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Mandolesi M, Das H, de Vries L, Yang Y, Kim C, Dhinakaran M, Castro Dopico X, Fischbach J, Kim S, Guryleva MV, Àdori M, Chernyshev M, Stålmarck A, Hanke L, McInerney GM, Sheward DJ, Corcoran M, Hällberg BM, Murrell B, Karlsson Hedestam GB. Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques. Nat Commun 2024; 15:6338. [PMID: 39068149 PMCID: PMC11283548 DOI: 10.1038/s41467-024-50286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024] Open
Abstract
The continued evolution of SARS-CoV-2 underscores the need to understand qualitative aspects of the humoral immune response elicited by spike immunization. Here, we combine monoclonal antibody (mAb) isolation with deep B cell receptor (BCR) repertoire sequencing of rhesus macaques immunized with prefusion-stabilized spike glycoprotein. Longitudinal tracing of spike-sorted B cell lineages in multiple immune compartments demonstrates increasing somatic hypermutation and broad dissemination of vaccine-elicited B cells in draining and non-draining lymphoid compartments, including the bone marrow, spleen and, most notably, periaortic lymph nodes. Phylogenetic analysis of spike-specific monoclonal antibody lineages identified through deep repertoire sequencing delineates extensive intra-clonal diversification that shaped neutralizing activity. Structural analysis of the spike in complex with a broadly neutralizing mAb provides a molecular basis for the observed differences in neutralization breadth between clonally related antibodies. Our findings highlight that immunization leads to extensive intra-clonal B cell evolution where members of the same lineage can both retain the original epitope specificity and evolve to recognize additional spike variants not previously encountered.
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MESH Headings
- Animals
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Macaca mulatta
- Antibodies, Neutralizing/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- B-Lymphocytes/immunology
- Antibodies, Viral/immunology
- Phylogeny
- Antibodies, Monoclonal/immunology
- Epitopes/immunology
- COVID-19/immunology
- COVID-19/virology
- Humans
- COVID-19 Vaccines/immunology
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, B-Cell/genetics
- Somatic Hypermutation, Immunoglobulin
- Immunization
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Affiliation(s)
- Marco Mandolesi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Liset de Vries
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Yiqiu Yang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Manojj Dhinakaran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Julian Fischbach
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mariia V Guryleva
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Monika Àdori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mark Chernyshev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Aron Stålmarck
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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2
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Janus BM, Wang R, Cleveland TE, Metcalf MC, Lemmer AC, van Dyk N, Jeong S, Astavans A, Class K, Fuerst TR, Ofek G. Macaque antibodies targeting Marburg virus glycoprotein induced by multivalent immunization. J Virol 2024; 98:e0015524. [PMID: 38832790 PMCID: PMC11329191 DOI: 10.1128/jvi.00155-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
Marburg virus infection in humans is associated with case fatality rates that can reach up to 90%, but to date, there are no approved vaccines or monoclonal antibody (mAb) countermeasures. Here, we immunized Rhesus macaques with multivalent combinations of filovirus glycoprotein (GP) antigens belonging to Marburg, Sudan, and Ebola viruses to generate monospecific and cross-reactive antibody responses against them. From the animal that developed the highest titers of Marburg virus GP-specific neutralizing antibodies, we sorted single memory B cells using a heterologous Ravn virus GP probe and cloned and characterized a panel of 34 mAbs belonging to 28 unique lineages. Antibody specificities were assessed by overlapping pepscan and binding competition analyses, revealing that roughly a third of the lineages mapped to the conserved receptor binding region, including potent neutralizing lineages that were confirmed by negative stain electron microscopy to target this region. Additional lineages targeted a protective region on GP2, while others were found to possess cross-filovirus reactivity. Our study advances the understanding of orthomarburgvirus glycoprotein antigenicity and furthers efforts to develop candidate antibody countermeasures against these lethal viruses. IMPORTANCE Marburg viruses were the first filoviruses characterized to emerge in humans in 1967 and cause severe hemorrhagic fever with average case fatality rates of ~50%. Although mAb countermeasures have been approved for clinical use against the related Ebola viruses, there are currently no approved countermeasures against Marburg viruses. We successfully isolated a panel of orthomarburgvirus GP-specific mAbs from a macaque immunized with a multivalent combination of filovirus antigens. Our analyses revealed that roughly half of the antibodies in the panel mapped to regions on the glycoprotein shown to protect from infection, including the host cell receptor binding domain and a protective region on the membrane-anchoring subunit. Other antibodies in the panel exhibited broad filovirus GP recognition. Our study describes the discovery of a diverse panel of cross-reactive macaque antibodies targeting orthomarburgvirus and other filovirus GPs and provides candidate immunotherapeutics for further study and development.
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Affiliation(s)
- Benjamin M Janus
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Ruixue Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Thomas E Cleveland
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Matthew C Metcalf
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Aaron C Lemmer
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Nydia van Dyk
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Sarah Jeong
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Anagh Astavans
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Kenneth Class
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Thomas R Fuerst
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Gilad Ofek
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
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3
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Weinfurter JT, Bennett SN, Reynolds MR. A SMART method for isolating monoclonal antibodies from individual rhesus macaque memory B cells. J Immunol Methods 2024; 525:113602. [PMID: 38103783 PMCID: PMC10842827 DOI: 10.1016/j.jim.2023.113602] [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: 06/09/2023] [Revised: 11/07/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Characterizing antigen-specific B cells is a critical component of vaccine and infectious disease studies in rhesus macaques (RMs). However, it is challenging to capture immunoglobulin variable (IgV) genes from individual RM B cells using 5' multiplex (MTPX) primers in nested PCR reactions. In particular, the diversity within RM IgV gene leader sequences necessitates large 5' MTPX primer sets to amplify IgV genes, decreasing PCR efficiency. To address this problem, we developed a switching mechanism at the 5' ends of the RNA transcript (SMART)-based method for amplifying IgV genes from single RM B cells to capture Ig heavy and light chain pairs. We demonstrate this technique by isolating simian immunodeficiency virus (SIV) envelope-specific antibodies from single-sorted RM memory B cells. This approach has several advantages over existing methods for cloning antibodies from RMs. First, optimized PCR conditions and SMART 5' and 3' rapid amplification of cDNA ends (RACE) reactions generate full-length cDNAs from individual B cells. Second, it appends synthetic primer binding sites to the 5' and 3' ends of cDNA during synthesis, allowing for PCR amplification of low-abundance antibody templates. Third, the nested PCR primer mixes are simplified by employing universal 5' primers, eliminating the need for complex 5' MTPX primer sets. We anticipate this method will enhance the isolation of antibodies from individual RM B cells, supporting the genetic and functional characterization of antigen-specific B cells.
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Affiliation(s)
- Jason T Weinfurter
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, United States of America
| | - Sarah N Bennett
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, United States of America
| | - Matthew R Reynolds
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, United States of America; Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, United States of America.
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4
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Weinfurter JT, Bennett SN, Reynolds M. A SMART method for efficiently isolating monoclonal antibodies from individual rhesus macaque memory B cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543510. [PMID: 37333083 PMCID: PMC10274751 DOI: 10.1101/2023.06.02.543510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Characterizing antigen-specific B cells is a critical component of vaccine and infectious disease studies in rhesus macaques (RMs). However, it is challenging to capture immunoglobulin variable (IgV) genes from individual RM B cells using 5' multiplex (MTPX) primers in nested PCR reactions. In particular, the diversity within RM IgV gene leader sequences necessitates the use of large 5' MTPX primer sets to amplify IgV genes, decreasing PCR efficiency. To address this problem, we developed a switching mechanism at the 5' ends of the RNA transcript (SMART)-based method for amplifying IgV genes from single RM B cells, providing unbiased capture of Ig heavy and light chain pairs for cloning antibodies. We demonstrate this technique by isolating simian immunodeficiency virus (SIV) envelope-specific antibodies from single-sorted RM memory B cells. This approach has several advantages over existing methods for PCR cloning antibodies from RMs. First, optimized PCR conditions and SMART 5' and 3' rapid amplification of cDNA ends (RACE) reactions generate full-length cDNAs from individual B cells. Second, it appends synthetic primer binding sites to the 5' and 3' ends of cDNA during synthesis, allowing for PCR amplification of low-abundance antibody templates. Third, universal 5' primers are employed to amplify the IgV genes from cDNA, simplifying the primer mixes in the nested PCR reactions and improving the recovery of matched heavy and light chain pairs. We anticipate this method will enhance the isolation of antibodies from individual RM B cells, supporting the genetic and functional characterization of antigen-specific B cells.
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Affiliation(s)
- Jason T. Weinfurter
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison WI
| | - Sarah N. Bennett
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison WI
| | - Matthew Reynolds
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison WI
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Wisconsin, Madison WI
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5
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A single donor is sufficient to produce a highly functional in vitro antibody library. Commun Biol 2021; 4:350. [PMID: 33742103 PMCID: PMC7979914 DOI: 10.1038/s42003-021-01881-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Antibody complementarity determining region diversity has been considered to be the most important metric for the production of a functional antibody library. Generally, the greater the antibody library diversity, the greater the probability of selecting a diverse array of high affinity leads. According to this paradigm, the primary means of elevating library diversity has been by increasing the number of donors. In the present study we explored the possibility of creating an in vitro antibody library from a single healthy individual, showing that the number of lymphocytes, rather than the number of donors, is the key criterion in the production of a diverse and functional antibody library. We describe the construction of a high-quality phage display library comprising 5 × 109 human antibodies by applying an efficient B cell extraction protocol from a single donor and a targeted V-gene amplification strategy favoring specific antibody families for their improved developability profiles. Each step of the library generation process was followed and validated by next generation sequencing to monitor the library quality and diversity. The functionality of the library was tested using several therapeutically relevant targets for which a vast number of different antibodies with desired biophysical properties were obtained.
