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Experimental Therapeutics, Molecular Targets, and Chemical Biology |
Departments of 1 Gynecology and Obstetrics and Oncology, and 2 Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland; and 3 Department of Pathology, Norwegian Radium Hospital, University of Oslo, Oslo, Norway
Requests for reprints: Tian-Li Wang, Departments of Gynecology/Obstetrics and Oncology, Johns Hopkins University School of Medicine, CRBII, 1550 East Jefferson Street, Room 306, Baltimore, MD 21231. Phone: 410-502-7774; Fax: 410-502-7943; E-mail: tlw{at}jhmi.edu.
| Abstract |
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-secretase inhibitor and Notch3-specific small interfering RNA suppressed cell proliferation and induced apoptosis in the cell lines that overexpressed Notch3 but not in those with minimal amount of Notch3 expression. These results indicate that Notch3 is required for proliferation and survival of Notch3-amplified tumors and inactivation of Notch3 can be a potential therapeutic approach for ovarian carcinomas. (Cancer Res 2006; 66(12): 6312-8) | Introduction |
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16,000 women will succumb to this disease. In ovarian carcinomas, amplifications of cyclin E1 (2), Her2/neu (3), AKT2 (4), L-Myc (5), and Rsf-1 (6) have been reported. Because these amplifications occur only in a subset of tumors, it is expected that additional oncogenic amplifications will be identified. Recent developments of molecular genetic techniques that allow a genome-wide exploration of DNA copy number in cancer have provided investigators unprecedented opportunities to analyze cancer genome in great details. For example, single nucleotide polymorphism (SNP) array has been recently shown as an effective tool in discovering amplified chromosomal regions (7, 8). In the current study, we did SNP array analysis on 31 high-grade ovarian serous carcinomas purified from fresh clinical samples and identified a chromosomal region at 19p13.12 that is frequently amplified. One of the genes within this amplicon, Notch3, showed the most significant correlation between gene copy numbers and transcript expression in ovarian cancer, suggesting that Notch3 is a candidate oncogene in the chr19p13.12 amplicon. | Materials and Methods |
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SNP array. SNPs were genotyped using 10K arrays (Affymetrix, Santa Clara, CA) in the Microarray Core Facility at the Dana-Farber Cancer Institute (Boston, MA). A detailed protocol is available at the Core center web page.4 Briefly, genomic DNA was cleaved with the restriction enzyme, XbaI, ligated with linkers, followed by PCR amplification. The PCR products were purified and then digested with DNaseI to a size ranging from 250 to 2,000 bp. Fragmented PCR products were then labeled with biotin and hybridized to the array. Arrays were then washed on the Affymetrix fluidics stations. The bound DNA was then fluorescently labeled using streptavidin-phycoerythrin conjugates and scanned using the Gene Chip Scanner 3000.
dChip software version 1.3 was used to analyze the SNP array data as described previously (7, 8). Data was normalized to a baseline array with median signal intensity at the probe intensity level using the invariant set normalization method. A model-based (PM/MM) method was used to obtain the signal values for each SNP in each array. Signal values for each SNP were compared with the average intensities from 13 normal samples. To infer the DNA copy number from the raw signal data, we used the Hidden-Markov model (7) based on the assumption of diploidy for normal samples. Mapping information of SNP locations and cytogenetic band were based on curation of Affymetrix and University of California Santa Cruz hg15. A cutoff of >2.8 copies in more than three consecutive SNPs was defined as amplification.
Digital karyotyping. Purified carcinoma cells as described in the SNP array method were used to generate digital karyotyping library as previously described (9). Approximate 120,000 genomic tags were obtained for each digital karyotyping library. After removing the nucleotide repeats in human genome, the average of filtered tags was 66,000 for each library. We set up a window size of 300 (300 virtual tags) for the analysis in this study. Based on Monte Carlo simulation, the variables used in this study can reliably detect >0.6 Mb amplicon with >5-fold amplification with >99% sensitivity and 100% positive predictive value.
Fluorescence in situ hybridization and quantitative real-time PCR. BAC clones (RP11-937H1 and RP11-319O10) containing the genomic sequences of the 19p13.12 amplicon at 15.00 to 15.25 Mb were purchased from Bacpac Resources (Children's Hospital, Oakland, CA). BAC clone (RP11-752A21), located at 19q13.42 (59.26-59.46 Mb), was used to generate the reference probe. The method for fluorescence in situ hybridization (FISH) has been detailed in a previous report (6).
Relative gene expression and genomic amplification levels were measured by quantitative real-time PCR using methods previously described (9, 10). PCR primers were designed using the Primer 3 program and the nucleotide sequences of the primers for determining transcript expression were listed in Supplementary Table S1. The primer sequences to determine the 19p13.12 genomic amplification were 5'-GCCTGTGGCTGAAAATTAAGG-3' and 5'-TCAATGTCCACCTCGCAATAG-3'.
