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Novel BRD4–NUT fusion isoforms increase the pathogenic complexity in NUT midline carcinoma

Oncogene volume 32, pages 4664–4674 (2013)Cite this article

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Abstract

Nuclear protein in testis (NUT)-midline carcinoma (NMC) is a rare, aggressive disease typically presenting with a single t(15;19) translocation that results in the generation of a bromodomain-containing protein 4 (BRD4)–NUT fusion. PER-624 is a cell line generated from an NMC patient with an unusually complex karyotype that gave no initial indication of the involvement of the NUT locus. Analysis of PER-624 next-generation transcriptome sequencing (RNA-Seq) using the algorithm FusionFinder identified a novel transcript in which Exon 15 of BRD4 was fused to Exon 2 of NUT, therefore differing from all published NMC fusion transcripts. The three additional exons contained in the PER-624 fusion encode a series of polyproline repeats, with one predicted to form a helix. In the NMC cell line PER-403, we identified the ‘standard’ NMC fusion and two novel isoforms. Knockdown by small interfering RNA in either cell line resulted in decreased proliferation, increased cell size and expression of cytokeratins consistent with epithelial differentiation. These data demonstrate that the novel BRD4–NUT fusion in PER-624 encodes a functional protein that is central to the oncogenic mechanism in these cells. Genomic PCR indicated that in both PER-624 and PER-403, the translocation fuses an intron of BRD4 to a region upstream of the NUT coding sequence. Thus, the generation of BRD4–NUT fusion transcripts through post-translocation RNA-splicing appears to be a common feature of these carcinomas that has not previously been appreciated, with the mechanism facilitating the expression of alternative isoforms of the fusion. Finally, ectopic expression of wild-type NUT, a protein normally restricted to the testis, could be demonstrated in PER-403, indicating additional pathways for aberrant cell signaling in NMC. This study contributes to our understanding of the genetic diversity of NMC, an important step towards finding therapeutic targets for a disease that is refractory to current treatments.

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References

  1. French CA . Pathogenesis of NUT midline carcinoma. Annu Rev Pathol 2012; 7: 247–265.

    Article  CAS  Google Scholar 

  2. French CA, Ramirez CL, Kolmakova J, Hickman TT, Cameron MJ, Thyne ME et al. BRD-NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and maintain the growth of carcinoma cells. Oncogene 2008; 27: 2237–2242.

    Article  CAS  Google Scholar 

  3. Shehata BM, Steelman CK, Abramowsky CR, Olson TA, French CA, Saxe DF et al. NUT midline carcinoma in a newborn with multiorgan disseminated tumor and a 2-year-old with a pancreatic/hepatic primary. Pediatr Dev Pathol 2010; 13: 481–485.

    Article  Google Scholar 

  4. French CA . Demystified molecular pathology of NUT midline carcinomas. J Clin Pathol 2010; 63: 492–496.

    Article  Google Scholar 

  5. Kees UR, Mulcahy MT, Willoughby ML . Intrathoracic carcinoma in an 11-year-old girl showing a translocation t(15;19). Am J Pediatr Hematol Oncol 1991; 13: 459–464.

    Article  CAS  Google Scholar 

  6. Kubonishi I, Takehara N, Iwata J, Sonobe H, Ohtsuki Y, Abe T et al. Novel t(15;19)(q15;p13) chromosome abnormality in a thymic carcinoma. Cancer Res 1991; 51: 3327–3328.

    CAS  PubMed  Google Scholar 

  7. Kuzume T, Kubonishi I, Takeuchi S, Takeuchi T, Iwata J, Sonobe H et al. Establishment and characterization of a thymic carcinoma cell line (Ty-82) carrying t(15;19)(q15;p13) chromosome abnormality. Int J Cancer 1992; 50: 259–264.

    Article  CAS  Google Scholar 

  8. Bauer D, Mitchell C, Strait K, Lathan C, Stelow E, Lueer S et al. Clinicopathologic features and long-term outcomes of NUT midline carcinoma. Clin Cancer Res 2012; 18: 5773–5779.

    Article  Google Scholar 

  9. French CA, Kutok JL, Faquin WC, Toretsky JA, Antonescu CR, Griffin CA et al. Midline carcinoma of children and young adults with NUT rearrangement. J Clin Oncol 2004; 22: 4135–4139.

    Article  CAS  Google Scholar 

  10. Reynoird N, Schwartz BE, Delvecchio M, Sadoul K, Meyers D, Mukherjee C et al. Oncogenesis by sequestration of CBP/p300 in transcriptionally inactive hyperacetylated chromatin domains. EMBO J 2010; 29: 2943–2952.

    Article  CAS  Google Scholar 

  11. Schwartz BE, Hofer MD, Lemieux ME, Bauer DE, Cameron MJ, West NH et al. Differentiation of NUT midline carcinoma by epigenomic reprogramming. Cancer Res 2011; 71: 2686–2696.

    Article  CAS  Google Scholar 

  12. Toretsky JA, Jenson J, Sun CC, Eskenazi AE, Campbell A, Hunger SP et al. Translocation (11;15;19): a highly specific chromosome rearrangement associated with poorly differentiated thymic carcinoma in young patients. Am J Clin Oncol 2003; 26: 300–306.

    PubMed  Google Scholar 

  13. Vargas SO, French CA, Faul PN, Fletcher JA, Davis IJ, Dal Cin P et al. Upper respiratory tract carcinoma with chromosomal translocation 15;19: evidence for a distinct disease entity of young patients with a rapidly fatal course. Cancer 2001; 92: 1195–1203.

