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LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly
OA Location
Author(s)
Attig, Jan
Young, George R
Hosie, Louise
Perkins, David
Encheva-Yokoya, Vesela
Type
Journal Article
Abstract
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.
Date Issued
2019-10-01
Date Acceptance
2019-08-21
Citation
Genome Research, 2019, 29 (10), pp.1578-1590
URI
DOI
ISSN
1054-9803
Publisher
Cold Spring Harbor Laboratory Press
Start Page
1578
End Page
1590
Journal / Book Title
Genome Research
Volume
29
Issue
10
Copyright Statement
© 2019 Attig et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/31537638
PII: gr.248922.119
Subjects
06 Biological Sciences
11 Medical and Health Sciences
Bioinformatics
Publication Status
Published
Coverage Spatial
United States
Date Publish Online
2019-09-19