[en] The tumor suppressor and deubiquitinase (DUB) BAP1 and its Drosophila ortholog Calypso assemble DUB complexes with the transcription regulators Additional sex combs-like (ASXL1, ASXL2, ASXL3) and Asx respectively. ASXLs and Asx use their DEUBiquitinase ADaptor (DEUBAD) domain to stimulate BAP1/Calypso DUB activity. Here we report that monoubiquitination of the DEUBAD is a general feature of ASXLs and Asx. BAP1 promotes DEUBAD monoubiquitination resulting in an increased stability of ASXL2, which in turn stimulates BAP1 DUB activity. ASXL2 monoubiquitination is directly catalyzed by UBE2E family of Ubiquitin-conjugating enzymes and regulates mammalian cell proliferation. Remarkably, Calypso also regulates Asx monoubiquitination and transgenic flies expressing monoubiquitination-defective Asx mutant exhibit developmental defects. Finally, the protein levels of ASXL2, BAP1 and UBE2E enzymes are highly correlated in mesothelioma tumors suggesting the importance of this signaling axis for tumor suppression. We propose that monoubiquitination orchestrates a molecular symbiosis relationship between ASXLs and BAP1.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Daou, Salima; Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada ; Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
Barbour, Haithem; Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
Ahmed, Oumaima; Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
Masclef, Louis ; Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
Baril, Caroline; Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, University of Montréal, Montréal, QC, H3T 1J4, Canada
Sen Nkwe, Nadine; Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
Tchelougou, Daméhan ; Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
Uriarte, Maxime ; Université de Liège - ULiège > Département des sciences biomédicales et précliniques ; Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
Bonneil, Eric ; Institute for Research in Immunology and Cancer, Laboratory of Proteomics and Bioanalytical Mass Spectrometry, University of Montréal, Montréal, QC, H3T 1J4, Canada
Ceccarelli, Derek ; Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
Mashtalir, Nazar; Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
Tanji, Mika; University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
Masson, Jean-Yves; CHU de Quebec Research Center (Oncology Axis), Laval University Cancer Research Center, 9 McMahon, Quebec, PQ, G1R 2J6, Canada
Thibault, Pierre; Institute for Research in Immunology and Cancer, Laboratory of Proteomics and Bioanalytical Mass Spectrometry, University of Montréal, Montréal, QC, H3T 1J4, Canada
Sicheri, Frank; Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
Yang, Haining; University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
Carbone, Michele; University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
Therrien, Marc; Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, University of Montréal, Montréal, QC, H3T 1J4, Canada. marc.therrien@umontreal.ca ; Département de pathologie et biologie cellulaire, University of Montréal, Montréal, QC, H3C 3J7, Canada. marc.therrien@umontreal.ca
Affar, El Bachir; Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada. el.bachir.affar@umontreal.ca
We thank Jürg Muller for insightful comments and reagents. We thank Diana Adjaoud, Ian Hammond-Martel, Pham My-An, and Erlinda Diaz Fernandez for technical assistance. This work was supported by grants from the Canadian Institutes of Health Research (CIHR) to E.B.A. (399244), a Foundation grant from the CIHR to M.T. (388023), a Foundation grant from the CIHR to J.Y.M. (388879), and grants from the Natural Sciences and Engineering Research Council of Canada (2015-2020) and Mesothelioma Applied Research Foundation (MARF) to E.B.A. E.B.A. is a senior scholar of the Fonds de la Recherche du Québec-Santé (FRQ-S). J.Y.M. is a Fonds de la Recherche du Québec-Santé (FRQ-S) research chair in genome stability . This work was supported by Department of Defense Grant No. CA150220 toH.Y. and M.C.; National Cancer Institute (NCI) GrantNo. R01 CA198138 to M.C.; the University of Hawaii Foundation, whichreceived unrestricted donations to support cancer and mesotheliomaresearch from: The Melohn family endowment (M.C.); HoneywellInternational (M.C.); The Riviera United 4-a Cure to M.C. and H.Y. S.D. has a Banting postdoctoral fellowship. H.B. has a PhD scholarship from the Ministry of Higher Education and Scientific Research of Tunisia and the Cole Foundation. O.A. has a MSc scholarship from the The Canadian Francophonie Scholarship Program. The Institute for Research in Immunology and Cancer (IRIC) receives infrastructure support from Genome Canada and Génome Québec, IRICoR, the Canadian Foundation for Innovation, and the Fonds de Recherche du Québec - Santé (FRQS).
