Abstract
Small ubiquitin-like modifier (SUMO) family proteins regulate target-protein functions by post-translational modification. However, a potent and selective inhibitor targeting the SUMO pathway has been lacking. Here we describe ML-792, a mechanism-based SUMO-activating enzyme (SAE) inhibitor with nanomolar potency in cellular assays. ML-792 selectively blocks SAE enzyme activity and total SUMOylation, thus decreasing cancer cell proliferation. Moreover, we found that induction of the MYC oncogene increased the ML-792-mediated viability effect in cancer cells, thus indicating a potential application of SAE inhibitors in treating MYC-amplified tumors. Using ML-792, we further explored the critical roles of SUMOylation in mitotic progression and chromosome segregation. Furthermore, expression of an SAE catalytic-subunit (UBA2) S95N M97T mutant rescued SUMOylation loss and the mitotic defect induced by ML-792, thus confirming the selectivity of ML-792. As a potent and selective SAE inhibitor, ML-792 provides rapid loss of endogenously SUMOylated proteins, thereby facilitating novel insights into SUMO biology.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Geiss-Friedlander, R. & Melchior, F. Concepts in sumoylation: a decade on. Nat. Rev. Mol. Cell Biol. 8, 947–956 (2007).
Gareau, J.R. & Lima, C.D. The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat. Rev. Mol. Cell Biol. 11, 861–871 (2010).
Wan, J., Subramonian, D. & Zhang, X.D. SUMOylation in control of accurate chromosome segregation during mitosis. Curr. Protein Pept. Sci. 13, 467–481 (2012).
Matunis, M.J., Coutavas, E. & Blobel, G. A novel ubiquitin-like modification modulates the partitioning of the Ran-GTPase-activating protein RanGAP1 between the cytosol and the nuclear pore complex. J. Cell Biol. 135, 1457–1470 (1996).
Girdwood, D. et al. P300 transcriptional repression is mediated by SUMO modification. Mol. Cell 11, 1043–1054 (2003).
Ouyang, J., Valin, A. & Gill, G. Regulation of transcription factor activity by SUMO modification. Methods Mol. Biol. 497, 141–152 (2009).
Verger, A., Perdomo, J. & Crossley, M. Modification with SUMO: a role in transcriptional regulation. EMBO Rep. 4, 137–142 (2003).
Sarangi, P. & Zhao, X. SUMO-mediated regulation of DNA damage repair and responses. Trends Biochem. Sci. 40, 233–242 (2015).
Bergink, S. & Jentsch, S. Principles of ubiquitin and SUMO modifications in DNA repair. Nature 458, 461–467 (2009).
Ivanschitz, L., De Thé, H. & Le Bras, M. PML, SUMOylation, and senescence. Front. Oncol. 3, 171 (2013).
Mo, Y.Y., Yu, Y., Theodosiou, E., Ee, P.L. & Beck, W.T. A role for Ubc9 in tumorigenesis. Oncogene 24, 2677–2683 (2005).
Chen, S.F. et al. Ubc9 expression predicts chemoresistance in breast cancer. Chin. J. Cancer 30, 638–644 (2011).
Moschos, S.J. et al. Expression analysis of Ubc9, the single small ubiquitin-like modifier (SUMO) E2 conjugating enzyme, in normal and malignant tissues. Hum. Pathol. 41, 1286–1298 (2010).
Liu, X. et al. Knockdown of SUMO-activating enzyme subunit 2 (SAE2) suppresses cancer malignancy and enhances chemotherapy sensitivity in small cell lung cancer. J. Hematol. Oncol. 8, 67 (2015).
He, X. et al. Characterization of the loss of SUMO pathway function on cancer cells and tumor proliferation. PLoS One 10, e0123882 (2015).
Kessler, J.D. et al. A SUMOylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis. Science 335, 348–353 (2012).
Hoellein, A. et al. Myc-induced SUMOylation is a therapeutic vulnerability for B-cell lymphoma. Blood 124, 2081–2090 (2014).
Yu, B. et al. Oncogenesis driven by the Ras/Raf pathway requires the SUMO E2 ligase Ubc9. Proc. Natl. Acad. Sci. USA 112, E1724–E1733 (2015).
Becker, J. et al. Detecting endogenous SUMO targets in mammalian cells and tissues. Nat. Struct. Mol. Biol. 20, 525–531 (2013).
Fukuda, I. et al. Ginkgolic acid inhibits protein SUMOylation by blocking formation of the E1-SUMO intermediate. Chem. Biol. 16, 133–140 (2009).
Takemoto, M. et al. Inhibition of protein SUMOylation by davidiin, an ellagitannin from Davidia involucrata. J. Antibiot. (Tokyo) 67, 335–338 (2014).
Suzawa, M. et al. A gene-expression screen identifies a non-toxic sumoylation inhibitor that mimics SUMO-less human LRH-1 in liver. eLife 4, e09003 (2015).
