Evidence map›Paper›PMID 29466756›Full record

ArticleImmunity2018

Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells.

John L Johnson, Georgios Georgakilas, Jelena Petrovic, Makoto Kurachi, Stanley Cai, Christelle Harly, Warren S Pear, Avinash Bhandoola, E John Wherry, Golnaz Vahedi

Open access · bronzeAbstract read
In one paragraph

Article in Immunity, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.

0numbers the graph read from it
0cells of the map it votes in
139citing papers in PubMed
9.9field-weighted citation impact, top 1% of its field
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

139 citing papers in PubMed, 223 citations in OpenAlex.

  1. Trial
  2. Single-cell epigenomics of colorectal cancer.Experimental & molecular medicine · 2026
    Review
  3. Article
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  5. Article
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  12. Pre-division TCF1 drop determines long-term CD8 T cell fates.bioRxiv : the preprint server for biology · 2025
    Article
  13. Article
  14. Article
  15. Article
  16. Biomolecular condensates in immune cell fate.Nature reviews. Immunology · 2025
    Review
  17. Article
  18. Article
  19. Review
  20. Article

79 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors at 3 institutions in 1 country.

John L JohnsonDepartment of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Georgios GeorgakilasDepartment of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Jelena PetrovicInstitute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Makoto KurachiInstitute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Stanley CaiDepartment of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Christelle HarlyNational Cancer Institute, National Institutes of Health, Bethesda, MD 20184, USA.
Warren S PearInstitute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Avinash BhandoolaNational Cancer Institute, National Institutes of Health, Bethesda, MD 20184, USA.
E John WherryInstitute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Golnaz VahediDepartment of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: vahedi@pennmedicine.upenn.edu.
University of Pennsylvania · USNational Cancer Institute · USNational Institutes of Health · US

Funding

Virology CoreU19AI082630 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI Michela Locci · 2009 to 2026
$48.1M
Synergies among inhibitory receptors in tolerance, cancer & antiviral immunityP01AI108545 · NIAID · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Dario AA Vignali · 2015 to 2026
$30.8M
T cell Development and RegenerationZIABC011633 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI BHANDOOLA, AVINASH · 2015 to 2025
$20.5M
Sequencing and Viral Evolution CoreU19AI117950 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI WHERRY, E. JOHN · 2015 to 2019
$12.0M
Protein CoreP01CA119070 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI BLACKLOW, STEPHEN C. · 2006 to 2016
$10.3M
P3: Chemokine-Mediated T Cell Trafficking in HIV Transmission and Immune ResponseP01AI112521 · NIAID · HARVARD MEDICAL SCHOOL · PI LUSTER, ANDREW · 2014 to 2018
$9.8M
Notch Regulation of Hematopoietic Cell FatesR01AI047833 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI JORDAN, MARTHA S, PEAR, WARREN S · 2000 to 2022
$7.4M
Testing the role of BATF as a pioneer transcription factor in effector T cellsR01AI115712 · NIAID · DANA-FARBER CANCER INST · PI KADOCH, CIGALL, WHERRY, E. JOHN · 2015 to 2019
$2.9M
Targeting the Notch:Myc axis in leukemia/lymphomaR01CA215518 · NCI · UNIVERSITY OF PENNSYLVANIA · PI PEAR, WARREN S · 2018 to 2022
$2.3M
Cellular and transcriptional control of exhausted CD8 T cells lineage dynamicsR01AI105343 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI WHERRY, E. JOHN · 2014 to 2017
$1.6M
Defining the role of microRNAs in CD8 T cell exhaustionR21AI117718 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI WHERRY, E. JOHN · 2015 to 2016
$440k
Super-enhancer structure defines a signature of inflammatory bowel disease (IBD)K22AI112570 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI VAHEDI, GOLNAZ · 2015 to 2016
$266k
NCI NIH HHS P01 CA119070NCI NIH HHS R01 CA215518NIAID NIH HHS K22 AI112570NIAID NIH HHS P01 AI108545NIAID NIH HHS P01 AI112521NIAID NIH HHS R01 AI047833NIAID NIH HHS R01 AI105343NIAID NIH HHS R01 AI115712NIAID NIH HHS R21 AI117718NIAID NIH HHS U19 AI082630NIAID NIH HHS U19 AI117950
6 · The paper itself

Abstract

T cell development is orchestrated by transcription factors that regulate the expression of genes initially buried within inaccessible chromatin, but the transcription factors that establish the regulatory landscape of the T cell lineage remain unknown. Profiling chromatin accessibility at eight stages of T cell development revealed the selective enrichment of TCF-1 at genomic regions that became accessible at the earliest stages of development. TCF-1 was further required for the accessibility of these regulatory elements and at the single-cell level, it dictated a coordinate opening of chromatin in T cells. TCF-1 expression in fibroblasts generated de novo chromatin accessibility even at chromatin regions with repressive marks, inducing the expression of T cell-restricted genes. These results indicate that a mechanism by which TCF-1 controls T cell fate is through its widespread ability to target silent chromatin and establish the epigenetic identity of T cells.

Indexed as

Cell LineageEpigenomicsAnimalsChromatinChromatin Assembly and DisassemblyFibroblastsHepatocyte Nuclear Factor 1-alphaMiceNIH 3T3 CellsT Cell Transcription Factor 1T-LymphocytesTranscription, GeneticChromatinHepatocyte Nuclear Factor 1-alphaHnf1a protein, mouseT Cell Transcription Factor 1chromatin accessibilityepigeneticsLineage-determining transcription factornucleosomesrepressed chromatinreprogrammingsingle-cell epigenomicsT cell developmentTCF-1

Identifiers

PMID29466756
PMCPMC5824646
OpenAlexW2788726131

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.