Evidence map›Paper›PMID 42054357›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2026

Deep mining of the human antibody repertoire identifies frequent and genetically diverse CDRH3 topologies targetable by vaccination.

Rumi Habib, Shahlo O Solieva, Zi Jie Lin, Sukanya Ghosh, Kelly Bayruns, Maya Singh, Colby J Agostino, Nicholas J Tursi, Kirsten J Sowers, Jinwei Huang and 29 more

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Trial
  2. Deletions in variable region 1 of the HIV envelope accelerate V3-glycan bNAb induction in SHIV-infected rhesus macaques.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  3. Article
  4. Nanoparticle Immunoadjuvant Complexes Augment Germinal Center Responses to Vaccination.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

39 authors.

Rumi Habib *Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Shahlo O Solieva *Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Zi Jie Lin *Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Sukanya Ghosh *Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Kelly BayrunsVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Maya SinghVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Colby J AgostinoVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.ORCID 0000-0002-1864-1848
Nicholas J TursiVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Kirsten J SowersDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
Jinwei HuangVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Ryan S RoarkDepartment of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
Mansi PurwarVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Younghoon ParkDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
Kasirajan AyyanathanDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
Hui LiDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
John W CareyDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
Amber KimVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Joyce ParkVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Madison E McCannaVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Ashwin N SkellyDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.ORCID 0000-0002-1565-3376
Neethu ChokkalingamVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Sinja KrieteVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Nicholas ShupinVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Alana HuynhVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Susanne WalkerVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Roopak SadeeshVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Niklas LaengerVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Jianqiu DuVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Jiayan CuiVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Ami PatelVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Amelia EscolanoVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Peter D KwongAaron Diamond AIDS Research Center and Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032.ORCID 0000-0003-3560-232X
Lawrence ShapiroAaron Diamond AIDS Research Center and Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032.
Gregory R BowmanDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.ORCID 0000-0002-2083-4892
Beatrice H HahnDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.ORCID 0000-0002-9400-9887
George M ShawDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
David B WeinerVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.
Jesper PallesenVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.ORCID 0000-0002-3270-1587
Daniel W KulpVaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104.

Funding

Vaccine and adjuvant Clinical GMP product development and DNA Technology platform enhancementsU19AI166916 · NIAID · WISTAR INSTITUTE · PI DAVID B. WEINER · 2023 to 2026
$24.0M
TRAINING PROGRAM IN BASIC CANCER RESEARCHT32CA009171 · NCI · WISTAR INSTITUTE · PI Alessandro Gardini · 1985 to 2026
$15.3M
TRAINING IN HIV PATHOGENESIST32AI007632 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI Frederic D Bushman, James L. Riley · 2000 to 2026
$10.6M
Optimizing glycan shield coverage, germline B cell receptor binding and epitope diversity of V2-apex targeted HIV-1 Env immunogensR37AI150590 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI Beatrice H Hahn · 2019 to 2026
$6.9M
HIV-1 Q23.17 Env: Engineering a novel immunogen to elicit broadly neutralizing antibodiesR01AI165080 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI GEORGE M SHAW · 2021 to 2026
$6.6M
Structural biology and molecular biophysics training programT32GM132039 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI Ben E. Black, Elizabeth Rhoades · 2019 to 2026
$3.3M
A New Cryo-Transmission Electron Microscope at Thomas Jefferson UniversityS10OD030457 · OD · THOMAS JEFFERSON UNIVERSITY · PI CINGOLANI, GINO · 2022 to 2022
$2.0M
HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) AI007632HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) AI165080HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) AI166916HHS | NIH | National Institute of General Medical Sciences (NIGMS) GM132039NCI NIH HHS T32 CA009171NIAID NIH HHS R01 AI165080NIAID NIH HHS R37 AI150590NIAID NIH HHS T32 AI007632NIAID NIH HHS U19 AI166916NIGMS NIH HHS T32 GM132039NIH HHS S10 OD030457
6 · The paper itself

Abstract

Germline targeting vaccination strategies against highly variable pathogens such as HIV aim to elicit broadly neutralizing antibodies (bnAbs) with particular immunogenetic or structural features. The V2 apex of the HIV Env protein is a promising target for a class of bnAbs that contain conserved structural motifs in the heavy chain complementarity determining region 3 (CDRH3). Here, we show that these structural motifs are targetable by vaccination by characterizing V2 apex "axe-like" CDRH3s in the human repertoire and developing immunogens capable of engaging them. We determined the frequency and diversity of axe-like CDRH3s in healthy human donors using a series of structural informatics approaches, finding these precursors in nearly 90% of donors. Axe-targeting immunogens based on the HIV Env Q23.17 bound axe-like precursors in cryo-electron microscopy structures, induced V2 apex-specific antibody responses in humanized mice, and induced axe-like heterologous neutralizing antibodies in rhesus macaques infected with a germline-targeted simian-HIV. These results illustrate a structure-guided immunoinformatic vaccine design paradigm that can be employed to elicit immunogenetically diverse yet structurally conserved classes of antibodies.

Indexed as

AIDS VaccinesAntibodies, NeutralizingComplementarity Determining Regionsenv Gene Products, Human Immunodeficiency VirusHIV AntibodiesAmino Acid SequenceAnimalsCryoelectron MicroscopyGenetic VariationHIV-1HIV InfectionsHumansMacaca mulattaMiceVaccinationAIDS VaccinesAntibodies, NeutralizingComplementarity Determining Regionsenv Gene Products, Human Immunodeficiency VirusHIV AntibodiesB cell repertoirebroadly neutralizing antibodiesHIVvaccines

Identifiers

PMID42054357
PMCPMC13143044

What Socratic holds

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Read underepoch 390

Registered trials

None linked

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 Socratic graph.