Genetic Characterization of Bone and Soft Tissue Tumors

Bone and soft tissue tumors (BSTT) constitute a heterogeneous group of neoplasms of mesenchymal and neuroectodermal origin. Although many BSTT are rare, it has become clear that BSTT are characterized by recurrent acquired chromosomal aberrations, and the general aim of this thesis have been to apply molecular genetic and molecular cytogenetic techniques to further characterize recurrent breakpoints and deletions, and to search for candidate target genes. In the first study, 27 lipomatous tumors with 13q-rearrangements were analyzed by fluorescence in situ hybridization (FISH). The selected probes were dispersed over 22.5 Mb within 13q12-21. In 4 cases, the rearrangement was seemingly balanced; in the other 23 cases, unbalanced changes resulting in loss of 13q-material were detected. The deletions varied greatly in size, but a common region (~2.5 Mb) of deletion in band 13q14, distal to the RB1 gene locus, was deleted in 20 of the 23 cases. Deletion of one or more genes within this region could thus be of importance for the development of lipomatous tumors. In the second study, the status of the HMGA2 gene (12q15) was investigated by reverse transcription polymerase chain reaction (RT-PCR) in chondromatous tumors. The HMGA2 gene was activated by breakpoints within or upstream of the coding region in all chondromas with 12q13-15 changes. An HMGA2-LPP fusion gene, resulting from a t(3;12)(q27;q15), was detected in one soft tissue chondroma. Not all chondromas, however, showed 12q13-15/HMGA2 rearrangements, suggesting that other mechanisms than HMGA2 activation must be of importance. Among chondrosarcomas, no clear correspondence between cytogenetic findings and HMGA2 gene activation could be found. In the third study, combined FISH and RT-PCR analyses were used to identify and characterize of a previously undescribed ACTB-GLI fusion gene. An ACTB-GLI fusion transcript was detected in 5 tumors displaying a t(7;12)(p21-22;q13-15). A reciprocal GLI-ACTB fusion transcript was detected in 2 of the 5 cases. All tumors were highly vascularized and composed of spindle cells that expressed pericytic features. The tumors constitute a new entity: ?pericytoma with t(7;12)?. The ACTB-GLI and GLI-ACTB fusion breakpoints were further investigated at the DNA level by genomic PCR in the last study. Breakpoints were found in exonic and intronic sequences, and all cases were unbalanced at the DNA-level. Short common oligomers, possibly of importance for recombination, were present at the breakpoints.