Evidence map›Paper›PMID 40106578›Full record

ArticleScience translational medicine2025

The T cell receptor landscape of childhood brain tumors.

Itay Raphael, Zujian Xiong, Chaim T Sneiderman, Rebecca A Raphael, Moshe Mash, Lance Schwegman, Sydney A Jackson, Casey O'Brien, Kevin J Anderson, ReidAnn E Sever and 23 more

Abstract read
In one paragraph

Article in Science translational medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. 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

33 authors.

Itay RaphaelDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.ORCID 0000-0002-7369-2752
Zujian XiongDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.ORCID 0000-0003-2943-1931
Chaim T SneidermanDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
Rebecca A RaphaelDepartment of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.ORCID 0009-0004-6869-7382
Moshe MashRobotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA.ORCID 0000-0002-1017-4608
Lance SchwegmanDepartment of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA.
Sydney A JacksonDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
Casey O'BrienDivision of Health Informatics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
Kevin J AndersonDivision of Health Informatics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.ORCID 0009-0006-6749-3999
ReidAnn E SeverDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
Liam D HendrikseArthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.ORCID 0000-0002-0253-8512
Sarah R VinczeDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
Aaron DiazDepartment of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
James FelkerPediatric Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.ORCID 0000-0003-4585-8126
Javad NazarianDepartment of Pediatrics, University of Zurich, 8001 Zurich, Switzerland.ORCID 0000-0002-1951-9828
Yael Nechemia-ArbelyDepartment of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.ORCID 0000-0001-5753-5485
Baoli HuDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.ORCID 0000-0002-2737-6871
Udai S KammulaUPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.ORCID 0000-0001-6894-4356
Sameer AgnihotriDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.ORCID 0000-0001-6584-3795
Jeremy N RichUPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.ORCID 0000-0001-7845-5302
Alberto BroniscerPediatric Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.
Jan DrappatzNeuro-oncology Program, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.
Taylor J AbelDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
Shikhar UttamDepartment of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.ORCID 0000-0002-0897-2918
Eugene I HwangDepartment of Pediatrics, Division of Oncology, Children's National Hospital, Washington, DC 20010, USA.ORCID 0000-0002-3923-1135
Thomas M PearceDivision of Neuropathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.ORCID 0000-0002-5712-9492
Michael D TaylorArthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.ORCID 0000-0001-7009-3466
Michal NisnboymDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
Thomas G ForsthuberDepartment of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA.
Ian F PollackDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.ORCID 0000-0003-1765-357X
Maria ChikinaDepartment of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.ORCID 0000-0003-2550-5403
Dhivyaa RajasundaramDivision of Health Informatics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.ORCID 0000-0001-7417-8002
Gary KohanbashDepartment of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.ORCID 0000-0002-3953-8022

Funding

The role of TNFR2 in ameliorating progressive encephalomyelitisR01NS117742 · NINDS · UNIVERSITY OF TEXAS SAN ANTONIO · PI FORSTHUBER, THOMAS G. · 2021 to 2025
$1.8M
Peptide vaccine immunotherapy for children with recurrent low-grade astrocytomasR01CA187219 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI POLLACK, IAN F. · 2016 to 2020
$1.8M
UTSA ESTEEMED ProgramR25EB027605 · NIBIB · UNIVERSITY OF TEXAS SAN ANTONIO · PI ABU-LAIL, NEHAL IBRAHIM · 2019 to 2024
$1.6M
MARC at the University of Texas at San AntonioT34GM145507 · NIGMS · UNIVERSITY OF TEXAS SAN ANTONIO · PI BAREA-RODRIGUEZ, EDWIN J, CASSILL, AARON · 2022 to 2024
$1.5M
Peptide vaccine-based immunotherapy for children with recurrent ependymomas.R01CA174858 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI POLLACK, IAN F. · 2013 to 2015
$945k
High-Throughput Computing for Genomics and Bioinformatics ResearchS10OD028483 · OD · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI LEE, ADRIAN V · 2021 to 2021
$574k
NCI NIH HHS R01 CA174858NCI NIH HHS R01 CA187219NIBIB NIH HHS R25 EB027605NIGMS NIH HHS T34 GM145507NIH HHS S10 OD028483NINDS NIH HHS R01 NS117742
6 · The paper itself

Abstract

The diverse T cell receptor (TCR) repertoire confers the ability to recognize an almost unlimited array of antigens. Characterization of antigen specificity of tumor-infiltrating lymphocytes (TILs) is key for understanding antitumor immunity and for guiding the development of effective immunotherapies. Here, we report a large-scale comprehensive examination of the TCR landscape of TILs across the spectrum of pediatric brain tumors, the leading cause of cancer-related mortality in children. We show that a T cell clonality index can inform patient prognosis, where more clonality is associated with more favorable outcomes. Moreover, TCR similarity groups' assessment revealed patient clusters with defined human leukocyte antigen associations. Computational analysis of these clusters identified putative tumor antigens and peptides as targets for antitumor T cell immunity, which were functionally validated by T cell stimulation assays in vitro. Together, this study presents a framework for tumor antigen prediction based on in situ and in silico TIL TCR analyses. We propose that TCR-based investigations should inform tumor classification and precision immunotherapy development.

Indexed as

Brain NeoplasmsReceptors, Antigen, T-CellAntigens, NeoplasmChildChild, PreschoolFemaleHumansLymphocytes, Tumor-InfiltratingMaleAntigens, NeoplasmReceptors, Antigen, T-Cell

Identifiers

PMID40106578
PMCPMC12360399

What Socratic 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 Socratic graph.