Pancreatic cancer is a devastating disease with high mortality. This is mainly due to the lack of effective treatment regimens and tools to identify tumors at early stage of development. To improve the poor prognosis of this disease, we need to identify new molecular markers for earlier diagnosis as well as new therapeutic targets. Microarray-based technologies have provided us better tools to identify putative novel cancer genes. Previously, we performed a genome-wide copy number survey in pancreatic cancer cell lines using comparative genomic hybridization (CGH) on cDNA microarrays and identified 24 independent amplified regions. Here, we aimed to characterize more precisely one of the amplified regions, the 19q13 locus, to identify genes that might be of importance in pancreatic carcinogenesis. Public genome databases (http://www.ncbi.nlm.nih.gov/ and http://www.genome.ucsc.edu/) were used to select 15 BAC clones evenly distributed over this 2.9 Mb amplicon. Fluorescence in situ hybridization (FISH) with labeled BAC probes was performed in 16 pancreatic cell lines to define copy number alterations. FISH analyses confirmed the array CGH results and revealed extremely high level amplification (up to 20-fold) in PANC-1 cell line as well as lower level amplification in SU.86.86 and HPAC cell lines. FISH analysis also allowed us to narrow down the amplicon core to 1.1 Mb. The cell line copy number data was further validated in primary pancreatic tumors using FISH to a tissue microarray containing 33 indi vidual pancreatic cancer samples. High-level copy number increase of the 19q13 region was observed in three cases (9%). The 1.1 Mb core region of amplification contains 40 genes, including 24 known genes and 16 hypothetical proteins. expression levels of these transcripts were evaluated in the same set of cell lines using quantitative real-time RT-PCR. Interestingly, PANC-1 cells showed highly elevated expression levels of all genes located within the amplified region, thus suggesting that the high level amplification observed in this cell line overrules general transcription regulation mechanisms. In contrast, the SU.86.86 and HPAC cell lines with low level amplification showed a more specific expression pattern with a subset of genes having elevated expression levels. Taken together, a detailed characterization of the 19q13 amplicon in pancreatic cancer cell lines delineated a minimal region of amplification to 1.1 Mb. The presence of this amplicon was validated also in primary pancreatic tumors. expression profiling revealed a small set of biologically interesting genes that were more strongly expressed in the amplified cell lines than in the non-amplified group. In addition, a unique pattern of overexpression throughout the amplicon was observed in PANC-1 cells.
[Proc Amer Assoc Cancer Res, Volume 47, 2006]