Gene expression analysis of bone tumors

Subungual exostosis is a benign bone- and cartilage-forming tumor known to harbour a pathognomonic t(X;6)(q22;q13-14). Using global gene expression analysis and quantitative real-time PCR we could show that this translocation results in increased expression of the IRS4 gene, presumably due to disruption and/or exchange of regulatory sequences with the translocation partner, the COL12A1 gene. A corresponding deregulation at the protein level could be demonstrated in primary cell cultures using a combination of fluorescence in situ hybridization and immunostaining. As the t(X;6) usually is the sole cytogenetic aberration in subungual exostosis, the deregulated expression of IRS4 is likely to be pathogenetically essential. Gene expression analysis of bone tumors. Total RNA was extracted from five frozen bone tumor biopsies (two osteochondromas, two cases of BPOP, one subungual exostosis), cDNA was generated, fragmented and end-labelled. The fragmented and biotinylated cDNA was hybridized to the GeneChipR Human Gene 1.0 ST Arrays (Affymetrix).