Next-generation sequencing reveals novel rare fusion events with functional implication in prostate cancer.
Gene fusions, mainly between TMPRSS2 and ERG, are frequent early genomic rearrangements in prostate cancer (PCa). In order to discover novel genomic fusion events, we applied whole-genome paired-end sequencing to identify structural alterations present in a primary PCa patient (G089) and in a PCa cell line (PC346C). Overall, we identified over 3800 genomic rearrangements in each of the two samples as compared with the reference genome. Correcting these structural variations for polymorphisms using whole-genome sequences of 46 normal samples, the numbers of cancer-related rearrangements were 674 and 387 for G089 and PC346C, respectively. From these, 192 in G089 and 106 in PC346C affected gene structures. Exclusion of small intronic deletions left 33 intergenic breaks in G089 and 14 in PC346C. Out of these, 12 and 9 reassembled genes with the same orientation, capable of generating a feasible fusion transcript. Using PCR we validated all the reliable predicted gene fusions. Two gene fusions were in-frame: MPP5-FAM71D in PC346C and ARHGEF3-C8ORF38 in G089. Downregulation of FAM71D and MPP5-FAM71D transcripts in PC346C cells decreased proliferation; however, no effect was observed in the RWPE-1-immortalized normal prostate epithelial cells. Together, our data showed that gene rearrangements frequently occur in PCa genomes but result in a limited number of fusion transcripts. Most of these fusion transcripts do not encode in-frame fusion proteins. The unique in-frame MPP5-FAM71D fusion product is important for proliferation of PC346C cells.
Department of Urology and Pathology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
I
I
Teles Alves
Department of Urology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
T
T
Hartjes
1] Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands [2] Department of Mathematical and Computer Sciences, Metropolitan State University of Denver, Colorado, USA.
E
E
McClellan
Department of Urology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
S
S
Hiltemann
Department of Urology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
R
R
Böttcher
Department of Urology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
N
N
Dits
CMNS-Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA.
M R
MR
Temanni
ServiceXS B.V., Leiden, The Netherlands.
B
B
Janssen
ServiceXS B.V., Leiden, The Netherlands.
W
W
van Workum
Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands.
P
P
van der Spek
Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands.
A
A
Stubbs
Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
A
A
de Klein
Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
B
B
Eussen
Department of Pathology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
J
J
Trapman
Department of Urology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
G
G
Jenster
D049109:Cell Proliferation / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008565:Membrane Proteins / Q000096:biosynthesis / Q000235:genetics*; D024101:Mitochondrial Proteins / Q000096:biosynthesis / Q000235:genetics; D009703:Nucleoside-Phosphate Kinase / Q000096:biosynthesis / Q000235:genetics*; D015514:Oncogene Proteins, Fusion / Q000235:genetics* / Q000302:isolation & purification; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000473:pathology; D064067:Rho Guanine Nucleotide Exchange Factors / Q000096:biosynthesis / Q000235:genetics
C576601:ARHGEF3 protein, human; D008565:Membrane Proteins; D024101:Mitochondrial Proteins; C530233:NDUFAF6 protein, human; D015514:Oncogene Proteins, Fusion; D064067:Rho Guanine Nucleotide Exchange Factors; D009703:Nucleoside-Phosphate Kinase; C501307:MPP5 protein, human