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E-GEOD-34800 - A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion

Status
Released on 3 March 2012, last updated on 24 June 2012
Organism
Homo sapiens
Samples (14)
Array (1)
Protocols (7)
Description
The identification of subtype-specific translocations has revolutionized diagnostics of sarcoma and provided new insight into oncogenesis. We used RNA-Seq to investigate samples diagnosed as small round cell tumors of bone, possibly Ewing sarcoma, but lacking the canonical EWSR1-ETS translocation. A new fusion was observed between the BCL6 co-repressor (BCOR) and the testis specific cyclin B3 (CCNB3) genes on chromosome X. RNA-Seq results were confirmed by RT-PCR and cloning the tumor-specific genomic translocation breakpoints. 24 BCOR-CCNB3-positive tumors were identified among a series of 594 sarcomas. Gene profiling experiments indicate that BCOR-CCNB3-positive cases are biologically distinct from other sarcomas, particularly Ewing’s sarcoma. Finally, we show that CCNB3 immunohistochemistry is a powerful diagnostic marker for this group of sarcoma and that over-expression of BCOR-CCNB3 or of a truncated CCNB3 activates S-phase in NIH3T3 cells. Thus the intrachromosomal X fusion described here represents a new subtype of bone sarcoma caused by a novel gene fusion mechanism. Comparison of expression profiles of 10 BCOR-CCNB3 samples (plus 4 EWS-FLI1 Ewing sarcomas samples as control) with publicly available profiles of other tumor types.
Experiment type
transcription profiling by array 
Contacts
Franck Tirode <geo@ncbi.nlm.nih.gov>, Carlo Lucchesi, Gaelle Pierron, Jean-Michel Coindre, Olivier Delattre, Sarah Cohen-Gogo, Stelly Ballet, Stéphanie Reynaud, Virginie Perrin
Citation
A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion. Pierron G, Tirode F, Lucchesi C, Reynaud S, Ballet S, Cohen-Gogo S, Perrin V, Coindre JM, Delattre O. , PMID:22387997
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-34800.idf.txt
Sample and data relationshipE-GEOD-34800.sdrf.txt
Raw data (1)E-GEOD-34800.raw.1.zip
Processed data (1)E-GEOD-34800.processed.1.zip
Array designA-AFFY-44.adf.txt
Links