibody-like molecules also inhibit HIV replication both in vitro and in vivo To expand the available array of multispecific HIV inhibitors, we designed single-component molecules that incorporate two (bispecific) or three (trispecific) bNAbs that recognize HIV Env exclusively, a bispecific CrossMAb targeting two epitopes on the major HIV coreceptor, CCR5, and bi- and trispecifics that cross-target both Env and CCR5. These newly designed molecules displayed exceptional breadth, neutralizing 98 to 100% of a 109-virus panel, as well as additivity and potency compared to those of the individual parental control IgGs. The bispecific molecules, designed as tandem single-chain variable fragments (scFvs) (10E8fv-N6fv and m36.4-PRO 140fv), displayed median 50% inhibitory concentration (IC50s) of 0.0685 and 0.0131 μg/ml, respectively. A trispecific containing 10E8-PGT121-PGDM1400 Env-specific binding sites was equally potent (median IC50 of 0.0135 μg/ml), while a trispecific molecule targeting Env and CCR5 simultaneously (10E8Fab-PGDM1400fv-PRO 140fv) demonstrated even greater potency, with a median IC50 of 0.007 μg/ml. By design, some of these molecules lacked Fc-mediated effector function; therefore, we also constructed a trispecific prototype possessing reconstituted CH2-CH3 domains to restore Fc receptor binding capacity. The molecules developed here, along with those described previously, possess promise as prophylactic and therapeutic agents against HIV.IMPORTANCE Broadly neutralizing antibodies (bNAbs) prevent HIV infection in monkey challenge models and suppress HIV replication in infected humans. Combinations of bNAbs are more effective at suppression, and antibody-like molecules engineered to have two or three bNAb combining sites also inhibit HIV replication in monkeys and other animal models. To expand the available array of multispecific HIV inhibitors, we designed single-component molecules that incorporate two (bispecific) or three (trispecific) bNAb binding sites that recognize the HIV envelope glycoprotein (Env) or the HIV coreceptor (CCR5) or that cross-target both Env and CCR5. Several of the bi- and trispecific molecules neutralized most viruses in a diverse cross-clade panel, with greater breadth and potency than those of the individual parental bNAbs. The molecules described here provide additional options for preventing or suppressing HIV infection.
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13
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Yang L, Sharma SK, Cottrell C, Guenaga J, Tran K, Wilson R, Behrens AJ, Crispin M, de Val N, Wyatt RT. Structure-Guided Redesign Improves NFL HIV Env Trimer Integrity and Identifies an Inter-Protomer Disulfide Permitting Post-Expression Cleavage. Front Immunol 2018; 9:1631. [PMID: 30065725 PMCID: PMC6056610 DOI: 10.3389/fimmu.2018.01631] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/02/2018] [Indexed: 11/13/2022] Open
Abstract
Soluble HIV-1 envelope glycoprotein (Env) trimers are under active investigation as vaccine candidates in relevant pre-clinical models. Like SOSIPs, the cleavage-independent native flexibly linked (NFL) trimers are faithful mimics of the Env spike. Here, we analyzed multiple new designs to explore alternative modifications, informing tertiary interactions, while maintaining NFL trimer homogeneity and integrity. Accordingly, we performed a proline (P) substitution screen in the gp41 heptad repeat 1 region, identifying other trimer-enhancing Ps, including L555P. This P improved trimer integrity compared to I559P in selected properties. Next, we screened 15 structure-guided potential cysteine pairs in gp140 and found that A501C-L663C ("CC2") forms an inter-protomer disulfide bond that demonstrably increased NFL trimer thermostability. We combined these two approaches with trimer-derived substitutions, coupled with glycine substitutions at helix-to-coil transitions, developed by our group. To increase the exposure of the fusion peptide (FP) N-terminus, we engineered an enterokinase (EK) cleavage site upstream of the FP for controlled post-expression cleavage. In combination, the redesigns resulted in highly stable and homogeneous NFL mimics derived from different clades. Following recombinant EK cleavage, the NFL trimers retained covalent linkage, maintaining a native-like structure while displaying enhanced stability and favorable antigenic features. These trimers also displayed increased exposure of neutralizing epitopes in the FP and gp120/gp41 interface, while retaining other neutralizing epitopes and occluding non-neutralizing elements. This array of Env-structure-guided designs reveals additional interactive regions in the prefusion state of the HIV Env spike, affording the development of novel antigens and immunogens.
