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Title: Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses

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.

Authors:
ORCiD logo [1];  [1];  [2]; ORCiD logo [2];  [1]; ORCiD logo [1];  [1]; ORCiD logo [3];  [4];  [5];  [1];  [1]; ORCiD logo [6]; ORCiD logo [6]; ORCiD logo [6];  [1];  [5];  [4];  [3];  [7] more »;  [1];  [2]; ORCiD logo [1] « less
  1. Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
  2. International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
  3. Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
  4. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
  5. Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
  6. Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
  7. Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1573531
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Journal of Experimental Medicine
Additional Journal Information:
Journal Name: Journal of Experimental Medicine; Journal ID: ISSN 0022-1007
Publisher:
Rockefeller University Press
Country of Publication:
United States
Language:
English

Citation Formats

Phad, Ganesh E., Pushparaj, Pradeepa, Tran, Karen, Dubrovskaya, Viktoriya, Àdori, Monika, Martinez-Murillo, Paola, Vázquez Bernat, Néstor, Singh, Suruchi, Dionne, Gilman, O’Dell, Sijy, Bhullar, Komal, Narang, Sanjana, Sorini, Chiara, Villablanca, Eduardo J., Sundling, Christopher, Murrell, Benjamin, Mascola, John R., Shapiro, Lawrence, Pancera, Marie, Martin, Marcel, Corcoran, Martin, Wyatt, Richard T., and Karlsson Hedestam, Gunilla B. Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses. United States: N. p., 2019. Web. doi:10.1084/jem.20191155.
Phad, Ganesh E., Pushparaj, Pradeepa, Tran, Karen, Dubrovskaya, Viktoriya, Àdori, Monika, Martinez-Murillo, Paola, Vázquez Bernat, Néstor, Singh, Suruchi, Dionne, Gilman, O’Dell, Sijy, Bhullar, Komal, Narang, Sanjana, Sorini, Chiara, Villablanca, Eduardo J., Sundling, Christopher, Murrell, Benjamin, Mascola, John R., Shapiro, Lawrence, Pancera, Marie, Martin, Marcel, Corcoran, Martin, Wyatt, Richard T., & Karlsson Hedestam, Gunilla B. Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses. United States. doi:10.1084/jem.20191155.
Phad, Ganesh E., Pushparaj, Pradeepa, Tran, Karen, Dubrovskaya, Viktoriya, Àdori, Monika, Martinez-Murillo, Paola, Vázquez Bernat, Néstor, Singh, Suruchi, Dionne, Gilman, O’Dell, Sijy, Bhullar, Komal, Narang, Sanjana, Sorini, Chiara, Villablanca, Eduardo J., Sundling, Christopher, Murrell, Benjamin, Mascola, John R., Shapiro, Lawrence, Pancera, Marie, Martin, Marcel, Corcoran, Martin, Wyatt, Richard T., and Karlsson Hedestam, Gunilla B. Fri . "Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses". United States. doi:10.1084/jem.20191155.
@article{osti_1573531,
title = {Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses},
author = {Phad, Ganesh E. and Pushparaj, Pradeepa and Tran, Karen and Dubrovskaya, Viktoriya and Àdori, Monika and Martinez-Murillo, Paola and Vázquez Bernat, Néstor and Singh, Suruchi and Dionne, Gilman and O’Dell, Sijy and Bhullar, Komal and Narang, Sanjana and Sorini, Chiara and Villablanca, Eduardo J. and Sundling, Christopher and Murrell, Benjamin and Mascola, John R. and Shapiro, Lawrence and Pancera, Marie and Martin, Marcel and Corcoran, Martin and Wyatt, Richard T. and Karlsson Hedestam, Gunilla B.},
abstractNote = {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.},
doi = {10.1084/jem.20191155},
journal = {Journal of Experimental Medicine},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {11}
}

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Works referenced in this record:

Broadly neutralizing antibodies and the search for an HIV-1 vaccine: the end of the beginning
journal, August 2013

