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Original Article |
1 Department of General Surgery, University of Muenster, Waldeyerstrasse 1, 48149 Muenster, Germany
2 Institute of Pathology, University of Duesseldorf, Duesseldorf, Germany
Correspondence: Address correspondence and reprint requests to: Christina Schleicher; E-mail: christina.schleicher{at}ukmuenster.de
| ABSTRACT |
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Methods: Specimens of 33 PCA were investigated by comparative genomic hybridization. Microdissection was used for separation of PCA from the normal cells before isolation of DNA; nick-end labeling and hybridization were performed according to standard protocols. Aberrations were correlated with staging and grading using log-rank test and Cox regression. Survival rates were plotted using the KaplanMeier method.
Results: Twenty-eight (85%) PCA showed aberrations. Gains of chromosomal material were most frequently identified on 8q (42%), 13q (30%), 18p (21%), and 3q (18%). Genetic losses were frequently detected on 1p (45%), 22 (42%), 19 (36%), 17p (27%), 18q and 8p (15% each), and 3p (12%). Losses of 8p (n = 5) and 3p (n = 4) were only detected in stages III and IV (P < 0.05). Median survival time of all patients was 13 months. Median survival time of patients with aberration of 8q (n = 14) was 8.5 months compared to 16 months in patients without gain of 8q (n = 19; P = 0.029).
Conclusions: The chromosomal regions containing genetic alterations represent potential loci for new target genes in PCA. The significant correlation of gain of chromosome 8q with short survival time suggests that 8q may be a new marker to assess prognosis and malignant potential of resected PCA in the individual patient, thereby helping to identify patients at risk for recurrence that might profit from adjuvant therapy.
Key Words: Pancreatic carcinoma Comparative genomic hybridization CGH Chromosome 8q Cytogenetics
| INTRODUCTION |
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In recent years, extensive molecular profiling of PCA has been accomplished and several cancer-related genes have been identified. In general, the development of PCA is thought to be driven by a multi-step process of a critical accumulation of genetic alterations. p53, p16/CDKN2 and DPC4/SMAD4 are the most frequently inactivated tumor suppressor genes in sporadic PCA,3 while k-ras is the oncogene commonly mutated in PCA.4 Some other cancer-related genes are Her-2/neu, COX-2 and VEGF.57 Modern molecular biological techniques such as Comparative Genomic Hybridization (CGH) and Spectral Karyotyping (SKY) have shown a high chromosomal instability of malignant pancreatic tumors with frequent losses and gains of genetic material.816 Some of these chromosomal regions correspond to the loci of the aforementioned genes which are frequently mutated in PCA, indicating that other chromosomal regions with genomic imbalances might harbor new potential target genes.
Nevertheless, currently no effective biomarkers useful for early detection or prognostic assessment of PCA are available. Therefore, the investigation of molecular markers for early diagnosis of PCA and the identification of new prognostic markers to identify patients at high risk for recurrent or meta-static disease that might benefit from new adjuvant or neoadjuvant therapeutic strategies are of utmost importance. The objective of the present study was to detect specific genomic alterations potentially involved in early initiation as well as progression of PCA by CGH. The identified chromosomal imbalances were correlated with histopathological and clinical data to verify their prognostic significance.
| MATERIALS AND METHODS |
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DNA Isolation
Ten to 20 consecutive sections (10 µm) from paraffin-embedded material with a high share of malignant tissue were stained with hematoxylin. Areas of pancreatic adenocarcinoma were defined by an experienced pathologist (C.P.). Then, the marked lesions were carefully separated from normal cells by microdissection using a light microscope-based micromanipulator (Zeiss). Only microdissections that consisted of at least 70% malignant cells were used for further DNA extraction.
The tissue was treated with 2040 µl of proteinase K (20 mg/ml) for 34 days. Then, DNA was isolated by standard phenol-chloroform extraction. After extraction, DNA was dissolved in 50 µl of TE (Tris-EDTA) buffer at 45°C and stored at 4°C. Fragmentation of the extracted DNA was examined by gel electrophoresis with ethidiumbromide.
Comparative Genomic Hybridization
CGH analysis was performed as previously described.17 About 900 ng of tumor DNA and 300 ng of reference DNA from a healthy female donor were labeled by a standard nick-translation reaction with biotin-16-dUTP and digoxigenin-11-dUTP (Boeh-ringer, Mannheim), respectively. In order to obtain an average fragment size of 5001000 base pairs, the DNAase concentration was adjusted individually. Using a standardized PCR purification kit (Qiagen, QIAquick Mini Columns) the labeled DNA fragments were purified from the remaining nucleotides and fragments smaller than 100 base pairs. Of the remaining DNA, 500 ng of tumor DNA and 300 ng of reference DNA were used for hybridization.