Nijman, S. M. et al. A genomic and functional inventory of deubiquitinating enzymes. Cell 123, 773–786 (2005)
Murali, R., Wiesner, T. & Scolyer, R. A. Tumours associated with BAP1 mutations. Pathology 45, 116–126 (2013)
Carbone, M. et al. BAP1 and cancer. Nat. Rev. Cancer 13, 153–159 (2013)
Dey, A. et al. Loss of the tumor suppressor BAP1 causes myeloid transformation. Science 337, 1541–1546 (2012)
Kadariya, Y. et al. Bap1 is a bona fide tumor suppressor: genetic evidence from mouse models carrying heterozygous germline Bap1 mutations. Cancer Res. 76, 2836–2844 (2016)
Napolitano, A. et al. Minimal asbestos exposure in germline BAP1 heterozygous mice is associated with deregulated inflammatory response and increased risk of mesothelioma. Oncogene 35, 1996–2002 (2016)
Gu, Y. F. et al. Modeling renal cell carcinoma in mice: Bap1 and Pbrm1 inactivation drive tumor grade. Cancer Discov. 7, 900–917 (2017)
Machida, Y. J., Machida, Y., Vashisht A. A., Wohlschlegel, J. A. & Dutta A. The deubiquitinating enzyme BAP1 regulates cell growth via interaction with HCF-1. J. Biol. Chem. 284, 34179–34188 (2009)
Sowa, M. E., Bennett, E. J., Gygi, S. P. & Harper, J. W. Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389–403 (2009)
Yu, H. et al. The ubiquitin carboxyl hydrolase BAP1 forms a ternary complex with YY1 and HCF-1 and is a critical regulator of gene expression. Mol. Cell. Biol. 30, 5071–5085 (2010)
Yu, H. et al. Tumor suppressor and deubiquitinase BAP1 promotes DNA double-strand break repair. Proc. Natl Acad. Sci. USA 111, 285–290 (2014)
Ismail, I. H. et al. Germ-line mutations in BAP1 impair its function in DNA double-strand break repair. Cancer Res. 74, 4282–4294 (2014)
Lee, H. S., Lee, S. A., Hur, S. K., Seo, J. W. & Kwon, J. Stabilization and targeting of INO80 to replication forks by BAP1 during normal DNA synthesis. Nat. Commun. 5, 5128 (2014)
Mashtalir, N. et al. Autodeubiquitination protects the tumor suppressor BAP1 from cytoplasmic sequestration mediated by the atypical ubiquitin ligase UBE2O. Mol. Cell 54, 392–406 (2014)
Bononi, A. et al. BAP1 regulates IP3R3-mediated Ca2 + flux to mitochondria suppressing cell transformation. Nature 546, 549–553 (2017)
Scheuermann, J. C. et al. Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature 465, 243–247 (2010)
Pengelly, A. R., Kalb, R., Finkl, K. & Muller, J. Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation. Genes Dev. 29, 1487–1492 (2015)
Milne, T. A., Sinclair, D. A. & Brock, H. W. The Additional sex combs gene of Drosophila is required for activation and repression of homeotic loci, and interacts specifically with Polycomb and super sex combs. Mol. Gen. Genet. 261, 753–761 (1999)
Gildea, J. J., Lopez, R. & Shearn, A. A screen for new trithorax group genes identified little imaginal discs, the Drosophila melanogaster homologue of human retinoblastoma binding protein 2. Genetics 156, 645–663 (2000)
Cho, Y. S., Kim, E. J., Park, U. H., Sin, H. S. & Um, S. J. Additional sex comb-like 1 (ASXL1), in cooperation with SRC-1, acts as a ligand-dependent coactivator for retinoic acid receptor. J. Biol. Chem. 281, 17588–17598 (2006)
Park, U. H., Yoon, S. K., Park, T., Kim, E. J. & Um, S. J. Additional sex comb-like (ASXL) proteins 1 and 2 play opposite roles in adipogenesis via reciprocal regulation of peroxisome proliferator-activated receptor {gamma}. J. Biol. Chem. 286, 1354–1363 (2011)