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Affiliation(s)
- Lifei Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Shailendra Kumar Sharma
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Christopher Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Javier Guenaga
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Karen Tran
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Richard Wilson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Anna-Janina Behrens
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, United Kingdom
| | - Max Crispin
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, United Kingdom
- Centre for Biological Sciences, Institute of Life Sciences, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - Natalia de Val
- Center for Molecular Microscopy (CMM), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Richard T. Wyatt
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, 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
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14
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Hessell AJ, Malherbe DC, Haigwood NL. Passive and active antibody studies in primates to inform HIV vaccines. Expert Rev Vaccines 2018; 17:127-144. [PMID: 29307225 PMCID: PMC6587971 DOI: 10.1080/14760584.2018.1425619] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Prevention of infection remains the ultimate goal for HIV vaccination, and there is compelling evidence that antibodies directed to Envelope are necessary to block infection. Generating antibodies that are sufficiently broad, potent, and sustained to block infection by the diverse HIV-1 strains circulating worldwide remains an area of intense study. AREAS COVERED In this review, we have summarized progress from publications listed as PubMed citations in 2016-17 in the areas of passive antibody studies using human neutralizing monoclonal antibodies in nonhuman primates, HIV Envelope vaccine development and active vaccination studies to generate potent neutralizing antibodies. EXPERT COMMENTARY Passive transfer studies in nonhuman primates using human neutralizing monoclonal antibodies have informed the potency, specificity, and cooperativity of antibodies needed to prevent infection, leading to clinical studies now testing potent antibodies for prevention of HIV. Progress in understanding the structure of Envelope has led to novel vaccine constructs, including mimetics, scaffolds and native-like proteins. As yet, no single approach ensures protection against the circulating global HIV-1 strains, but there is progress in understanding why, and intense research continues in these and other areas for a solution. We offer perspectives on how this knowledge may shape the design of future HIV vaccines.
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15
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Roychowdhury S, Oh YJ, Kajiura H, Hamorsky KT, Fujiyama K, Matoba N. Hydroponic Treatment of Nicotiana benthamiana with Kifunensine Modifies the N-glycans of Recombinant Glycoprotein Antigens to Predominantly Man9 High-Mannose Type upon Transient Overexpression. FRONTIERS IN PLANT SCIENCE 2018; 9:62. [PMID: 29441088 PMCID: PMC5797603 DOI: 10.3389/fpls.2018.00062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/12/2018] [Indexed: 05/17/2023]
Abstract
Nicotiana benthamiana transient overexpression systems offer unique advantages for rapid and scalable biopharmaceuticals production, including high scalability and eukaryotic post-translational modifications such as N-glycosylation. High-mannose-type glycans (HMGs) of glycoprotein antigens have been implicated in the effectiveness of some subunit vaccines. In particular, Man9GlcNAc2 (Man9) has high binding affinity to mannose-specific C-type lectin receptors such as the mannose receptor and dendritic cell-specific intracellular adhesion molecule 3-grabbing non-integrin (DC-SIGN). Here, we investigated the effect of kifunensine, an α-mannosidase I inhibitor, supplemented in a hydroponic culture of N. benthamiana for the production of Man9-rich HMG glycoproteins, using N-glycosylated cholera toxin B subunit (gCTB) and human immunodeficiency virus gp120 that are tagged with a H/KDEL endoplasmic reticulum retention signal as model vaccine antigens. Biochemical analysis using anti-fucose and anti-xylose antibodies as well as Endo H and PNGase F digestion showed that kifunensine treatment effectively reduced plant-specific glycoforms while increasing HMGs in the N-glycan compositions of gCTB. Detailed glycan profiling revealed that plant-produced gp120 had a glycan profile bearing mostly HMGs regardless of kifunensine treatment. However, the gp120 produced under kifunensine-treatment conditions showed Man9 being the most prominent glycoform (64.5%), while the protein produced without kifunensine had a substantially lower Man9 composition (20.3%). Our results open up possibilities for efficient production of highly mannosylated recombinant vaccine antigens in plants.
