Gene Expression Profiling of Microdissected Pancreatic Ductal Carcinomas Using High-Density DNA Microarrays

Abstract

Pancreatic ductal adenocarcinoma (PDAC) remains an important cause of malignancy-related death and is the eighth most common cancer with the lowest overall 5-year relative survival rate. To identify new molecular markers and candidates for new therapeutic regimens, we investigated the gene expression profile of microdissected cells from 11 normal pancreatic ducts, 14 samples of PDAC, and 4 well-characterized pancreatic cancer cell lines using the Affymetrix U133 GeneChip set. RNA was extracted from microdissected samples and cell lines, amplified, and labeled using a repetitive in vitro transcription protocol. Differentially expressed genes were identified using the significance analysis of microarrays program. We found 616 differentially expressed genes. Within these, 140 were also identified in PDAC by others, such as Galectin-1, Galectin-3, and MT-SP2. We validated the differential expression of several genes (e.g., CENPF, MCM2, MCM7, RAMP, IRAK1, and PTTG1) in PDAC by immunohistochemistry and reverse transcription polymerase chain reaction. We present a whole genome expression study of microdissected tissues from PDAC, from microdissected normal ductal pancreatic cells and pancreatic cancer cell lines using high-density microarrays. Within the panel of genes, we identified novel differentially expressed genes, which have not been associated with the pathogenesis of PDAC before.

Co-expression of KLK6 and KLK10 as prognostic factors for survival in pancreatic ductal adenocarcinoma

“…We scored genes as differentially expressed if they displayed a fold change 42. To identify signature genes we used the method described elsewhere (Grutzmann et al, 2004). Datasets are accessible (Arrayexpress E-MEXP-1121 and E-MEXP-950).…”

Tumor-associated CD75s- and iso-CD75s-gangliosides are potential targets for adjuvant therapy in pancreatic cancer

“…The study was carried out with institutional review board consent using tissue samples from 38 patients that have undergone surgery for their primary tumors under an approved protocol of the local ethic committees of the University Hospital Dresden (20) and the University Hospital Mü nster (15). Tumor histology was determined according to the criteria of the WHO.…”

Complementary effects of HDAC inhibitor 4-PB on gap junction communication and cellular export mechanisms support restoration of chemosensitivity of PDAC cells

“…Pancreatic carcinoma cell lines COLO 357, Panc 1, T3M-4; BxPc3 (Sipos et al, 2003) and primary human fibroblasts were grown as described (Grutzmann et al, 2004). HPDE6-E6E7-c7 cells (H6c7) (Furukawa et al, 1996;Ouyang et al, 2000) were grown in a medium containing FCS (10%, PAN Biotech, Aidenbach, Germany), RPMI 1640 (45%), Keratinocyte-SFM (45%), Bovine Pituitary Extract (25 mg l À1 ) and hEGF (2.5 mg l À1 , all Invitrogen, Karlsruhe, Germany).…”

“…Deregulated genes in PDAC have been published recently by us and others (Crnogorac-Jurcevic et al, 2002;Iacobuzio-Donahue et al, 2003;Logsdon et al, 2003;Grutzmann et al, 2004). These genes included candidates involved in cell cycle control, apoptosis, cell motility or other tumour relevant pathways, but druggable key players have to be defined yet.…”