Evidence map›Paper›PMID 41379955›Full record

ArticleScience (New York, N.Y.)2025

Chromothripsis and ecDNA initiated by N4BP2 nuclease fragmentation of cytoplasm-exposed chromosomes.

Ksenia Krupina, Alexander Goginashvili, Michael W Baughn, Stephen Moore, Christopher D Steele, Amy T Nguyen, Daniel L Zhang, Jonas Koeppel, Prasad Trivedi, Aarti Malhotra and 9 more

Abstract read
In one paragraph

Article in Science (New York, N.Y.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Review
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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

19 authors.

Ksenia KrupinaDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.ORCID 0009-0003-7864-8069
Alexander GoginashviliDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.ORCID 0000-0002-3305-5898
Michael W BaughnDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.ORCID 0000-0001-8525-8024
Stephen MooreDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.ORCID 0009-0004-3908-3920
Christopher D SteeleDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.ORCID 0000-0002-6110-0086
Amy T NguyenDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.
Daniel L ZhangDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.ORCID 0009-0005-8505-2831
Jonas KoeppelDepartment of Haematology, University of Cambridge, Cambridge, UK.ORCID 0000-0003-1306-3994
Prasad TrivediDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.ORCID 0000-0002-7150-4324
Aarti MalhotraDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.
David JenkinsDepartment of Cell and Developmental Biology, University of California at San Diego, La Jolla, USA.ORCID 0009-0000-3001-0996
Andrew K ShiauDepartment of Cell and Developmental Biology, University of California at San Diego, La Jolla, USA.
Yohei MiyakeSanford Stem Cell Institute, University of California San Diego, La Jolla, USA.
Tomoyuki KogaDepartment of Medicine, University of California at San Diego, La Jolla, USA.ORCID 0000-0002-8330-117X
Shunichiro MikiDepartment of Medicine, University of California at San Diego, La Jolla, USA.ORCID 0000-0002-9625-8668
Frank B FurnariSanford Stem Cell Institute, University of California San Diego, La Jolla, USA.ORCID 0000-0003-1909-4361
Peter J CampbellDepartment of Haematology, University of Cambridge, Cambridge, UK.ORCID 0000-0002-3921-0510
Ludmil B AlexandrovDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.ORCID 0000-0003-3596-4515
Don W ClevelandDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, USA.ORCID 0000-0002-1934-3682

Funding

Mechanisms of chromosome segregation, aneuploidy, and tumorigenesisR35GM122476 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Don W Cleveland · 2017 to 2026
$9.0M
Detecting Mutational Signatures of Environmental Mutagens in Heathy Individuals for Personalized Cancer PreventionR01ES032547 · NIEHS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ALEXANDROV, LUDMIL B · 2021 to 2025
$3.4M
Mapping immuno-genomic drivers of the head and neck precancer invasive-disease transitionU01CA290479 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ludmil B Alexandrov, Jorge Silvio Gutkind · 2023 to 2026
$3.1M
Credentialing next-generation human glioma models for precision therapeuticsR01CA258248 · NCI · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI Frank Furnari, Christopher Ryan Miller · 2022 to 2026
$3.0M
Mutational Signatures of a Combined Environmental Exposure: Arsenic and Ultraviolet RadiationR01ES030993 · NIEHS · UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR · PI HUDSON, LAURIE G, LIU, KE JIAN · 2020 to 2024
$2.5M
Comprehensive identification of germline-somatic interactionsR01CA269919 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ludmil B Alexandrov, Hannah Kathryn Carter · 2022 to 2026
$2.2M
Therapeutic targeting mesenchymal transition in newly diagnosed and recurrent GBMR01NS134798 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Frank Furnari, Christopher Ryan Miller · 2024 to 2026
$1.9M
Genotypic Interactions in Brain Cancer HeterogeneityR56NS080939 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FURNARI, FRANK · 2023 to 2023
$537k
NCI NIH HHS R01 CA258248NCI NIH HHS R01 CA269919NCI NIH HHS U01 CA290479NIEHS NIH HHS R01 ES030993NIEHS NIH HHS R01 ES032547NIGMS NIH HHS R35 GM122476NINDS NIH HHS R01 NS134798NINDS NIH HHS R56 NS080939Wellcome Trust
6 · The paper itself

Abstract

Genome instability, including chromothripsis, is a hallmark of cancer. Cancer cells frequently contain micronuclei-small, nucleus-like structures formed by chromosome missegregation-that are susceptible to rupture, exposing chromatin to cytoplasmic nucleases. Through an unbiased, imaging-based small interfering RNA screen that targeted all 204 known and putative human nucleases, we identified a previously uncharacterized cytoplasmic endonuclease, NEDD4-binding protein 2 (N4BP2), that enters ruptured micronuclei and initiates DNA damage, leading to chromosome fragmentation. N4BP2 promoted genome rearrangements (including chromothripsis), formation of extrachromosomal DNA (ecDNA) in drug-induced gene amplification, tumorigenesis, and tumor cell proliferation in an induced model of human high-grade glioma. Analysis of more than 10,000 human cancer genomes revealed elevated N4BP2 expression to be predictive of chromothripsis and copy number amplifications, including ecDNA.

Indexed as

ChromothripsisCytoplasmDNA FragmentationDNA Repair EnzymesEndonucleasesMicronuclei, Chromosome-DefectiveAnimalsCarcinogenesisCell Line, TumorCell ProliferationDNA DamageGene AmplificationGenome, HumanGenomic InstabilityHumansMiceDNA Repair EnzymesEndonucleasesN4BP2 protein, human

Identifiers

PMID41379955
PMCPMC12795017

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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.