Abstract

Translocation events are frequent in cancer and may create chimeric fusions or 'regulatory rearrangements' that drive oncogene overexpression. Here we identify super-enhancer translocations that drive overexpression of the oncogenic transcription factor MYB as a recurrent theme in adenoid cystic carcinoma (ACC). Whole-genome sequencing data and chromatin maps highlight distinct chromosomal rearrangements that juxtapose super-enhancers to the MYB locus. Chromosome conformation capture confirms that the translocated enhancers interact with the MYB promoter. Remarkably, MYB protein binds to the translocated enhancers, creating a positive feedback loop that sustains its expression. MYB also binds enhancers that drive different regulatory programs in alternate cell lineages in ACC, cooperating with TP63 in myoepithelial cells and a Notch program in luminal epithelial cells. Bromodomain inhibitors slow tumor growth in ACC primagraft models in vivo. Thus, our study identifies super-enhancer translocations that drive MYB expression and provides insight into downstream MYB functions in alternate ACC lineages.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

Referenced accessions

References

  1. 1.

    et al. Molecular analysis of a chromosomal translocation, t(9;14)(p13;q32), in a diffuse large-cell lymphoma cell line expressing the Ki-1 antigen. Proc. Natl. Acad. Sci. USA 87, 628–632 (1990).

  2. 2.

    Chromosomal translocations in human cancer. Nature 372, 143–149 (1994).

  3. 3.

    et al. A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia. Cell 157, 369–381 (2014).

  4. 4.

    et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511, 428–434 (2014).

  5. 5.

    et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310, 644–648 (2005).

  6. 6.

    , , & Biology and management of salivary gland cancers. Semin. Radiat. Oncol. 22, 245–253 (2012).

  7. 7.

    et al. The mutational landscape of adenoid cystic carcinoma. Nat. Genet. 45, 791–798 (2013).

  8. 8.

    & MYB function in normal and cancer cells. Nat. Rev. Cancer 8, 523–534 (2008).

  9. 9.

    et al. Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck. Proc. Natl. Acad. Sci. USA 106, 18740–18744 (2009).

  10. 10.

    et al. Comprehensive analysis of the MYB-NFIB gene fusion in salivary adenoid cystic carcinoma: incidence, variability, and clinicopathologic significance. Clin. Cancer Res. 16, 4722–4731 (2010).

  11. 11.

    et al. Whole exome sequencing of adenoid cystic carcinoma. J. Clin. Invest. 123, 2965–2968 (2013).

  12. 12.

    et al. Development and characterization of xenograft model systems for adenoid cystic carcinoma. Lab. Invest. 91, 1480–1490 (2011).

  13. 13.

    & Mapping human epigenomes. Cell 155, 39–55 (2013).

  14. 14.

    et al. In vitro transformation of cell lines from human salivary gland tumors. Int. J. Cancer 81, 793–798 (1999).

  15. 15.

    et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).

  16. 16.

    et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320–334 (2013).

  17. 17.

    , , & Identification and regulation of c-Myb target genes in MCF-7 cells. BMC Cancer 11, 30 (2011).

  18. 18.

    et al. Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb. Nucleic Acids Res. 39, 4664–4679 (2011).

  19. 19.

    et al. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science 346, 1373–1377 (2014).

  20. 20.

    et al. Tissue-based map of the human proteome. Science 347, 1260419 (2015).

  21. 21.

    , , , & Developmental transcription factor EN1—a novel biomarker in human salivary gland adenoid cystic carcinoma. Cancer 118, 1288–1292 (2012).

  22. 22.

    , , & Histological changes during progression of adenoid cystic carcinoma. J. Laryngol. Otol. 106, 1016–1020 (1992).

  23. 23.

    et al. Adenoid cystic carcinoma of the maxillary sinus with gradual histologic transformation to high-grade adenocarcinoma: a comparative report with dedifferentiated carcinoma. Virchows Arch. 448, 204–208 (2006).

  24. 24.

    et al. p63, a p53 homologue, is a selective nuclear marker of myoepithelial cells of the human breast. Am. J. Surg. Pathol. 25, 1054–1060 (2001).

