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

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Abstract

The identification of subtype-specific translocations has revolutionized the diagnostics of sarcoma and has provided new insight into oncogenesis. We used RNA-seq to investigate samples from individuals diagnosed with small round cell tumors of bone, possibly Ewing sarcoma, but which lacked the canonical EWSR1-ETS translocation. A new fusion was observed between BCOR (encoding the BCL6 co-repressor) and CCNB3 (encoding the testis-specific cyclin B3) on the X chromosome. RNA-seq results were confirmed by RT-PCR and through cloning of the tumor-specific genomic translocation breakpoints. In total, 24 BCOR-CCNB3–positive tumors were identified among a series of 594 sarcoma cases. Gene profiling experiments indicated that BCOR-CCNB3–positive cases are biologically distinct from other sarcomas, particularly Ewing sarcoma. Finally, we show that CCNB3 immunohistochemistry is a powerful diagnostic marker for this subgroup of sarcoma and that overexpression of BCOR-CCNB3 or of truncated CCNB3 activates S phase in NIH3T3 cells. Thus, the intrachromosomal X-chromosome fusion described here represents a new subtype of bone sarcoma caused by a newly identified gene fusion mechanism.

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Figure 1: RNA-seq identification of the BCOR-CCNB3 fusion.
Figure 2: Characterization of the BCOR-CCNB3 genomic rearrangement and demonstration of its recurrence in small round cell sarcomas.
Figure 3: BCOR-CCNB3–positive cases are distinct from other small round cell tumors and particularly from Ewing sarcoma.
Figure 4: Functional consequences of BCOR-CCNB3 expression.
Figure 5: Expression of CCNB3 across a series of tumors.

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Acknowledgements

We thank S. Chanock for fruitful discussions and critical reading of the manuscript. We are indebted to V. Raynal, P. Legoix-Ne, A. Nicolas, D. Gentien, S. Lair, A. Lermine and E. Barillot for critical technical help. We thank the following individuals for contributing cases and paraffin blocks or for supplying clinical information: J. Champigneulle, A. Croue, P. Dechelotte, J.M. Guinebretière, C. Jeanne-Pasquier, A. Moreau, J.M. Picquenot, D. Ranchère-Vince, X. Sastre-Garau, P. Terrier, M.C. Vacher-Lavenue, V. Verkaere and L. Guillou. We thank E. Louis, S. Thoraval and T. Scarcez from the Life Science Company for help in applying SOLiD technology. We also thank N. Bretschneider, C. Gugenmus, M. Scherf and M. Seifert from the Genomatix company for the analysis of data. This work was supported by grants from the Ligue Nationale Contre le Cancer (Equipe Labellisée and Carte d'ldentité des Tumeurs program), the Région Île de France, the Institut National du Cancer (INCa; 2008-044, 0627 and ZP09-027-EPI), the European Union (European Embryonal Tumors pipeline) and the following associations: Courir pour Mathieu, Dans les Pas du Géant, Olivier Chape, Les Bagouzamanon and Les Amis de Claire.

Author information

S.B. performed the next-generation sequencing analysis. G.P., S.R. and S.B. characterized the initial case and screened the individuals with sarcoma. C.L. and F.T. performed all the bioinformatics analyses. J.-M.C. performed pathological review of the cases and CCNB3 immunohistochemistery experiments. S.C.-G. contributed the analysis of clinical files and, with V.P. performed the cloning and cell cycle analyses for BCOR-CCNB3 and ΔCCNB3 cDNA. G.P., F.T. and O.D. planned and supervised the work, and all authors contributed to writing the manuscript.

Correspondence to Olivier Delattre.

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