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Priority Report |
Departments of 1 Pathology and 2 Urology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
Requests for reprints: Jan Trapman, Department of Pathology, Josephine Nefkens Institute, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, the Netherlands. Phone: 31-107043933; Fax: 31-107044762; E-mail: j.trapman{at}erasmusmc.nl.
| Abstract |
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| Introduction |
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Most frequent genomic alterations in primary prostate cancers are losses of large fragments of chromosome arms 6q, 8p, 13q, and 16q and gain of 8q (4, 5). In a subset of tumors, a small region of loss of chromosome 21q22 has been detected. This genomic alteration is associated with recurrent fusion of prostate-specific and androgen-regulated TMPRSS2 (6) to the ETS transcription factor gene ERG, which maps at a distance of 3 Mbp from TMPRSS2 on 21q (7).
TMPRSS2-ERG fusion is present in 40% to 70% of clinical prostate cancers (7, 8).3 The gene fusion is an early event that has also been detected in a proportion of precursor lesions (9). Although in many tumors, TMPRSS2-ERG overexpression is accompanied by loss of the region between TMPRSS2 and ERG, in others, this region has been retained, indicative of different mechanisms of gene fusion (10). At low frequency, fusion of TMPRSS2 to a second ETS gene, ETV1, which maps to chromosome band 7p21, has been reported (7, 10). TMPRSS2 seems the only fusion partner of ERG, but it has recently been shown that ETV1 has more fusion partners (11).4
For a third ETS gene, ETV4, only fusion to TMPRSS2 has been described (12). In the present study, we identified in clinical prostate cancer samples two unique novel ETV4 fusion partners: Kallikrein 2 (KLK2) and Calcium-Activated Nucleotidase 1 (CANT1). KLK2, or hGK1, is a well-known prostate marker highly homologous to KLK3 or prostate-specific antigen (13). Like KLK3, KLK2 is prostate-specific and androgen-regulated expressed (13, 14). We show that CANT1 expression is also androgen regulated. CANT1 possesses two alternative first exons, but only one of these is present in the CANT1-ETV4 fusion transcript. In contrast to the majority of CANT1 transcripts, this mRNA is preferentially expressed in the prostate. The novel fusion genes indicate prostate-specificity and androgen-regulation as important characteristics of ETV4 fusion partners in prostate cancer.
| Materials and Methods |
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DNA and RNA isolation. RNA from clinical prostate cancer specimens was isolated using the RNA-Bee kit (Campro Scientific). DNA was isolated using the DNeasy DNA extraction kit (Qiagen). Xenograft RNA was isolated according to the LiCl protocol. RNA from the prostate cancer cell line LNCaP cultured in the presence of 10-9M R1881, or in the absence of hormone, was isolated using the RNeasy RNA extraction kit (Qiagen).
mRNA expression analysis. Analysis of mRNA expression was performed by reverse transcription-PCR (RT-PCR) or by QPCR. Two micrograms of RNA were reverse transcribed using 400 U M-MLV RT (Invitrogen) and an oligo-dT12 primer. cDNAs of 16 different tissues were purchased from Clontech. RT-PCR products were analyzed on a 1.5% agarose gel. QPCR was performed in an ABI Prism 7700 Sequence Detection System (Applied Biosystems), using Power SYBR Green PCR Master Mix (Applied Biosystems), containing 330 nmol/L forward and reverse primer, in a total volume of 25 µL. Thermocycling conditions were according to the recommendations of the manufacturer. Messenger RNA expression was determined relative to Porphobilinogen deaminase (PBDG) by the Standard curve method (Applied Biosystems). Primers are listed in Supplementary Table S1.
RNA ligase–mediated rapid amplification of cDNA ends. 5' RNA ligase–mediated rapid amplification of cDNA ends (RLM-RACE) was performed using the GeneRacer kit from Invitrogen according to instructions of the manufacturer. To obtain the 5'-sequence, cDNA was amplified with Qiagen Taq (Qiagen) using the Generacer 5'-primer and an ETV4 exon 6 primer. PCR products were separated over a 1.5% agarose gel, bands were excised, purified, and sequenced on an ABI 3100 genetic analyzer (Applied Biosystems).
