Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Loss of BAP1 function leads to EZH2-dependent transformation

Abstract

The tumor suppressors BAP1 and ASXL1 interact to form a polycomb deubiquitinase complex that removes monoubiquitin from histone H2A lysine 119 (H2AK119Ub). However, BAP1 and ASXL1 are mutated in distinct cancer types, consistent with independent roles in regulating epigenetic state and malignant transformation. Here we demonstrate that Bap1 loss in mice results in increased trimethylated histone H3 lysine 27 (H3K27me3), elevated enhancer of zeste 2 polycomb repressive complex 2 subunit (Ezh2) expression, and enhanced repression of polycomb repressive complex 2 (PRC2) targets. These findings contrast with the reduction in H3K27me3 levels seen with Asxl1 loss. Conditional deletion of Bap1 and Ezh2 in vivo abrogates the myeloid progenitor expansion induced by Bap1 loss alone. Loss of BAP1 results in a marked decrease in H4K20 monomethylation (H4K20me1). Consistent with a role for H4K20me1 in the transcriptional regulation of EZH2, expression of SETD8—the H4K20me1 methyltransferase—reduces EZH2 expression and abrogates the proliferation of BAP1-mutant cells. Furthermore, mesothelioma cells that lack BAP1 are sensitive to EZH2 pharmacologic inhibition, suggesting a novel therapeutic approach for BAP1-mutant malignancies.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Bap1 deletion results in increased levels of H3K27me3.
Figure 2: Proliferation induced by Bap1 deletion is rescued by the loss of Ezh2.
Figure 3: BAP1 loss leads to increased PRC2 expression and decreased H4K20me1 levels.
Figure 4: BAP1-mutant mesothelioma models are sensitive to EZH2 inhibition.

Accession codes

Primary accessions

Gene Expression Omnibus

Referenced accessions

Gene Expression Omnibus

References

  1. 1

    Abdel-Wahab, O. et al. Concomitant analysis of EZH2 and ASXL1 mutations in myelofibrosis, chronic myelomonocytic leukemia and blast-phase myeloproliferative neoplasms. Leukemia 25, 1200–1202 (2011).

    CAS  Article  Google Scholar 

  2. 2

    Gelsi-Boyer, V. et al. Mutations of polycomb-associated gene ASXL1 in myelodysplastic syndromes and chronic myelomonocytic leukaemia. Br. J. Haematol. 145, 788–800 (2009).

    CAS  Article  Google Scholar 

  3. 3

    Bejar, R. et al. Clinical effect of point mutations in myelodysplastic syndromes. N. Engl. J. Med. 364, 2496–2506 (2011).

    CAS  Article  Google Scholar 

  4. 4

    Bott, M. et al. The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat. Genet. 43, 668–672 (2011).

    CAS  Article  Google Scholar 

  5. 5

    Peña-Llopis, S. et al. BAP1 loss defines a new class of renal cell carcinoma. Nat. Genet. 44, 751–759 (2012).

    Article  Google Scholar 

  6. 6

    Harbour, J.W. et al. Frequent mutation of BAP1 in metastasizing uveal melanomas. Science 330, 1410–1413 (2010).

    CAS  Article  Google Scholar 

  7. 7

    Scheuermann, J.C. et al. Histone H2A deubiquitinase activity of the polycomb repressive complex PR-DUB. Nature 465, 243–247 (2010).

    CAS  Article  Google Scholar 

  8. 8

    Dey, A. et al. Loss of the tumor suppressor BAP1 causes myeloid transformation. Science 337, 1541–1546 (2012).

    CAS  Article  Google Scholar 

  9. 9

    Abdel-Wahab, O. et al. Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo. J. Exp. Med. 210, 2641–2659 (2013).

    CAS  Article  Google Scholar 

  10. 10

    Abdel-Wahab, O. et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell 22, 180–193 (2012).

    CAS  Article  Google Scholar 

  11. 11

    Béguelin, W. et al. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell 23, 677–692 (2013).

    Article  Google Scholar 

  12. 12

    Su, I.H. et al. Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement. Nat. Immunol. 4, 124–131 (2003).

    CAS  Article  Google Scholar 

  13. 13

    Campbell, J.E. et al. EPZ011989, a potent, orally available EZH2 inhibitor with robust in vivo activity. ACS Med. Chem. Lett. 6, 491–495 (2015).

    CAS  Article  Google Scholar 

  14. 14

    Nishioka, K. et al. PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol. Cell 9, 1201–1213 (2002).

    CAS  Article  Google Scholar 

  15. 15

    Blum, G. et al. Small-molecule inhibitors of SETD8 with cellular activity. ACS Chem. Biol. 9, 2471–2478 (2014).

    CAS  Article  Google Scholar 

  16. 16

    Guo, Y. et al. Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. Nucleic Acids Res. 37, 2204–2210 (2009).

    CAS  Article  Google Scholar 

  17. 17

    Qin, J. et al. The polycomb group protein L3mbtl2 assembles an atypical PRC1-family complex that is essential in pluripotent stem cells and early development. Cell Stem Cell 11, 319–332 (2012).

    CAS  Article  Google Scholar 

  18. 18

    Trojer, P. et al. L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. Mol. Cell 42, 438–450 (2011).

    CAS  Article  Google Scholar 

  19. 19

    Trojer, P. et al. L3MBTL1, a histone-methylation-dependent chromatin lock. Cell 129, 915–928 (2007).

