Evidence map›Paper›PMID 40938954›Full record

ArticleScience immunology2025

Single-cell multiomics identifies Tcf1 and Lef1 as key initiators of early thymic progenitor fate.

Xin Zhao, Shengen Shawn Hu, Wen-Han Lee, Johannes L Zakrzewski, Qing-Sheng Mi, Rachel K Rosenstein, Chongzhi Zang, Xiaoke Ma, Hai-Hui Xue

Abstract read
In one paragraph

Article in Science immunology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Exhausted CD8Nature immunology · 2026
    Article
  2. Article
  3. The LEF1-LAG3 axis regulates CD4Parasites & vectors · 2026
    Article
  4. Review
  5. Article
  6. 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

9 authors.

Xin ZhaoZhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.ORCID 0000-0002-9303-7675
Shengen Shawn HuDepartment of Genome Sciences, University of Virginia, Charlottesville, VA 22908, USA.ORCID 0000-0002-9691-7344
Wen-Han LeeCenter for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA.ORCID 0000-0001-9450-8072
Johannes L ZakrzewskiCenter for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA.ORCID 0000-0002-5323-0630
Qing-Sheng MiCenter for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI 48202, USA.ORCID 0000-0002-1411-6827
Rachel K RosensteinCenter for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA.ORCID 0000-0001-6375-6129
Chongzhi ZangDepartment of Genome Sciences, University of Virginia, Charlottesville, VA 22908, USA.ORCID 0000-0003-4812-3627
Xiaoke MaSchool of Computer Science and Technology, Xidian University, Xi'an, Shaanxi 215123, China.ORCID 0000-0002-5604-7137
Hai-Hui XueCenter for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA.ORCID 0000-0002-9163-7669

Funding

Tissue Culture Shared ResourceP30CA051008 · NCI · GEORGETOWN UNIVERSITY · PI MARCUS S NOEL · 1990 to 2026
$71.5M
Tcf/Lef-b-catenin in T cell identity and cancerR01AI112579 · NIAID · UNIVERSITY OF IOWA · PI Hai-Hui Xue · 2015 to 2026
$5.4M
Tcf/Lef and B-catenin pathway in follicular helper T cellsR01AI121080 · NIAID · UNIVERSITY OF IOWA · PI Hai-Hui Xue · 2016 to 2026
$4.6M
Harnessing the thymus for long-term tumor control with hematopoietic stem cell-derived naive CAR T cellsR37CA250661 · NCI · HACKENSACK UNIVERSITY MEDICAL CENTER · PI Johannes Zakrzewski · 2022 to 2026
$2.7M
Ezh2 regulates follicular helper T cell differentiationR01AI139874 · NIAID · UNIVERSITY OF IOWA · PI PENG, WEIQUN, XUE, HAI-HUI · 2018 to 2022
$2.4M
ID3 regulation of tissue-infiltrating T cells mediating graft-versus-host disease and leukemia rejectionR01CA290808 · NCI · HACKENSACK UNIVERSITY MEDICAL CENTER · PI Hai-Hui Xue, YI ZHANG · 2024 to 2026
$2.2M
BLRD VA I01 BX005771NCI NIH HHS P30 CA051008NCI NIH HHS R01 CA290808NCI NIH HHS R37 CA250661NIAID NIH HHS R01 AI112579NIAID NIH HHS R01 AI121080NIAID NIH HHS R01 AI139874
6 · The paper itself

Abstract

Bone marrow-derived multipotent hematopoietic progenitors seed the thymus and generate early thymic progenitors (ETPs). However, the factors governing ETP formation remain poorly defined. Using single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), we dissected the heterogeneity of transcriptomic and chromatin accessibility landscapes in murine ETPs. Whereas Tcf1

Indexed as

Hepatocyte Nuclear Factor 1-alphaLymphoid Enhancer-Binding Factor 1Thymus GlandAnimalsCell DifferentiationCell LineageMiceMice, Inbred C57BLMice, KnockoutMultiomicsSingle-Cell AnalysisThymocytesHepatocyte Nuclear Factor 1-alphaHnf1a protein, mouseLef1 protein, mouseLymphoid Enhancer-Binding Factor 1

Identifiers

PMID40938954
PMCPMC12700322

What OpenQuestion holds

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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 OpenQuestion graph.