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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
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).
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).
Bejar, R. et al. Clinical effect of point mutations in myelodysplastic syndromes. N. Engl. J. Med. 364, 2496–2506 (2011).
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).
Peña-Llopis, S. et al. BAP1 loss defines a new class of renal cell carcinoma. Nat. Genet. 44, 751–759 (2012).
Harbour, J.W. et al. Frequent mutation of BAP1 in metastasizing uveal melanomas. Science 330, 1410–1413 (2010).
Scheuermann, J.C. et al. Histone H2A deubiquitinase activity of the polycomb repressive complex PR-DUB. Nature 465, 243–247 (2010).
Dey, A. et al. Loss of the tumor suppressor BAP1 causes myeloid transformation. Science 337, 1541–1546 (2012).
Abdel-Wahab, O. et al. Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo. J. Exp. Med. 210, 2641–2659 (2013).
Abdel-Wahab, O. et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell 22, 180–193 (2012).
Béguelin, W. et al. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell 23, 677–692 (2013).
Su, I.H. et al. Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement. Nat. Immunol. 4, 124–131 (2003).
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).
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).
Blum, G. et al. Small-molecule inhibitors of SETD8 with cellular activity. ACS Chem. Biol. 9, 2471–2478 (2014).
Guo, Y. et al. Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. Nucleic Acids Res. 37, 2204–2210 (2009).
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).
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).
Trojer, P. et al. L3MBTL1, a histone-methylation-dependent chromatin lock. Cell 129, 915–928 (2007).
Qin, J. et al. Chromatin protein L3MBTL1 is dispensable for development and tumor suppression in mice. J. Biol. Chem. 285, 27767–27775 (2010).
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).
Morin, R.D. et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 476, 298–303 (2011).
Pasqualucci, L. et al. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat. Genet. 43, 830–837 (2011).
McCabe, M.T. et al. EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations. Nature 492, 108–112 (2012).
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).
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).
Wilson, B.G. et al. Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. Cancer Cell 18, 316–328 (2010).
Skarnes, W.C. et al. A conditional knockout resource for the genome-wide study of mouse gene function. Nature 474, 337–342 (2011).
Su, I.H. et al. Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement. Nature immunology 4, 124–131 (2003).
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN] (2013).
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).
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).
Garcia, B.A. et al. Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat. Protoc. 2, 933–938 (2007).
MacLean, B. et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966–968 (2010).
Krivtsov, A.V. et al. H3K79 methylation profiles define murine and human MLL-AF4 leukemias. Cancer Cell 14, 355–368 (2008).
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).
Langmead, B. & Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Quinlan, A.R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Béguelin, W. et al. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell 23, 677–692 (2013).
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).
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).
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
Authors and Affiliations
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
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)
Rights and permissions
About this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nm.3947
This article is cited by
-
BAP1 as a guardian of genome stability: implications in human cancer
Experimental & Molecular Medicine (2023)
-
CAMK2D: a novel molecular target for BAP1-deficient malignant mesothelioma
Cell Death Discovery (2023)
-
BAP1 loss induces mitotic defects in mesothelioma cells through BRCA1-dependent and independent mechanisms
Oncogene (2023)
-
Roles for the methyltransferase SETD8 in DNA damage repair
Clinical Epigenetics (2022)
-
BAP1 loss augments sensitivity to BET inhibitors in cancer cells
Acta Pharmacologica Sinica (2022)