Array comparative genomic hybridization. Arrays were produced from the human 3600 BAC/PAC genomic clone set of the Welcome Trust Sanger Institute, covering the full genome at
1-Mb spacing. DNA labeling and hybridization were performed as previously described (10). After hybridization, arrays were scanned in a ScanArray Express HT (Perkin-Elmer). The resulting images were analyzed with GenePix Pro 5.0 software (Axon Instruments) and subsequently visualized with an excel macro.
Interphase fluorescent in situ hybridization. Interphase fluorescence in situ hybridization (FISH) was done on 5-µm frozen tissue sections as described previously (10). BAC clones RP11-100E5 and RP11-209M4 (both flanking ETV4) were purchased from BacPac Resources. Specificity of BACs was confirmed on metaphase chromosome spreads. BAC DNAs were either Spectrum Orange– or Spectrum Green–labeled using a Nick Translation Reagent kit (Vysis). Tissue sections were counterstained with 4',6-diamidino-2-phenylindole in antifade solution (Vector Laboratories). Images of the three fluorochromes were collected on an epifluorescence microscope (Leica DM) equipped with appropriate filter sets (Leica) and a CCD cooled camera (Photometrics).
Breakpoint mapping. Fusion points were mapped by standard long-range PCR on 200 ng genomic DNA in the presence of 0.5 µmol/L of each forward (fusion partner) and reverse (ETV4) primer with Taq polymerase and Proofstart DNA polymerase (Qiagen). Primers are given in Supplementary Table S1. PCR products were separated on a 1% agarose gel. Specific amplified fragments were isolated and sequenced.
| Results and Discussion |
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The KLK2-ETV4 mRNA fragment, detected by RLM-RACE, was composed of KLK2 exon 1 linked to a new ETV4 exon (here denoted exon 4a), followed by ETV4 exon 5 and 6 sequences (Fig. 1C). The novel ETV4 exon 4a has a length of 133 bp and delivers the ATG start codon of the longest predicted open reading frame in the KLK2-ETV4 fusion transcript (Fig. 1D). KLK2 maps to chromosome band 19q13 and ETV4 on chromosome band 17q21. Because of the orientations of KLK2 and ETV4, KLK2-ETV4 gene fusion cannot be explained by a single chromosomal translocation.
The CANT1-ETV4 fragment detected by RLM-RACE contained one of the two described exons 1 of CANT1 (here denoted exon 1a). This exon maps
4 Kbp downstream of the other first exon (here denoted exon 1; Fig. 1C). CANT1 exon 1a delivers the ATG start codon of the predicted ETV4 open reading frame. Remarkably, CANT1-ETV4 fusion transcripts starting at CANT1 exon 1 were not detected, although wild-type CANT1 transcripts starting either at exon 1 or 1a of the nonrearranged second allele were present in the tumor sample and in normal prostate (data not shown). CANT1 and ETV4 map in the same orientation on 17q, at a distance of
35 Mbp. However, array-based comparative genomic hybridization showed that the genomic region between ETV4 and CANT1 was not lost (data not shown), indicating that either an internal rearrangement of 17q had occurred or that this region was reintegrated in another part of the genome.
ETV4 rearrangements in samples 98 and 206 were confirmed by split signal FISH with probes flanking ETV4 at both sites (Fig. 2A ). Next, the genomic fusion points were mapped by long-range PCR and sequencing (Fig. 2B and C). As expected, the breakpoints of CANT1-ETV4 were located in CANT1 intron 1, downstream from exon 1a, and in ETV4 intron 5, respectively. This latter breakpoint was located in a MER20 repeat, a low copy repetitive element known to be involved in unstable genomic regions prone to chromosomal rearrangement (16). Breakpoints in KLK2 and ETV4 in sample 98 were not in repetitive sequences. The breakpoint in ETV4 intron 4 of the KLK2-ETV4 rearrangement was 2 bp upstream of ETV4 exon 4a (Figs. 1D and 2C). Due to the gene fusion the purine-rich ETV4, intron sequence was replaced by a more pyrimidine-rich sequence of KLK2 intron 1, generating a novel splice acceptor sequence. To confirm that the rearrangement induced ETV4 exon 4a, a splicing assay was performed (Supplementary Fig. S1). ETV4 exon 4a was indeed retained if the KLK2-ETV4 fusion sequence was used, but not if intron 4 sequence of wild-type ETV4 was used in the assay (Supplementary Fig. S1).
