Evidence map›Paper›PMID 39672954›Full record

ArticleNature biotechnology2025

Targeting peptide antigens using a multiallelic MHC I-binding system.

Haotian Du, Leena Mallik, Daniel Hwang, Yi Sun, Chengzi Kaku, Daniel Hoces, Shirley M Sun, Reem Ghinnagow, Stephen D Carro, Hoang Anh T Phan and 19 more

Abstract read
In one paragraph

Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing 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

23 citing papers in PubMed.

  1. Article
  2. Article
  3. Discovery of TCR-like antibodies to the KRAS G12D neoantigen via in silico-in vitro workflow.Molecular therapy : the journal of the American Society of Gene Therapy · 2026
    Article
  4. Article
  5. Review
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  8. Article
  9. Article
  10. Review
  11. Article
  12. Antigen-conjugated scaffolds enable sustained delivery of antigen and enrichment of antigen-specific T-cells.Journal of controlled release : official journal of the Controlled Release Society · 2026
    Article
  13. Article
  14. Computational Design of a TCR-like Human VComputational and structural biotechnology journal · 2026
    Article
  15. Article
  16. Article
  17. CIMT 2025: Report on the 22Human vaccines & immunotherapeutics · 2025
    Article
  18. Article
  19. Molecular Insights into Tumor Immunogenicity.Current issues in molecular biology · 2025
    Article
  20. Article
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

29 authors.

Haotian DuDepartment of Chemistry, Stanford University, Stanford, CA, USA.
Leena MallikCenter for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Daniel HwangCenter for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Yi SunCenter for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Chengzi KakuDepartment of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA.
Daniel HocesDepartment of Bioengineering, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-1451-5166
Shirley M SunCenter for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.ORCID http://orcid.org/0009-0007-6764-5750
Reem GhinnagowDepartment of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Stephen D CarroDepartment of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Hoang Anh T PhanCenter for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0001-6488-0404
Sagar GuptaCenter for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Wyatt BlacksonDepartment of Chemical Engineering, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-2452-5915
Hyejin LeeDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Christian A ChoeDepartment of Bioengineering, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-8871-9682
Devin DershDepartment of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-3763-4192
Jingjia LiuDepartment of Bioengineering, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-6038-593X
Braxton BellDepartment of Chemistry, Stanford University, Stanford, CA, USA.
Hongli YangDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Georgia F PapadakiCenter for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Michael C YoungCenter for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-8420-2149
Emily ZhouDepartment of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA.
Gina El NesrBiophysics Program, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-4857-9464
Kimia Dasteh GoliCenter for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Laurence C EisenlohrDepartment of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Andy J MinnDepartment of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Rogelio A Hernandez-LopezDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Joseph G JardineDepartment of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA.
Nikolaos G SgourakisCenter for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Nikolaos.Sgourakis@Pennmedicine.upenn.edu.
Po-Ssu HuangDepartment of Chemistry, Stanford University, Stanford, CA, USA. possu@stanford.edu.ORCID http://orcid.org/0000-0002-7948-2895

Funding

Human Pancreas Analysis Program for Type 1 Diabetes - HPAP-T1DU01DK112217 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI MARK A. ATKINSON, KLAUS H KAESTNER · 2021 to 2026
$46.8M
X-ray Scattering Technology CoreP30GM133893 · NIGMS · BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB · PI Sean McSweeney · 2019 to 2026
$38.6M
cGMP Manufacture, Fill-Finish, Release, Analytical and Stability Testing and Stability Program of a Nanoparticle Based HIV Envelope Vaccine75N93022D00005 · NIAID · INTERNATIONAL AIDS VACCINE INITIATIVE · PI HASSELL, THOMAS · 2022 to 2025
$8.0M
Task Area A shall encompass annual follow-up of cohort members, clinical events investigations, study operations, and data analysis and manuscript writing. If implemented, Task A.1 will provide fundin75N92020D00005 · NHLBI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI WATSON, KAROL E · 2020 to 2025
$5.1M
An integrative structural biology approach to understanding metabolite recognition by cellular receptorsR35GM125034 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI SGOURAKIS, NIKOLAOS · 2017 to 2025
$4.7M
Molecular mechanism of antigen editing by Class-I MHC ChaperonesR01AI143997 · NIAID · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI SGOURAKIS, NIKOLAOS · 2019 to 2023
$4.0M
Graduate Training Program in BiotechnologyT32GM141819 · NIGMS · STANFORD UNIVERSITY · PI Eric Andrew Appel, Fan Yang · 2021 to 2026
$1.9M
American Cancer Society (American Cancer Society, Inc.) ACS134055-IRG-218NHLBI NIH HHS 75N92020D00005NIAID NIH HHS 75N93022D00005NIAID NIH HHS 75N93023D00005NIAID NIH HHS R01 AI143997NIDA NIH HHS 75N95020D00005NIDDK NIH HHS U01 DK112217NIGMS NIH HHS P30 GM133893NIGMS NIH HHS R35 GM125034NIGMS NIH HHS T32 GM141819ORFDO NIH HHS 75N99020D00005U.S. Department of Health & Human Services | National Institutes of Health (NIH) T32GM141819
6 · The paper itself

Abstract

Identifying highly specific T cell receptors (TCRs) or antibodies against epitopic peptides presented by class I major histocompatibility complex (MHC I) proteins remains a bottleneck in the development of targeted therapeutics. Here, we introduce targeted recognition of antigen-MHC complex reporter for MHC I (TRACeR-I), a generalizable platform for targeting peptides on polymorphic HLA-A*, HLA-B* and HLA-C* allotypes while overcoming the cross-reactivity challenges of TCRs. Our TRACeR-MHC I co-crystal structure reveals a unique antigen recognition mechanism, with TRACeR forming extensive contacts across the entire peptide length to confer single-residue specificity at the accessible positions. We demonstrate rapid screening of TRACeR-I against a panel of disease-relevant HLAs with peptides derived from human viruses (human immunodeficiency virus, Epstein-Barr virus and severe acute respiratory syndrome coronavirus 2), and oncoproteins (Kirsten rat sarcoma virus, paired-like homeobox 2b and New York esophageal squamous cell carcinoma 1). TRACeR-based bispecific T cell engagers and chimeric antigen receptor T cells exhibit on-target killing of tumor cells with high efficacy in the low nanomolar range. Our platform empowers the development of broadly applicable MHC I-targeting molecules for research, diagnostic and therapeutic applications.

Indexed as

Histocompatibility Antigens Class IPeptidesAllelesHumansReceptors, Antigen, T-CellT-LymphocytesHistocompatibility Antigens Class IPeptidesReceptors, Antigen, T-Cell

Identifiers

PMID39672954
PMCPMC12163099

What OpenQuestion holds

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Registered trials

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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.