Evidence map›Paper›PMID 33664368›Full record

ArticleScientific reports2021

Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL).

Timothy I Shaw, Li Dong, Liqing Tian, Chenxi Qian, Yu Liu, Bensheng Ju, Anthony High, Kanisha Kavdia, Vishwajeeth R Pagala, Bridget Shaner and 14 more

Open access · goldAbstract read
In one paragraph

Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed, 1 pooled it
0.9field-weighted citation impact, top 28% 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

10 citing papers in PubMed, 1 synthesis or guideline pooled it, 12 citations in OpenAlex.

  1. Pooled it
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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

24 authors at 3 institutions in 1 country.

Timothy I Shaw *Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA.
Li Dong *Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA.
Liqing TianDepartment of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA.
Chenxi QianDepartment of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA.
Yu LiuDepartment of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA.
Bensheng JuDepartment of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA.
Anthony HighCenter for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, USA.
Kanisha KavdiaCenter for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, USA.
Vishwajeeth R PagalaCenter for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, USA.
Bridget ShanerDepartment of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA.
Deqing PeiDepartment of Biostatistics, St Jude Children's Research Hospital, Memphis, USA.
John EastonDepartment of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA.
Laura J JankeDepartment of Pathology, St Jude Children's Research Hospital, Memphis, USA.
Shaina N PorterDepartment of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, USA.
Xiaotu MaDepartment of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA.
Cheng ChengDepartment of Biostatistics, St Jude Children's Research Hospital, Memphis, USA.
Shondra M Pruett-MillerDepartment of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, USA.
John ChoiDepartment of Pathology, St Jude Children's Research Hospital, Memphis, USA.
Jiyang YuDepartment of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA.
Junmin PengCenter for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, USA.
Wei GuDepartment of Pathology and Cell Biology and Institute for Cancer Genetics, Columbia University, New York, USA.
A Thomas LookDepartment of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02216, USA.
James R DowningDepartment of Pathology, St Jude Children's Research Hospital, Memphis, USA.
Jinghui ZhangDepartment of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS321, Memphis, TN, 38105, USA. jinghui.zhang@stjude.org.
St. Jude Children's Research Hospital · USColumbia University · USHarvard University · US

Funding

Mechanisms and Vulnerabilities of Aberrant Transcriptional Enhancers in CancerR35CA210064 · NCI · DANA-FARBER CANCER INST · PI LOOK, A. THOMAS · 2016 to 2022
$7.3M
Discovery of Somatic Noncoding Variants that Serve as Drivers in Pediatric CancersR01CA216391 · NCI · ST. JUDE CHILDREN'S RESEARCH HOSPITAL · PI ZHANG, JINGHUI · 2018 to 2022
$2.8M
Intracellular and Intercellular Network Rewiring and Hidden Driver Inference from Single-Cell DataR01GM134382 · NIGMS · ST. JUDE CHILDREN'S RESEARCH HOSPITAL · PI YU, JIYANG · 2019 to 2023
$1.7M
NCI NIH HHS R01 CA216391NCI NIH HHS R35 CA210064NIGMS NIH HHS R01 GM134382
6 · The paper itself

Abstract

USP7, which encodes a deubiquitylating enzyme, is among the most frequently mutated genes in pediatric T-ALL, with somatic heterozygous loss-of-function mutations (haploinsufficiency) predominantly affecting the subgroup that has aberrant TAL1 oncogene activation. Network analysis of > 200 T-ALL transcriptomes linked USP7 haploinsufficiency with decreased activities of E-proteins. E-proteins are also negatively regulated by TAL1, leading to concerted down-regulation of E-protein target genes involved in T-cell development. In T-ALL cell lines, we showed the physical interaction of USP7 with E-proteins and TAL1 by mass spectrometry and ChIP-seq. Haploinsufficient but not complete CRISPR knock-out of USP7 showed accelerated cell growth and validated transcriptional down-regulation of E-protein targets. Our study unveiled the synergistic effect of USP7 haploinsufficiency with aberrant TAL1 activation on T-ALL, implicating USP7 as a haploinsufficient tumor suppressor in T-ALL. Our findings caution against a universal oncogene designation for USP7 while emphasizing the dosage-dependent consequences of USP7 inhibitors currently under development as potential cancer therapeutics.

Indexed as

Cell LineageCell Line, TumorCell ProliferationCRISPR-Cas SystemsGene Expression Regulation, LeukemicHaploinsufficiencyHumansOncogenesPediatricsPrecursor T-Cell Lymphoblastic Leukemia-LymphomaT-Cell Acute Lymphocytic Leukemia Protein 1Transcriptional ActivationUbiquitin-Specific Peptidase 7TAL1 protein, humanT-Cell Acute Lymphocytic Leukemia Protein 1Ubiquitin-Specific Peptidase 7USP7 protein, human

Identifiers

PMID33664368
PMCPMC7933146
OpenAlexW3133926535

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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.