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6
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Charles TP, Burton SL, Arunachalam PS, Cottrell CA, Sewall LM, Bollimpelli VS, Gangadhara S, Dey AK, Ward AB, Shaw GM, Hunter E, Amara RR, Pulendran B, van Gils MJ, Derdeyn CA. The C3/465 glycan hole cluster in BG505 HIV-1 envelope is the major neutralizing target involved in preventing mucosal SHIV infection. PLoS Pathog 2021; 17:e1009257. [PMID: 33556148 PMCID: PMC7895394 DOI: 10.1371/journal.ppat.1009257] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/19/2021] [Accepted: 12/23/2020] [Indexed: 01/08/2023] Open
Abstract
Stabilized HIV-1 envelope (Env) trimers elicit tier 2 autologous neutralizing antibody (nAb) responses in immunized animals. We previously demonstrated that BG505 SOSIP.664.T332N gp140 (BG505 SOSIP) immunization of rhesus macaques (RM) provided robust protection against autologous intra-vaginal simian-human immunodeficiency virus (SHIV) challenge that was predicted by high serum nAb titers. Here, we show that nAb in these protected RM targeted a glycan hole proximal to residue 465 in gp120 in all cases. nAb also targeted another glycan hole at residues 241/289 and an epitope in V1 at varying frequencies. Non-neutralizing antibodies directed at N611-shielded epitopes in gp41 were also present but were more prevalent in RM with low nAb titers. Longitudinal analysis demonstrated that nAb broadened in some RM during sequential immunization but remained focused in others, the latter being associated with increases in nAb titer. Thirty-eight monoclonal antibodies (mAbs) isolated from a protected RM with an exceptionally high serum neutralization titer bound to the trimer in ELISA, and four of the mAbs potently neutralized the BG505 Env pseudovirus (PV) and SHIV. The four neutralizing mAbs were clonally related and targeted the 465 glycan hole to varying degrees, mimicking the serum. The data demonstrate that the C3/465 glycan hole cluster was the dominant neutralization target in high titer protected RM, despite other co-circulating neutralizing and non-neutralizing specificities. The isolation of a neutralizing mAb family argues that clonotype expansion occurred during BG505 SOSIP immunization, leading to high titer, protective nAb and setting a desirable benchmark for HIV vaccines.
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Affiliation(s)
- Tysheena P. Charles
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Samantha L. Burton
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Prabhu S. Arunachalam
- Departments of Pathology, and Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, United States of America
| | - Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Leigh M. Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Venkata S. Bollimpelli
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Sailaja Gangadhara
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Antu K. Dey
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - George M. Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Rama R. Amara
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
| | - Bali Pulendran
- Departments of Pathology, and Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail: (MJVG); (CAD)
| | - Cynthia A. Derdeyn
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail: (MJVG); (CAD)
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7
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Tsuji I, Dominguez D, Egan MA, Dean HJ. Development of a novel assay to assess the avidity of dengue virus-specific antibodies elicited in response to a tetravalent dengue vaccine. J Infect Dis 2021; 225:1533-1544. [PMID: 33534885 PMCID: PMC9071338 DOI: 10.1093/infdis/jiab064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/29/2021] [Indexed: 11/28/2022] Open
Abstract
Antibody affinity maturation is a critical step in development of functional antiviral immunity; however, accurate measurement of affinity maturation of polyclonal serum antibody responses to particulate antigens such as virions is challenging. We describe a novel avidity assay employing biolayer interferometry and dengue virus-like particles. After validation using anti-dengue monoclonal antibodies, the assay was used to assess avidity of antibody responses to a tetravalent dengue vaccine candidate (TAK-003) in children, adolescents, and adults during two phase 2 clinical trials conducted in dengue-endemic regions. Vaccination increased avidity index and avidity remained high through 1 year postvaccination. Neutralizing antibody titers and avidity index did not correlate overall; however, a correlation was observed between neutralizing antibody titer and avidity index in those subjects with the highest degree of antibody affinity maturation. Therefore, vaccination with TAK-003 stimulates polyclonal affinity maturation and functional antibody responses, including neutralizing antibodies.
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8
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Hartley GE, Edwards ESJ, Bosco JJ, Ojaimi S, Stirling RG, Cameron PU, Flanagan K, Plebanski M, Hogarth PM, O'Hehir RE, van Zelm MC. Influenza-specific IgG1 + memory B-cell numbers increase upon booster vaccination in healthy adults but not in patients with predominantly antibody deficiency. Clin Transl Immunology 2020; 9:e1199. [PMID: 33088507 PMCID: PMC7563650 DOI: 10.1002/cti2.1199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 09/15/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
Background Annual influenza vaccination is recommended to all individuals over 6 months of age, including predominantly antibody deficiency (PAD) patients. Vaccination responses are typically evaluated by serology, and because PAD patients are by definition impaired in generating IgG and receive immunoglobulin replacement therapy (IgRT), it remains unclear whether they can mount an antigen-specific response. Objective To quantify and characterise the antigen-specific memory B (Bmem) cell compartment in healthy controls and PAD patients following an influenza booster vaccination. Methods Recombinant hemagglutinin (HA) from the A/Michigan/2015 H1N1 (AM15) strain with an AviTag was generated in a mammalian cell line, and following targeted biotinylation, was tetramerised with BUV395 or BUV737 streptavidin conjugates. Multicolour flow cytometry was applied on blood samples before and 28 days after booster influenza vaccination in 16 healthy controls and five PAD patients with circulating Bmem cells. Results Recombinant HA tetramers were specifically recognised by 0.5-1% of B cells in previously vaccinated healthy adults. HA-specific Bmem cell numbers were significantly increased following booster vaccination and predominantly expressed IgG1. Similarly, PAD patients carried HA-specific Bmem cells, predominantly expressing IgG1. However, these numbers were lower than in controls and did not increase following booster vaccination. Conclusion We have successfully identified AM15-specific Bmem cells in healthy controls and PAD patients. The presence of antigen-specific Bmem cells could offer an additional diagnostic tool to aid in the clinical diagnosis of PAD. Furthermore, alterations in the number or immunophenotype of HA-specific Bmem cells post-booster vaccination could assist in the evaluation of immune responses in individuals receiving IgRT.
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Affiliation(s)
- Gemma E Hartley
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia.,The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies Melbourne VIC Australia
| | - Emily S J Edwards
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia.,The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies Melbourne VIC Australia
| | - Julian J Bosco
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies Melbourne VIC Australia.,Department of Allergy, Immunology and Respiratory Medicine Central Clinical School Alfred Hospital Monash University and Allergy, Asthma and Clinical Immunology Service Melbourne VIC Australia
| | - Samar Ojaimi
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies Melbourne VIC Australia.,Infectious Diseases Monash Health Clayton VIC Australia.,Immunology Laboratory Monash Pathology Clayton VIC Australia.,Allergy and Immunology Monash Health Clayton VIC Australia
| | - Robert G Stirling
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies Melbourne VIC Australia.,Department of Allergy, Immunology and Respiratory Medicine Central Clinical School Alfred Hospital Monash University and Allergy, Asthma and Clinical Immunology Service Melbourne VIC Australia
| | - Paul U Cameron
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies Melbourne VIC Australia.,Department of Allergy, Immunology and Respiratory Medicine Central Clinical School Alfred Hospital Monash University and Allergy, Asthma and Clinical Immunology Service Melbourne VIC Australia
| | - Katie Flanagan
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia.,School of Medicine University of Tasmania Launceston TAS Australia.,School of Health and Biomedical Sciences RMIT Bundoora VIC Australia
| | | | - Philip Mark Hogarth
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia.,Immune Therapies Group Burnet Institute Melbourne VIC Australia
| | - Robyn E O'Hehir
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia.,The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies Melbourne VIC Australia.,Department of Allergy, Immunology and Respiratory Medicine Central Clinical School Alfred Hospital Monash University and Allergy, Asthma and Clinical Immunology Service Melbourne VIC Australia
| | - Menno C van Zelm
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia.,The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies Melbourne VIC Australia.,Department of Allergy, Immunology and Respiratory Medicine Central Clinical School Alfred Hospital Monash University and Allergy, Asthma and Clinical Immunology Service Melbourne VIC Australia
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9
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Brochu HN, Tseng E, Smith E, Thomas MJ, Jones AM, Diveley KR, Law L, Hansen SG, Picker LJ, Gale M, Peng X. Systematic Profiling of Full-Length Ig and TCR Repertoire Diversity in Rhesus Macaque through Long Read Transcriptome Sequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:3434-3444. [PMID: 32376650 PMCID: PMC7276939 DOI: 10.4049/jimmunol.1901256] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/13/2020] [Indexed: 12/19/2022]
Abstract
The diversity of Ig and TCR repertoires is a focal point of immunological studies. Rhesus macaques (Macaca mulatta) are key for modeling human immune responses, placing critical importance on the accurate annotation and quantification of their Ig and TCR repertoires. However, because of incomplete reference resources, the coverage and accuracy of the traditional targeted amplification strategies for profiling rhesus Ig and TCR repertoires are largely unknown. In this study, using long read sequencing, we sequenced four Indian-origin rhesus macaque tissues and obtained high-quality, full-length sequences for over 6000 unique Ig and TCR transcripts, without the need for sequence assembly. We constructed, to our knowledge, the first complete reference set for the constant regions of all known isotypes and chain types of rhesus Ig and TCR repertoires. We show that sequence diversity exists across the entire variable regions of rhesus Ig and TCR transcripts. Consequently, existing strategies using targeted amplification of rearranged variable regions comprised of V(D)J gene segments miss a significant fraction (27-53% and 42-49%) of rhesus Ig/TCR diversity. To overcome these limitations, we designed new rhesus-specific assays that remove the need for primers conventionally targeting variable regions and allow single cell level Ig and TCR repertoire analysis. Our improved approach will enable future studies to fully capture rhesus Ig and TCR repertoire diversity and is applicable for improving annotations in any model organism.
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Affiliation(s)
- Hayden N Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | | | - Elise Smith
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Matthew J Thomas
- Department of Immunology, University of Washington, Seattle, WA 98109
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109
| | - Aiden M Jones
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
- Genetics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Kayleigh R Diveley
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
- Genetics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Lynn Law
- Department of Immunology, University of Washington, Seattle, WA 98109
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA 98109
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109
- Washington National Primate Research Center, University of Washington, Seattle, WA 98121; and
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607;
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695
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10
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Wong J, Tai CM, Hurt AC, Tan HX, Kent SJ, Wheatley AK. Sequencing B cell receptors from ferrets (Mustela putorius furo). PLoS One 2020; 15:e0233794. [PMID: 32470013 PMCID: PMC7259655 DOI: 10.1371/journal.pone.0233794] [Citation(s) in RCA: 4] [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: 02/26/2020] [Accepted: 05/12/2020] [Indexed: 12/16/2022] Open
Abstract
The domestic ferret (Mustela putorius furo) provides a critical animal model to study human respiratory diseases. However immunological insights are restricted due to a lack of ferret-specific reagents and limited genetic information about ferret B and T cell receptors. Here, variable, diversity and joining genes within the ferret kappa, lambda and heavy chain immunoglobulin loci were annotated using available genomic information. A multiplex PCR approach was derived that facilitated the recovery of paired heavy and light chain immunoglobulin sequences from single sorted ferret B cells, allowing validation of predicted germline gene sequences and the identification of putative novel germlines. Eukaryotic expression vectors were developed that enabled the generation of recombinant ferret monoclonal antibodies. This work advances the ferret as an informative immunological model for viral diseases by allowing the in-depth interrogation of antibody-based immunity.