    Article  CAS  Google Scholar 

  14. Haack H, Johnson LA, Fry CJ, Crosby K, Polakiewicz RD, Stelow EB et al. Diagnosis of NUT midline carcinoma using a NUT-specific monoclonal antibody. Am J Surg Pathol 2009; 33: 984–991.

    Article  Google Scholar 

  15. French CA, Miyoshi I, Aster JC, Kubonishi I, Kroll TG, Dal Cin P et al. BRD4 bromodomain gene rearrangement in aggressive carcinoma with translocation t(15;19). Am J Pathol 2001; 159: 1987–1992.

    Article  CAS  Google Scholar 

  16. French CA, Miyoshi I, Kubonishi I, Grier HE, Perez-Atayde AR, Fletcher JA . BRD4-NUT fusion oncogene: a novel mechanism in aggressive carcinoma. Cancer Res 2003; 63: 304–307.

    CAS  Google Scholar 

  17. Tanaka M, Kato K, Gomi K, Yoshida M, Niwa T, Aida N et al. NUT midline carcinoma: Report of 2 Cases Suggestive of Pulmonary Origin. Am J Surg Pathol 2012; 36: 381–388.

    Article  Google Scholar 

  18. Engleson J, Soller M, Panagopoulos I, Dahlen A, Dictor M, Jerkeman M . Midline carcinoma with t(15;19) and BRD4-NUT fusion oncogene in a 30-year-old female with response to docetaxel and radiotherapy. BMC Cancer 2006; 6: 69.

    Article  Google Scholar 

  19. Haruki N, Kawaguchi KS, Eichenberger S, Massion PP, Gonzalez A, Gazdar AF et al. Cloned fusion product from a rare t(15;19)(q13.2;p13.1) inhibit S phase in vitro. J Med Genet 2005; 42: 558–564.

    Article  CAS  Google Scholar 

  20. Francis RW, Thompson-Wicking K, Carter KW, Anderson D, Kees UR, Beesley AH . FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data. PLoS One 2012; 7: e39987.

    Article  CAS  Google Scholar 

  21. Yan J, Diaz J, Jiao J, Wang R, You J . Perturbation of BRD4 protein function by BRD4-NUT protein abrogates cellular differentiation in NUT midline carcinoma. J Biol Chem 2011; 286: 27663–27675.

    Article  CAS  Google Scholar 

  22. Mertens F, Wiebe T, Adlercreutz C, Mandahl N, French CA . Successful treatment of a child with t(15;19)-positive tumor. Pediatr Blood Cancer 2007; 49: 1015–1017.

    Article  Google Scholar 

  23. Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O et al. Selective inhibition of BET bromodomains. Nature 2010; 468: 1067–1073.

    Article  CAS  Google Scholar 

  24. Dawson MA, Prinjha RK, Dittmann A, Giotopoulos G, Bantscheff M, Chan WI et al. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature 2011; 478: 529–533.

    Article  CAS  Google Scholar 

  25. Zuber J, Shi J, Wang E, Rappaport AR, Herrmann H, Sison EA et al. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 2011; 478: 524–528.

    Article  CAS  Google Scholar 

  26. Ott CJ, Kopp N, Bird L, Paranal RM, Qi J, Bowman T et al. BET bromodomain inhibition targets both c-MYC and IL7R in high-risk acute lymphoblastic leukemia. Blood 2012; 120: 2843–2852.

    Article  CAS  Google Scholar 

  27. Delmore JE, Issa GC, Lemieux ME, Rahl PB, Shi J, Jacobs HM et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 2011; 146: 904–917.

    Article  CAS  Google Scholar 

  28. Prinjha RK, Witherington J, Lee K . Place your BETs: the therapeutic potential of bromodomains. Trends Pharmacol Sci 2012; 33: 146–153.

    Article  CAS  Google Scholar 

  29. Belkina AC, Denis GV . BET domain co-regulators in obesity, inflammation and cancer. Nat Rev Cancer 2012; 12: 465–477.

    Article  CAS  Google Scholar 

  30. Trapnell C, Pachter L, Salzberg SL . TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25: 1105–1111.

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by grants from the Children’s Leukemia and Cancer Research Foundation (CLCRF, Perth, Western Australia, Australia), Apache Energy Limited, the Cancer Council of Western Australia, the University of Western Australia and the WA State Government Centers of Excellence Program. We would like to thank Maxine Crook, Senior Medical Scientist, PathWest Laboratory Medicine, Perth, for performing the IHC used in this study.

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Authors and Affiliations

  1. Division of Children’s Leukaemia and Cancer Research, Telethon Institute for Child Health Research, University of Western Australia Centre for Child Health Research, Perth, Australia

    K Thompson-Wicking, A Stirnweiss, E Ferrari, M D Welch, A M Gout, U R Kees & A H Beesley

  2. Division of Bioinformatics, Telethon Institute for Child Health Research, University of Western Australia Centre for Child Health Research, Perth, Australia

    R W Francis & K W Carter

  3. Cytogenetics Department, PathWest Laboratory Medicine, King Edward Memorial Hospital for Women, Perth, Western Australia, Australia

    E Baker & A R Murch

  4. School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia

    A R Murch & A K Charles

  5. Department of Pathology, PathWest Laboratory Medicine, Perth, Western Australia, Australia

    A K Charles

  6. Department of Oncology and Haematology, Princess Margaret Hospital for Children, Perth, Western Australia, Australia

    M B Phillips

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  1. K Thompson-Wicking
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Correspondence to U R Kees.

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Thompson-Wicking, K., Francis, R., Stirnweiss, A. et al. Novel BRD4–NUT fusion isoforms increase the pathogenic complexity in NUT midline carcinoma. Oncogene 32, 4664–4674 (2013). https://doi.org/10.1038/onc.2012.487

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