Evidence map›Paper›PMID 34937926›Full record

ArticleNature immunology2022

TET deficiency perturbs mature B cell homeostasis and promotes oncogenesis associated with accumulation of G-quadruplex and R-loop structures.

Vipul Shukla, Daniela Samaniego-Castruita, Zhen Dong, Edahí González-Avalos, Qingqing Yan, Kavitha Sarma, Anjana Rao

Open access · greenAbstract read
In one paragraph

Article in Nature immunology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
53citing papers in PubMed, 1 pooled it
6.2field-weighted citation impact, top 2% 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

53 citing papers in PubMed, 1 synthesis or guideline pooled it, 86 citations in OpenAlex.

  1. Pooled it
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  7. CTCF directly binds G-quadruplex structures to regulate genome topology and gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2026
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  19. Mechanisms underlining R-loop biology and implications for human disease.Frontiers in cell and developmental biology · 2025
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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

7 authors at 3 institutions in 1 country.

Vipul Shukla *Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-1422-5182
Daniela Samaniego-Castruita *Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6082-6603
Zhen DongDivision of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
Edahí González-AvalosDivision of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
Qingqing YanGene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA.
Kavitha SarmaGene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA.
Anjana RaoDivision of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA. arao@lji.org.ORCID http://orcid.org/0000-0002-1870-1775
La Jolla Institute for Immunology · USThe Wistar Institute · USNorthwestern University · US

Funding

Tumor Microenvironment and MetastasisP30CA010815 · NCI · WISTAR INSTITUTE · PI Dario C Altieri · 1985 to 2026
$75.9M
The TET-DNMT-ASXL1-OGT axis: relevance to clonal hematopoiesis, heterochromatin integrity and cancerR35CA210043 · NCI · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI Anjana Rao · 2016 to 2026
$10.6M
NFAT, bZIP proteins, and transcriptional programs in lymphocytesR01AI109842 · NIAID · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI Patrick Hogan, Anjana Rao · 2014 to 2026
$8.6M
Investigating the role of TET deficiency in promoting T cell expansion and inflammationR01AI128589 · NIAID · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI RAO, ANJANA · 2017 to 2025
$5.3M
Epigenetic regulation through the formation and resolution of R loopsDP2NS105576 · NINDS · WISTAR INSTITUTE · PI SARMA, KAVITHA · 2017 to 2017
$2.9M
NovaSeq5000 High Throughput SequencerS10OD025052 · OD · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI SEUMOIS, GREGORY · 2018 to 2018
$832k
Illumina HiSeq 2500 Sequencing SystemS10OD016262 · OD · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI RAO, ANJANA · 2013 to 2013
$600k
FACSAria II Cell SorterS10RR027366 · NCRR · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI CROFT, MICHAEL · 2011 to 2011
$514k
Tumor suppressive functions of TET proteins in B cell malignancies: role of G-quadruplex structuresK99CA248835 · NCI · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI SHUKLA, VIPUL · 2020 to 2021
$289k
NCI NIH HHS K99 CA248835NCI NIH HHS P30 CA010815NCI NIH HHS R35 CA210043NCRR NIH HHS S10 RR027366NIAID NIH HHS R01 AI109842NIAID NIH HHS R01 AI128589NIH HHS S10 OD016262NIH HHS S10 OD025052NINDS NIH HHS DP2 NS105576
6 · The paper itself

Abstract

Enzymes of the TET family are methylcytosine dioxygenases that undergo frequent mutational or functional inactivation in human cancers. Recurrent loss-of-function mutations in TET proteins are frequent in human diffuse large B cell lymphoma (DLBCL). Here, we investigate the role of TET proteins in B cell homeostasis and development of B cell lymphomas with features of DLBCL. We show that deletion of Tet2 and Tet3 genes in mature B cells in mice perturbs B cell homeostasis and results in spontaneous development of germinal center (GC)-derived B cell lymphomas with increased G-quadruplexes and R-loops. At a genome-wide level, G-quadruplexes and R-loops were associated with increased DNA double-strand breaks (DSBs) at immunoglobulin switch regions. Deletion of the DNA methyltransferase DNMT1 in TET-deficient B cells prevented expansion of GC B cells, diminished the accumulation of G-quadruplexes and R-loops and delayed B lymphoma development, consistent with the opposing functions of DNMT and TET enzymes in DNA methylation and demethylation. Clustered regularly interspaced short palindromic repeats (CRISPR)-mediated depletion of nucleases and helicases that regulate G-quadruplexes and R-loops decreased the viability of TET-deficient B cells. Our studies suggest a molecular mechanism by which TET loss of function might predispose to the development of B cell malignancies.

Indexed as

AnimalsB-LymphocytesCarcinogenesisCell DifferentiationDioxygenasesDNA-Binding ProteinsDNA MethylationGerminal CenterG-QuadruplexesHomeostasisMiceMice, Inbred C57BLR-Loop StructuresDioxygenasesDNA-Binding Proteins

Identifiers

PMID34937926
PMCPMC8772520
OpenAlexW4200575273

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

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.