Oligonucleotide microarray expression analysis of genes whose expression is correlated with tumorigenic and non-tumorigenic phenotype of HeLa X humanfibroblast hybrid cells

In order to understand the differences and similarities between tumorigenic and non-tumorigenic HeLa x human fibroblast hybrids, gene expression profi les were examined with synthetic oligonucleotide arrays containing nearly 7 000 gene probe sets. We used two pairs of genetically related hybrids, each pair representing individual clones of non-tumorigenic and tumorigenic seg regant hybrids, respectively. Analysis of six possible comparisons, utilizi ng two algorithms, identified 204 genes with differential expression. The g reater number of differentially expressed genes was observed when non-tumor igenic hybrids were compared with tumorigenic segregants. Fifteen and 14 ge nes, respectively, were consistently found to be differentially expressed i n non-tumorigenic and tumorigenic cells. Among those 29 differentially expr essed genes, three (intestinal alkaline phosphatase, caveolin-1, and solute carrier family2, member3) have been reported previously to be associated w ith the tumorigenic phenotype, using the same hybrid pairs. In addition, am ong the genes previously detected by differential display, 78% of them exhi bited more than 5-fold change, demonstrating a high consistency between the two methods of differential gene expression. These findings suggest that s ynthetic oligonucleotide arrays are a powerful and highly reproducible tool to identify those genes whose expression is associated with certain phenot ypes. (C) 2001 Elsevier Science Ireland Ltd. All rights reserved.