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Affiliation(s)
- Sugata Roychowdhury
- James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, United States
| | - Young J. Oh
- James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, United States
| | - Hiroyuki Kajiura
- The International Center for Biotechnology, Osaka University, Suita, Japan
| | - Krystal T. Hamorsky
- James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, United States
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, United States
| | - Kazuhito Fujiyama
- The International Center for Biotechnology, Osaka University, Suita, Japan
| | - Nobuyuki Matoba
- James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, United States
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY, United States
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, United States
- *Correspondence: Nobuyuki Matoba
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16
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Pinder CL, Kratochvil S, Cizmeci D, Muir L, Guo Y, Shattock RJ, McKay PF. Isolation and Characterization of Antigen-Specific Plasmablasts Using a Novel Flow Cytometry-Based Ig Capture Assay. THE JOURNAL OF IMMUNOLOGY 2017; 199:4180-4188. [PMID: 29118244 DOI: 10.4049/jimmunol.1701253] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/10/2017] [Indexed: 11/19/2022]
Abstract
We report the development of a novel flow cytometry-based Ig capture assay (ICA) for the identification and sorting of individual Ab-secreting cells based on their Ag reactivity. The ICA represents a fast and versatile tool for single-cell sorting of peripheral plasmablasts, streamlining subsequent Ab analysis, and cloning. We demonstrate the utility of the assay by isolating Ag-reactive plasmablasts from cryopreserved PBMC obtained from volunteers vaccinated with a recombinant HIV envelope protein. To show the specificity of the ICA, we produced Ag-specific Abs from these cells and subsequently verified their Ag reactivity via ELISA. Furthermore, we used the ICA to track Ag-specific plasmablast responses in HIV-vaccine recipients over a period of 42 d and performed a head-to-head comparison with a conventional B cell ELISpot. Results were highly comparable, highlighting that this assay is a viable alternative for monitoring Ag-specific plasmablast responses at early time points after infection or vaccination. The ICA provides important added benefits in that phenotypic information can be obtained from the identified Ag-specific cells that can then be captured for downstream applications such as B cell sequencing and/or Ab cloning. We envisage the ICA as being a useful tool in Ab repertoire analysis for future clinical trials.
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Affiliation(s)
- Christopher L Pinder
- Division of Medicine, Department of Infectious Diseases, Imperial College London, London W2 1PG, United Kingdom; and
| | - Sven Kratochvil
- Division of Medicine, Department of Infectious Diseases, Imperial College London, London W2 1PG, United Kingdom; and
| | - Deniz Cizmeci
- Division of Medicine, Department of Infectious Diseases, Imperial College London, London W2 1PG, United Kingdom; and
| | - Luke Muir
- Division of Medicine, Department of Infectious Diseases, Imperial College London, London W2 1PG, United Kingdom; and
| | - Yanping Guo
- Flow Cytometry Core Facility, National Heart and Lung Institute, Imperial College London, London W2 1PG, United Kingdom
| | - Robin J Shattock
- Division of Medicine, Department of Infectious Diseases, Imperial College London, London W2 1PG, United Kingdom; and
| | - Paul F McKay
- Division of Medicine, Department of Infectious Diseases, Imperial College London, London W2 1PG, United Kingdom; and
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17
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Sun Z, Yan L, Tang J, Qian Q, Lenberg J, Zhu D, Liu W, Wu K, Wang Y, Lu S. Brief introduction of current technologies in isolation of broadly neutralizing HIV-1 antibodies. Virus Res 2017; 243:75-82. [PMID: 29051051 PMCID: PMC7114535 DOI: 10.1016/j.virusres.2017.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/13/2017] [Accepted: 10/15/2017] [Indexed: 12/11/2022]
Abstract
HIV/AIDS has become a worldwide pandemic. Before an effective HIV-1 vaccine eliciting broadly neutralizing monoclonal antibodies (bnmAbs) is fully developed, passive immunization for prevention and treatment of HIV-1 infection may alleviate the burden caused by the pandemic. Among HIV-1 infected individuals, about 20% of them generated cross-reactive neutralizing antibodies two to four years after infection, the details of which could provide knowledge for effective vaccine design. Recent progress in techniques for isolation of human broadly neutralizing antibodies has facilitated the study of passive immunization. The isolation and characterization of large panels of potent human broadly neutralizing antibodies has revealed new insights into the principles of antibody-mediated neutralization of HIV. In this paper, we review the current effective techniques in broadly neutralizing antibody isolation.
