Oncotarget

Research Papers:

Novel transcription-induced fusion RNAs in prostate cancer

Sen Zhao, Marthe Løvf, Kristina Totland Carm, Anne Cathrine Bakken, Andreas M. Hoff and Rolf I. Skotheim _

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Oncotarget. 2017; 8:49133-49143. https://doi.org/10.18632/oncotarget.17099

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Abstract

Sen Zhao1,2, Marthe Løvf1,2, Kristina Totland Carm1,2, Anne Cathrine Bakken1,2, Andreas M. Hoff1,2 and Rolf I. Skotheim1,2,3

1Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway

2Center for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway

3Department of Informatics, Faculty of Natural Science and Mathematics, University of Oslo, Oslo Norway

Correspondence to:

Rolf I. Skotheim, email: rolf.i.skotheim@rr-research.no

Keywords: prostate cancer, fusion transcript, RNA sequencing, expression profile

Received: July 07, 2016     Accepted: April 03, 2017     Published: April 13, 2017

ABSTRACT

Prostate cancer is a clinically and pathologically heterogeneous disease with a broad spectrum of molecular abnormalities in the genome and transcriptome. One key feature is the involvement of chromosomal rearrangements creating fusion genes. Recent RNA-sequencing technology has uncovered that fusions which are not caused by chromosomal rearrangements, but rather meditated at transcription level, are common in both healthy and diseased cells. Such fusion transcripts have been proven highly associated with prostate cancer development and progression. To discover novel fusion transcripts, we analyzed RNA sequencing data from 44 primary prostate tumors and matched benign tissues from The Cancer Genome Atlas. Twenty-one high-confident candidates were significantly enriched in malignant vs. benign samples. Thirteen of the candidates have not previously been described in prostate cancer, and among them, five long intergenic non-coding RNAs are involved as fusion partners. Their expressions were validated in 50 additional prostate tumor samples and seven prostate cancer cell lines. For four fusion transcripts, we found a positive correlation between their expression and the expression of the 3′ partner gene. Among these, differential exon usage and qRT-PCR analyses in particular support that SLC45A3-ELK4 is mediated by an RNA polymerase read-through mechanism.


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