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Molecular Biology and Genetics |
Urology Research Laboratory, University Hospital Nijmegen, 6500 HB Nijmegen, the Netherlands [M. J. G. B., A. v. B., G. W. V., F. P. S., J. A. S., F. M. J. D.]; Department of Urology, Canisius Wilhelmina Hospital, 6500 GS Nijmegen, the Netherlands [H. F. M. K.]; and James Buchanan Brady Urological Institute, Johns Hopkins Hospital, Baltimore, Maryland 21287-2101 [N. R., W. B. I.]
| ABSTRACT |
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| INTRODUCTION |
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A better understanding of the molecular changes associated with the onset and progression of prostate cancer may provide a rational basis for the development of new diagnostic and prognostic tools as well as new targets for therapy. Likewise, the recent identification of critical biochemical pathways, including angiogenesis, programmed cell death, cell adhesion, and signal transduction have offered promising targets for new therapeutic approaches (6) . The identification and characterization of new prostate cancer-specific antigens or genes could provide new markers and could be instrumental for the development of new treatment modalities. Here we describe the identification and molecular characterization of a new prostate cancer-specific gene, DD3. DD3 is highly overexpressed in prostate cancer tissue in comparison to adjacent nonmalignant prostatic tissue. Moreover, because its expression appears to be restricted to the prostate, DD3 is one of the most prostate cancer-specific genes yet described and provides a promising tool for the early diagnosis of prostate cancer and the development of new treatment modalities.
| MATERIALS AND METHODS |
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Northern Blot Analysis.
Total RNA (10 µg) was glyoxalated, separated on a 1% agarose gel in 20 mM phosphate buffer, and transferred to Hybond-N+ (Amersham) by capillary blotting. Probes for DD3 (original differential display clone, nucleotides 513987, GenBank accession number AF103907), PSA, and rRNA were radioactively labeled with [
-32P]dATP by random prime labeling. Hybridizations were performed as described previously (8)
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RT-PCR Analysis.
Total RNA (1 µg) was treated with DNase I, and cDNA was synthesized using Superscript Moloney murine leukemia virus reverse transcriptase (Life Technologies, Inc.). Upon quantification of the reverse transcription reaction, 10 ng of cDNA were used for a PCR reaction using DD3-specific primers: (a) forward primer (located in exon 1), 5'-AGATTTGTGGTGCTGCAGCC-3'; and (b) reverse primer (located in exon 3), 5'-TCCTGCCCATCCTTTAAGG-3'. The amplification was performed as follows: 30s, 94°C/30s, 60°C/30s, 72°C/35 cycles/10 min., 72°C. To verify the quality of the cDNA synthesized, control reactions were performed using primers derived from the
2 microglobulin gene (9)
, a ubiquitous housekeeping gene: (a) forward primer (located in exon 2), 5'-AGCAGAGAATGGAAAGTCAAA-3'; and (b) reverse primer (located in exon 4), 5'-TGTTGATGTTGGATAAGAGAA-3'. The amplification was performed as follows: 1 min., 94°C/1 min., 58°C/1 min., 72°C/35 cycles/10 min., 72°C. PCR products were analyzed by agarose gel electrophoresis. RNA that was not subjected to reverse transcription was used as a negative control for PCR amplification.
The following cell lines were analyzed for the expression of DD3: (a) human prostate cancer cell lines ALVA-31, DU-145, JCA-1, LNCaP, PC-3, PPC-1, and TSU-pr1; (b) human breast cancer cell lines 734B, BT-20, CAMA, MCF-7, MDA-MB-175, MDA-MB-231, MDA-MB-331, MDA-MB-361, and MDA-MB-469; (c) human bladder cancer cell lines 253J, 575A, 647V, 5637, J82, JON, RT-4, RT112, Scaber, SD, SW780, SW800, SW1710, T24, VMCUB-1, VMCUB-2, and VMCUB-3; (d) renal cell carcinoma cell lines SK-RC-1, SK-RC-7, SK-RC-10, SK-RC-12, SK-RC-14, SK-RC-17, SK-RC-28, SK-RC-35, SK-RC-42, SK-RC-52, and SK-RC-59; and (e) ovarian cancer cell lines COLO-316, OV2774, SK-OV-3, SK-OV-4, SK-OV-6, and SW626. Other human tumor specimens that were analyzed for DD3 expression included four breast, three ovarian, two testicular, two cervical, and two endometrial tumors.
Construction and Screening of a cDNA Library.
A cDNA library was constructed from total cellular RNA extracted from human prostate cancer specimens using the ZAP-cDNA Gigapack II Gold Cloning kit (Stratagene). Approximately 1.5 x 106 phages were screened according to Sambrook et al. (10)
using the original differential display clone DD3 as a probe. Positive clones were purified, and plasmids were rescued by in vivo excision, according to manufacturers procedures.
Screening of the Genomic Library.
A genomic library, constructed of human placenta genomic DNA, cloned in
FIX2 (Stratagene) was screened according to Sambrook et al. (10)
using the original differential display clone DD3 as a probe. Four different clones were obtained (
FIX-ME1,
FIX-ME2,
FIX-ME3, and
FIX-ME4). Screening of the genomic library with a more 5'-located probe, pME4.5.3, resulted in the identification of another two DD3-related genomic clones,
FIX-IH1 and
FIX-IH2.
Genomic Mapping.
