Differential expression of multiple genes in association with MADH4/DPC4/SMAD4 inactivation in pancreatic cancer

The Gene Logic Inc. Gene Express(R) tools and Affymetrix GeneChip(R) arrays were utilized to discover genes differentially expressed in pancreatic cancers with MADH4/DPC4/SMAD4 gene inactivation. cDNA was prepared from thirteen pancreas cancer cell lines with known MADH4 status (5 with wild-type MADH4 and 8 with inactivated MADH4) and hybridized to the complete Affymetrix Human Genome U133 GeneChip(R) set (arrays U133 A,B) for simultaneous analysis of 45,000 gene fragments corresponding to 33,000 known genes. 25 known genes were identified as down-regulated at least three fold in the MADH4 mutant cancer cell lines. 9 were decreased in expression at least 5 fold, and 1 in particular (ID3) was decreased 23 fold. Only 2 of the 25 down-regulated genes (ID1 and ID3) have been previously reported as MADH4-dependent targets, and the remaining 23 genes represent potential novel direct or indirect MADH4 downstream targets. Immunolabeling for Id1 and Id3 did not show a relationship with known MADH4 status in pancreatic cancer tissues, suggesting additional regulation of these two genes than activation by MadH4. Further investigations to validate and to determine the significance of these candidate target genes in pancreatic carcinogenesis and progression are warranted.