Oncotarget

Research Papers:

Novel RNA variants in colorectal cancers

Andreas M. Hoff _, Bjarne Johannessen, Sharmini Alagaratnam, Sen Zhao, Torfinn Nome, Marthe Løvf, Anne C. Bakken, Merete Hektoen, Anita Sveen, Ragnhild A. Lothe, Rolf I. Skotheim

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Oncotarget. 2015; 6:36587-36602. https://doi.org/10.18632/oncotarget.5500

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Abstract

Andreas M. Hoff1,2,3,*, Bjarne Johannessen1,2,3,*, Sharmini Alagaratnam1,2,3, Sen Zhao1,2,3, Torfinn Nome1,2,3, Marthe Løvf1,2,3, Anne C. Bakken1,2,3, Merete Hektoen1,2,3, Anita Sveen1,2,3, Ragnhild A. Lothe1,2,3, Rolf I. Skotheim1,2,3

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

2KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway

3Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway

*These authors have contributed equally to this work

Correspondence to:

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

Keywords: colorectal cancer, fusion genes, transcript variants, RACE-seq, splicing

Received: July 01, 2015     Accepted: September 30, 2015     Published: October 12, 2015

ABSTRACT

With an annual estimated incidence of 1.4 million, and a five-year survival rate of 60%, colorectal cancer (CRC) is a major clinical burden. To identify novel RNA variants in CRC, we analyzed exon-level microarray expression data from a cohort of 202 CRCs. We nominated 25 genes with increased expression of their 3′ parts in at least one cancer sample each. To efficiently investigate underlying transcript structures, we developed an approach using rapid amplification of cDNA ends followed by high throughput sequencing (RACE-seq). RACE products from the targeted genes in 23 CRC samples were pooled together and sequenced. We identified VWA2-TCF7L2, DHX35-BPIFA2 and CASZ1-MASP2 as private fusion events, and novel transcript structures for 17 of the 23 other candidate genes. The high-throughput approach facilitated identification of CRC specific RNA variants. These include a recurrent read-through fusion transcript between KLK8 and KLK7, and a splice variant of S100A2. Both of these were overrepresented in CRC tissue and cell lines from external RNA-seq datasets.

Author Information

Andreas M. Hoff
Primary Contact  _

Bjarne Johannessen

Sharmini Alagaratnam

Sen Zhao

Torfinn Nome

Marthe Løvf

Anne C. Bakken

Merete Hektoen

Anita Sveen

Ragnhild A. Lothe

Rolf I. Skotheim


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