  • Kwong, Peter D.; Mascola, John R.; Nabel, Gary J.
  • Nature Reviews Immunology, Vol. 13, Issue 9
  • DOI: 10.1038/nri3516

Targeted N-glycan deletion at the receptor-binding site retains HIV Env NFL trimer integrity and accelerates the elicited antibody response
journal, September 2017


Broad and potent neutralization of HIV-1 by a gp41-specific human antibody
journal, September 2012


Broad and potent HIV-1 neutralization by a human antibody that binds the gp41–gp120 interface
journal, September 2014

  • Huang, Jinghe; Kang, Byong H.; Pancera, Marie
  • Nature, Vol. 515, Issue 7525
  • DOI: 10.1038/nature13601

Broad neutralization coverage of HIV by multiple highly potent antibodies
journal, September 2011

  • Walker, Laura M.; Huber, Michael; Doores, Katie J.
  • Nature, Vol. 477, Issue 7365
  • DOI: 10.1038/nature10373

Practical guidelines for B-cell receptor repertoire sequencing analysis
journal, November 2015


Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning
journal, January 2008

  • Tiller, Thomas; Meffre, Eric; Yurasov, Sergey
  • Journal of Immunological Methods, Vol. 329, Issue 1-2
  • DOI: 10.1016/j.jim.2007.09.017

Vaccine-Induced Protection from Homologous Tier 2 SHIV Challenge in Nonhuman Primates Depends on Serum-Neutralizing Antibody Titers
journal, January 2019


Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding
journal, July 2011


Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity
journal, December 2016

  • Corcoran, Martin M.; Phad, Ganesh E.; Bernat, Néstor Vázquez
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13642

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1
journal, June 2018


Tissue memory B cell repertoire analysis after ALVAC/AIDSVAX B/E gp120 immunization of rhesus macaques
journal, December 2016


Crystal Structure of a Soluble Cleaved HIV-1 Envelope Trimer
journal, October 2013


Soluble HIV-1 Env trimers in adjuvant elicit potent and diverse functional B cell responses in primates
journal, August 2010

  • Sundling, Christopher; Forsell, Mattias N. E.; O'Dell, Sijy
  • The Journal of Experimental Medicine, Vol. 207, Issue 9
  • DOI: 10.1084/jem.20100025

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization
journal, July 2019


Diverse Antibody Genetic and Recognition Properties Revealed following HIV-1 Envelope Glycoprotein Immunization
journal, May 2015

  • Phad, Ganesh E.; Vázquez Bernat, Néstor; Feng, Yu
  • The Journal of Immunology, Vol. 194, Issue 12
  • DOI: 10.4049/jimmunol.1500122

Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1
journal, July 2010


The CCP4 suite programs for protein crystallography
journal, September 1994


Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection
journal, April 2015


Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody
journal, April 2016


HIV-1 neutralizing antibodies induced by native-like envelope trimers
journal, June 2015


Cleavage-Independent HIV-1 Env Trimers Engineered as Soluble Native Spike Mimetics for Vaccine Design
journal, April 2015


Structure and Diversity of the Rhesus Macaque Immunoglobulin Loci through Multiple De Novo Genome Assemblies
journal, October 2017


HIV-1 Receptor Binding Site-Directed Antibodies Using a VH1-2 Gene Segment Orthologue Are Activated by Env Trimer Immunization
journal, August 2014


Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination
journal, February 2013


Single-Cell and Deep Sequencing of IgG-Switched Macaque B Cells Reveal a Diverse Ig Repertoire following Immunization
journal, March 2014

  • Sundling, Christopher; Zhang, Zhenhai; Phad, Ganesh E.
  • The Journal of Immunology, Vol. 192, Issue 8
  • DOI: 10.4049/jimmunol.1303334

The promise and challenge of high-throughput sequencing of the antibody repertoire
journal, January 2014

  • Georgiou, George; Ippolito, Gregory C.; Beausang, John
  • Nature Biotechnology, Vol. 32, Issue 2
  • DOI: 10.1038/nbt.2782