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Affiliation(s)
- Zehua Sun
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, United States.
| | - Lixin Yan
- Harbin Medical University Affiliated 2nd Hospital, 246 Xuefu Road, Harbin, 150086, China.
| | - Jiansong Tang
- Department of Technical Specialist, China Bioengineering Technology Group Limited, Unit 209,Building 16W, Hong Kong Science Park, Shatin, NT, HK, 999077, Hong Kong
| | - Qian Qian
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, United States
| | - Jerica Lenberg
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, United States; Augustana University, 2001 S Summit Avenue, Sioux Falls, SD, 571977, United States
| | - Dandan Zhu
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX, 77030, United States
| | - Wan Liu
- Harbin Medical University Affiliated 2nd Hospital, 246 Xuefu Road, Harbin, 150086, China
| | - Kao Wu
- Glyn O. Philips Hydrocolloid Research Center at HUT, Hubei University of Technology, Wuhan 430068, China
| | - Yilin Wang
- University of California, Irvine. 100 Pacific, Irvine, CA, 92618, United States
| | - Shiqiang Lu
- AIDS Institute, Faculty of Medicine, The University of Hong Kong, No21 Sassoon Road, 999077, Hong Kong, Hong Kong.
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18
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Martinez-Murillo P, Tran K, Guenaga J, Lindgren G, Àdori M, Feng Y, Phad GE, Vázquez Bernat N, Bale S, Ingale J, Dubrovskaya V, O'Dell S, Pramanik L, Spångberg M, Corcoran M, Loré K, Mascola JR, Wyatt RT, Karlsson Hedestam GB. Particulate Array of Well-Ordered HIV Clade C Env Trimers Elicits Neutralizing Antibodies that Display a Unique V2 Cap Approach. Immunity 2017; 46:804-817.e7. [PMID: 28514687 DOI: 10.1016/j.immuni.2017.04.021] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/27/2017] [Accepted: 04/26/2017] [Indexed: 01/22/2023]
Abstract
The development of soluble envelope glycoprotein (Env) mimetics displaying ordered trimeric symmetry has ushered in a new era in HIV-1 vaccination. The recently reported native, flexibly linked (NFL) design allows the generation of native-like trimers from clinical isolates at high yields and homogeneity. As the majority of infections world-wide are of the clade C subtype, we examined responses in non-human primates to well-ordered subtype C 16055 trimers administered in soluble or high-density liposomal formats. We detected superior germinal center formation and enhanced autologous neutralizing antibodies against the neutralization-resistant (tier 2) 16055 virus following inoculation of liposome-arrayed trimers. Epitope mapping of the neutralizing monoclonal antibodies (mAbs) indicated major contacts with the V2 apex, and 3D electron microscopy reconstructions of Fab-trimer complexes revealed a horizontal binding angle to the Env spike. These vaccine-elicited mAbs target the V2 cap, demonstrating a means to accomplish tier 2 virus neutralization by penetrating the dense N-glycan shield.
