Molecular Characterization of Genomic Amplifications in Pancreatic Cancer

Abstract: Pancreatic cancer includes multiple histologic subtypes that show large differences in their clinical and biological characteristics. Despite this diversity, more than 85% of the neoplasms in the organ are malignant ductal adenocarcinomas, which are the focus of the present thesis. At the genetic level this tumor type is characterized by highly rearranged karyotypes, resulting in a large number of DNA copy number alterations. As these are believed to play a major role in pancreatic tumorigenesis, the aim of the present thesis was to molecularly characterize such imbalances, particularly genomic amplifications, in a panel of 32 pancreatic carcinoma cell lines. The first study was based on previously generated CGH data, which indicated frequent local amplifications of 12p11-12. For precise characterization of this region, we used single-copy FISH analysis and PCR-based STS mapping. This delineated a commonly amplified segment of 3.5 Mb in six cases. To identify potential target genes in this region, a chromosome segment-specific cDNA array containing 29 genes/ESTs, were used to search for consistently overexpressed genes. This analysis identified four genes/ESTs, including PPFIBP1 and DEC2. In the second study we performed array-based CGH for high-resolution mapping of genome-wide DNA copy number alterations. For this purpose, two separate microarray platforms were used, the first containing >3,500 BAC clones and the second encompassing >25,000 cDNA clones. In total, 60 amplifications at 32 different genomic loci were characterized in detail. The most frequently amplified regions were located in 8q23-24 and 12p11-12. Apart from the large number of genomic amplifications, the array-based CGH analyses identified several homozygously deleted segments, including sequences within 9p24, 9p21, 9q32, 10p12, 10q22, 12q24, and 18q23. In the third study we performed expression profiling to investigate the transcriptional consequences of the genomic alterations identified by the array-based CGH analyses. This investigation showed a strong correlation between DNA copy numbers and gene expression levels in pancreatic cancer. Moreover, the expression analysis revealed that the most commonly amplified regions do not appear to have a single target gene. Instead, the results suggested that several target genes may be of importance in each amplified segment, and that these may show varying degrees of overexpression in individual amplifications. Nevertheless, the expression profiling study identified new genes in both the 8q23-24, and the 12p11-12, amplicons of potential importance for the development of pancreatic cancer.