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In prostate cancer, TMPRSS2 is the common fusion partner of the ETS family members ERG, ETV1, and ETV4. Recently, several novel ETV1 fusion partners have been identified: SLC45A3, HERV-K_22q11.23, C15orf21, and HNRPA2B1 (11), with different expression characteristics. Based on expression profiles, the fusion partners were divided into distinct classes of ETV1 rearrangements, separating prostate-specific, androgen up-regulated genes and down-regulated genes, and ubiquitously regulated genes. Recently, we identified three novel ETV1 fusion partners: FOXP1, HERVK17, and EST14.4 Both HERVK17 and EST14 have a prostate-specific and androgen-induced expression pattern; FOXP1 seems expressed in many tissues. The three ETV4 partners identified, TMPRSS2, KLK2, and CANT1, show identical expression profiles: up-regulation by androgens and prostate-specificity.
The common expression pattern of ETV4 fusion partners indicates a similar mechanism of gene fusion. It is tempting to speculate that the genomic region of prostate-specific genes is unstable in a specific cell type. Based on the stem cell/progenitor cell concept of tumor development (17), progenitor cells of the luminal epithelial prostate cells, in which expression of the prostate-specific fusion partners is expected to be activated, are interesting candidates. In this regard, we could confirm TMPRSS2 induction during development of the mouse prostate.4 Unfortunately, there are no appropriate mouse counterparts of KLK2 and CANT1(exon 1a).
A second process that might play a role in a common mechanism of gene fusion includes the nuclear compartmentalization of gene expression. It might be proposed that prostate-specific genes are all expressed in a limited number of nuclear compartments, or so-called transcription factories (18, 19). Possibly, ETV4 is expressed in the same compartments. In accordance with the latter hypothesis, it has recently been shown that IGH and cMYC, which are fusion partners in Burkitt lymphoma and plasmacytoma, are preferentially expressed in the same nuclear regions at in vitro B cell stimulation (20).
Taken together, the results from this study show that ETV4 has multiple fusion partners and highlight the importance of meticulous examination of gene fusions. Importantly, key determinants of ETV4 fusion partners are not chromosomal location or expression level, but their androgen-regulated and prostate-specific expression pattern.
| Acknowledgments |
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We thank Theo van der Kwast and Arno van Leenders for pathology, Chris Bangma and Wilma Teubel for clinical samples, Wytske van Weerden for xenograft tissues, and Anieta Siewerts for RNA isolation of clinical samples.
| Footnotes |
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3 K.G. Hermans, J.L. Boormans, D. Gasi, G. Jenster, P. Verhagen, and J. Trapman, unpublished. ![]()
4 K.G. Hermans, H.A. van der Korput, R. van Marion, A. Ziel-van der Made, N.F. Dits, T.H. van der Kwast, H. van Dekken, C.H. Bangma, H. Korsten, G. Jenster, and J. Trapman, unpublished. ![]()
Received 1/16/08. Revised 3/ 5/08. Accepted 3/ 6/08.
| References |
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This article has been cited by other articles:
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K. G. Hermans, H. A. van der Korput, R. van Marion, D. J. van de Wijngaart, A. Ziel-van der Made, N. F. Dits, J. L. Boormans, T. H. van der Kwast, H. van Dekken, C. H. Bangma, et al. Truncated ETV1, Fused to Novel Tissue-Specific Genes, and Full-Length ETV1 in Prostate Cancer Cancer Res., September 15, 2008; 68(18): 7541 - 7549. [Abstract] [Full Text] [PDF] |
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B. Han, R. Mehra, S. M. Dhanasekaran, J. Yu, A. Menon, R. J. Lonigro, X. Wang, Y. Gong, L. Wang, S. Shankar, et al. A Fluorescence In situ Hybridization Screen for E26 Transformation-Specific Aberrations: Identification of DDX5-ETV4 Fusion Protein in Prostate Cancer Cancer Res., September 15, 2008; 68(18): 7629 - 7637. [Abstract] [Full Text] [PDF] |
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