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Affiliation(s)
- Julius Wong
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Celeste M. Tai
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Aeron C. Hurt
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- ARC Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AKW); (SJK)
| | - Adam K. Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- ARC Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AKW); (SJK)
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11
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Olbrich A, Wardemann H, Böhm S, Rother K, Colpitts CC, Wrensch F, Baumert TF, Berg T, Benckert J. Repertoire and Neutralizing Activity of Antibodies Against Hepatitis C Virus E2 Peptide in Patients With Spontaneous Resolution of Hepatitis C. J Infect Dis 2020; 220:1209-1218. [PMID: 31165162 DOI: 10.1093/infdis/jiz274] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/03/2019] [Indexed: 12/15/2022] Open
Abstract
Neutralizing antibodies can prevent hepatitis C virus (HCV) infection, one of the leading causes of cirrhosis and liver cancer. Here, we characterized the immunoglobulin repertoire of memory B-cell antibodies against a linear epitope in the central front layer of the HCV envelope (E2; amino acids 483-499) in patients who were infected in a single-source outbreak. A reverse transcription polymerase chain reaction-based immunoglobulin gene cloning and recombinant expression approach was used to express monoclonal antibodies from HCV E2 peptide-binding immunoglobulin G-positive memory B cells. We identified highly mutated antibodies with a neutralizing effect in vitro against different genotype isolates sharing similar gene features. Our data confirm the importance of VH1-69 use for neutralizing activity. The data offer a promising basis for vaccine research and the use of anti-E2 antibodies as a means of passive immunization.
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Affiliation(s)
- Anne Olbrich
- Laboratory for Clinical and Experimental Hepatology, Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, Leipzig, Germany
| | - Hedda Wardemann
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Stephan Böhm
- Laboratory for Clinical and Experimental Hepatology, Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, Leipzig, Germany.,Max von Pettenkofer Institute, Munich, Germany
| | - Karen Rother
- Laboratory for Clinical and Experimental Hepatology, Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, Leipzig, Germany
| | - Che C Colpitts
- Inserm U1110, University of Strasbourg, France.,Division of Infection and Immunity, University College London, United Kingdom
| | - Florian Wrensch
- Clinic for Hepatology and Gastroenterology, Charité, CVK, Berlin, Germany
| | - Thomas F Baumert
- Clinic for Hepatology and Gastroenterology, Charité, CVK, Berlin, Germany
| | - Thomas Berg
- Laboratory for Clinical and Experimental Hepatology, Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, Leipzig, Germany
| | - Julia Benckert
- Laboratory for Clinical and Experimental Hepatology, Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, Leipzig, Germany.,Inserm U1110, University of Strasbourg, France
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12
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Sannier G, Dubé M, Kaufmann DE. Single-Cell Technologies Applied to HIV-1 Research: Reaching Maturity. Front Microbiol 2020; 11:297. [PMID: 32194526 PMCID: PMC7064469 DOI: 10.3389/fmicb.2020.00297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
The need for definitive answers probably explains our natural tendency to seek simplicity. The reductionist “bulk” approach, in which a mean behavior is attributed to a heterogeneous cell population, fulfills this need by considerably helping the conceptualization of complex biological processes. However, the limits of this methodology are becoming increasingly clear as models seek to explain biological events occurring in vivo, where heterogeneity is the rule. Research in the HIV-1 field is no exception: the challenges encountered in the development of preventive and curative anti-HIV-1 strategies may well originate in part from inadequate assumptions built on bulk technologies, highlighting the need for new perspectives. The emergence of diverse single-cell technologies set the stage for potential breakthrough discoveries, as heterogeneous processes can now be investigated with an unprecedented depth in topics as diverse as HIV-1 tropism, dynamics of the replication cycle, latency, viral reservoirs and immune control. In this review, we summarize recent advances in the HIV-1 field made possible by single-cell technologies, and contextualize their importance.
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Affiliation(s)
- Gérémy Sannier
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada.,Consortium for HIV/AIDS Vaccine Development (Scripps CHAVD), La Jolla, CA, United States
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13
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Phad GE, Pushparaj P, Tran K, Dubrovskaya V, Àdori M, Martinez-Murillo P, Vázquez Bernat N, Singh S, Dionne G, O’Dell S, Bhullar K, Narang S, Sorini C, Villablanca EJ, Sundling C, Murrell B, Mascola JR, Shapiro L, Pancera M, Martin M, Corcoran M, Wyatt RT, Karlsson Hedestam GB. Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses. J Exp Med 2020; 217:e20191155. [PMID: 31704807 PMCID: PMC7041718 DOI: 10.1084/jem.20191155] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022] Open
Abstract
Well-ordered HIV-1 envelope glycoprotein (Env) trimers are prioritized for clinical evaluation, and there is a need for an improved understanding about how elicited B cell responses evolve following immunization. To accomplish this, we prime-boosted rhesus macaques with clade C NFL trimers and identified 180 unique Ab lineages from ∼1,000 single-sorted Env-specific memory B cells. We traced all lineages in high-throughput heavy chain (HC) repertoire (Rep-seq) data generated from multiple immune compartments and time points and expressed several as monoclonal Abs (mAbs). Our results revealed broad dissemination and high levels of somatic hypermutation (SHM) of most lineages, including tier 2 virus neutralizing lineages, following boosting. SHM was highest in the Ab complementarity determining regions (CDRs) but also surprisingly high in the framework regions (FRs), especially FR3. Our results demonstrate the capacity of the immune system to affinity-mature large numbers of Env-specific B cell lineages simultaneously, supporting the use of regimens consisting of repeated boosts to improve each Ab, even those belonging to less expanded lineages.
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Affiliation(s)
- Ganesh E. Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Karen Tran
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Viktoriya Dubrovskaya
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Monika Àdori
- 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
| | - Néstor Vázquez Bernat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Suruchi Singh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Gilman Dionne
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Komal Bhullar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sanjana Narang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Chiara Sorini
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Eduardo J. Villablanca
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Christopher Sundling
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Benjamin Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Marcel Martin
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Richard T. Wyatt
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
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14
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Li R, Fu F, Feng L, Liu P. Next-generation sequencing and single-cell RT-PCR reveal a distinct variable gene usage of porcine antibody repertoire following PEDV vaccination. SCIENCE CHINA-LIFE SCIENCES 2019; 63:1240-1250. [PMID: 31321668 PMCID: PMC7088813 DOI: 10.1007/s11427-019-9576-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/12/2019] [Indexed: 11/24/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is the most common diarrhea-causing pathogen in newborn piglets. The clarifications of the overall antibody repertoire and antigen-specific antibody repertoire are essential to provide important insights into the B-cell response and reshape new vaccines. Here, we applied next-generation sequencing (NGS) technology to investigate immunoglobulin (Ig) variable (V) gene segment usage of swine B-cells from peripheral blood lymphocytes (PBL) and mesenteric lymph node (MLN) cells following PEDV vaccination. We identified the transcripts of all functional Ig V-genes in antibody repertoire. IgHV1S2, IgKV1-11, and IgLV3-4 were the most prevalent gene segments for heavy, kappa, and lambda chains, respectively, in PBL and MLN. Unlike previous studies, IgKV1, instead of IgKV2, and IgLV3, instead of IgLV8, were the prevalent Ig V-gene families for kappa and lambda light chains, respectively. We further examined the antibody repertoire of PEDV spike-specific B cells by single-cell RT-PCR. In contrast to the overall antibody repertoire, Ig V-gene segments of PEDV spike-specific B cells preferentially adopted IgHV1-4 and IgHV1-14 for heavy chain, IgKV1-11 for kappa chain, and IgLV3-3 for lambda chain. These results represent a comprehensive analysis to characterize the Ig V-gene segment usage in the overall and PEDV spike-specific antibody repertoire in PBL and MLN.
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Affiliation(s)
- Ren Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Fang Fu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - PingHuang Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
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15
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Gadala-Maria D, Gidoni M, Marquez S, Vander Heiden JA, Kos JT, Watson CT, O'Connor KC, Yaari G, Kleinstein SH. Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data. Front Immunol 2019; 10:129. [PMID: 30814994 PMCID: PMC6381938 DOI: 10.3389/fimmu.2019.00129] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/16/2019] [Indexed: 01/10/2023] Open
Abstract
The adaptive immune receptor repertoire (AIRR) contains information on an individuals' immune past, present and potential in the form of the evolving sequences that encode the B cell receptor (BCR) repertoire. AIRR sequencing (AIRR-seq) studies rely on databases of known BCR germline variable (V), diversity (D), and joining (J) genes to detect somatic mutations in AIRR-seq data via comparison to the best-aligning database alleles. However, it has been shown that these databases are far from complete, leading to systematic misidentification of mutated positions in subsets of sample sequences. We previously presented TIgGER, a computational method to identify subject-specific V gene genotypes, including the presence of novel V gene alleles, directly from AIRR-seq data. However, the original algorithm was unable to detect alleles that differed by more than 5 single nucleotide polymorphisms (SNPs) from a database allele. Here we present and apply an improved version of the TIgGER algorithm which can detect alleles that differ by any number of SNPs from the nearest database allele, and can construct subject-specific genotypes with minimal prior information. TIgGER predictions are validated both computationally (using a leave-one-out strategy) and experimentally (using genomic sequencing), resulting in the addition of three new immunoglobulin heavy chain V (IGHV) gene alleles to the IMGT repertoire. Finally, we develop a Bayesian strategy to provide a confidence estimate associated with genotype calls. All together, these methods allow for much higher accuracy in germline allele assignment, an essential step in AIRR-seq studies.
