Evidence map›Paper›PMID 37502711›Full record

ArticleNAR cancer2023

The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes.

Anastasiya Kazachenka, Jane Hc Loong, Jan Attig, George R Young, Piyali Ganguli, Ginny Devonshire, Nicola Grehan, The OCCAMS Consortium, Francesca D Ciccarelli, Rebecca C Fitzgerald and 1 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in NAR cancer, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.9field-weighted citation impact, top 25% 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

5 citing papers in PubMed, 6 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
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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

11 authors at 3 institutions in 1 country.

Anastasiya KazachenkaRetroviral Immunology Laboratory, The Francis Crick Institute, London, UK.
Jane Hc LoongRetroviral Immunology Laboratory, The Francis Crick Institute, London, UK.
Jan AttigRetroviral Immunology Laboratory, The Francis Crick Institute, London, UK.
George R YoungBioinformatics and Biostatistics Facility, The Francis Crick Institute, London, UK.
Piyali GanguliCancer Systems Biology Laboratory, The Francis Crick Institute, London, UK.
Ginny DevonshireCancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
Nicola GrehanEarly Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK.
The OCCAMS Consortium
Francesca D CiccarelliCancer Systems Biology Laboratory, The Francis Crick Institute, London, UK.
Rebecca C FitzgeraldEarly Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK.
George KassiotisRetroviral Immunology Laboratory, The Francis Crick Institute, London, UK.ORCID https://orcid.org/0000-0002-8457-2633
University of Cambridge · GBThe Francis Crick Institute · GBKing's College London · GB

Funding

Medical Research Council MR/W014122/1Wellcome Trust CC2088
6 · The paper itself

Abstract

Most cancer types exhibit aberrant transcriptional activity, including derepression of retrotransposable elements (RTEs). However, the degree, specificity and potential consequences of RTE transcriptional activation may differ substantially among cancer types and subtypes. Representing one extreme of the spectrum, we characterize the transcriptional activity of RTEs in cohorts of esophageal adenocarcinoma (EAC) and its precursor Barrett's esophagus (BE) from the OCCAMS (Oesophageal Cancer Clinical and Molecular Stratification) consortium, and from TCGA (The Cancer Genome Atlas). We found exceptionally high RTE inclusion in the EAC transcriptome, driven primarily by transcription of genes incorporating intronic or adjacent RTEs, rather than by autonomous RTE transcription. Nevertheless, numerous chimeric transcripts straddling RTEs and genes, and transcripts from stand-alone RTEs, particularly KLF5- and SOX9-controlled

Identifiers

PMID37502711
PMCPMC10370457
OpenAlexW4385275722

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.