To block repetitive sequences each DNA probe was ethanol-precipitated with 40 µg of unlabeled human Cot-1 DNA (Gibco) and resuspended in 5 µl of formamid. After application of 5 µl Mastermix (20% dextran sulfate in 2x SSC) the hybridization probe was denatured for 5 min at 75°C and incubated for 45 min at 37°C to allow preannealing of Cot-1 DNA. Slides containing metaphase chromosomes of a healthy individualpretreated in standard fashion were denatured in 70% formamid/2x SSC at 73°C for 5 min and subsequently dehydrated in a series of 70%, 90% and 100% ethanol before and after a 3-min incubation with 30 µl of proteinase K (0.1 µl/ml). The preannealed probe mixture was hybridized to the denatured metaphase chromosomes in a humidified chamber at 37°C. After 3 days, the slides were washed in 50% formamid/2x SSC (45°C) and 0.1x SSC (60°C). For detection of biotin-labeled tumor-DNA 100 µl of Avidin-FITC (1:200) was added, digoxigenin-labeled reference DNA was detected by sheep anti-digoxigenin rhodamine (TRITC, 1:33). After 45 min of incubation at 37°C, chromosomes were counterstained with 20 µl of DAPI solution (1 mg/5ml) for 710 min and subsequently stored with antifade solution (Vecta-Shield).
Digital Image Analysis
Hybridization pictures were generated by a charged coupled device camera (CCD camera, Cohu 6X-924) connected to a Leica DMRBE fluorescence microscope. The Cytovision 3.1 (Applied Imaging) software package was used for karyotyping and subsequent evaluation of green-to-red ratios of fluorescence intensities, which were determined from ten meta-phase spreads for each chromosome. The resulting average ratio profile was plotted along the chromosomal ideograms. Ratio profiles were evaluated only if the 95% confidence limits did not exceed 0.15. The diagnostic cut-o3 level representing chromosomal gains and losses was set at 1.15 and 0.85, respectively. All CGH experiments were repeated at least once.
Statistical Analysis
All statistical calculations were performed with SPSS 12.0.1 software (SPSS Inc., Chicago, IL, USA). Characteristics of the cohorts were compared by Students t-test for independent groups, ANOVA, Chi-square test and Mann-Whitney rank sum test. P values <0.05 were considered statistically significant.
| RESULTS |
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10) were detected in two PCA (6%), 12 tumors (36%) had intermediate copy number abnormalities (59) and 14 tumors (42%) had 14 chromosomal aberrations (low-frequency copy number abnormalities). There was an average of 4.7 total aberrations per tumor (range 013). Losses (6.8, range 07) were more frequently observed than gains (4.4, range 06; P > 0.05).
Figure 1
shows a schematic overview of genetic imbalances detected in the 28 cases of PCA. Gains of chromosomal material were most frequently identified on chromosome 8q (42%), 13q (30%), 18p (21%), 3q (18%), 9p (12%) and 12p (12%). Genetic losses were frequently detected on chromosome 1p (45%), 22 (42%) and 19 (36%), 17p (27%), 18q (15%), 8p (15%) and 3p (12%).
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The average number of aberrations per tumor in patients with intermediate differentiation (G2, n = 17) was 4.8 [213]. This was not significantly different from poorly differentiated tumors (G3, n = 16), which had an average of 3.4 [110] aberrations per tumor (P = 0.162, Students t). Specific chromosomal aberrations showed no association with histopathological tumor grading except for losses of 1p (n = 12) which was significantly higher in G2 tumors (P = 0.005, Chi square; Fig. 2
). Median survival time of patients with G2 tumors was 15 months [485], median survival time of patients with G3 tumors was 10 months ([340]; P = 0.2795, log rank).
