Elevated levels of protein kinase C (PKC) are associated with increased metastatic capacity in both human breast cancer cells and breast tumors. MCF-7 breast cancer cells stably transfected with PKC-alpha were recently shown to display a more aggressive phenotype and increased tumorigenicity in nude mice. To identify genes involved in the progression to the aggressive phenotype, mRNA differential display was performed to isolate cDNAs that are differentially expressed between the parental, non-metastatic MCF-7 cell line and the metastatic derivative MCF-7-PKC-alpha cell line. One cDNA was identified which was upregulated and four cDNAs were downregulated in MCF-7-PKC-alpha cells. The upregulated cDNA may be a differentiation-specific gene as it is 100% homologous to a putative glialblastoma cell differentiation-related protein, GBDR1. DNA sequence analysis and flow cytometry revealed that three of the downregulated cDNAs correspond to histone 3.B, and integrins alpha3 and alpha6. The fourth downregulated cDNA clone, G2Q, is a novel sequence. G2Q is expressed in normal breast and bronchial tissue, but is downregulated in a variety of tumor cell lines and in aggressive primary and secondary breast tumors, suggesting that G2Q may be a useful prognostic indicator of tumor aggressiveness. Further, downregulation of G2Q expression in the non-metastatic MCF-7 cells by antisense oligonucleotides resulted in increased in vitro invasive capacity of these cells in a Matrigel matrice. This study provides the basis for identifying new genes involved in breast tumor progression and the role that PKC plays in the pathogenesis of this cancer.