Abdel-Wahab, O. et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell. 22, 180–193 (2012)
Huether, R. et al. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat. Commun. 5, 3630 (2014)
Katoh, M. Functional proteomics of the epigenetic regulators ASXL1, ASXL2 and ASXL3: a convergence of proteomics and epigenetics for translational medicine. Expert Rev. Proteom. 12, 317–328 (2015)
Robinson, D. R. et al. Integrative clinical genomics of metastatic cancer. Nature 548, 297–303 (2017)
Sanchez-Pulido, L., Kong, L. & Ponting, C. P. A common ancestry for BAP1 and Uch37 regulators. Bioinformatics 28, 1953–1956 (2012)
Qiu, X. B. et al. hRpn13/ADRM1/GP110 is a novel proteasome subunit that binds the deubiquitinating enzyme, UCH37. EMBO J. 25, 5742–5753 (2006)
Hamazaki, J. et al. A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes. EMBO J. 25, 4524–4536 (2006)
Yao, T. et al. Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and in the Ino80 chromatin-remodeling complex. Mol. Cell 31, 909–917 (2008)
Yao, T. et al. Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nat. Cell Biol. 8, 994–1002 (2006)
Sahtoe, D. D. et al. Mechanism of UCH-L5 activation and inhibition by DEUBAD domains in RPN13 and INO80G. Mol. Cell 57, 887–900 (2015)
Vander Linden, R. T. et al. Structural basis for the activation and inhibition of the UCH37 deubiquitylase. Mol. Cell 57, 901–911 (2015)
Daou, S. et al. The BAP1/ASXL2 histone H2A deubiquitinase complex regulates cell proliferation and is disrupted in cancer. J. Biol. Chem. 290, 28643–28663 (2015)
Sahtoe, D. D., van Dijk, W. J., Ekkebus, R., Ovaa, H. & Sixma, T. K. BAP1/ASXL1 recruitment and activation for H2A deubiquitination. Nat. Commun. 7, 10292 (2016)
Inoue, D., Nishimura, K., Kozuka-Hata, H., Oyama, M. & Kitamura, T. The stability of epigenetic factor ASXL1 is regulated through ubiquitination and USP7-mediated deubiquitination. Leukemia 29, 2257–2260 (2015)
Borodovsky, A. et al. A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14. EMBO J. 20, 5187–5196 (2001)
Ovaa, H., Galardy, P. J. & Ploegh, H. L. Mechanism-based proteomics tools based on ubiquitin and ubiquitin-like proteins: synthesis of active site-directed probes. Methods Enzymol. 399, 468–478 (2005)
Petersen, B. O. et al. Cell cycle- and cell growth-regulated proteolysis of mammalian CDC6 is dependent on APC-CDH1. Genes Dev. 14, 2330–2343 (2000)
Sun, L. & Fang, J. E3-independent constitutive monoubiquitination complements histone methyltransferase activity of SETDB1. Mol. Cell 62, 958–966 (2016)
Weatherbee, S. D., Halder, G., Kim, J., Hudson, A. & Carroll, S. Ultrabithorax regulates genes at several levels of the wing-patterning hierarchy to shape the development of the Drosophila haltere. Genes Dev. 12, 1474–1482 (1998)
Gaytan de Ayala Alonso, A. et al. A genetic screen identifies novel polycomb group genes in Drosophila. Genetics 176, 2099–2108 (2007)
Brand, A. H. & Perrimon, N. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118, 401–415 (1993)
Perez-Garijo, A., Fuchs, Y. & Steller, H. Apoptotic cells can induce non-autonomous apoptosis through the TNF pathway. eLife 2, e01004 (2013)
Dutta, D. et al. Deltex interacts with Eiger and consequently influences the cell death in Drosophila melanogaster. Cell. Signal. 49, 17–29 (2018)
Testa, J. R. et al. Germline BAP1 mutations predispose to malignant mesothelioma. Nat. Genet. 43, 1022–1025 (2011)