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Comparing tumors of the node-negative stage I (T1-2N0M0) and II (T3N0M0) with node-positive and advanced stage III (T1-3N1M0) and IVa/b (T4N0-1M0-1) tumors, certain aberrations were detected only in stage III and IV tumors, including loss of the short arms of chromosome 3 (n = 4, P = 0.044, Chi square) and chromosome 8 (n = 5; P = 0.018, Chi square). However, gain of the short arm of chromosome 12 was identified exclusively in stage I and II tumors (n = 4; P = 0.103, Chi square) but not in advanced stage carcinomas (Fig. 3
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Univariate analysis unveiled tumor stage (P < 104), resection margin (P = 0.025) and gain of chromosome 8q (P = 0.029) as significant prognostic factors for tumor-related survival, while other tested factors were insignificant (age, gender, G category, T category, N category, tumor localization). Multivariate analysis identified gain of chromosome 8q as the only independent significant predictor of survival (P = 0.025) with a hazard ratio of 2.415 (95% confidence interval [2.022.81]). Furthermore gain of chromosome 8q was the only aberration correlated with patient survival. Median survival of patients with aberration of 8q (n = 14) was 8.5 months [450] while median survival of patients without gain of chromosome 8q (n = 19) was 16 months [385] (P = 0.029, Fig. 5
). The 1-, 2-and 5-year-survival rates were 28%, 7% and 0% for patients with aberration of 8q, and 74%, 11% and 5% for patients without gain of 8q, respectively. This difference remained statistically significant when adjusted for factors like age, sex, grading, staging, tumor localization, resection margin status and adjuvant treatment (Table 1
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10, n = 2) copy number abnormalities had a median survival time of 10 months [418]. Although this difference did not become statistically significant (P = 0.48), it suggests that the total number of chromosomal aberrations per tumor is associated with patient survival since comparing the two groupslow-frequency versus intermediate-/high-frequency abnormalitiesno differences according to patient characteristics and tumor pathology could be found. | DISCUSSION |
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Such discrepancies among CGH results obtained from in vivo or in vitro tumor material can be due to several reasons. PCA are very heterogeneous with typically high numbers of stromal and inflammatory cells bearing the risk of contamination of DNA probes. In studies using pancreatic tumor specimens, the failure to detect chromosomal aberrations may therefore result from inadequate microdissection and consecutive contamination of the samples by non-neoplastic cells leading to a suboptimal ratio of tumor versus normal DNA for CGH analysis. Kallioniemi et al.18 assessed that CGH tolerates about 3050% contamination of tumor cell DNA by stromal DNA. The threshold of at least 70% neoplastic cells per sample chosen in our study seems to be adequate for detection of a high frequency of chromosomal aberrations in PCA. Moreover, the use of paraffin-embedded material for CGH analysis is well established in our laboratory.17 In PCA, equivalent chromosomal imbalances had been described, no matter whether paraffin-embedded or fresh-frozen samples were used.10 On the other hand, cell lines due to genetic instability often harbor genomic alterations acquired during long-term culture conditions. Moreover ex vivo selection pressures can give rise to sub-clones that do not reflect the genetic profile of the native tumor in vivo.
In this study, our concern was to evaluate the clinical significance of chromosomal aberrations detected in pancreatic cancer. Therefore we analyzed the association of specific genomic imbalances with histopathological data and patient survival.
The total number of aberrations per tumor was not associated with tumor stage or G-category. However there was a tendency toward shorter survival times in patients showing intermediate- or high-frequency copy number abnormalities compared to those with low-frequency copy number changes. Moch et al.19 and Isola et al.20 had found a significant correlation between total number of genetic losses per tumor and poor survival in renal cell carcinoma and node-negative breast cancer, respectively. A correlation between number of genetic abnormalities per tumor and prognosis might support the hypothesis that development and progression of PCA is driven by a multistep process of a critical accumulation of genetic alterations comparable with the adenoma-carcinoma-sequence in colorectal cancer. However, this difference did not reach statistical significance in our study, possibly due to the small number of cases investigated.
Every single aberration was tested for association with clinico-pathologic staging according to UICC criteria and histological tumor grading. There were no significant differences between intermediately differentiated and poorly differentiated tumors with reference to specific chromosomal gains or losses except for losses of 1p in G2 tumors. Although gain of the short arm of chromosome 7 was only detected in three patients with poorly differentiated PCA this finding did not reach statistical significance. Concerning the analysis of association of chromosomal imbalances with UICC criteria, a diagnostic cut-off was set between tumors without (UICC I and II) and such with lymph node metastasis, that is, more advanced (UICC III and IV) tumors. Most of the aberrations showed no association with UICC stages and were detected in early and advanced tumors alike.
However, three specific chromosomal aberrations were correlated with tumor stages: gain of the short arm of chromosome 12 was only detected in stages I and II, that is, without metastatic spread but not in stages III and IV. Losses of chromosome 3p as well as 8p could only be identified in stages III and IV, that is, more advanced tumors, while other chromosomal imbalances were not associated with stages.
The overrepresentation of 12p coincides with the localization of the proto-oncogene k-RAS (12p12), which is known to be activated by point mutation in 90% of pancreatic adenocarcinomas.21 Since gain of 12p is a commonly described event in PCA, it can be suggested that overexpression of k-RAS by gene amplification may be another way of oncogene activation. Heidenblad et al.14 performed detailed genomic mapping and expression analysis of 12p amplifications in PCA cell lines and identified two genes (DEC 2 and PPFIBP1) at 12p1112, in addition to k-RAS, which showed increased expression in cell lines with amplifications of 12p. This implies that the short arm of chromosome 12 might harbor more than one gene critically involved in the tumorigenesis of PCA. The fact that gains of the short arm of chromosome 12 were selectively detected in small, node-negative tumors indicates that activation of oncogenes located on 12p is an early event involved in tumor initiation rather than in tumor progression.
