RT Journal
A1 Attig, Jan
A1 Young, George R.
A1 Hosie, Louise
A1 Perkins, David
A1 Encheva-Yokoya, Vesela
A1 Stoye, Jonathan P.
A1 Snijders, Ambrosius P.
A1 Ternette, Nicola
A1 Kassiotis, George
T1 LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly
JF Genome Research 
JO Genome Research 
YR 2019 
FD October 01 
VO 29 
IS 10 
SP 1578 
OP 1590 
DO 10.1101/gr.248922.119 
UL http://genome.cshlp.org/content/29/10/1578.abstract 
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.