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Affiliation(s)
- Daniel Gadala-Maria
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Moriah Gidoni
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Jason A. Vander Heiden
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Justin T. Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Kevin C. O'Connor
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, United States
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Steven H. Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, United States
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT, United States
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16
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Zhang W, Li X, Wang L, Deng J, Lin L, Tian L, Wu J, Tang C, Yang H, Wang J, Qiu P, Fu TM, Saksena NK, Wang IM, Liu X. Identification of Variable and Joining Germline Genes and Alleles for Rhesus Macaque from B Cell Receptor Repertoires. THE JOURNAL OF IMMUNOLOGY 2019; 202:1612-1622. [DOI: 10.4049/jimmunol.1800342] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 12/20/2018] [Indexed: 11/19/2022]
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17
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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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18
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Kovaltsuk A, Leem J, Kelm S, Snowden J, Deane CM, Krawczyk K. Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires. THE JOURNAL OF IMMUNOLOGY 2018; 201:2502-2509. [PMID: 30217829 DOI: 10.4049/jimmunol.1800708] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/19/2018] [Indexed: 11/19/2022]
Abstract
Abs are immune system proteins that recognize noxious molecules for elimination. Their sequence diversity and binding versatility have made Abs the primary class of biopharmaceuticals. Recently, it has become possible to query their immense natural diversity using next-generation sequencing of Ig gene repertoires (Ig-seq). However, Ig-seq outputs are currently fragmented across repositories and tend to be presented as raw nucleotide reads, which means nontrivial effort is required to reuse the data for analysis. To address this issue, we have collected Ig-seq outputs from 55 studies, covering more than half a billion Ab sequences across diverse immune states, organisms (primarily human and mouse), and individuals. We have sorted, cleaned, annotated, translated, and numbered these sequences and make the data available via our Observed Antibody Space (OAS) resource at http://antibodymap.org The data within OAS will be regularly updated with newly released Ig-seq datasets. We believe OAS will facilitate data mining of immune repertoires for improved understanding of the immune system and development of better biotherapeutics.
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Affiliation(s)
- Aleksandr Kovaltsuk
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| | - Jinwoo Leem
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| | | | | | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| | - Konrad Krawczyk
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
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19
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Abstract
Humans have a close phylogenetic relationship with nonhuman primates (NHPs) and share many physiological parallels, such as highly similar immune systems, with them. Importantly, NHPs can be infected with many human or related simian viruses. In many cases, viruses replicate in the same cell types as in humans, and infections are often associated with the same pathologies. In addition, many reagents that are used to study the human immune response cross-react with NHP molecules. As such, NHPs are often used as models to study viral vaccine efficacy and antiviral therapeutic safety and efficacy and to understand aspects of viral pathogenesis. With several emerging viral infections becoming epidemic, NHPs are proving to be a very beneficial benchmark for investigating human viral infections.
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Affiliation(s)
- Jacob D Estes
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, USA
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, USA
| | - Scott W Wong
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, USA
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
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20
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Upadhyay AA, Kauffman RC, Wolabaugh AN, Cho A, Patel NB, Reiss SM, Havenar-Daughton C, Dawoud RA, Tharp GK, Sanz I, Pulendran B, Crotty S, Lee FEH, Wrammert J, Bosinger SE. BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data. Genome Med 2018; 10:20. [PMID: 29558968 PMCID: PMC5859752 DOI: 10.1186/s13073-018-0528-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/23/2018] [Indexed: 01/21/2023] Open
Abstract
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells. BALDR enables matching of clonotype identity with single-cell transcriptional information in B cell lineages and will have broad application in the fields of vaccines, human immunodeficiency virus broadly neutralizing antibody development, and cancer. BALDR is available at https://github.com/BosingerLab/BALDR.
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Affiliation(s)
- Amit A Upadhyay
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Robert C Kauffman
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Amber N Wolabaugh
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Alice Cho
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Nirav B Patel
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA
| | - Samantha M Reiss
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, USA
| | - Colin Havenar-Daughton
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, USA
| | - Reem A Dawoud
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Gregory K Tharp
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA
| | - Iñaki Sanz
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.,Division of Rheumatology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, USA.,Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - F Eun-Hyung Lee
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.,Divisions of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA, USA
| | - Jens Wrammert
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA. .,Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA. .,Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, USA.
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21
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Han SY, Antoine A, Howard D, Chang B, Chang WS, Slein M, Deikus G, Kossida S, Duroux P, Lefranc MP, Sebra RP, Smith ML, Fofana IBF. Coupling of Single Molecule, Long Read Sequencing with IMGT/HighV-QUEST Analysis Expedites Identification of SIV gp140-Specific Antibodies from scFv Phage Display Libraries. Front Immunol 2018; 9:329. [PMID: 29545792 PMCID: PMC5837965 DOI: 10.3389/fimmu.2018.00329] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/06/2018] [Indexed: 12/20/2022] Open
Abstract
The simian immunodeficiency virus (SIV)/macaque model of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome pathogenesis is critical for furthering our understanding of the role of antibody responses in the prevention of HIV infection, and will only increase in importance as macaque immunoglobulin (IG) gene databases are expanded. We have previously reported the construction of a phage display library from a SIV-infected rhesus macaque (Macaca mulatta) using oligonucleotide primers based on human IG gene sequences. Our previous screening relied on Sanger sequencing, which was inefficient and generated only a few dozen sequences. Here, we re-analyzed this library using single molecule, real-time (SMRT) sequencing on the Pacific Biosciences (PacBio) platform to generate thousands of highly accurate circular consensus sequencing (CCS) reads corresponding to full length single chain fragment variable. CCS data were then analyzed through the international ImMunoGeneTics information system® (IMGT®)/HighV-QUEST (www.imgt.org) to identify variable genes and perform statistical analyses. Overall the library was very diverse, with 2,569 different IMGT clonotypes called for the 5,238 IGHV sequences assigned to an IMGT clonotype. Within the library, SIV-specific antibodies represented a relatively limited number of clones, with only 135 different IMGT clonotypes called from 4,594 IGHV-assigned sequences. Our data did confirm that the IGHV4 and IGHV3 gene usage was the most abundant within the rhesus antibodies screened, and that these genes were even more enriched among SIV gp140-specific antibodies. Although a broad range of VH CDR3 amino acid (AA) lengths was observed in the unpanned library, the vast majority of SIV gp140-specific antibodies demonstrated a more uniform VH CDR3 length (20 AA). This uniformity was far less apparent when VH CDR3 were classified according to their clonotype (range: 9–25 AA), which we believe is more relevant for specific antibody identification. Only 174 IGKV and 588 IGLV clonotypes were identified within the VL sequences associated with SIV gp140-specific VH. Together, these data strongly suggest that the combination of SMRT sequencing with the IMGT/HighV-QUEST querying tool will facilitate and expedite our understanding of polyclonal antibody responses during SIV infection and may serve to rapidly expand the known scope of macaque V genes utilized during these responses.
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Affiliation(s)
- Seung Yub Han
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Alesia Antoine
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United States
| | - David Howard
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Bryant Chang
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Woo Sung Chang
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Matthew Slein
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United States
| | - Sofia Kossida
- The international ImMunoGeneTics information system® (IMGT®), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UMR CNRS, Montpellier University, Montpellier, France
| | - Patrice Duroux
- The international ImMunoGeneTics information system® (IMGT®), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UMR CNRS, Montpellier University, Montpellier, France
| | - Marie-Paule Lefranc
- The international ImMunoGeneTics information system® (IMGT®), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UMR CNRS, Montpellier University, Montpellier, France
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United States
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United States
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22
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HIV Broadly Neutralizing Antibodies: VRC01 and Beyond. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1075:53-72. [PMID: 30030789 DOI: 10.1007/978-981-13-0484-2_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Developing an effective prophylaxis HIV-1 vaccine is likely to require the elicitation of broadly neutralizing antibodies (bnAbs). As the HIV-1 envelope (Env) glycoprotein - the sole target of bnAbs - has evolved multiple mechanisms to evade antibody neutralization, the processes for bnAb generation are highly selective and time-consuming. Benefiting from antibody isolation technologies of single B cell culturing and direct single B cell sorting and cloning, a new generation of monoclonal bnAbs has been isolated since 2009, exhibiting remarkable breadths and potencies, thus breaking through a nearly 20-year-long limit of four monoclonal bnAbs with moderate breadth and potency. The discovery of a long list of monoclonal bnAbs has provided in-depth understanding of the sites of vulnerability on the HIV-1 Env and the complexity of human B cell immunology to generate such responses, thus presenting both guidance and challenges to move the Env immunogen design effort forward.
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23
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Farfán-Arribas DJ, Liu S, Wang S, Lu S. The dynamics of immunoglobulin V-gene usage and clonotype expansion in mice after prime and boost immunizations as analyzed by NGS. Hum Vaccin Immunother 2017; 13:2987-2995. [PMID: 29049006 PMCID: PMC5718813 DOI: 10.1080/21645515.2017.1379638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the current study, an improved NGS approach was developed to study the B-cell repertoire evolution in a simple mouse immunization model including only two DNA immunizations. The combination of 5′RACE and Ion Torrent long reads enabled unbiased immunoglobulin repertoire analysis even from small amounts of peripheral mouse blood. The B-cell population expanded by the vaccine displayed a relatively strong clonality. Upon priming with the first vaccine dose, we observed a consistent pattern of V-segment gene and CDR3 usage (public specificities). Interestingly, this pattern diversified with the second dose of immunization —it was relatively different in individual mice in spite of having received the same vaccine regimen (private specificities). Nevertheless, there were several instances in which the same public V-segment genes and CDR3s that were expanded after the first dose were further amplified after the second immunization. Taken together, it appears that the major clonotypes expanded by vaccination were originally a homogeneous subset that later diversified after a second dose leading to diverse “private” clonal compositions in different mice. These results established a new platform valuable to perform longitudinal analyses of the Ig germline gene usage and clonotype evolution throughout an immunization regimen in a commonly used animal model.