Immunohistochemistry. A rabbit polyclonal anti-Notch3 antibody was purchased from Santa Cruz Biotechnology (Santa Cruz, CA) and was used in the immunohistochemistry. An EnVision+System peroxidase kit (DAKO, Carpinteria, CA) was used for staining following the protocol provided by the manufacturer. Tissue microarrays (triplicate 1.5 mm cores from each specimen) including 111 high-grade serous carcinomas and 10 normal ovaries were used to facilitate immunohistochemistry. Immunointensity was scored as negative (0), negligible (1+), moderate (2+), and intense (3+), and two investigators independently scored all the samples. For discordant cases, a third investigator scored and the final intensity score was determined by the majority scores.
Cell proliferation and apoptosis assays. Cells were grown in 96-well plates at a density of 4,000 per well. Type 1
-secretase inhibitor was purchased from Calbiochem (San Diego, CA) and was dissolved in DMSO as 4 mmol/L stock solution. Cells were treated with
-secretase inhibitor with DMSO final concentration <0.1%. Notch3-specific small interfering RNA (siRNA) (rGrUrCrArArUrGrUrUrCrArCrUrUrCrGrCrArGrUrU and rGrCrGrUrGrGrArUrUrCrGrGrArCrCrArGrUrCrUrGrArGrArGrGrG) and control siRNA that targets the Luciferase gene (rGrArUrUrArArArUrCrUrUrCrUrArGrCrGrArCrUrGrCrUrUrCrGrC) were synthesized by Integrated DNA Technologies (Coralville, IA). Cells were treated with siRNA at a final concentration of 200 nmol/L.
Cell number was measured by the fluorescence intensity of SYBR green I nucleic acid gel stain (Molecular Probes, Eugene, OR) using a fluorescence microplate reader (Fluostar from BMG, Durham, NC). Data was determined from five replicates and was expressed as the percentage of the inhibitor or Notch3 siRNA-treated cells versus DMSO or control siRNA-treated cells. BrdUrd uptake and staining were done using a cell proliferation kit (Amersham, Buckinghamshire, England, United Kingdom) and apoptotic cells were detected using an Annexin V staining kit (BioVision, Mountain View, CA). The percentage of BrdUrd-positive and Annexin Vpositive cells was determined by counting
400 cells from each well in 96-well plates. The data was expressed as mean ± 1 SD from triplicates.
| Results and Discussion |
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Notch3 as the candidate cancer-related gene in the 19p13.12 amplicon. To select the most promising tumor-associated gene within the minimal amplicon, we aligned the amplicons from these six tumors and delineated a common region of amplification (minimal amplicon), which spanned from 14.60 to 16.47 Mb on chromosome 19p and contained 34 genes (Fig. 2 ). To identify the candidate-amplified tumor-associated gene within the amplicon, we correlated the gene copy number and gene expression levels for all 34 genes based on the rationale that a tumor-driving gene, when amplified, should overexpress to activate its tumorigenic pathway, whereas coamplified "passenger" genes that are not related to tumor development may or may not do so (14). This approach can be useful to narrow down the candidate gene lists, although some amplification events may not necessarily have overexpression of the gene of interest. The mRNA levels were measured using quantitative RT-PCR on five high-grade carcinomas with 19p13.12 amplification, 11 high-grade tumors without such amplification, and five benign ovarian tissues including four OSE samples and a benign ovarian cyst. The expression levels for each gene were normalized to the average value of benign tissues (Fig. 2). Mann-Whitney U test was used to compute and compare the difference in gene expression levels between the 19p13.12 amplified versus nonamplified high-grade carcinomas. Among the 34 genes within the minimal amplicon, Notch3 showed the most consistent and significant up-regulation in 19p13.12-amplified tumors compared with nonamplified tumors (P = 0.0018). Other genes in the amplicon, such as DDX39 and ADHD9, also showed a significant overexpression in the amplified versus nonamplified tumors (P = 0.01 and P = 0.02, respectively). It is plausible that these genes also contribute to the tumorigenesis in ovarian cancer. In this study, we selected Notch3 for further characterization because it showed the most significant P value. We further correlated Notch3 DNA and mRNA copy number in a set of 31 samples in which both tissues and RNA samples were available for FISH and quantitative RT-PCR analyses. Our data showed a moderate positive correlation of these two variables with a correlation coefficient of 0.481 (Spearman rank-order test, P < 0.05).
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2). This finding implies that in addition to gene amplification, mechanisms such as epigenetic activation of the Notch3 promoter in response to environmental cues may contribute to Notch overexpressing in those tumors. Although a positive correlation of Notch3 gene copy ratio and protein expression was observed, there are some tumors (5 of 50 tumors) with Notch3 DNA copy ratio >2 but with only weak Notch3 protein expression (0/1+). This result suggests that these carcinomas may use other oncogene(s) that resides on the same chromosomal arm as the Notch3 locus to promote tumor progression in ovarian serous carcinomas.
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The genetic findings are supported by mouse models. For example, expression of the intracellular domain (a constitutively active form) of Notch3 in mouse thymus induced T-cell leukemia/lymphoma (17). Furthermore, constitutive expression of activated Notch3 in the central nervous system initiates the formation of brain tumors in the choroid plexus in mice (18), suggesting that deregulation of Notch3 plays a role in neoplastic transformation.