Chromosome arms 3p and 8p are two of the most frequently altered regions in human cancers including several potential oncogenes and tumor suppressor genes. The FHIT tumor suppressor gene is one of the best known examples. Inactivation of FHIT is frequently involved in several human cancers such as lung,22 gastric,23 prostate24 and hepato-cellular carcinoma.25 Sorio et al.26 demonstrated FHIT expression in normal ductular epithelium of the pancreas. In PCA, FHIT expression was reduced and the authors concluded that cancer cells derived from FHIT-positive epithelial cells might have lost their FHIT expression during cancer development and progression. Moreover, FHIT expression was shown to delay tumor development, induce apoptosis and regulate cell cycle arrest in PCA.27,28 Other possible target genes at 3p include BRCA1 which is associated with increased risk of cancer of the breast, ovary, prostate and colon29 or the Von-Hippel-Lindau (VHL) gene which is associated with familial PCA as well as renal cell carcinoma.19
Similarly, 8p shows alterations in many human cancer types such as carcinomas of the lung, colon, breast or melanomas and lymphomas.30 Several gene candidates have been suggested. The N33 gene has been proposed as a tumor suppressor gene in prostate tumors.31 A role of DLC1 is assumed in hepato-cellular carcinoma as well as cancer of the lung, prostate, breast and colon. In PCA, expression of FGFR1 inhibits tumor growth in cancer cell lines.32 Seibold et al.33 described a new tumor suppressor gene located on 8p21.322, which they called MTSG1 (mitochondrial tumor suppressor gene 1). They found that MTSG1 is involved in the regulation of cellular transition from proliferation to quiescence and is associated with differentiation of PCA cell lines.
Selective losses of the short arm of chromosomes 3 and 8 in stage III and IV tumors in our study give support to the hypothesis that potential tumor suppressor genes located at these chromosomal sites might play a role in tumor progression of PCA.
However, the most important finding of our study was the statistically significant association of the gain of chromosome 8q with reduced survival time. This biomarker retained its significance when adjusted for factors such as age, gender, tumor grade, tumor stage and resection margin status. This suggests a potential biological significance for 8q gain in assessing malignant potential and prognosis of PCA.
Similar to other aberrations genetic alterations involving 8q have been reported in a number of solid tumors. In breast cancer,20 osteosarcomas,34 bladder cancer35 and prostate cancer36 gains of 8q have been correlated with poor prognosis and progression of the disease. The target gene for this gain is not known yet, but a number of potential oncogenes are located on the long arm of chromosome 8. The MYC oncogene correlates with poor survival in prostate cancer37 and tumor grading in PCA.38 Gain of EIF3S3, located at the distal part of 8q and encoding a eukaryotic translation initiation factor was found associated with high-grade and high-stage prostatic cancer.39 Furthermore, EIF3S3 seems to be associated with aggressive phenotype of hepatocellular carcinomas.40 Another candidate gene may be the PSCA which was found to be overexpressed in PCA.41 Overexpression of RCAS1, another potential oncogene located on 8q, correlates with poor prognosis of PCA.42 Focal adhesion kinase (FAK), also found at 8q24, has been shown to be overexpressed in several cancer types43 including PCA.44 Finally, a variety of other genes that have not yet been implicated in cancer development but are functionally related to processes involved in tumorigenesis are located on 8q, for example MMP16, a matrix metalloproteinase, ANGPT1, involved in development of vascular structures during embryogenesis or a number of zinc finger proteins, often involved in cancerous changes.36,45
In conclusion, we have created a map of genetic changes in early and advanced PCA and propose a new prognostic marker associated with poor patient outcome. Specifically, the presence of gain of chromosome 8q markedly was correlated with statistically reduced survival time. However, the statistic difference in survival cannot be called biologically significant in the long-term follow-up. This might be due to other tumorbiological factors that influence survival after resection of PCA. Infiltration of nerves and vessels, DNA-ploidy and wild-type mutations of p53, p16/CDKN2 and DPC4/SMAD4 are examples for significant prognostic parameters46 that were not analyzed but might have influenced survival of our patients.
Nevertheless, gain of chromosome 8q may be a new marker to assess prognosis and malignant potential of surgically resected PCA in the individual patient, thereby helping to identify patients at risk for recurrence that might profit from adjuvant therapy. However, the current findings are based on a relatively small number of patients and screening of large numbers of tumor probes will be necessary to further investigate the role of 8q in PCA and to delineate potential target genes at this chromosomal region that characterize development, progression and aggressiveness of PCA.
Received for publication May 26, 2006. Accepted for publication May 31, 2006.
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