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Affiliation(s)
- Diego J Farfán-Arribas
- a Department of Medicine , University of Massachusetts Medical School , Worcester , MA , USA
| | - Shuying Liu
- a Department of Medicine , University of Massachusetts Medical School , Worcester , MA , USA
| | - Shixia Wang
- a Department of Medicine , University of Massachusetts Medical School , Worcester , MA , USA
| | - Shan Lu
- a Department of Medicine , University of Massachusetts Medical School , Worcester , MA , USA
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24
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HIV-1 Cross-Reactive Primary Virus Neutralizing Antibody Response Elicited by Immunization in Nonhuman Primates. J Virol 2017; 91:JVI.00910-17. [PMID: 28835491 DOI: 10.1128/jvi.00910-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/10/2017] [Indexed: 12/15/2022] Open
Abstract
Elicitation of broadly neutralizing antibody (bNAb) responses is a major goal for the development of an HIV-1 vaccine. Current HIV-1 envelope glycoprotein (Env) vaccine candidates elicit predominantly tier 1 and/or autologous tier 2 virus neutralizing antibody (NAb) responses, as well as weak and/or sporadic cross-reactive tier 2 virus NAb responses with unknown specificity. To delineate the specificity of vaccine-elicited cross-reactive tier 2 virus NAb responses, we performed single memory B cell sorting from the peripheral blood of a rhesus macaque immunized with YU2gp140-F trimers in adjuvant, using JR-FL SOSIP.664, a native Env trimer mimetic, as a sorting probe to isolate monoclonal Abs (MAbs). We found striking genetic and functional convergence of the SOSIP-sorted Ig repertoire, with predominant VH4 or VH5 gene family usage and Env V3 specificity. Of these vaccine-elicited V3-specific MAbs, nearly 20% (6/33) displayed cross-reactive tier 2 virus neutralization, which recapitulated the serum neutralization capacity. Substantial similarities in binding specificity, neutralization breadth and potency, and sequence/structural homology were observed between selected macaque cross-reactive V3 NAbs elicited by vaccination and prototypic V3 NAbs derived from natural infections in humans, highlighting the convergence of this subset of primate V3-specific B cell repertories. Our study demonstrated that cross-reactive primary virus neutralizing B cell lineages could be elicited by vaccination as detected using a standardized panel of tier 2 viruses. Whether these lineages could be expanded to acquire increased breadth and potency of neutralization merits further investigation.IMPORTANCE Elicitation of antibody responses capable of neutralizing diverse HIV-1 primary virus isolates (designated broadly neutralizing antibodies [bNAbs]) remains a high priority for the vaccine field. bNAb responses were so far observed only in response to natural infection within a subset of individuals. To achieve this goal, an improved understanding of vaccine-elicited responses, including at the monoclonal Ab level, is essential. Here, we isolated and characterized a panel of vaccine-elicited cross-reactive neutralizing MAbs targeting the Env V3 loop that moderately neutralized several primary viruses and recapitulated the serum neutralizing antibody response. Striking similarities between the cross-reactive V3 NAbs elicited by vaccination in macaques and natural infections in humans illustrate commonalities between the vaccine- and infection-induced responses to V3 and support the feasibility of exploring the V3 epitope as a HIV-1 vaccine target in nonhuman primates.
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25
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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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26
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Karlsson Hedestam GB, Guenaga J, Corcoran M, Wyatt RT. Evolution of B cell analysis and Env trimer redesign. Immunol Rev 2017; 275:183-202. [PMID: 28133805 DOI: 10.1111/imr.12515] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
HIV-1 and its surface envelope glycoproteins (Env), gp120 and gp41, have evolved immune evasion strategies that render the elicitation of effective antibody responses to the functional Env entry unit extremely difficult. HIV-1 establishes chronic infection and stimulates vigorous immune responses in the human host; forcing selection of viral variants that escape cellular and antibody (Ab)-mediated immune pressure, yet possess contemporary fitness. Successful survival of fit variants through the gauntlet of the human immune system make this virus and these glycoproteins a formidable challenge to target by vaccination, requiring a systematic approach to Env mimetic immunogen design and evaluation of elicited responses. Here, we review key aspects of HIV-1 Env immunogenicity and immunogen re-design, based on experimental data generated by us and others over the past decade or more. We further provide rationale and details regarding the use of newly evolving tools to analyze B cell responses, including approaches to use next generation sequencing for antibody lineage tracing and B cell fate mapping. Together, these developments offer opportunities to address long-standing questions about the establishment of effective B cell immunity elicited by vaccination, not just against HIV-1.
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Affiliation(s)
| | - Javier Guenaga
- Department of Immunology and Microbial Science, IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, USA
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Richard T Wyatt
- Department of Immunology and Microbial Science, IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, USA.,The Scripps CHAVI-ID, La Jolla, CA, USA
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27
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Antibody therapies for the prevention and treatment of viral infections. NPJ Vaccines 2017; 2:19. [PMID: 29263875 PMCID: PMC5627241 DOI: 10.1038/s41541-017-0019-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/08/2017] [Accepted: 05/16/2017] [Indexed: 12/18/2022] Open
Abstract
Antibodies are an important component in host immune responses to viral pathogens. Because of their unique maturation process, antibodies can evolve to be highly specific to viral antigens. Physicians and researchers have been relying on such high specificity in their quest to understand host–viral interaction and viral pathogenesis mechanisms and to find potential cures for viral infection and disease. With more than 60 recombinant monoclonal antibodies developed for human use in the last 20 years, monoclonal antibodies are now considered a viable therapeutic modality for infectious disease targets, including newly emerging viral pathogens such as Ebola representing heightened public health concerns, as well as pathogens that have long been known, such as human cytomegalovirus. Here, we summarize some recent advances in identification and characterization of monoclonal antibodies suitable as drug candidates for clinical evaluation, and review some promising candidates in the development pipeline.
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28
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Kwong PD, Chuang G, DeKosky BJ, Gindin T, Georgiev IS, Lemmin T, Schramm CA, Sheng Z, Soto C, Yang A, Mascola JR, Shapiro L. Antibodyomics: bioinformatics technologies for understanding B-cell immunity to HIV-1. Immunol Rev 2017; 275:108-128. [PMID: 28133812 PMCID: PMC5516196 DOI: 10.1111/imr.12480] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Numerous antibodies have been identified from HIV-1-infected donors that neutralize diverse strains of HIV-1. These antibodies may provide the basis for a B cell-mediated HIV-1 vaccine. However, it has been unclear how to elicit similar antibodies by vaccination. To address this issue, we have undertaken an informatics-based approach to understand the genetic and immunologic processes controlling the development of HIV-1-neutralizing antibodies. As DNA sequencing comprises the fastest growing database of biological information, we focused on incorporating next-generation sequencing of B-cell transcripts to determine the origin, maturation pathway, and prevalence of broadly neutralizing antibody lineages (Antibodyomics1, 2, 4, and 6). We also incorporated large-scale robotic analyses of serum neutralization to identify and quantify neutralizing antibodies in donor cohorts (Antibodyomics3). Statistical analyses furnish another layer of insight (Antibodyomics5), with physical characteristics of antibodies and their targets through molecular dynamics simulations (Antibodyomics7) and free energy perturbation analyses (Antibodyomics8) providing information-rich output. Functional interrogation of individual antibodies (Antibodyomics9) and synthetic antibody libraries (Antibodyomics10) also yields multi-dimensional data by which to understand and improve antibodies. Antibodyomics, described here, thus comprise resolution-enhancing tools, which collectively embody an information-driven discovery engine aimed toward the development of effective B cell-based vaccines.
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Affiliation(s)
- Peter D. Kwong
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
| | - Gwo‐Yu Chuang
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Brandon J. DeKosky
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Tatyana Gindin
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
| | - Ivelin S. Georgiev
- Vanderbilt Vaccine Center and Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTNUSA
| | - Thomas Lemmin
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCAUSA
| | - Chaim A. Schramm
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Zizhang Sheng
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Cinque Soto
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - An‐Suei Yang
- Genomics Research CenterAcademia SinicaTaipeiTaiwan
| | - John R. Mascola
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Lawrence Shapiro
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
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29
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Heydarchi B, Center RJ, Bebbington J, Cuthbertson J, Gonelli C, Khoury G, Mackenzie C, Lichtfuss M, Rawlin G, Muller B, Purcell D. Trimeric gp120-specific bovine monoclonal antibodies require cysteine and aromatic residues in CDRH3 for high affinity binding to HIV Env. MAbs 2016; 9:550-566. [PMID: 27996375 PMCID: PMC5384801 DOI: 10.1080/19420862.2016.1270491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
We isolated HIV-1 Envelope (Env)-specific memory B cells from a cow that had developed high titer polyclonal immunoglobulin G (IgG) with broad neutralizing activity after a long duration vaccination with HIV-1AD8 Env gp140 trimers. We cloned the bovine IgG matched heavy (H) and light (L) chain variable (V) genes from these memory B cells and constructed IgG monoclonal antibodies (mAbs) with either a human constant (C)-region/bovine V-region chimeric or fully bovine C and V regions. Among 42 selected Ig+ memory B cells, two mAbs (6A and 8C) showed high affinity binding to gp140 Env. Characterization of both the fully bovine and human chimeric isoforms of these two mAbs revealed them as highly type-specific and capable of binding only to soluble AD8 uncleaved gp140 trimers and covalently stabilized AD8 SOSIP gp140 cleaved trimers, but not monomeric gp120. Genomic sequence analysis of the V genes showed the third heavy complementarity-determining region (CDRH3) of 6A mAb was 21 amino acids in length while 8C CDRH3 was 14 amino acids long. The entire V heavy (VH) region was 27% and 25% diverged for 6A and 8C, respectively, from the best matched germline V genes available, and the CDRH3 regions of 6A and 8C were 47.62% and 78.57% somatically mutated, respectively, suggesting a high level of somatic hypermutation compared with CDRH3 of other species. Alanine mutagenesis of the VH genes of 6A and 8C, showed that CDRH3 cysteine and tryptophan amino acids were crucial for antigen binding. Therefore, these bovine vaccine-induced anti-HIV antibodies shared some of the notable structural features of elite human broadly neutralizing antibodies, such as CDRH3 size and somatic mutation during affinity-maturation. However, while the 6A and 8C mAbs inhibited soluble CD4 binding to gp140 Env, they did not recapitulate the neutralizing activity of the polyclonal antibodies against HIV infection.
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Affiliation(s)
- Behnaz Heydarchi
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - Rob J Center
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - Jonathan Bebbington
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - Jack Cuthbertson
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - Christopher Gonelli
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - Georges Khoury
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - Charlene Mackenzie
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - Marit Lichtfuss
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - Grant Rawlin
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - Brian Muller
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - Damian Purcell
- a Department of Microbiology and Immunology , The University of Melbourne at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
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30
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McCoy LE, van Gils MJ, Ozorowski G, Messmer T, Briney B, Voss JE, Kulp DW, Macauley MS, Sok D, Pauthner M, Menis S, Cottrell CA, Torres JL, Hsueh J, Schief WR, Wilson IA, Ward AB, Sanders RW, Burton DR. Holes in the Glycan Shield of the Native HIV Envelope Are a Target of Trimer-Elicited Neutralizing Antibodies. Cell Rep 2016; 16:2327-38. [PMID: 27545891 DOI: 10.1016/j.celrep.2016.07.074] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/25/2016] [Accepted: 07/27/2016] [Indexed: 10/21/2022] Open
Abstract
A major advance in the search for an HIV vaccine has been the development of a near-native Envelope trimer (BG505 SOSIP.664) that can induce robust autologous Tier 2 neutralization. Here, potently neutralizing monoclonal antibodies (nAbs) from rabbits immunized with BG505 SOSIP.664 are shown to recognize an immunodominant region of gp120 centered on residue 241. Residue 241 occupies a hole in the glycan defenses of the BG505 isolate, with fewer than 3% of global isolates lacking a glycan site at this position. However, at least one conserved glycan site is missing in 89% of viruses, suggesting the presence of glycan holes in most HIV isolates. Serum evidence is consistent with targeting of holes in natural infection. The immunogenic nature of breaches in the glycan shield has been under-appreciated in previous attempts to understand autologous neutralizing antibody responses and has important potential consequences for HIV vaccine design.