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Affiliation(s)
- Paola Martinez-Murillo
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Karen Tran
- IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Javier Guenaga
- IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gustaf Lindgren
- Immunology and Allergy Unit, Department of Medicine, Karolinska Institutet, 171 77 Solna, Sweden
| | - Monika Àdori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Yu Feng
- IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ganesh E Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Néstor Vázquez Bernat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Shridhar Bale
- IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jidnyasa Ingale
- IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Viktoriya Dubrovskaya
- IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lotta Pramanik
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Mats Spångberg
- Astrid Fagraeus Laboratory, Comparative Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Karin Loré
- Immunology and Allergy Unit, Department of Medicine, Karolinska Institutet, 171 77 Solna, Sweden
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard T Wyatt
- IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Soldemo M, Karlsson Hedestam GB. Env-Specific Antibodies in Chronic Infection versus in Vaccination. Front Immunol 2017; 8:1057. [PMID: 28928737 PMCID: PMC5591324 DOI: 10.3389/fimmu.2017.01057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/15/2017] [Indexed: 12/22/2022] Open
Abstract
Antibodies are central in vaccine-mediated protection. For HIV-1, a pathogen that displays extreme antigenic variability, B cell responses against conserved determinants of the envelope glycoproteins (Env) are likely required to achieve broadly protective vaccine-induced responses. To understand antibodies in chronic infection, where broad serum neutralizing activity is observed in a subset of individuals, monoclonal antibodies mediating this activity have been isolated. Studies of their maturation pathways reveal that years of co-evolution between the virus and the adaptive immune response are required for such responses to arise. Furthermore, they do so in subjects who display alterations of their B cell subsets caused by the chronic infection, conditions that are distinctly different from those in healthy hosts. So far, broadly neutralizing antibody responses were not induced by vaccination in primates or small animals with natural B cell repertoires. An increased focus on the development vaccine-induced responses in healthy subjects is therefore needed to delineate how the immune system recognizes different forms of HIV-1 Env and to optimize approaches to stimulate antibody responses against relevant neutralizing antibody epitopes. In this review, we describe aspects of Env-directed antibody responses that differ between chronic HIV-1 infection and subunit vaccination for an increased appreciation of these differences; and we highlight the need for an improved understanding of vaccine-induced B cell responses to complex glycoproteins such as Env, in healthy subjects.
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Affiliation(s)
- Martina Soldemo
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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Abstract
Despite major advances in our understanding of the biology of HIV-1 infection, and advances in antiretroviral therapy to treat the disease, there were 2.1 million new cases of HIV-1 infection in 2015, and 36.7 million people living with AIDS (http://www.unaids.org/en/resources/fact-sheet ). Thus, a vaccine that can prevent HIV-infection remains a global priority. Thirty-three years after the discovery of HIV-1(1 ), and the demonstration it was the cause of AIDS(2 ) and after 6 HIV-1 vaccine efficacy trials (3 –8 ), no HIV-1 candidate vaccine has shown enough efficacy to be approved for clinical use. Of several vaccine concepts tested in efficacy trials, only one, the RV144 pox virus prime, protein boost (ALVAC/AIDSVAX B/E) vaccine, showed a low level of vaccine protection with an estimated 31% vaccine efficacy (8 ). Candidate vaccines have sought to elicit both antibody and T-cell responses, but to fully prevent the acquisition of infection, a major focus has been on the induction of protective antibody responses (9 , 10 ). Hence, the focus of this issue of Immunologic Reviews is “Antibodies and Immunity to HIV”. Animal models have demonstrated that passive administration of HIV-1-- neutralizing antibodies can fully protect against infection, but the induction of such antibodies via immunization remains a major scientific challenge. With recent advances in the isolation and characterization of broadly neutralizing antibodies (bnAbs) from HIV-1-infected subjects, in elucidating structures of the HIV-1 envelope glycoprotein (Env), in defining novel approaches to immunogen design, and in improved understanding of the immunological pathways leading to bNAb elicitation, the challenge developing an HIV-1 vaccine appears to be more tractable. The articles in this issue highlight both major areas of HIV-1 vaccine development progress and remaining obstacles, and provide context for the renewed optimism that a highly effective vaccine, while not imminent, is possible.
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Affiliation(s)
- Barton F. Haynes
- Duke Human Vaccine Institute, Departments of Medicine and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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