Functional analysis of Notch3 expression. To determine if Notch3 is essential for cell growth and survival in cell lines that overexpress Notch3, we used
-secretase inhibitor 1, which prevents the activation of Notch3 by inhibiting the proteolysis and translocation of Notch3 cytoplasmic domain to the nucleus. This compound has been shown to be a potent and specific inhibitor of Notch pathway (19, 20).
-Secretase inhibitor was applied to the culture medium in nine cell lines, including three cancer cell lines with Notch3 overexpression (OVCAR3, A2780, and MCF7), an immortalized OSE cell line (OSE 29), and five cancer cell lines (SKOV3, MPSC1, HTB75, TOV-G21, and ES-2) without Notch3 overexpression (Fig. 5A
). We first determined the concentration of
-secretase inhibitor to be used and found that the IC50 was lowest in OVCAR3 (1 µmol/L). Therefore, we treated different cell lines with inhibitor at 1 µmol/L in culture and found that there was a substantial reduction in cell number of OVCAR3, A2780, and MCF7 cells that overexpressed Notch3 compared with other cell lines that did not have Notch3 overexpression (Fig. 5B, P < 0.001, Student's t test). To assess the mechanisms underlying the growth inhibition by the
-secretase inhibitor in OVCAR3, A2780, and MCF-7 cells, we measured the percentage of BrdUrd-labeled cells for cellular proliferation and Annexin Vlabeled cells for apoptosis (Fig. 5C and D). We found that
-secretase inhibitor significantly reduced cellular proliferation and induced apoptosis in all three cell lines with Notch3 overexpression compared with the DMSO controls (P < 0.001, Student's t test). siRNA was used to knock down the expression of Notch3 in the same nine cell lines used for the
-secretase inhibitor assay. The knockdown effect of siRNA was shown by Western blot (Fig. 6A
). siRNA treatment significantly reduced the Notch3 protein expression compared with the mock or control siRNA-treated groups. Similar to the effects of
-secretase inhibitor, Notch3 siRNA reduced cell number most significantly in OVCAR3, A2780, and MCF7 cells, which overexpressed Notch3 compared with the other cell lines (Fig. 6B, P < 0.001, Student's t test). The BrdUrd-positive cells decreased and the Annexin Vlabeled cells increased in Notch3 siRNA-treated cells compared with control siRNA-treated cells (Fig. 6C and D, P < 0.001, Student's t test).
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-secretase inhibitor and siRNA may have clinical implications for ovarian cancer patients and suggest that Notch3 can be a candidate therapeutic target.
-Secretase inhibitors have been studied in the past several years as a potential therapeutic intervention in Alzheimer's disease. Very recently,
-secretase inhibitors have been shown to inhibit the epithelial cell proliferation and induce goblet cell differentiation in intestinal adenomas Apc/ (min) mice (20). Furthermore,
-secretase was shown to be able to inhibit the growth of Kaposi's sarcoma cells in mouse tumor model (19). Therefore, with the promising effects at both in vitro and in vivo systems,
-secretase inhibitors can be used as new target-based therapy for those tumors with Notch3 activation. The current study suggests that Notch3 is a strong candidate oncogene among the genes within the ch19p13.12 amplicon in ovarian carcinomas. This is because Notch3 gene shows a high correlation of gene amplification and overexpression and is functionally essential for tumor growth and survival. Although the above represents our preferred interpretation, other alternative interpretations should be pointed out. For example, Notch3 may not be the only gene with high correlation of DNA copy number and gene expression level after analyzing a large series of amplified and nonamplified tumors. It is possible that other coamplified gene(s) within the Notch3 amplicon also plays a role in tumorigenesis and they may cooperate with Notch3 in propelling tumor progression.
In conclusion, we have identified Notch3 as a candidate amplified oncogene that overexpressed in 66% of ovarian serous carcinomas. Our findings suggest that Notch3 amplification may play an important role in the development of ovarian carcinomas; moreover, these findings provide a rationale for future development of Notch3-based therapy for ovarian cancer.
| Acknowledgments |
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The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
We thank Dr. Edward Fox and Dr. Changzhong Chen at the microarray core facility of the Dana-Farber Cancer Institute for valuable suggestions.
| Footnotes |
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4 http://chip.dfci.harvard.edu/lab/services.php. ![]()
Received 10/ 6/05. Revised 3/10/06. Accepted 4/11/06.
| References |
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B and T-cell leukemia/lymphoma in Notch3 transgenic mice. EMBO J 2000;19:333748.[CrossRef][Medline]
-Secretase inhibitor blocks Notch activation and induces apoptosis in Kaposi's sarcoma tumor cells. Oncogene 2005;24:633344.[Medline]
-secretase inhibition turns proliferative cells in intestinal crypts and adenomas into goblet cells. Nature 2005;435:95963.[CrossRef][Medline]This article has been cited by other articles:
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