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Affiliation(s)
- Laura E McCoy
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Infection & Immunity, University College London, London WC1E 6BT, UK
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Gabriel Ozorowski
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Terrence Messmer
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James E Voss
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthew S Macauley
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthias Pauthner
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A Cottrell
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Torres
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica Hsueh
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Ian A Wilson
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; Weill Medical College of Cornell University, New York, NY 10065, USA.
| | - Dennis R Burton
- Department of Immunology & Microbial Science, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.
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31
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Vigdorovich V, Oliver BG, Carbonetti S, Dambrauskas N, Lange MD, Yacoob C, Leahy W, Callahan J, Stamatatos L, Sather DN. Repertoire comparison of the B-cell receptor-encoding loci in humans and rhesus macaques by next-generation sequencing. Clin Transl Immunology 2016; 5:e93. [PMID: 27525066 PMCID: PMC4973324 DOI: 10.1038/cti.2016.42] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/15/2016] [Accepted: 06/16/2016] [Indexed: 12/29/2022] Open
Abstract
Rhesus macaques (RMs) are a widely used model system for the study of vaccines, infectious diseases and microbial pathogenesis. Their value as a model lies in their close evolutionary relationship to humans, which, in theory, allows them to serve as a close approximation of the human immune system. However, despite their prominence as a human surrogate model system, many aspects of the RM immune system remain ill characterized. In particular, B cell-mediated immunity in macaques has not been sufficiently characterized, and the B-cell receptor-encoding loci have not been thoroughly annotated. To address these gaps, we analyzed the circulating heavy- and light-chain repertoires in humans and RMs by next-generation sequencing. By comparing V gene segment usage, J-segment usage and CDR3 lengths between the two species, we identified several important similarities and differences. These differences were especially notable in the IgM(+) B-cell repertoire. However, the class-switched, antigen-educated B-cell populations converged on a set of similar characteristics, implying similarities in how each species responds to antigen. Our study provides the first comprehensive overview of the circulating repertoires of the heavy- and light-chain sequences in RMs, and provides insight into how they may perform as a model system for B cell-mediated immunity in humans.
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Affiliation(s)
- Vladimir Vigdorovich
- Center for Infectious Disease Research (formerly Seattle BioMed) , Seattle, WA, USA
| | - Brian G Oliver
- Center for Infectious Disease Research (formerly Seattle BioMed) , Seattle, WA, USA
| | - Sara Carbonetti
- Center for Infectious Disease Research (formerly Seattle BioMed) , Seattle, WA, USA
| | - Nicholas Dambrauskas
- Center for Infectious Disease Research (formerly Seattle BioMed) , Seattle, WA, USA
| | - Miles D Lange
- Center for Infectious Disease Research (formerly Seattle BioMed) , Seattle, WA, USA
| | - Christina Yacoob
- Fred Hutchinson Cancer Research Center, Viral and Infectious Disease Division , Seattle, WA, USA
| | | | | | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Viral and Infectious Disease Division , Seattle, WA, USA
| | - D Noah Sather
- Center for Infectious Disease Research (formerly Seattle BioMed) , Seattle, WA, USA
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32
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Highly sensitive and unbiased approach for elucidating antibody repertoires. Proc Natl Acad Sci U S A 2016; 113:7846-51. [PMID: 27354528 DOI: 10.1073/pnas.1608649113] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Developing B lymphocytes undergo V(D)J recombination to assemble germ-line V, D, and J gene segments into exons that encode the antigen-binding variable region of Ig heavy (H) and light (L) chains. IgH and IgL chains associate to form the B-cell receptor (BCR), which, upon antigen binding, activates B cells to secrete BCR as an antibody. Each of the huge number of clonally independent B cells expresses a unique set of IgH and IgL variable regions. The ability of V(D)J recombination to generate vast primary B-cell repertoires results from a combinatorial assortment of large numbers of different V, D, and J segments, coupled with diversification of the junctions between them to generate the complementary determining region 3 (CDR3) for antigen contact. Approaches to evaluate in depth the content of primary antibody repertoires and, ultimately, to study how they are further molded by secondary mutation and affinity maturation processes are of great importance to the B-cell development, vaccine, and antibody fields. We now describe an unbiased, sensitive, and readily accessible assay, referred to as high-throughput genome-wide translocation sequencing-adapted repertoire sequencing (HTGTS-Rep-seq), to quantify antibody repertoires. HTGTS-Rep-seq quantitatively identifies the vast majority of IgH and IgL V(D)J exons, including their unique CDR3 sequences, from progenitor and mature mouse B lineage cells via the use of specific J primers. HTGTS-Rep-seq also accurately quantifies DJH intermediates and V(D)J exons in either productive or nonproductive configurations. HTGTS-Rep-seq should be useful for studies of human samples, including clonal B-cell expansions, and also for following antibody affinity maturation processes.
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33
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Yamamoto T, Lynch RM, Gautam R, Matus-Nicodemos R, Schmidt SD, Boswell KL, Darko S, Wong P, Sheng Z, Petrovas C, McDermott AB, Seder RA, Keele BF, Shapiro L, Douek DC, Nishimura Y, Mascola JR, Martin MA, Koup RA. Quality and quantity of TFH cells are critical for broad antibody development in SHIVAD8 infection. Sci Transl Med 2016. [PMID: 26223303 DOI: 10.1126/scitranslmed.aab3964] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Broadly neutralizing antibodies (bNAbs) protect against HIV-1 infection, yet how they are generated during chronic infection remains unclear. It is known that T follicular helper (TFH) cells are needed to promote affinity maturation of B cells during an immune response; however, the role of TFH during HIV-1 infection is undefined within lymph node germinal centers (GCs). We use nonhuman primates to investigate the relationship in the early stage of chronic SHIVAD8 (simian-human immunodeficiency virus AD8) infection between envelope (Env)-specific TFH cells, Env-specific B cells, virus, and the generation of bNAbs during later infection. We found that both the frequency and quality of Env-specific TFH cells were associated with an expansion of Env-specific immunoglobulin G-positive GC B cells and broader neutralization across HIV clades. We also found a correlation between breadth of neutralization and the degree of somatic hypermutation in Env-specific memory B cells. Finally, we observed high viral loads and greater diversity of Env sequences in rhesus macaques that developed cross-reactive neutralization as compared to those that did not. These studies highlight the importance of boosting high-quality TFH populations as part of a robust vaccine regimen aimed at eliciting bNabs.
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Affiliation(s)
- Takuya Yamamoto
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Rebecca M Lynch
- Humoral Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Rajeev Gautam
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Rodrigo Matus-Nicodemos
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Stephen D Schmidt
- Humoral Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Kristin L Boswell
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Sam Darko
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Patrick Wong
- Humoral Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Constantinos Petrovas
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Robert A Seder
- Cellular Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - John R Mascola
- Humoral Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Malcolm A Martin
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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34
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Wang Y, Sundling C, Wilson R, O'Dell S, Chen Y, Dai K, Phad GE, Zhu J, Xiao Y, Mascola JR, Karlsson Hedestam GB, Wyatt RT, Li Y. High-Resolution Longitudinal Study of HIV-1 Env Vaccine-Elicited B Cell Responses to the Virus Primary Receptor Binding Site Reveals Affinity Maturation and Clonal Persistence. THE JOURNAL OF IMMUNOLOGY 2016; 196:3729-43. [PMID: 27001953 DOI: 10.4049/jimmunol.1502543] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/01/2016] [Indexed: 01/01/2023]
Abstract
Because of the genetic variability of the HIV-1 envelope glycoproteins (Env), the elicitation of neutralizing Abs to conserved neutralization determinants including the primary receptor binding site, CD4 binding site (CD4bs), is a major focus of vaccine development. To gain insight into the evolution of Env-elicited Ab responses, we used single B cell analysis to interrogate the memory B cell Ig repertoires from two rhesus macaques after five serial immunizations with Env/adjuvant. We observed that the CD4bs-specific repertoire displayed unique features in the third CDR of Ig H chains with minor alterations along the immunization course. Progressive affinity maturation occurred as evidenced by elevated levels of somatic hypermutation (SHM) in Ab sequences isolated at the late immunization time point compared with the early time point. Abs with higher SHM were associated with increased binding affinity and virus neutralization capacity. Moreover, a notable portion of the CD4bs-specific repertoire was maintained between early and late immunization time points, suggesting that persistent clonal lineages were induced by Env vaccination. Furthermore, we found that the predominant persistent CD4bs-specific clonal lineages had larger population sizes and higher affinities than that from the rest of the repertoires, underscoring the critical role of Ag affinity selection in Ab maturation and clonal expansion. Genetic and functional analyses revealed that the accumulation of SHM in both framework regions and CDRs contributed to the clonal affinity and antigenicity evolution. Our longitudinal study provides high-resolution understanding of the dynamically evolving CD4bs-specific B cell response after Env immunization in primates.
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Affiliation(s)
- Yimeng Wang
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Christopher Sundling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden; Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Richard Wilson
- International AIDS Vaccine Initiative Neutralizing Antibody Center at The Scripps Research Institute, La Jolla, CA 92037
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Yajing Chen
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Kaifan Dai
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Ganesh E Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jiang Zhu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037; Scripps Center for HIV Vaccine Immunogen Discovery, La Jolla, CA 92037; and
| | - Yongli Xiao
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | | | - Richard T Wyatt
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037; International AIDS Vaccine Initiative Neutralizing Antibody Center at The Scripps Research Institute, La Jolla, CA 92037; Scripps Center for HIV Vaccine Immunogen Discovery, La Jolla, CA 92037; and
| | - Yuxing Li
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850; International AIDS Vaccine Initiative Neutralizing Antibody Center at The Scripps Research Institute, La Jolla, CA 92037;
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35
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Abstract
Recent biological, structural, and technical advances are converging within the HIV-1 vaccine field to harness the power of antibodies for prevention and therapy. Numerous monoclonal antibodies with broad neutralizing activity against diverse HIV-1 isolates have now been identified, revealing at least five sites of vulnerability on the envelope (Env) glycoproteins. While there are practical and technological barriers blocking a clear path from broadly neutralizing antibodies (bNAb) to a protective vaccine, this is not a dead end. Scientists are revisiting old approaches with new technology, cutting new trails through unexplored territory, and paving new roads in the hopes of preventing HIV-1 infection. Other promising avenues to capitalize on the power of bNAbs are also being pursued, such as passive antibody immunotherapy and gene therapy approaches. Moreover, non-neutralizing antibodies have inhibitory activities that could have protective potential, alone or in combination with bNAbs. With a new generation of bNAbs, and a clinical trial that associated antibodies with reduced acquisition, the field is closer than ever to developing strategies to use antibodies against HIV-1.
