Comparative analysis of imbalances in genomic DNA and mRNA expression levels in chondrosarcoma-derived cell line FSCP-1

Malignant cell transformation results from multiple biological alterations including chromosomal abnormalities, oncogene activation, loss of suppressor gene function and a imbalance in cell regulating processes. The aim of our study was to combine gene expression and genomic analysis to evaluate the cellular phenotype of a chondrosarcoma cell line, which is potentially a useful in vitro model system for physiological and/or neoplastic chondrocytes. cDNA-array, quantitative PCR and comparative genomic hybridization (CGH) technologies were used to analyze gene expression profiles of chondrosarcoma cell line FSCP-1 in correlation to changes of DNA copy number on corresponding chromosomal sections. Gene expression analysis revealed similarities, but also great differences in between the chondrosarcoma cell line and physiological chondrocytes. In particular the proliferative activity was up-regulated and molecules involved in matrix synthesis and turnover down-regulated. CGH analysis revealed a heterogeneous pattern of DNA gains or losses. The c-myc oncogene, located on 8q24.12-q24.13, was the only gene with a marked up-regulation located on a chromosome section with a gain of DNA copy number. The inability of the chondrosarcoma cell line FSCP-1 to maintain an adequate matrix turnover as well as a notable proliferative activity is similar to neoplastic chondrosarcoma in vivo. The limited correlation between the CGH analysis and the gene expression pattern supports the notion that also in neoplastic cells most genes are not primarily regulated by the gene dosage, but by cellular regulation pathways. However, genes such as c-myc might represent significant exceptions potentially relevant for the clinico-biological behavior of the neoplasms.