Evidence map›Paper›PMID 39506153›Full record

ArticleNature2024

Enhancing transcription-replication conflict targets ecDNA-positive cancers.

Jun Tang, Natasha E Weiser, Guiping Wang, Sudhir Chowdhry, Ellis J Curtis, Yanding Zhao, Ivy Tsz-Lo Wong, Georgi K Marinov, Rui Li, Philip Hanoian and 20 more

Registry-linked trialAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05827614 (An Open-Label, Multicenter, First-in-Human, Dose-Escalation and Dose-Expansion, Phase 1/2 Study of BBI-355 and BBI-355 in Combination With Select Targeted Therapies in Subjects With Locally Advanced or Metastatic Solid Tumors With Oncogene Amplifications), which is not on this map. Cited by 69 papers.

0numbers the graph read from it
0cells of the map it votes in
69citing 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.

NCT05827614 phase1terminatednot on this map

An Open-Label, Multicenter, First-in-Human, Dose-Escalation and Dose-Expansion, Phase 1/2 Study of BBI-355 and BBI-355 in Combination With Select Targeted Therapies in Subjects With Locally Advanced or Metastatic Solid Tumors With Oncogene Amplifications

TypeinterventionalSponsorBoundless Bio, Inc.Ran2023 to 2026Enrolled85ConditionsTriple Negative Breast Cancer (TNBC), High Grade Serous Ovarian Carcinoma, High Grade Endometrial Carcinoma, Anogenital CancerArmsBBI-355, Erlotinib, Futibatinib, BBI-825
3 · Its place in the literature

Who cites it

69 citing papers in PubMed.

  1. Evolution of AR and Non-AR Alterations in ctDNA of Patients with Metastatic Prostate Cancer Treated in the Phase III Alliance A031201 Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026
    Trial
  2. Review
  3. Article
  4. Article
  5. Review
  6. Article
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  8. Review
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  10. Review
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  12. Review
  13. Examining the role of extrachromosomal DNA in lung cancer.Journal of the National Cancer Institute · 2026
    Article
  14. Review
  15. Article
  16. Review
  17. Review
  18. Article
  19. Review
  20. Review

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

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

30 authors.

Jun Tang *Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Natasha E Weiser *Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-9971-2961
Guiping Wang *Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.ORCID 0000-0002-6347-0419
Sudhir ChowdhryBoundless Bio, San Diego, CA, USA.
Ellis J CurtisDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Yanding ZhaoCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Ivy Tsz-Lo WongDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-9761-3422
Georgi K MarinovDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-1822-7273
Rui LiCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Philip HanoianDepartment of Chemistry, Pennsylvania State University, University Park, PA, USA.
Edison TseBoundless Bio, San Diego, CA, USA.
Salvador Garcia MojicaBoundless Bio, San Diego, CA, USA.
Ryan HansenBoundless Bio, San Diego, CA, USA.
Joshua PlumBoundless Bio, San Diego, CA, USA.
Auzon SteffyBoundless Bio, San Diego, CA, USA.
Snezana MilutinovicBoundless Bio, San Diego, CA, USA.
S Todd MeyerBoundless Bio, San Diego, CA, USA.
Jens LuebeckDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0003-4391-979X
Yanbo WangDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Shu ZhangDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-2543-5943
Nicolas AltemoseDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-7231-6026
Christina CurtisDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
William J GreenleafDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-1409-3095
Vineet BafnaDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Stephen J BenkovicDepartment of Chemistry, Pennsylvania State University, University Park, PA, USA.ORCID 0000-0003-3680-3481
Anthony B PinkertonBoundless Bio, San Diego, CA, USA.ORCID 0000-0003-4571-152X
Shailaja KasibhatlaBoundless Bio, San Diego, CA, USA.
Christian A HassigBoundless Bio, San Diego, CA, USA. chassig@boundlessbio.com.ORCID 0009-0005-7431-9166
Paul S MischelDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA. pmischel@stanford.edu.ORCID 0000-0002-4560-2211
Howard Y ChangCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. howchang@stanford.edu.ORCID 0000-0002-9459-4393

Funding

Center for Personal Dynamic RegulomesRM1HG007735 · NHGRI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2019 to 2023
$13.8M
eDyNAmiC - STANFORDOT2CA278688 · NCI · STANFORD UNIVERSITY · PI PAUL S MISCHEL · 2022 to 2026
$7.7M
Software and algorithms for elucidating the structure, function, and evolution of extrachromosomal DNAU24CA264379 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET, MESIROV, JILL P. · 2021 to 2025
$3.5M
Computational methods for detecting patterns of complex genomic variationR01GM114362 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna · 2016 to 2026
$3.1M
eDyNAmiC - UCSDOT2CA278635 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna · 2022 to 2026
$1.8M
Cancer Research UK CGCATF-2021/100012NCI NIH HHS OT2 CA278635NCI NIH HHS OT2 CA278688NCI NIH HHS U24 CA264379NHGRI NIH HHS RM1 HG007735NIGMS NIH HHS R01 GM114362
6 · The paper itself

Abstract

Extrachromosomal DNA (ecDNA) presents a major challenge for cancer patients. ecDNA renders tumours treatment resistant by facilitating massive oncogene transcription and rapid genome evolution, contributing to poor patient survival

Indexed as

DNA ReplicationStomach NeoplasmsTranscription, GeneticAnimalsAntineoplastic AgentsCell DeathCell Line, TumorCheckpoint Kinase 1DNA Breaks, Double-StrandedDNA RepairDNA, Single-StrandedFemaleHumansMaleMicePhenylurea CompoundsAntineoplastic AgentsCheckpoint Kinase 1CHEK1 protein, humanDNA, Single-StrandedFGFR2 protein, humaninfigratinibPhenylurea CompoundsProtein Kinase InhibitorsPyrimidinesReceptor, Fibroblast Growth Factor, Type 2Replication Protein ARPA2 protein, human

Identifiers

PMID39506153
PMCPMC11540844

What OpenQuestion holds

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Registered trials

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.