  25. 25.

    et al. Cross-regulation between Notch and p63 in keratinocyte commitment to differentiation. Genes Dev. 20, 1028–1042 (2006).

  26. 26.

    et al. Antagonistic roles of Notch and p63 in controlling mammary epithelial cell fates. Cell Death Differ. 17, 1600–1612 (2010).

  27. 27.

    et al. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. Cancer Discov. 4, 1154–1167 (2014).

  28. 28.

    et al. Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer. Nat. Med. 17, 1646–1651 (2011).

  29. 29.

    et al. An activating intragenic deletion in NOTCH1 in human T-ALL. Blood 119, 5211–5214 (2012).

  30. 30.

    & p63 and p73: roles in development and tumor formation. Mol. Cancer Res. 2, 371–386 (2004).

  31. 31.

    et al. Expression and regulation of the ΔN and TAp63 isoforms in salivary gland tumorigenesis: clinical and experimental findings. Am. J. Pathol. 179, 391–399 (2011).

  32. 32.

    , , , & BET bromodomain inhibition suppresses the function of hematopoietic transcription factors in acute myeloid leukemia. Mol. Cell 58, 1028–1039 (2015).

  33. 33.

    et al. An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. Nat. Genet. 46, 364–370 (2014).

  34. 34.

    et al. Selective inhibition of BET bromodomains. Nature 468, 1067–1073 (2010).

  35. 35.

    , , , & Positive autoregulation of c-myb expression via Myb binding sites in the 5′ flanking region of the human c-myb gene. Mol. Cell. Biol. 11, 6166–6176 (1991).

  36. 36.

    et al. Negative autoregulation of c-Myb activity by homodimer formation through the leucine zipper. J. Biol. Chem. 268, 21914–21923 (1993).

  37. 37.

    et al. Analysis of MYB expression and MYB-NFIB gene fusions in adenoid cystic carcinoma and other salivary neoplasms. Mod. Pathol. 24, 1169–1176 (2011).

  38. 38.

    et al. Clinical significance of Myb protein and downstream target genes in salivary adenoid cystic carcinoma. Cancer Biol. Ther. 12, 569–573 (2011).

  39. 39.

    et al. The genomic complexity of primary human prostate cancer. Nature 470, 214–220 (2011).

  40. 40.

    et al. Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Res. 23, 228–235 (2013).

  41. 41.

    , , , & The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 42, D986–D992 (2014).

  42. 42.

    et al. Detection of enhancer-associated rearrangements reveals mechanisms of oncogene dysregulation in B-cell lymphoma. Cancer Discov. 5, 1058–1071 (2015).

  43. 43.

    , & Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).

  44. 44.

    et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 4, e1000242 (2008).

  45. 45.

    et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43–49 (2011).

  46. 46.

    & Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

  47. 47.

    et al. Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell 157, 580–594 (2014).

  48. 48.

    et al. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell 26, 668–681 (2014).

  49. 49.

    et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

  50. 50.

    et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495–501 (2010).

  51. 51.

    et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29 (2000).

  52. 52.

    et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).

  53. 53.

    et al. Annotating cancer variants and anti-cancer therapeutics in Reactome. Cancers (Basel) 4, 1180–1211 (2012).

  54. 54.

    et al. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 149, 1233–1244 (2012).

Download references

Acknowledgements

We thank M. Rivera, N. Riggi, S. Puram, P. van Galen, J. Lohr and J. Kaufman for helpful discussions and critical comments on the manuscript; J. Voisine, R. Isenhart, R. Issner, H. Whitton, A. Spooner, M. Uziel, C. Epstein and N. Shoresh for technical assistance; T. Chan and V. Makarov for help with whole-genome sequencing data access; and the Salivary Gland Tumor Biorepository for providing the primary tumors (National Institute of Dental and Craniofacial Research (NIDCR) award reference HHSN268200900039C 04). This work was supported by the Adenoid Cystic Carcinoma Research Foundation (B.E.B. and B.K.), the Temares Family Foundation and the Howard Hughes Medical Institute. B.E.B. is an American Cancer Society Research Professor.

Author information

Author notes

    • Birgit Knoechel
    •  & Bradley E Bernstein

    These authors contributed equally to this work.

