Evidence map›Paper›PMID 37961138›Full record

ArticlebioRxiv : the preprint server for biology2023

Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair.

John C Rose, Ivy Tsz-Lo Wong, Bence Daniel, Matthew G Jones, Kathryn E Yost, King L Hung, Ellis J Curtis, Paul S Mischel, Howard Y Chang

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed, 3 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors at 2 institutions in 1 country.

John C RoseCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.ORCID 0000-0003-1810-4337
Ivy Tsz-Lo WongSarafan ChEM-H, Stanford University, Stanford, CA, USA.
Bence DanielCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Matthew G JonesCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Kathryn E YostCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
King L HungCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.ORCID 0000-0002-3662-4662
Ellis J CurtisSarafan ChEM-H, Stanford University, Stanford, CA, USA.
Paul S MischelSarafan ChEM-H, Stanford University, Stanford, CA, USA.
Howard Y ChangCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Stanford University · USHoward Hughes Medical Institute · US

Funding

Molecular dissection of extrachromosomal DNA formation, development, and evolutionK99CA279512 · NCI · STANFORD UNIVERSITY · PI ROSE, JOHN CHRISTOPHER · 2023 to 2024
$253k
NCI NIH HHS K99 CA279512
6 · The paper itself

Abstract

Oncogene amplification on extrachromosomal DNA (ecDNA) is a pervasive driver event in cancer, yet our understanding of how ecDNA forms is limited. Here, we couple a CRISPR-based method for induction of ecDNA with extensive characterization of newly formed ecDNA to examine ecDNA biogenesis. We find that DNA circularization is efficient, irrespective of 3D genome context, with formation of a 1 Mb and 1.8 Mb ecDNA both reaching 15%. We show non-homologous end joining and microhomology mediated end joining both contribute to ecDNA formation, while inhibition of DNA-PKcs and ATM have opposing impacts on ecDNA formation. EcDNA and the corresponding chromosomal excision scar form at significantly different rates and respond differently to DNA-PKcs and ATM inhibition. Taken together, our results support a model of ecDNA formation in which double strand break ends dissociate from their legitimate ligation partners prior to joining of illegitimate ends to form the ecDNA and excision scar.

Identifiers

PMID37961138
PMCPMC10634728
OpenAlexW4387874525

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.