Characterizing Candidate Oncogenes at 8q21 in Breast Cancer

Abstract : Breast cancer carcinogenesis is caused by molecular genetic changes. These genetic changes ultimately affect the transcriptome. Copy number alterations of the genome is a cardinal feature of cancer and plays an important role in tumor progression by altering the gene expression program. These regions of alteration are associated with oncogenes and tumor suppressor genes of known and unknown identity. Characterization of both CNA's and gene expression profiles have been carried out on breast tumor specimens using microarray technology to gain further insight into the progression of this disease. We comprehensively characterized both DNA copy number changes and captured the gene expression profiles of 50 breast cancer cell lines, widely used model systems for the study of breast cancer. We found that the cell lines could be classified into three main subtypes, Luminal, Basal A, and Basal B by clustering of gene expression. Overall, this is similar to what is seen in the gene expression analysis of the tumors however, distinct differences were found. Analysis of the copy number profile revealed that the cell lines recapitulated the main genetic changes represented in the tumor data set but contained more changes. Finally, caution should be employed with choosing the appropriate cell line model system when studying specific processes in breast cancer.