New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays

Amplification of the ERBB2 oncogene at 17q12 has been well documented in br east cancer and has been shown to contribute to a poor clinical outcome. Ho wever, systematic surveys of copy number and expression levels of all genes within the 17q12 region have not been performed. Here, we used cDNA and co mparative genomic hybridization microarray technologies to undertake a broa d survey of genes involved in the 17q12 amplification in breast cancer. A c hromosomal region-specific cDNA microarray containing 217 expressed sequenc e tag (EST) clones from 17q12 was constructed and used for parallel analysi s of gene copy numbers and expression levels in seven breast cancer cell li nes allowing direct identification of genes whose expression is elevated be cause of an increase in copy number in this chromosomal region. The copy nu mber and expression survey identified 12 transcripts that showed a consiste nt pattern of increased copy number and expression in three or more of the 17q12-amplified cell lines. As expected, these included ERBB2 as well as th e GRB7 and MLN64 genes previously shown to be coamplified with ERBB2. In ad dition, five other known genes and four uncharacterized ESTs were also foun d to be consistently activated by amplification in these breast cancer cell lines. Amplicon mapping by fluorescence in situ hybridization revealed a m inimal common region of amplification containing four highly expressed gene s, ERBB2, GRB7, MLN64, and an uncharacterized EST 48582. Furthermore, sever al other genes, although not located in the minimal common region of amplif ication, showed a correlated pattern of amplification and expression indica ting that they might play a role in breast cancers with the 17q12 amplifica tion. In conclusion, parallel analysis of gene copy number and expression l evels by cDNA microarray can be used to directly identify candidate target genes involved in amplifications. Our results show that the 17q12 amplifica tion in breast cancer leads to the simultaneous elevation of expression lev els of several genes.