title: Microarray analyses reveal strong influence of DNA copy number alterations on the transcriptional patterns in pancreatic cancer: implications for the interpretation of genomic amplifications.
abstract: DNA copy number alterations are believed to play a major role in the development and progression of human neoplasms. Although most of these genomic imbalances have been associated with dysregulation of individual genes, their large-scale transcriptional consequences remain unclear. Pancreatic carcinomas frequently display gene copy number variation of entire chromosomes as well as of chromosomal subregions. These changes range from homozygous deletions to high-level amplifications and are believed to constitute key genetic alterations in the cellular transformation of this tumor type. To investigate the transcriptional consequences of the most drastic genomic changes, that is, genomic amplifications, and to analyse the genome-wide transcriptional effects of DNA copy number changes, we performed expression profiling of 29 pancreatic carcinoma cell lines and compared the results with matching genomic profiling data. We show that a strong association between DNA copy numbers and mRNA expression levels is present in pancreatic cancer, and demonstrate that as much as 60% of the genes within highly amplified genomic regions display associated overexpression. Consequently, we identified 67 recurrently overexpressed genes located in seven precisely mapped commonly amplified regions. The presented findings indicate that more than one putative target gene may be of importance in most pancreatic cancer amplicons.
authors.affiliation: Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden. markus.heidenblad@klingen.lu.se
authors.forename: Markus
authors.initials: M
authors.lastname: Heidenblad
authors.forename: David
authors.initials: D
authors.lastname: Lindgren
authors.forename: Joris A
authors.initials: JA
authors.lastname: Veltman
authors.forename: Tord
authors.initials: T
authors.lastname: Jonson
authors.forename: Eija H
authors.initials: EH
authors.lastname: Mahlamäki
authors.forename: Ludmila
authors.initials: L
authors.lastname: Gorunova
authors.forename: Ad Geurts
authors.initials: AG
authors.lastname: van Kessel
authors.forename: Eric F P M
authors.initials: EF
authors.lastname: Schoenmakers
authors.forename: Mattias
authors.initials: M
authors.lastname: Höglund
mesh_terms: D002874:Chromosome Mapping; D005784:Gene Amplification; D018628:Gene Dosage; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010190:Pancreatic Neoplasms / Q000235:genetics*