Gene expression analysis of bone tumors. Homo sapiens

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. Overall design: 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).