Affiliations

  1. Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Yotam Drier
    • , Matthew J Cotton
    • , Kaylyn E Williamson
    • , Shawn M Gillespie
    • , Russell J H Ryan
    • , Amir H Afrogheh
    • , William C Faquin
    • , Birgit Knoechel
    •  & Bradley E Bernstein
  2. Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA.

    • Yotam Drier
    • , Matthew J Cotton
    • , Kaylyn E Williamson
    • , Shawn M Gillespie
    • , Russell J H Ryan
    •  & Bradley E Bernstein
  3. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

    • Yotam Drier
    • , Matthew J Cotton
    • , Kaylyn E Williamson
    • , Shawn M Gillespie
    • , Russell J H Ryan
    • , James E Bradner
    • , Birgit Knoechel
    •  & Bradley E Bernstein
  4. Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

    • Yotam Drier
    • , Matthew J Cotton
    • , Kaylyn E Williamson
    • , Shawn M Gillespie
    • , Russell J H Ryan
    •  & Bradley E Bernstein
  5. Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Michael J Kluk
    • , Christopher D Carey
    • , Scott J Rodig
    • , Lynette M Sholl
    •  & Jon C Aster
  6. Department of Otorhinolaryngology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.

    • Lurdes Queimado
  7. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

    • Jun Qi
    •  & James E Bradner
  8. South Texas Accelerated Research Therapeutics (START), San Antonio, Texas, USA.

    • Michael J Wick
  9. Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.

    • Adel K El-Naggar
  10. Department of Pathology, University of Virginia Health Sciences Center, Charlottesville, Virginia, USA.

    • Christopher A Moskaluk
  11. Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Birgit Knoechel
  12. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

    • Birgit Knoechel

Authors

  1. Search for Yotam Drier in:

  2. Search for Matthew J Cotton in:

  3. Search for Kaylyn E Williamson in:

  4. Search for Shawn M Gillespie in:

  5. Search for Russell J H Ryan in:

  6. Search for Michael J Kluk in:

  7. Search for Christopher D Carey in:

  8. Search for Scott J Rodig in:

  9. Search for Lynette M Sholl in:

  10. Search for Amir H Afrogheh in:

  11. Search for William C Faquin in:

  12. Search for Lurdes Queimado in:

  13. Search for Jun Qi in:

  14. Search for Michael J Wick in:

  15. Search for Adel K El-Naggar in:

  16. Search for James E Bradner in:

  17. Search for Christopher A Moskaluk in:

  18. Search for Jon C Aster in:

  19. Search for Birgit Knoechel in:

  20. Search for Bradley E Bernstein in:

Contributions

B.K. and Y.D. designed and performed experiments and analyzed the data. B.K. and B.E.B. designed the experimental strategy and supervised the study and analysis. Y.D. carried out computational analyses. Y.D., B.K. and B.E.B. wrote the manuscript. J.C.A., M.J.C., K.E.W., S.M.G., C.D.C., S.J.R., L.M.S. and M.J.W. contributed to experiments and data analysis. A.H.A., R.J.H.R., M.J.K., W.C.F., L.Q., J.Q., J.E.B., C.A.M., A.K.E.-N. and J.E.B. provided reagents, contributed to analysis and gave conceptual advice. All authors discussed the results and implications and reviewed the manuscript.

Competing interests

J.E.B. is a scientific founder of Tensha Therapeutics, which has licensed drug-like derivatives of the JQ1 bromodomain inhibitor from the Dana-Farber Cancer Institute. The remaining authors declare no competing financial interests.

Corresponding authors

Correspondence to Birgit Knoechel or Bradley E Bernstein.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–11 and Supplementary Table 5

Excel files

  1. 1.

    Supplementary Table 1

    Rearrangements detected in six ACC primagrafts from whole-genome sequencing.

  2. 2.

    Supplementary Table 2

    MYB high-confidence peaks and associated nearby genes.

  3. 3.

    Supplementary Table 3

    Enriched annotations of MYB targets.

  4. 4.

    Supplementary Table 4

    Transcriptional regulators targeted by MYB ranked by MYB binding, with expression levels in ACC and normal gland.

  5. 5.

    Supplementary Table 6

    Primer and reporter sequences used in this study.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/ng.3502

Further reading