Evidence map›Paper›PMID 29973404›Full record

ArticleScience translational medicine2018

The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen.

Colin Havenar-Daughton, Anita Sarkar, Daniel W Kulp, Laura Toy, Xiaozhen Hu, Isaiah Deresa, Oleksandr Kalyuzhniy, Kirti Kaushik, Amit A Upadhyay, Sergey Menis and 13 more

Abstract read
In one paragraph

Article in Science translational medicine, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.

0numbers the graph read from it
0cells of the map it votes in
100citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

100 citing papers in PubMed.

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  15. Structural insights into VRC01-class bnAb precursors with diverse light chains elicited in the IAVI G001 human vaccine trial.Proceedings of the National Academy of Sciences of the United States of America · 2025
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40 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

23 authors.

Colin Havenar-DaughtonDivision of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. chavenar@lji.org shane@lji.org.ORCID 0000-0002-2880-3927
Anita SarkarCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.
Daniel W KulpCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.ORCID 0000-0002-0527-3804
Laura ToyDivision of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.ORCID 0000-0002-4636-2731
Xiaozhen HuCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.ORCID 0000-0003-3890-0533
Isaiah DeresaDivision of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
Oleksandr KalyuzhniyCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.ORCID 0000-0002-5273-1951
Kirti KaushikDivision of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
Amit A UpadhyayEmory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.ORCID 0000-0002-0952-4164
Sergey MenisCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.
Elise LandaisInternational AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.ORCID 0000-0002-8183-5565
Liwei CaoCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.
Jolene K DiedrichDepartment of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.ORCID 0000-0001-6489-4558
Sonu KumarCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.
Torben SchiffnerCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.
Samantha M ReissDivision of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.ORCID 0000-0001-5273-0898
Grégory SeumoisDivision of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.ORCID 0000-0002-8164-6852
John R YatesDepartment of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.ORCID 0000-0001-5267-1672
James C PaulsonCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.ORCID 0000-0003-4589-5322
Steven E BosingerEmory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.ORCID 0000-0002-2116-5061
Ian A WilsonCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.ORCID 0000-0002-6469-2419
William R SchiefCenter for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.ORCID 0000-0002-1120-0150
Shane CrottyDivision of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. chavenar@lji.org shane@lji.org.ORCID 0000-0002-6484-6262

Funding

Yerkes National Primate Research Center Role of type-I IFN in regulating COVID-19 induced inflammation and pathogenesisP51OD011132 · OD · EMORY UNIVERSITY · PI Joon Sup Lee · 2012 to 2026
$167.0M
Support Component D/Vaccine Discovery, Concept to ClinicUM1AI100663 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI BURTON, DENNIS R. · 2012 to 2018
$131.5M
Project 3 - Ex vivo immune profiling of dengue viruses and vaccinesU19AI118610 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI HARRIS, EVA · 2015 to 2021
$46.6M
B and T Cell Biology of Protection from and Eradication of SIV/SHIV Infection - Administrative SupplementUM1AI124436 · NIAID · EMORY UNIVERSITY · PI AMARA, RAMA RAO, HUNTER, ERIC · 2016 to 2021
$42.3M
Simultaneous antigen receptor repertoire profiling and single-cell transcriptomics in T and B lymphocytes from limited clinical samplesU24AI120134 · NIAID · EMORY UNIVERSITY · PI BOSINGER, STEVEN EDWARD · 2015 to 2024
$6.5M
Glycan dependent epitopes of HIV broadly neutralizing antibodiesR01AI113867 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI PAULSON, JAMES C, SCHIEF, WILLIAM R. · 2014 to 2018
$4.8M
Illumina HiSeq 2500 Sequencing SystemS10OD016262 · OD · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI RAO, ANJANA · 2013 to 2013
$600k
FACSAria II Cell SorterS10RR027366 · NCRR · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI CROFT, MICHAEL · 2011 to 2011
$514k
NCRR NIH HHS S10 RR027366NIAID NIH HHS R01 AI113867NIAID NIH HHS U19 AI118610NIAID NIH HHS U24 AI120134NIAID NIH HHS UM1 AI100663NIAID NIH HHS UM1 AI124436NIH HHS P51 OD011132NIH HHS S10 OD016262
6 · The paper itself

Abstract

Traditional vaccine development to prevent some of the worst current pandemic diseases has been unsuccessful so far. Germline-targeting immunogens have potential to prime protective antibodies (Abs) via more targeted immune responses. Success of germline-targeting vaccines in humans will depend on the composition of the human naive B cell repertoire, including the frequencies and affinities of epitope-specific B cells. However, the human naive B cell repertoire remains largely undefined. Assessment of antigen-specific human naive B cells among hundreds of millions of B cells from multiple donors may be used as pre-phase 1 ex vivo human testing to potentially forecast B cell and Ab responses to new vaccine designs. VRC01 is an HIV broadly neutralizing Ab (bnAb) against the envelope CD4-binding site (CD4bs). We characterized naive human B cells recognizing eOD-GT8, a germline-targeting HIV-1 vaccine candidate immunogen designed to prime VRC01-class Abs. Several distinct subclasses of VRC01-class naive B cells were identified, sharing sequence characteristics with inferred precursors of known bnAbs VRC01, VRC23, PCIN63, and N6. Multiple naive B cell clones exactly matched mature VRC01-class bnAb L-CDR3 sequences. Non-VRC01-class B cells were also characterized, revealing recurrent public light chain sequences. Unexpectedly, we also identified naive B cells related to the IOMA-class CD4bs bnAb. These different subclasses within the human repertoire had strong initial affinities (

Indexed as

AIDS VaccinesAmino Acid SequenceAntibodiesAntibodies, NeutralizingBinding SitesB-LymphocytesCD4 AntigensEpitopes, B-LymphocyteHIV-1HumansTissue DonorsAIDS VaccinesAntibodiesAntibodies, NeutralizingCD4 AntigensEpitopes, B-Lymphocyte

Identifiers

PMID29973404
PMCPMC6145074

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.