Renal cell carcinoma primary cultures as in vitro model to study genomic profile of parental tumor tissues

Clear cell renal carcinoma (RCC) accounts for 80% of all primary kidney malignancies. It is characterized by recurrent copy number (CN) alterations (amplifications and deletions) and loss of heterozygosity (LOH) events and many evidences suggest that this peculiar pattern of genomic instability may be useful in diagnostic and prognostic applications. However, molecular analyses of this pathology are complicated because bioptic tumor tissues are highly variegated and comprise a mixture of tumor and normal cells. In the context of an Italian oncological research project aimed to the identification of novel RCC molecular markers, we investigated the possibility to use short-term primary cultures as in vitro model of the parental tumors to study their genomic profiles and characterize their CN alterations. Using the Affymetrix 50K SNP Mapping microarray platform, we performed a high-throughput genomic profiling analysis of 10 pairs of RCC primary culture/original tumor tissue sample and assembled a genome-wide map of amplifications, deletions and LOH occurring in each sample by CNAGv3.0 software. Comparing each primary culture to the corresponding tissue, we found that 9 out of 10 cultures had a genomic profile concordant to the parental tumors: all CN alterations and LOH events occurring in matched tumor tissues were maintained and the typical RCC molecular signature was confirmed (e.g chromosome 3p loss and 5q gain); moreover, in 6 out of these 9 cultures CN alterations were better discriminated than in tumor parental tissues, and this phenomenon particularly affected the CN loss events. We observed that 4 cultures acquired additional CN alterations, such as amplifications or deletions on one or two chromosomes. Additionally, one RCC primary culture showed a diploid status as compared to parental tissue, suggesting the possibility that a normal clone population has been selected by culturing. We concluded that RCC primary cultures at early passages maintained the genomic profile of parental tumor tissues and showed an increased cell homogeneity and enrichment in tumor cells. Thus, we suggest that the short-term RCC primary cultures are a reliable model to study this pathology and to identify novel genetic elements potentially involved in its etiology and useful in clinical applications. This work was supported by MIUR grants RBLA03ER38 and PRIN 2006.