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Affiliation(s)
- S Abigail Smith
- Yerkes National Primate Research Center, Atlanta, Georgia, 30322, USA
| | - Cynthia A Derdeyn
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, 30322, USA; Yerkes National Primate Research Center, Atlanta, Georgia, 30322, USA
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36
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Rhesus Macaque B-Cell Responses to an HIV-1 Trimer Vaccine Revealed by Unbiased Longitudinal Repertoire Analysis. mBio 2015; 6:e01375-15. [PMID: 26530382 PMCID: PMC4631801 DOI: 10.1128/mbio.01375-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Next-generation sequencing (NGS) has been used to investigate the diversity and maturation of broadly neutralizing antibodies (bNAbs) in HIV-1-infected individuals. However, the application of NGS to the preclinical assessment of human vaccines, particularly the monitoring of vaccine-induced B-cell responses in a nonhuman primate (NHP) model, has not been reported. Here, we present a longitudinal NGS analysis of memory B-cell responses to an HIV-1 trimer vaccine in a macaque that has been extensively studied by single B-cell sorting and antibody characterization. We first established an NHP antibodyomics pipeline using the available 454 pyrosequencing data from this macaque and developed a protocol to sequence the NHP antibody repertoire in an unbiased manner. Using these methods, we then analyzed memory B-cell repertoires at four time points of NHP immunization and traced the lineages of seven CD4-binding site (CD4bs)-directed monoclonal antibodies previously isolated from this macaque. Longitudinal analysis revealed distinct patterns of B-cell lineage development in response to an HIV-1 trimer vaccine. While the temporal B-cell repertoire profiles and lineage patterns provide a baseline for comparison with forthcoming HIV-1 trimer vaccines, the newly developed NHP antibody NGS technologies and antibodyomics tools will facilitate future evaluation of human vaccine candidates. The nonhuman primate model has been widely used in the preclinical assessment of human vaccines. Next-generation sequencing of B-cell repertoires provides a quantitative tool to analyze B-cell responses to a vaccine. In this study, the longitudinal B-cell repertoire analysis of a rhesus macaque immunized with an HIV-1 trimer vaccine revealed complex B-cell lineage patterns and showed the potential to facilitate the evaluation of future HIV-1 vaccines. The repertoire sequencing technologies and antibodyomics methods reported here can be extended to vaccine development for other human pathogens utilizing the nonhuman primate model.
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37
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Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires. Trends Immunol 2015; 36:738-749. [DOI: 10.1016/j.it.2015.09.006] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 01/16/2023]
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38
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Cotugno N, De Armas L, Pallikkuth S, Rossi P, Palma P, Pahwa S. Paediatric HIV infection in the ‘omics era: defining transcriptional signatures of viral control and vaccine responses. J Virus Erad 2015. [DOI: 10.1016/s2055-6640(20)30507-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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39
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Cotugno N, De Armas L, Pallikkuth S, Rossi P, Palma P, Pahwa S. Paediatric HIV infection in the 'omics era: defining transcriptional signatures of viral control and vaccine responses. J Virus Erad 2015; 1:153-158. [PMID: 26807446 PMCID: PMC4721557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Modern technologies and their increased accessibility have shifted 'benchtop' medical research to the larger dimension of 'omics. The huge amount of data derived from gene expression and sequencing experiments has propelled physicians, basic scientists and bioinformaticians towards a common goal to transform 'big data' into predictive constructs that are readily available and will offer clinical utility. Although most of the studies available in the literature have been performed on healthy subjects and in peripheral blood mononuclear cells (PBMC), which are a heterogenous and extremely variable pool of cells, scientists are now trying to address mechanistic questions in purified cell subsets in pathological conditions. In the field of HIV, few attempts have been made to comprehensively evaluate gene-expression profiles of infected patients with different disease status. With the view of discovering a path towards remission or viral eradication, perinatally HIV-infected children represent a unique model. In fact the well-defined time of infection and the resulting opportunity to start early treatment, thereby generating a smaller size of viral reservoir and a more intact immune system, allow for investigation of therapeutic strategies to defeat the virus. In this scenario, 'transcriptomic' or gene expression technologies and supporting bioinformatics applications need to be strategically integrated to provide novel information about immune correlates of virus control following treatment interruption. Here we review modern techniques for gene expression analysis and discuss the best transcriptomic strategies applicable to the field of functional cure in paediatric HIV infection.
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Affiliation(s)
- Nicola Cotugno
- University Department of Pediatrics, DPUO, Unit of Immune and Infectious Diseases,
Bambino Gesù Children's Hospital,
Rome,
Italy,Department of Systems Medicine,
University of Rome,‘Tor Vergata’,
Italy
| | - Lesley De Armas
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami,
Miami,
Florida,
USA
| | - Suresh Pallikkuth
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami,
Miami,
Florida,
USA
| | - Paolo Rossi
- University Department of Pediatrics, DPUO, Unit of Immune and Infectious Diseases,
Bambino Gesù Children's Hospital,
Rome,
Italy,Department of Systems Medicine,
University of Rome,‘Tor Vergata’,
Italy
| | - Paolo Palma
- University Department of Pediatrics, DPUO, Unit of Immune and Infectious Diseases,
Bambino Gesù Children's Hospital,
Rome,
Italy
| | - Savita Pahwa
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami,
Miami,
Florida,
USA,Corresponding author: Savita Pahwa,
Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami1580 NW 10th Avenue,
Miami,
FL33136,
USA
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40
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Phad GE, Vázquez Bernat N, Feng Y, Ingale J, Martinez Murillo PA, O'Dell S, Li Y, Mascola JR, Sundling C, Wyatt RT, Karlsson Hedestam GB. Diverse antibody genetic and recognition properties revealed following HIV-1 envelope glycoprotein immunization. THE JOURNAL OF IMMUNOLOGY 2015; 194:5903-14. [PMID: 25964491 DOI: 10.4049/jimmunol.1500122] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/15/2015] [Indexed: 11/19/2022]
Abstract
Isolation of mAbs elicited by vaccination provides opportunities to define the development of effective immunity. Ab responses elicited by current HIV-1 envelope glycoprotein (Env) immunogens display narrow neutralizing activity with limited capacity to block infection by tier 2 viruses. Intense work in the field suggests that improved Env immunogens are forthcoming, and it is therefore important to concurrently develop approaches to investigate the quality of vaccine-elicited responses at a higher level of resolution. In this study, we cloned a representative set of mAbs elicited by a model Env immunogen in rhesus macaques and comprehensively characterized their genetic and functional properties. The mAbs were genetically diverse, even within groups of Abs targeting the same subregion of Env, consistent with a highly polyclonal response. mAbs directed against two subdeterminants of Env, the CD4 binding site and V region 3, could in part account for the neutralizing activity observed in the plasma of the animal from which they were cloned, demonstrating the power of mAb isolation for a detailed understanding of the elicited response. Finally, through comparative analyses of mAb binding and neutralizing capacity of HIV-1 using matched Envs, we demonstrate complex relationships between epitope recognition and accessibility, highlighting the protective quaternary packing of the HIV-1 spike relative to vaccine-induced mAbs.
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Affiliation(s)
- Ganesh E Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Néstor Vázquez Bernat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Yu Feng
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Jidnyasa Ingale
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | | | - Sijy O'Dell
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892
| | - Yuxing Li
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850; and
| | - John R Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892
| | - Christopher Sundling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Richard T Wyatt
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
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41
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Doria-Rose NA, Joyce MG. Strategies to guide the antibody affinity maturation process. Curr Opin Virol 2015; 11:137-47. [PMID: 25913818 DOI: 10.1016/j.coviro.2015.04.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/02/2015] [Accepted: 04/06/2015] [Indexed: 11/16/2022]
Abstract
Antibodies with protective activity are critical for vaccine efficacy. Affinity maturation increases antibody activity through multiple rounds of somatic hypermutation and selection in the germinal center. Identification of HIV-1 specific and influenza-specific antibody developmental pathways, as well as characterization of B cell and virus co-evolution in patients, has informed our understanding of antibody development. In order to counteract HIV-1 and influenza viral diversity, broadly neutralizing antibodies precisely target specific sites of vulnerability and require high levels of affinity maturation. We present immunization strategies that attempt to recapitulate these natural processes and guide the affinity maturation process.
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Affiliation(s)
- Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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42
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Francica JR, Sheng Z, Zhang Z, Nishimura Y, Shingai M, Ramesh A, Keele BF, Schmidt SD, Flynn BJ, Darko S, Lynch RM, Yamamoto T, Matus-Nicodemos R, Wolinsky D, Nason M, Valiante NM, Malyala P, De Gregorio E, Barnett SW, Singh M, O'Hagan DT, Koup RA, Mascola JR, Martin MA, Kepler TB, Douek DC, Shapiro L, Seder RA. Analysis of immunoglobulin transcripts and hypermutation following SHIV(AD8) infection and protein-plus-adjuvant immunization. Nat Commun 2015; 6:6565. [PMID: 25858157 PMCID: PMC4403371 DOI: 10.1038/ncomms7565] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/09/2015] [Indexed: 01/28/2023] Open
Abstract
Developing predictive animal models to assess how candidate vaccines and infection influence the ontogenies of Envelope (Env)-specific antibodies is critical for the development of an HIV vaccine. Here we use two nonhuman primate models to compare the roles of antigen persistence, diversity and innate immunity. We perform longitudinal analyses of HIV Env-specific B-cell receptor responses to SHIV(AD8) infection and Env protein vaccination with eight different adjuvants. A subset of the SHIV(AD8)-infected animals with higher viral loads and greater Env diversity show increased neutralization associated with increasing somatic hypermutation (SHM) levels over time. The use of adjuvants results in increased ELISA titres but does not affect the mean SHM levels or CDR H3 lengths. Our study shows how the ontogeny of Env-specific B cells can be tracked, and provides insights into the requirements for developing neutralizing antibodies that should facilitate translation to human vaccine studies.
