Imperial College London
Alternate

Emeritus ProfessorJonathanStoye

Faculty of Medicine, Department of Infectious Disease

Emeritus Professor of Endogenous Retroviruses
 
 
 
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Contact

 

j.stoye Website

 
 
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Location

 

Francis Crick InstituteThe Francis Crick Institute

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Summary

 

Publications

Citation

BibTex format

@article{Attig:2019:10.1101/gr.248922.119,
author = {Attig, J and Young, GR and Hosie, L and Perkins, D and Encheva-Yokoya, V and Stoye, JP and Snijders, AP and Ternette, N and Kassiotis, G},
doi = {10.1101/gr.248922.119},
journal = {Genome Research},
pages = {1578--1590},
title = {LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly},
url = {http://dx.doi.org/10.1101/gr.248922.119},
volume = {29},
year = {2019}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Dysregulated endogenous retroelements (EREs) are increasingly implicated in the initiation, progression, and immune surveillance of human cancer. However, incomplete knowledge of ERE activity limits mechanistic studies. By using pan-cancer de novo transcript assembly, we uncover the extent and complexity of ERE transcription. The current assembly doubled the number of previously annotated transcripts overlapping with long-terminal repeat (LTR) elements, several thousand of which were expressed specifically in one or a few related cancer types. Exemplified in melanoma, LTR-overlapping transcripts were highly predictable, disease prognostic, and closely linked with molecularly defined subtypes. They further showed the potential to affect disease-relevant genes, as well as produce novel cancer-specific antigenic peptides. This extended view of LTR elements provides the framework for functional validation of affected genes and targets for cancer immunotherapy.
AU  - Attig,J
AU  - Young,GR
AU  - Hosie,L
AU  - Perkins,D
AU  - Encheva-Yokoya,V
AU  - Stoye,JP
AU  - Snijders,AP
AU  - Ternette,N
AU  - Kassiotis,G
DO  - 10.1101/gr.248922.119
EP  - 1590
PY  - 2019///
SN  - 1054-9803
SP  - 1578
TI  - LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly
T2  - Genome Research
UR  - http://dx.doi.org/10.1101/gr.248922.119
UR  - https://www.ncbi.nlm.nih.gov/pubmed/31537638
UR  - http://hdl.handle.net/10044/1/74021
VL  - 29
ER  -
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