CDNA-based comparative genomic hybridization (cCGH) analysis of genomic aberrations of pancreatic cancer cells

Abstract

4122 Introduction: Pancreatic carcinoma (PanCa) is the fourth leading cause of cancer mortality in US with a 5-year survival rate of 5%. urrent treatments have only a minimal survival benefit. In this study, we are using cDNA-based comparative genomic hybridization (cCGH) technologies to search for common genomic alternations in human PanCa cell lines. Methods: Genomic DNA from seven human PanCa cell lines was extracted and labeled with Cyanine 3-dUTP. Normal human genomic DNA isolated from leukocytes of healthy male and female volunteers was labeled with Cyanine 5-dUTP. The labeled probe mixtures were then hybridized with 10K (5K in replicates) cDNA slides prepared by the UT MD Anderson Cancer Genomics Core Laboratory. The gain or loss of individual genes after background subtraction and appropriate normalization. The identified genomic alternations were then verified by florescent in situ hybridization (FISH) analysis in pancreatic cells and biopsy tissues with human BAC clone DNA and the centromere controls. Results: We successfully performed cCGH analysis using 7 pancreatic cancer cell lines. Our data revealed that human hepatocyte nuclear factor-6 (HNF6), telomeric repeat binding factor 2 (TRF2), reticulocalbin 2 EF-hand calcium binding domain (RCN2), and bromodomain testis-specific (BRDT) were amplified by more than 6 copies and fucose-1-phosphate guanyltransferase (FPGT) lost two endogenous copies in 43 to 71% of the PanCa cell lines studied (see the attached table). The genomic amplifications of HNF6 and TRF2 have been validated by FISH assays. We are validating FISH analysis for RCN3, BRDT and FPGT and with PanCa tissues from primary and metastatic tumors. Conclusions: We identified 4 genes with 6+fold gain and one gene with complete loss in PanCa cell lines. Two of these genes have been validated by the FISH analysis. Using similar analyses with patient tissues, we are searching for predictive and prognostic genomic markers and new therapeutic targets for improving PanCa survival (Supported by a pilot study grant and a T32 training grant from UT MD Anderson Cancer Center and NCI). Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration M.D. Anderson Cancer Center; National Cancer Institute