Abstract 5124: Genomic and proteomic characterization of tamoxifen sensitive and resistant MCF7 cells
Authors: Gonzalez-Malerva Laura G. , Park Jin , Velmurugan Karthik , LaBaer Joshua , Mumenthaler Shannon 
Published: August 2012

Abstract
Among the most common and challenging aspect to the management of breast cancer is the development of tumor resistance to virtually all therapies. Our major research focus is to investigate genes and pathways that contribute to this process. We have previously derived a series of cultured breast cancer cell lines that were either highly sensitive or naturally resistant to tamoxifen to study the factors that lead to drug resistance. By comparing tamoxifen sensitive and resistant sub-clones we identified 227 genes that responded to tamoxifen in sensitive but not in resistant cells. From these, a signature of 67 genes demonstrated that women whose tumors matched the resistance pattern had a significantly greater likelihood of early relapse while on tamoxifen. Using automated high-throughput cell-based assays; we identified 31 kinases that repeatedly conferred resistance to tamoxifen when ectopically expressed. To further expand our understanding of the development of tamoxifen resistance to a genome level, we employed 6 of our tamoxifen-sensitive and -resistant sister cell lines. We previously showed that all 6 of these cell lines, which were all sub-cloned from the same parent without any drug selection, were identical for a set of 24 single nucleotide polymorphism (SNPs), confirming that they all derived from the same parent MCF7 line. We reasoned that they should be nearly identical genetically, thus allowing us to find genetic differences that account for the profound difference in drug response. For the genotyping, genomic DNA from an early passage of three independent sensitive and three resistant sub-clones were analyzed for copy number variation (CNV) and SNP by Illumina BeadArray and HiSeq200 next-generation sequencing. Preliminary analysis showed segregation between the genomic profiles of sensitive and resistant sub-clones in general. Chromosomes that showed more variation between sensitive and resistant sub-clones included chromosome number 2, 7, 10, 15 and 20. Visual examination of the data identified several regions of sub-clone specific chromosomal gain or loss across all chromosomes, where overlap regions across both sub-clones and regions that are either copy number gain in one cell but loss in the other one. Furthermore, by comparative analysis with cDNA microarray data, we also found that mRNA expression levels of several genes in these chromosomal regions were indeed correlated with their chromosomal status. In addition to a gene-level analysis, we are performing quantitative mass spectrometry analysis (SILAC) to identify the differences in proteomes of sensitive and resistant cells, which may account for molecular mechanisms underlying drug resistance.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5124. doi:1538-7445.AM2012-5124