Screening of the National Institute of General Medical Sciences human X rodent somatic cell mapping panel (Coriell Cell Repositories, Camden, NJ) with DD3 as a probe indicated that the DD3 gene is located on chromosome 9. To more precisely determine the chromosomal location of the DD3 gene, we performed a hybridization of metaphase chromosomes of human lymphocytes using a probe specific for the centromere of chromosome 9 and a probe consisting of a mixture of four DD3-related genomic clones (
FIX-ME1,
FIX-ME2,
FIX-ME3, and
FIX-ME4). Chromosomes were counterstained using 4,6-diamidino-2-phenylindole.
| RESULTS |
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FIX-ME1,
FIX-ME2,
FIX-ME3, and
FIX-ME4), we determined that the DD3 gene is located on human chromosome 9q2122 (see Fig. 5
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| DISCUSSION |
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A number of prostate-specific genes are known, including PSA (16) and prostate-specific membrane antigen (17) , which have already been studied extensively for their application in the management of prostate cancer patients as either a marker or a tool or target for therapy. More recently, human kallikrein 2 (18) and prostate stem cell antigen (19) were identified as prostate-specific genes. Their usefulness in prostate cancer diagnosis and treatment remains to be established.
Molecular characterization of the DD3 transcription unit revealed that alternative polyadenylation at three different positions in exon 4 is the main mechanism giving rise to the differently sized transcripts detected by Northern blot analysis. In addition, alternative splicing occurs, by which exon 2 is deleted from most transcripts (exon 2 is present in only 5% of the transcripts). The most striking feature of the full-length DD3 cDNA is the high density of stop codons in all three reading frames and the resulting lack of an extensive open reading frame. The alternative splicing of exon 2 or the use of CTG or ACG as the initiation codon for translation (14) does not result in the extension of potential protein-encoding regions. Recently, a number of genes (e.g., H19, Xist, his-1, BORG) have been described, which are expressed as spliced and polyadenylated RNA molecules containing a high density of stop codons and lacking an extensive open reading frame (20, 21, 22, 23, 24, 25, 26) . Analogous to DD3, these genes are unlikely to be pseudogenes, and, moreover, it has been suggested that these genes may function as noncoding RNAs. Available evidence indicates that H19 plays a role in mammalian development (20) and that Xist RNA acts in the nucleus and contributes to X chromosome inactivation (21 , 22) . BORG has been suggested to be a noncoding RNA that plays a role in the differentiation process induced by bone morphogenetic proteins (26) . Recently, Lanz et al. (27) reported on SRA, a steroid receptor coactivator, which acts as a RNA transcript that functions as a component of a large multiprotein complex. DD3 may be another new member of the growing unique class of noncoding RNAs; however, we do not exclude the possibility that DD3 encodes a small peptide. Grail software predicted a potential protein-encoding region of DD3 to be located in exons 3 and 4a, which is present in all transcripts analyzed. In vitro transcription and translation of the full-length DD3 cDNA has not yet provided evidence that a small protein is produced. We are currently cloning the orthologues of DD3 from other mammalian species: if conservation of the nucleotide sequence is mainly limited to the potential open reading frame, this will indicate that a small protein may indeed be produced. However, if a strong conservation of the overall nucleotide sequence and genomic organization is found, as was shown for the his-1 gene (28) , this will suggest that the RNA is the final and functional product of the DD3gene.
Comparison of the nucleotide sequences of the full-length DD3 cDNA to the available computer databases revealed that no genes homologous to DD3 have been reported. However, three ESTs have been reported that are homologous to different parts of the DD3 cDNA. The fact that one of the ESTs was identified in human prostate epithelium supports our expectation that DD3 is expressed by the epithelial cells of the prostate rather than by the stromal cells, because DD3 is highly overexpressed in adenocarcinoma of the prostate, which arises from the epithelial cells. However, RISH will have to confirm this hypothesis. As mentioned before, several noncoding RNAs have been shown to localize to the nucleus and are involved in the regulation of expression of other genes. Therefore, determination of the subcellular localization of DD3 RNA by RISH may provide evidence for the functioning of DD3 as a noncoding RNA.
The gene encoding DD3 maps to chromosome 9q2122, a region that has not been shown to be frequently affected in prostatic tumors. Preliminary data provide no evidence that the overexpression of DD3 is due to amplification or rearrangements on chromosome 9. Additional studies will be needed to disclose the mechanism responsible for the observed increase of DD3 expression in prostatic tumors. Moreover, studies are required to investigate the putative biological functional relation of DD3 in the process of prostate cancer development.
In our efforts to establish the usefulness of DD3 for the management of prostate cancer patients, the value of DD3 as a marker for prostate cancer needs to be assessed. Considering the fact that DD3 may be a noncoding RNA, it is difficult to envision its utility in a protein/antibody-based test. Therefore, RISH will be used to analyze human prostate cancer specimens to establish the potential usefulness of DD3 as a diagnostic and/or prognostic marker for prostate cancer. Furthermore, we are currently establishing a RT-PCR-based assay to determine the usefulness of DD3 as a marker for the detection of circulating neoplastic prostate cells. Likewise, the DD3 gene promoter needs to be characterized: identification and characterization of the elements that regulate the prostate cancer-specific expression of the DD3gene may provide important tools for the development of new gene therapy approaches aimed at selectively driving the expression of therapeutic genes in prostate cancer cells.
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 Supported by a research award from the CaP CURE Foundation. ![]()
2 To whom requests for reprints should be addressed, at Urology Research Laboratory (814 URL), University Hospital Nijmegen, P. O. Box 9101, 6500 HB Nijmegen, the Netherlands. Phone: 31-24-3615157; Fax: 31-24-3541222; E-mail: M.Bussemakers{at}hetnet.nl ![]()
3 The abbreviations used are: BPH, benign prostatic hyperplasia; PSA, prostate-specific antigen; RT-PCR, reverse transcription-PCR; EST, expressed sequence tag; RISH, RNA in situ hybridization; GS, Gleason score. ![]()
Received 6/28/99. Accepted 10/ 5/99.
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