Nasu, M. et al. High Incidence of Somatic BAP1 alterations in sporadic malignant mesothelioma. J. Thorac. Oncol. 10, 565–576 (2015)
Yoshikawa, Y. et al. High-density array-CGH with targeted NGS unmask multiple noncontiguous minute deletions on chromosome 3p21 in mesothelioma. Proc. Natl Acad. Sci. USA 113, 13432–13437 (2016)
Desterro, J. M., Rodriguez, M. S., Kemp, G. D. & Hay, R. T. Identification of the enzyme required for activation of the small ubiquitin-like protein SUMO-1. J. Biol. Chem. 274, 10618–10624 (1999)
Desterro, J. M., Thomson, J. & Hay, R. T. Ubch9 conjugates SUMO but not ubiquitin. FEBS Lett. 417, 297–300 (1997)
Okuma, T., Honda, R., Ichikawa, G., Tsumagari, N. & Yasuda, H. In vitro SUMO-1 modification requires two enzymatic steps, E1 and E2. Biochem. Biophys. Res. Commun. 254, 693–698 (1999)
Johnson, E. S. & Gupta, A. A. An E3-like factor that promotes SUMO conjugation to the yeast septins. Cell 106, 735–744 (2001)
Sachdev, S., Bruhn, L., Sieber, H., Pichler, A. & Melchior, F. Grosschedl R. PIASy, a nuclear matrix-associated SUMO E3 ligase, represses LEF1 activity by sequestration into nuclear bodies. Genes Dev. 15, 3088–3103 (2001)
Pichler, A., Gast, A., Seeler, J. S., Dejean, A. & Melchior, F. The nucleoporin RanBP2 has SUMO1 E3 ligase activity. Cell 108, 109–120 (2002)
Schumacher, F. R., Wilson, G. & Day, C. L. The N-terminal extension of UBE2E ubiquitin-conjugating enzymes limits chain assembly. J. Mol. Biol. 425, 4099–4111 (2013)
Ventii, K. H. et al. BRCA1-associated protein-1 is a tumor suppressor that requires deubiquitinating activity and nuclear localization. Cancer Res. 68, 6953–6962 (2008)
Wang, H. et al. Role of histone H2A ubiquitination in Polycomb silencing. Nature 431, 873–878 (2004)
Douziech, M. et al. Bimodal regulation of RAF by CNK in Drosophila. EMBO J. 22, 5068–5078 (2003)
Affar el, B. et al. Targeted ablation of Par-4 reveals a cell type-specific susceptibility to apoptosis-inducing agents. Cancer Res. 66, 3456–3462 (2006)
Bateman, J. R., Lee, A. M. & Wu, C. T. Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange. Genetics 173, 769–777 (2006)
Ashton-Beaucage, D. et al. A functional screen reveals an extensive layer of transcriptional and splicing control underlying RAS/MAPK signaling in Drosophila. PLoS Biol. 12, e1001809 (2014)
Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783–784 (2014)
Hammond-Martel, I. et al. PI 3 kinase related kinases-independent proteolysis of BRCA1 regulates Rad51 recruitment during genotoxic stress in human cells. PLoS ONE 5, e14027 (2010)
Daou, S. et al. Crosstalk between O-GlcNAcylation and proteolytic cleavage regulates the host cell factor-1 maturation pathway. Proc. Natl Acad. Sci. USA 108, 2747–2752 (2011)
Bond, C. S. & Schuttelkopf, A. W. ALINE: a WYSIWYG protein-sequence alignment editor for publication-quality alignments. Acta Crystallogr. D Biol. Crystallogr. 65, 510–512 (2009)
Jiao, L. et al. Mechanism of the Rpn13-induced activation of Uch37. Protein Cell 5, 616–630 (2014)
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010)
Biasini, M. et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42, W252–W258 (2014)
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010)
Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847–2849 (2016)
Hosmer D., Lemeshow S., Sturdivant, R. X. Applied Logistic Regression. 3rd Ed. (A Wiley-Interscience Publication, John Wiley & Sons Inc., New York, NY, 2013)