The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes.
Journal
NAR cancer
ISSN: 2632-8674
Titre abrégé: NAR Cancer
Pays: England
ID NLM: 101769553
Informations de publication
Date de publication:
Sep 2023
Sep 2023
Historique:
received:
18
05
2023
revised:
01
07
2023
accepted:
14
07
2023
medline:
28
7
2023
pubmed:
28
7
2023
entrez:
28
7
2023
Statut:
epublish
Résumé
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
Identifiants
pubmed: 37502711
doi: 10.1093/narcan/zcad040
pii: zcad040
pmc: PMC10370457
doi:
Types de publication
Journal Article
Langues
eng
Pagination
zcad040Investigateurs
Rebecca C Fitzgerald
(RC)
Paul A W Edwards
(PAW)
Nicola Grehan
(N)
Barbara Nutzinger
(B)
Elwira Fidziukiewicz
(E)
Aisling M Redmond
(AM)
Sujath Abbas
(S)
Adam Freeman
(A)
Elizabeth C Smyth
(EC)
Maria O'Donovan
(M)
Ahmad Miremadi
(A)
Shalini Malhotra
(S)
Monika Tripathi
(M)
Calvin Cheah
(C)
Hannah Coles
(H)
Connor Flint
(C)
Matthew Eldridge
(M)
Maria Secrier
(M)
Ginny Devonshire
(G)
Sriganesh Jammula
(S)
Jim Davies
(J)
Charles Crichton
(C)
Nick Carroll
(N)
Richard H Hardwick
(RH)
Peter Safranek
(P)
Andrew Hindmarsh
(A)
Vijayendran Sujendran
(V)
Stephen J Hayes
(SJ)
Yeng Ang
(Y)
Andrew Sharrocks
(A)
Shaun R Preston
(SR)
Izhar Bagwan
(I)
Vicki Save
(V)
Richard J E Skipworth
(RJE)
Ted R Hupp
(TR)
J Robert O'Neill
(JR)
Olga Tucker
(O)
Andrew Beggs
(A)
Philippe Taniere
(P)
Sonia Puig
(S)
Gianmarco Contino
(G)
Timothy J Underwood
(TJ)
Robert C Walker
(RC)
Ben L Grace
(BL)
Jesper Lagergren
(J)
James Gossage
(J)
Andrew Davies
(A)
Fuju Chang
(F)
Ula Mahadeva
(U)
Vicky Goh
(V)
Francesca D Ciccarelli
(FD)
Grant Sanders
(G)
Richard Berrisford
(R)
David Chan
(D)
Ed Cheong
(E)
Bhaskar Kumar
(B)
L Sreedharan
(L)
Simon L Parsons
(SL)
Irshad Soomro
(I)
Philip Kaye
(P)
John Saunders
(J)
Laurence Lovat
(L)
Rehan Haidry
(R)
Michael Scott
(M)
Sharmila Sothi
(S)
Suzy Lishman
(S)
George B Hanna
(GB)
Christopher J Peters
(CJ)
Krishna Moorthy
(K)
Anna Grabowska
(A)
Richard Turkington
(R)
Damian McManus
(D)
Helen Coleman
(H)
Russell D Petty
(RD)
Freddie Bartlett
(F)
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Cancer.
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