ArticleCell2026
EcDNA-borne structural variants drive oncogenic fusion transcript amplification.
Abstract read
In one paragraph
Article in Cell, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
–field-weighted citation impact
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.
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.
Who cites it
11 citing papers in PubMed.
- Extrachromosomal DNA as a platform for epigenetic reprogramming in cancer.Molecular cancer · 2026Review
- Integrating molecular subtypes, genomics and functional dependencies to identify context-specific therapeutic vulnerabilities in small cell lung cancer.Biomarker research · 2026Review
- scAmp enables focal gene amplification analysis from single-cell data.Nature communications · 2026Article
- Hybrid extrachromosomal DNA in HPV-driven cancers.Journal of virology · 2026Review
- A Conserved Enhancer Locus in Extrachromosomal DNA and Homogeneously Staining Regions Activates MYC Transcription in Group 3 Medulloblastoma.Cancer research · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Targeting extrachromosomal DNA in human cancers.Nature reviews. Drug discovery · 2026Review
- Extrachromosomal DNA Gives Cancer a New Evolutionary Pathway.Research square · 2026Article
- Dysfunctional DNA Mismatch Repair Drives the Evolution of Gene Amplification in MTX-Resistant Human Colorectal Cancer Cells.International journal of molecular sciences · 2026Article
- Review
- The Extrachromosomal DNA Fusion Factory: Extrachromosomal Genesis of Oncogenic Fusion Transcripts.Research (Washington, D.C.) · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
28 authors.
Hyerim YiRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
Shu ZhangRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
Jason SwindermanArc Institute, Palo Alto, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
Yanbo WangRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
Vishnupriya KanakavetiDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
King L HungDepartments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Ivy Tsz-Lo WongDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
Suhas SrinivasanRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Ellis J CurtisDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA; School of Medicine, University of California at San Diego, La Jolla, CA, USA.
Aarohi Bhargava-ShahRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA; School of Medicine, Stanford University, Stanford, CA, USA.
Rui LiRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Matthew G JonesRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Jens LuebeckDepartment of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA.
Chris BaileyCancer Evolution and Genome Instability Laboratory, the Francis Crick Institute, London, UK.
Yanding ZhaoRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Julia A BelkRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Katerina KraftRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Quanming ShiRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Xiaowei YanRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
Simon K PritchardRNA Medicine Program, Stanford University, Stanford, CA, USA.
Kabir S MahajanRNA Medicine Program, Stanford University, Stanford, CA, USA.
Frances LiangRNA Medicine Program, Stanford University, Stanford, CA, USA.
Mariam Jamal-HanjaniCancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK.
Dean W FelsherDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Luke A GilbertArc Institute, Palo Alto, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
Vineet BafnaDepartment of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA; Halıcıoğlu Data Science Institute, University of California at San Diego, La Jolla, CA, USA.
Paul S MischelDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA. Electronic address: psmischel@stanford.edu.
Howard Y ChangRNA Medicine Program, Stanford University, Stanford, CA, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA. Electronic address: howchang@stanford.edu.
Funding
Translational Oncology Research Program (Project-005)P30CA124435 · NCI · STANFORD UNIVERSITY · PI MICHAEL KENNEY · 2007 to 2026
$71.4MPROMINENT - UCSFOT2CA278665 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ALLAN BALMAIN · 2022 to 2026
$8.9MSpatial multiomic mapping of gene function with CRISPRoffUM1HG012660 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Luke Gilbert · 2022 to 2026
$8.2MeDyNAmiC - STANFORDOT2CA278688 · NCI · STANFORD UNIVERSITY · PI PAUL S MISCHEL · 2022 to 2026
$7.7MTargeting the MYC Pathway for the Treatment of CancerR35CA253180 · NCI · STANFORD UNIVERSITY · PI DEAN W FELSHER · 2020 to 2026
$6.9MSoftware 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
$3.5MeDyNAmiC - UCSDOT2CA278635 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna · 2022 to 2026
$1.8MMolecular Mechanisms by which Statins Prevent and Reverse Hepatocellular CarcinomaU01CA288433 · NCI · STANFORD UNIVERSITY · PI FELSHER, DEAN W, VERNA, ELIZABETH CLARICE · 2023 to 2025
$1.3MQuantitative modeling of extrachromosomal DNA (ecDNA) evolution in tumorsK99CA286968 · NCI · STANFORD UNIVERSITY · PI JONES, MATTHEW GREGORY · 2024 to 2025
$335kRegulation and retention of extrachromosomal oncogene amplifications in cancerF99CA274692 · NCI · STANFORD UNIVERSITY · PI HUNG, KING L. · 2022 to 2023
$82kNCI NIH HHS F99 CA274692NCI NIH HHS K99 CA286968NCI NIH HHS OT2 CA278635NCI NIH HHS OT2 CA278665NCI NIH HHS OT2 CA278688NCI NIH HHS P30 CA124435NCI NIH HHS R35 CA253180NCI NIH HHS U01 CA288433NCI NIH HHS U24 CA264379NHGRI NIH HHS UM1 HG012660
Abstract
Extrachromosomal DNA (ecDNA) amplifications are key drivers of human cancers. Here, we show that ecDNAs are major platforms for generating and amplifying oncogene fusion transcripts across diverse cancer types. By integrating analysis of whole-genome and transcriptome sequences from tumor samples and cancer cell lines of a wide variety of tissue types, we reveal that ecDNAs have the highest rate of oncogene fusion events of any copy-number alteration. Focusing on the most common ecDNA fusion hotspot, we find that fusion of the 5' end of the long noncoding RNA gene, PVT1-with exon 1 joined to diverse 3' partners-confers increased RNA stability, potentially via an SRSF1-dependent mechanism, and enhances MYC-dependent transcription and cancer cell survival. These results demonstrate that ecDNA fosters genome instability and frequent oncogene fusion formation in cancer.
Indexed as
Gene AmplificationNeoplasmsOncogene FusionCell Line, TumorExtrachromosomal DNAGenomic InstabilityHumansRNA, Long NoncodingRNA StabilityExtrachromosomal DNARNA, Long NoncodingcancerecDNAextrachromosomal DNAoncogenePVT1RNA fusionRNA stabilitySRSF1
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
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.