    CAS  Article  Google Scholar 

  20. 20

    Qin, J. et al. Chromatin protein L3MBTL1 is dispensable for development and tumor suppression in mice. J. Biol. Chem. 285, 27767–27775 (2010).

    CAS  Article  Google Scholar 

  21. 21

    Morin, R.D. et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat. Genet. 42, 181–185 (2010).

    CAS  Article  Google Scholar 

  22. 22

    Morin, R.D. et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 476, 298–303 (2011).

    CAS  Article  Google Scholar 

  23. 23

    Pasqualucci, L. et al. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat. Genet. 43, 830–837 (2011).

    CAS  Article  Google Scholar 

  24. 24

    McCabe, M.T. et al. EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations. Nature 492, 108–112 (2012).

    CAS  Article  Google Scholar 

  25. 25

    Knutson, S.K. et al. Durable tumor regression in genetically altered malignant rhabdoid tumors by inhibition of methyltransferase EZH2. Proc. Natl. Acad. Sci. USA 110, 7922–7927 (2013).

    CAS  Article  Google Scholar 

  26. 26

    Alimova, I. et al. Inhibition of EZH2 suppresses self-renewal and induces radiation sensitivity in atypical rhabdoid teratoid tumor cells. Neuro-oncol. 15, 149–160 (2013).

    CAS  Article  Google Scholar 

  27. 27

    Wilson, B.G. et al. Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. Cancer Cell 18, 316–328 (2010).

    CAS  Article  Google Scholar 

  28. 28

    Skarnes, W.C. et al. A conditional knockout resource for the genome-wide study of mouse gene function. Nature 474, 337–342 (2011).

    CAS  Article  Google Scholar 

  29. 29

    Su, I.H. et al. Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement. Nature immunology 4, 124–131 (2003).

    CAS  Article  Google Scholar 

  30. 30

    Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN] (2013).

  31. 31

    Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article  Google Scholar 

  32. 32

    Suraokar, M.B. et al. Expression profiling stratifies mesothelioma tumors and signifies deregulation of spindle checkpoint pathway and microtubule network with therapeutic implications. Ann. Oncol. 25, 1184–1192 (2014).

    CAS  Article  Google Scholar 

  33. 33

    Garcia, B.A. et al. Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat. Protoc. 2, 933–938 (2007).

    CAS  Article  Google Scholar 

  34. 34

    MacLean, B. et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966–968 (2010).

    CAS  Article  Google Scholar 

  35. 35

    Krivtsov, A.V. et al. H3K79 methylation profiles define murine and human MLL-AF4 leukemias. Cancer Cell 14, 355–368 (2008).

    CAS  Article  Google Scholar 

  36. 36

    O'Geen, H., Echipare, L. & Farnham, P.J. Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods Mol. Biol. 791, 265–286 (2011).

    CAS  Article  Google Scholar 

  37. 37

    Langmead, B. & Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    CAS  Article  Google Scholar 

  38. 38

    Quinlan, A.R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    CAS  Article  Google Scholar 

  39. 39

    Béguelin, W. et al. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell 23, 677–692 (2013).

    Article  Google Scholar 

  40. 40

    Heinz, S. 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).

    CAS  Article  Google Scholar 

  41. 41

    Phung, Y.T., Barbone, D., Broaddus, V.C. & Ho, M. Rapid generation of in vitro multicellular spheroids for the study of monoclonal antibody therapy. J. Cancer 2, 507–514 (2011).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the Pershing Square Sohn Prize (R.L.L.), by grant 2R01GM096056 (M.L.), by grant CA172636 (R.L.L. and A.M.) and by grant F31 CA180642-02 (L.M.L.). Work in the Memorial Sloan Kettering Cancer Center (MSKCC) Core facilities that supported these studies is supported by P30 CA008748. R.L.L. is a Leukemia and Lymphoma Society Scholar. We would like to thank V. Rotter (Weizmann Institute of Science, Israel), X. Jiang (MSKCC), and M. Ladanyi (MSKCC) for generously providing plasmids for this work. We would like to thank D. Scheinberg (MSKCC) for generously sharing the mesothelioma cell lines used in this work.

Author information

Affiliations

Authors

Contributions

L.M.L., O.A.-W. and R.L.L. designed the study. L.M.L., W.B., A.C., E.P., M.D.K., K.K., J.-B.M., I.K., E.H.D., X.S., Y.R.C. and O.A.-W. performed the experiments. L.M.L., W.B., R.K., M.T., B.S., T.H., A.C. and O.A.-W. performed ChIP-and RNA-Seq, sequencing and subsequent downstream analyses. B.D., S.K.K., J.E.C., G.B., E.d.S., O.O., P.S.A., P.M.T., N.L.K., M.L., H.K., A.M., S.A.A. and R.L.L. participated in data analysis and discussions. L.M.L. and R.L.L. prepared the manuscript with input from all authors.

Corresponding author

Correspondence to Ross L Levine.

Ethics declarations

Competing interests

S.K.K., J.E.C. and H.K. are employees of Epizyme, Inc. S.A.A. is a consultant for Epizyme, Inc.

Supplementary information

Supplementary Text and Figures

Supplementary Table 1 and Supplementary Figures 1–9 (PDF 10368 kb)

Source data

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

LaFave, L., Béguelin, W., Koche, R. et al. Loss of BAP1 function leads to EZH2-dependent transformation. Nat Med 21, 1344–1349 (2015). https://doi.org/10.1038/nm.3947

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing