Evidence map›Paper›PMID 42288475›Full record

ArticleNature communications2026

Deciphering small sequence differences in T cell receptor-antigen pairing.

Yi Han, Yuqiu Yang, James Zhu, Farjana J Fattah, Mitchell S von Itzstein, Minying Zhang, Casey Bermack, Peixin Jiang, Shailbala Singh, Yanhua Tian and 28 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

38 authors.

Yi Han *Department of Bioinformatics & Comp Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Yuqiu Yang *Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0002-0975-1658
James ZhuDepartment of Bioinformatics & Comp Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Farjana J FattahHarold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
Mitchell S von ItzsteinDepartment of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0003-0530-3169
Minying ZhangDepartment of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Casey BermackDepartment of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Peixin JiangDepartment of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0009-0005-8033-1639
Shailbala SinghDepartment of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Yanhua TianDepartment of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0001-7095-8765
Yifei HuPeter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0009-0005-5709-4129
Yafang DengDepartment of Molecular Biology and Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Xiongbin KangDepartment of Bioinformatics & Comp Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Donghan M YangPeter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Jialiang LiuPeter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Yaming XueDepartment of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Chaoying LiangDepartment of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Indu RamanDepartment of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Chengsong ZhuDepartment of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0001-8872-9450
Olivia XiaoPeter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Jonathan E DowellDepartment of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Jade HomsiDepartment of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Sawsan RashdanDepartment of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Ke PanDepartment of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Shengjie YangPeter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Mary E GwinDepartment of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
David HsiehchenHarold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0001-9139-302X
Yvonne Gloria-McCutchenHarold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
Fangjiang WuPeter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0001-8812-8655
John V HeymachDepartment of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0001-9068-8942
Don GibbonsDepartment of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0003-2362-3094
Junzhou HuangComputer Science and Engineering, University of Texas at Arlington, Arlington, TX, USA.ORCID http://orcid.org/0000-0002-9548-1227
Chao ChengDepartment of Medicine, Baylor College of Medicine, Houston, TX, USA.ORCID http://orcid.org/0000-0002-5002-3417
Jianjun ZhangDepartment of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0001-7872-3477
Cassian YeeDepartment of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. CYee@mdanderson.org.ORCID http://orcid.org/0000-0002-4429-7307
Alexandre ReubenDepartment of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. AReuben@mdanderson.org.ORCID http://orcid.org/0000-0003-4510-0382
David E GerberHarold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA. David.Gerber@utsoutwestern.edu.ORCID http://orcid.org/0000-0002-7812-6741
Tao WangDepartment of Bioinformatics & Comp Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. twang10@mdanderson.org.ORCID http://orcid.org/0000-0002-4355-149X

Funding

Elucidating the Immune Suppressive Mechanism of SIGLEC-15 in the Tumor MicroenvironmentR01CA269898 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI JUN WANG · 2023 to 2026
$2.3M
Applying deep learning to predict T cell receptor binding specificity of neoantigens and response to checkpoint inhibitorsR01CA258584 · NCI · UT SOUTHWESTERN MEDICAL CENTER · PI WANG, TAO, WANG, XINLEI · 2021 to 2025
$1.4M
Machine learning for identifying antigen-antibody interactions from massive sequencing dataR01AI190103 · NIAID · UT SOUTHWESTERN MEDICAL CENTER · PI Junzhou Huang, JUN WANG · 2025 to 2026
$1.3M
TCR-antigen foundation model to empower TCR-based diagnostics and therapeuticsR01AI192499 · NIAID · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI David Eric Gerber, Jian Qiao · 2025 to 2026
$1.0M
Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas) RP230363Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID) R01AI190103NCI NIH HHS R01 CA258584NCI NIH HHS R01 CA269898NIAID NIH HHS R01 AI190103NIAID NIH HHS R01 AI192499U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) 5R01CA258584
6 · The paper itself

Abstract

T cells have important functions in development and disease processes through T cell receptor (TCR)-dependent activities. Many tools were developed to predict the binding between TCRs and antigens. However, one of the uncertainties is whether such tools can decipher how small changes in the TCRs or antigenic peptides contribute to binding. We develop a deep learning model, pMTnet-omni, which not only predicts the binding vs. non-binding of TCRs towards pMHCs, but also distinguishes the stronger vs. weaker binding of TCRs similar in sequence. We leverage this capability to interpret the biological rules that govern TCR-antigen pairing. This also enables pMTnet-omni to accurately predict variant TCRs with desired stronger or weaker binding to the antigen, in conjunction with a Lab-in-the-Loop (LiL) mechanism. We show that pMTnet-omni can also predict binding of TCRs towards similar pMHCs. Overall, we provide a flexible toolkit for research and translational applications involving antigens and TCRs.

Indexed as

AntigensReceptors, Antigen, T-CellAmino Acid SequenceHumansProtein BindingT-LymphocytesAntigensReceptors, Antigen, T-Cell

Identifiers

PMID42288475
PMCPMC13408770

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.