Targeting TLRs Expands the Antibody Repertoire in Response to a Malaria Vaccine
journal, July 2011


An atlas of B-cell clonal distribution in the human body
journal, August 2017

  • Meng, Wenzhao; Zhang, Bochao; Schwartz, Gregory W.
  • Nature Biotechnology, Vol. 35, Issue 9
  • DOI: 10.1038/nbt.3942

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Structure-Guided Redesign Increases the Propensity of HIV Env To Generate Highly Stable Soluble Trimers
journal, December 2015

  • Guenaga, Javier; Dubrovskaya, Viktoriya; de Val, Natalia
  • Journal of Virology, Vol. 90, Issue 6
  • DOI: 10.1128/JVI.02652-15

Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody
journal, May 2016


Particulate Array of Well-Ordered HIV Clade C Env Trimers Elicits Neutralizing Antibodies that Display a Unique V2 Cap Approach
journal, May 2017


Antibody neutralization and escape by HIV-1
journal, March 2003

  • Wei, Xiping; Decker, Julie M.; Wang, Shuyi
  • Nature, Vol. 422, Issue 6929
  • DOI: 10.1038/nature01470

Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization
journal, March 2013


Primate immune responses to HIV-1 Env formulated in the saponin-based adjuvant AbISCO-100 in the presence or absence of TLR9 co-stimulation
journal, March 2015

  • Martinez, Paola; Sundling, Christopher; O'Dell, Sijy
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep08925

B cell clonal lineage alterations upon recombinant HIV-1 envelope immunization of rhesus macaques
journal, June 2018


Studying the antibody repertoire after vaccination: practical applications
journal, July 2014

  • Galson, Jacob D.; Pollard, Andrew J.; Trück, Johannes
  • Trends in Immunology, Vol. 35, Issue 7
  • DOI: 10.1016/j.it.2014.04.005

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies
journal, March 2014

  • Doria-Rose, Nicole A.; Schramm, Chaim A.; Gorman, Jason
  • Nature, Vol. 509, Issue 7498
  • DOI: 10.1038/nature13036

High-Resolution Definition of Vaccine-Elicited B Cell Responses Against the HIV Primary Receptor Binding Site
journal, July 2012


Isolation of antibody V(D)J sequences from single cell sorted rhesus macaque B cells
journal, December 2012

  • Sundling, Christopher; Phad, Ganesh; Douagi, Iyadh
  • Journal of Immunological Methods, Vol. 386, Issue 1-2
  • DOI: 10.1016/j.jim.2012.09.003

Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance
journal, May 2019


Tracing Antibody Repertoire Evolution by Systems Phylogeny
journal, October 2018

  • Yermanos, Alexander Dimitri; Dounas, Andreas Kevin; Stadler, Tanja
  • Frontiers in Immunology, Vol. 9
  • DOI: 10.3389/fimmu.2018.02149

Flt3 ligand expands bona fide innate lymphoid cell precursors in vivo
journal, January 2018


Analysis of immunoglobulin transcripts and hypermutation following SHIVAD8 infection and protein-plus-adjuvant immunization
journal, April 2015

  • Francica, Joseph R.; Sheng, Zizhang; Zhang, Zhenhai
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms7565

The Essential Detail: The Genetics and Genomics of the Primate Immune Response
journal, January 2013


Comparative Analysis of B-Cell Receptor Repertoires Induced by Live Yellow Fever Vaccine in Young and Middle-Age Donors
journal, October 2018

  • Davydov, Alexey N.; Obraztsova, Anna S.; Lebedin, Mikhail Y.
  • Frontiers in Immunology, Vol. 9
  • DOI: 10.3389/fimmu.2018.02309

HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites
journal, December 2002

  • Kwong, Peter D.; Doyle, Michael L.; Casper, David J.
  • Nature, Vol. 420, Issue 6916
  • DOI: 10.1038/nature01188