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Affiliation(s)
- Joseph R. Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Zizhang Sheng
- Department of Biochemistry, Columbia University, New York, New York 10032, USA
| | - Zhenhai Zhang
- Department of Biochemistry, Columbia University, New York, New York 10032, USA
- State Key Laboratory of Organ Failure Research and National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Masashi Shingai
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Akshaya Ramesh
- Department of Microbiology and Immunology, Boston University, Boston, Massachusetts 02118, USA
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, Maryland 21702, USA
| | - Stephen D. Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Barbara J. Flynn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sam Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Rebecca M. Lynch
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Takuya Yamamoto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Rodrigo Matus-Nicodemos
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David Wolinsky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Martha Nason
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - Padma Malyala
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts 02139, USA
| | - Ennio De Gregorio
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts 02139, USA
| | - Susan W. Barnett
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts 02139, USA
| | - Manmohan Singh
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts 02139, USA
| | - Derek T. O'Hagan
- Novartis Vaccines and Diagnostics, Cambridge, Massachusetts 02139, USA
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Malcolm A. Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Thomas B. Kepler
- Department of Microbiology and Immunology, Boston University, Boston, Massachusetts 02118, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lawrence Shapiro
- Department of Biochemistry, Columbia University, New York, New York 10032, USA
| | - Robert A. Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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McCoy LE, Rutten L, Frampton D, Anderson I, Granger L, Bashford-Rogers R, Dekkers G, Strokappe NM, Seaman MS, Koh W, Grippo V, Kliche A, Verrips T, Kellam P, Fassati A, Weiss RA. Molecular evolution of broadly neutralizing Llama antibodies to the CD4-binding site of HIV-1. PLoS Pathog 2014; 10:e1004552. [PMID: 25522326 PMCID: PMC4270772 DOI: 10.1371/journal.ppat.1004552] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 11/04/2014] [Indexed: 11/20/2022] Open
Abstract
To date, no immunization of humans or animals has elicited broadly neutralizing sera able to prevent HIV-1 transmission; however, elicitation of broad and potent heavy chain only antibodies (HCAb) has previously been reported in llamas. In this study, the anti-HIV immune responses in immunized llamas were studied via deep sequencing analysis using broadly neutralizing monoclonal HCAbs as a guides. Distinct neutralizing antibody lineages were identified in each animal, including two defined by novel antibodies (as variable regions called VHH) identified by robotic screening of over 6000 clones. The combined application of five VHH against viruses from clades A, B, C and CRF_AG resulted in neutralization as potent as any of the VHH individually and a predicted 100% coverage with a median IC50 of 0.17 µg/ml for the panel of 60 viruses tested. Molecular analysis of the VHH repertoires of two sets of immunized animals showed that each neutralizing lineage was only observed following immunization, demonstrating that they were elicited de novo. Our results show that immunization can induce potent and broadly neutralizing antibodies in llamas with features similar to human antibodies and provide a framework to analyze the effectiveness of immunization protocols. Developing a vaccine against HIV-1 is a priority, but it remains unclear whether immunizations in humans can elicit potent broadly neutralizing antibodies able to prevent HIV-1 transmission. Llamas possess heavy chain only antibodies and conventional heavy and light chain antibodies. We previously reported the heavy chain only antibody J3, which potently neutralizes more than 95% of HIV strains, and was induced by immunization. Here we immunized two further llamas and elicited three novel broadly neutralizing heavy chain only antibodies, which were identified by high-throughput screening. These neutralizing llama antibodies target different areas of the CD4-binding site of the virus, therefore breadth and potency are increased when they are used in combination. To gain greater understanding of how the llama immunizations worked, deep sequencing of the HIV binding region of the antibodies was performed. This revealed that the antibodies were matured fully only in response to the protein immunogens. Furthermore, the VHH elicited in different animals, while sharing functional hallmarks, were encoded by distinct sequences and thus could not have been identified by a deep sequencing analysis alone. Our results show that immunization can potentially induce protective antibodies in llamas and provide a method to more extensively evaluate immunization studies.
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Affiliation(s)
- Laura E. McCoy
- Wohl Virion Centre and Medical Research Council (MRC) Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
- * E-mail: (LEM); (RAW)
| | | | - Dan Frampton
- Wohl Virion Centre and Medical Research Council (MRC) Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Ian Anderson
- Wohl Virion Centre and Medical Research Council (MRC) Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Luke Granger
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, London, United Kingdom
| | | | - Gillian Dekkers
- Wohl Virion Centre and Medical Research Council (MRC) Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | | | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Willie Koh
- Wohl Virion Centre and Medical Research Council (MRC) Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Vanina Grippo
- Centro de Virología Animal, Instituto de Ciencia y Tecnología Dr. César Milstein, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alexander Kliche
- Institute of Medical Microbiology, University of Regensburg, Regensburg, Germany
| | | | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Ariberto Fassati
- Wohl Virion Centre and Medical Research Council (MRC) Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Robin A. Weiss
- Wohl Virion Centre and Medical Research Council (MRC) Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
- * E-mail: (LEM); (RAW)
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Vaccine-induced plasmablast responses in rhesus macaques: phenotypic characterization and a source for generating antigen-specific monoclonal antibodies. J Immunol Methods 2014; 416:69-83. [PMID: 25445326 DOI: 10.1016/j.jim.2014.11.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/09/2014] [Accepted: 11/03/2014] [Indexed: 12/25/2022]
Abstract
Over 100 broadly neutralizing antibodies have been isolated from a minority of HIV infected patients, but the steps leading to the selection of plasma cells producing such antibodies remain incompletely understood, hampering the development of vaccines able to elicit them. Rhesus macaques have become a preferred animal model system used to study SIV/HIV, for the characterization and development of novel therapeutics and vaccines as well as to understand pathogenesis. However, most of our knowledge about the dynamics of antibody responses is limited to the analysis of serum antibodies or monoclonal antibodies generated from memory B cells. In a vaccine setting, relatively little is known about the early cellular responses that elicit long-lived plasma cells and memory B cells and the tools to dissect plasmablast responses are not available in macaques. In the current study, we show that the majority (>80%) of the vaccine-induced plasmablast response are antigen-specific by functional ELISPOT assays. While plasmablasts are easily defined and isolated in humans, those same phenotypic markers have not been useful for identifying macaque plasmablasts. Here we describe an approach that allows for the isolation and single cell sorting of vaccine-induced plasmablasts. Finally, we show that isolated plasmablasts can be used to efficiently recover antigen-specific monoclonal antibodies through single cell expression cloning. This will allow detailed studies of the early plasmablast responses in rhesus macaques, enabling the characterization of both their repertoire breadth as well as the epitope specificity and functional qualities of the antibodies they produce, not only in the context of SIV/HIV vaccines but for many other pathogens/vaccines as well.
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45
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HIV-1 Env-specific memory and germinal center B cells in C57BL/6 mice. Viruses 2014; 6:3400-14. [PMID: 25198199 PMCID: PMC4189027 DOI: 10.3390/v6093400] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/11/2014] [Accepted: 08/31/2014] [Indexed: 01/16/2023] Open
Abstract
Continued efforts to define the immunogenic properties of the HIV-1 envelope glycoproteins (Env) are needed to elicit effective antibody (Ab) responses by vaccination. HIV-1 is a highly neutralization-resistant virus due to conformational and glycan shielding of conserved Ab determinants on the virus spike. Elicitation of broadly neutralizing Abs that bind poorly accessible epitope regions on Env is therefore extremely challenging and will likely require selective targeting of specific sub-determinants. To evaluate such approaches there is a pressing need for in vivo studies in both large and small animals, including mice. Currently, most mouse immunization studies are performed in the BALB/c strain; however, the C57BL/6 strain offers improved possibilities for mechanistic studies due to the availability of numerous knock-out strains on this genetic background. Here, we compared Env immunogenicity in BALB/c and C57BL/6 mice and found that the magnitude of the antigen-specific response was somewhat lower in C57BL/6 than in BALB/c mice by ELISA but not significantly different by B cell ELISpot measurements. We then established protocols for the isolation of single Env-specific memory B cells and germinal center (GC) B cells from immunized C57BL/6 mice to facilitate future studies of the elicited response at the monoclonal Ab level. We propose that these protocols can be used to gain an improved understanding of the early recruitment of Env-specific B cells to the GC as well as the archiving of such responses in the memory B cell pool following immunization.
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46
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Mohanram V, Demberg T, Tuero I, Vargas-Inchaustegui D, Pavlakis GN, Felber BK, Robert-Guroff M. Improved flow-based method for HIV/SIV envelope-specific memory B-cell evaluation in rhesus macaques. J Immunol Methods 2014; 412:78-84. [PMID: 24953216 DOI: 10.1016/j.jim.2014.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/11/2014] [Accepted: 06/11/2014] [Indexed: 02/06/2023]
Abstract
The ability to elicit potent and long-lasting broadly neutralizing HIV envelope (Env)-specific antibodies has become a key goal for HIV vaccine development. Consequently, the ability to rapidly and efficiently monitor development of memory B cells in pre-clinical and clinical vaccine trails is critical for continued progress in vaccine design. We have developed an improved flow cytometry-based method for the rapid and efficient identification of gp120-specific memory B cells in peripheral blood, bone marrow, and mucosal tissues which allows their direct staining without the need for prior cell sorting or enrichment. We demonstrate staining of both HIV and SIV Env-specific memory B cells in PBMC, bone marrow, and rectal tissue of vaccinated and infected rhesus macaques. Validation of the method is illustrated by statistically significant correlations with memory B cell levels quantified by ELISPOT assay and with serum binding antibody titers determined by ELISA. In addition to quantification, this method will bring the power of flow cytometry to the study of homing and trafficking of Env-specific memory B cells.
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Affiliation(s)
- Venkatramanan Mohanram
- Section on Immune Biology of Retroviral Infection, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Thorsten Demberg
- Section on Immune Biology of Retroviral Infection, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Iskra Tuero
- Section on Immune Biology of Retroviral Infection, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Diego Vargas-Inchaustegui
- Section on Immune Biology of Retroviral Infection, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - George N Pavlakis
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, United States
| | - Barbara K Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, United States
| | - Marjorie Robert-Guroff
- Section on Immune Biology of Retroviral Infection, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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47
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Larsen PA, Campbell CR, Yoder AD. Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates. Mol Ecol Resour 2014; 14:1198-209. [DOI: 10.1111/1755-0998.12274] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 11/27/2022]
Affiliation(s)
- P. A. Larsen
- Department of Biology; Box 90338; Duke University; Durham NC 27708 USA
| | - C. R. Campbell
- Department of Biology; Box 90338; Duke University; Durham NC 27708 USA
| | - A. D. Yoder
- Department of Biology; Box 90338; Duke University; Durham NC 27708 USA
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