Evidence map›Paper›PMID 39824797›Full record

ArticleNature communications2025

Nr4a1 and Nr4a3 redundantly control clonal deletion and contribute to an anergy-like transcriptome in auto-reactive thymocytes to impose tolerance in mice.

Hailyn V Nielsen, Letitia Yang, James L Mueller, Alexander J Ritter, Ryosuke Hiwa, Irina Proekt, Elze Rackaityte, Dominik Aylard, Mansi Gupta, Christopher D Scharer and 3 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

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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

13 authors.

Hailyn V NielsenDivision of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, CA, 94143, USA.ORCID http://orcid.org/0000-0002-0843-0617
Letitia YangBiomedical Sciences Graduate Program, University of California, San Francisco, CA, 94143, USA.
James L MuellerDivision of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, CA, 94143, USA.
Alexander J RitterDivision of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, CA, 94143, USA.ORCID http://orcid.org/0000-0002-1998-7357
Ryosuke HiwaDepartment of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.ORCID http://orcid.org/0000-0001-6968-5712
Irina ProektDiabetes Center, Department of Medicine, University of California, San Francisco, CA, 94143, USA.ORCID http://orcid.org/0000-0003-3818-1102
Elze RackaityteDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA, 94143, USA.ORCID http://orcid.org/0000-0003-3889-8082
Dominik AylardDepartment of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA.
Mansi GuptaDepartment of Microbiology and Immunology, Emory University, Atlanta, GA, 30322, USA.ORCID http://orcid.org/0009-0005-5475-3838
Christopher D ScharerDepartment of Microbiology and Immunology, Emory University, Atlanta, GA, 30322, USA.ORCID http://orcid.org/0000-0001-7716-8504
Mark S AndersonDiabetes Center, Department of Medicine, University of California, San Francisco, CA, 94143, USA.ORCID http://orcid.org/0000-0002-3093-4758
Byron B Au-YeungDivision of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA, 30322, USA. byron.au-yeung@emory.edu.ORCID http://orcid.org/0000-0002-6446-9102
Julie ZikhermanDivision of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, CA, 94143, USA. julie.zikherman@ucsf.edu.ORCID http://orcid.org/0000-0002-0873-192X

Funding

UCSF IRACDA Scholars ProgramK12GM081266 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Raymond M. Esquerra, HOLLY A. INGRAHAM · 2007 to 2026
$19.4M
Regulation of CD4 T cell tolerance by the NR4A family of nuclear receptorsR01AI165706 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI JULIE ZIKHERMAN · 2022 to 2026
$3.0M
Academic Rheumatology and Clinical ImmunologyT32AR079068 · NIAMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Jinoos Yazdany, JULIE ZIKHERMAN · 2021 to 2026
$2.5M
Nuclear Receptors in B Cell Tolerance and Humoral Immune ResponsesR01AI148487 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ZIKHERMAN, JULIE · 2020 to 2024
$2.0M
The cell and molecular mechanisms underlying CD28 costimulationR01AI114575 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ZIKHERMAN, JULIE · 2024 to 2025
$795k
NIAID NIH HHS R01 AI114575NIAID NIH HHS R01 AI148487NIAID NIH HHS R01 AI165706NIAMS NIH HHS T32 AR079068NIGMS NIH HHS K12 GM081266U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) R01AI165706
6 · The paper itself

Abstract

The Nr4a nuclear hormone receptors are transcriptionally upregulated in response to antigen recognition by the T cell receptor (TCR) in the thymus and are implicated in clonal deletion, but the mechanisms by which they operate are not clear. Moreover, their role in central tolerance is obscured by redundancy among the Nr4a family members and by their reported functions in Treg generation and maintenance. Here we take advantage of competitive bone marrow chimeras and the OT-II/RIPmOVA model to show that Nr4a1 and Nr4a3 are essential for the upregulation of Bcl2l11/BIM and thymic clonal deletion by self-antigen. Importantly, thymocytes lacking Nr4a1/3 acquire an anergy-like signature after escaping clonal deletion and Treg lineage diversion. We further show that the Nr4a family helps mediate a broad transcriptional program in self-reactive thymocytes that resembles anergy and may operate at the margins of canonical thymic tolerance mechanisms to restrain self-reactive T cells after thymic egress.

Indexed as

Clonal AnergyClonal DeletionDNA-Binding ProteinsImmune ToleranceNuclear Receptor Subfamily 4, Group A, Member 1Receptors, SteroidReceptors, Thyroid HormoneThymocytesTranscriptomeAnimalsMiceMice, Inbred C57BLMice, KnockoutNerve Tissue ProteinsThymus GlandT-Lymphocytes, RegulatoryDNA-Binding ProteinsNerve Tissue ProteinsNr4a1 protein, mouseNr4a3 protein, mouseNuclear Receptor Subfamily 4, Group A, Member 1Receptors, SteroidReceptors, Thyroid Hormone

Identifiers

PMID39824797
PMCPMC11742425

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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.