TY  - JOUR
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
Y1  - 2019/10/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1578 
EP  - 1590 
DO  - 10.1101/gr.248922.119 
VL  - 29 
IS  - 10 
UR  - http://genome.cshlp.org/content/29/10/1578.abstract 
N2  - 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. 
ER  -