Fukuda, I. et al. Kerriamycin B inhibits protein SUMOylation. J. Antibiot. (Tokyo) 62, 221–224 (2009).
Kim, Y.S., Nagy, K., Keyser, S. & Schneekloth, J.S. Jr. An electrophoretic mobility shift assay identifies a mechanistically unique inhibitor of protein sumoylation. Chem. Biol. 20, 604–613 (2013).
Bogachek, M.V. et al. Sumoylation pathway is required to maintain the basal breast cancer subtype. Cancer Cell 25, 748–761 (2014).
Hirohama, M. et al. Spectomycin B1 as a novel SUMOylation inhibitor that directly binds to SUMO E2. ACS Chem. Biol. 8, 2635–2642 (2013).
Soucy, T.A. et al. An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer. Nature 458, 732–736 (2009).
Swords, R.T. et al. Pevonedistat (MLN4924), a first-in-class NEDD8-activating enzyme inhibitor, in patients with acute myeloid leukaemia and myelodysplastic syndromes: a phase 1 study. Br. J. Haematol. 169, 534–543 (2015).
Brownell, J.E. et al. Substrate-assisted inhibition of ubiquitin-like protein-activating enzymes: the NEDD8 E1 inhibitor MLN4924 forms a NEDD8-AMP mimetic in situ. Mol. Cell 37, 102–111 (2010).
Lee, Y.K., Thomas, S.N., Yang, A.J. & Ann, D.K. Doxorubicin down-regulates Kruppel-associated box domain-associated protein 1 sumoylation that relieves its transcription repression on p21WAF1/CIP1 in breast cancer MCF-7 cells. J. Biol. Chem. 282, 1595–1606 (2007).
Zhu, S. et al. Protection from isopeptidase-mediated deconjugation regulates paralog-selective sumoylation of RanGAP1. Mol. Cell 33, 570–580 (2009).
Yang, X. et al. Absolute quantification of E1, ubiquitin-like proteins and Nedd8-MLN4924 adduct by mass spectrometry. Cell Biochem. Biophys. 67, 139–147 (2013).
Chen, J.J. et al. Mechanistic studies of substrate-assisted inhibition of ubiquitin-activating enzyme by adenosine sulfamate analogues. J. Biol. Chem. 286, 40867–40877 (2011).
Nacerddine, K. et al. The SUMO pathway is essential for nuclear integrity and chromosome segregation in mice. Dev. Cell 9, 769–779 (2005).
Garcia-Dominguez, M. & Reyes, J.C. SUMO association with repressor complexes, emerging routes for transcriptional control. Biochim. Biophys. Acta 1789, 451–459 (2009).
Núñez-O'Mara, A. et al. PHD3-SUMO conjugation represses HIF1 transcriptional activity independently of PHD3 catalytic activity. J. Cell Sci. 128, 40–49 (2015).
Golebiowski, F. et al. System-wide changes to SUMO modifications in response to heat shock. Sci. Signal. 2, ra24 (2009).
Niskanen, E.A. et al. Global SUMOylation on active chromatin is an acute heat stress response restricting transcription. Genome Biol. 16, 153 (2015).
Nuro-Gyina, P.K. & Parvin, J.D. Roles for SUMO in pre-mRNA processing. Wiley Interdiscip. Rev. RNA 7, 105–112 (2016).
Psakhye, I. & Jentsch, S. Protein group modification and synergy in the SUMO pathway as exemplified in DNA repair. Cell 151, 807–820 (2012).
Morris, J.R. et al. The SUMO modification pathway is involved in the BRCA1 response to genotoxic stress. Nature 462, 886–890 (2009).
Moschos, S.J. et al. SAGE and antibody array analysis of melanoma-infiltrated lymph nodes: identification of Ubc9 as an important molecule in advanced-stage melanomas. Oncogene 26, 4216–4225 (2007).
Jacquemont, C. & Taniguchi, T. Proteasome function is required for DNA damage response and fanconi anemia pathway activation. Cancer Res. 67, 7395–7405 (2007).
Sakasai, R. & Tibbetts, R. RNF8-dependent and RNF8-independent regulation of 53BP1 in response to DNA damage. J. Biol. Chem. 283, 13549–13555 (2008).
Eifler, K. & Vertegaal, A.C. SUMOylation-mediated regulation of cell cycle progression and cancer. Trends Biochem. Sci. 40, 779–793 (2015).
Dasso, M. Emerging roles of the SUMO pathway in mitosis. Cell Div. 3, 5 (2008).
Milhollen, M.A. et al. Treatment-emergent mutations in NAEβ confer resistance to the NEDD8-activating enzyme inhibitor MLN4924. Cancer Cell 21, 388–401 (2012).
Minto, C.F. et al. Response surface model for anesthetic drug interactions. Anesthesiology 92, 1603–1616 (2000).
Chou, T.C. Drug combination studies and their synergy quantification using the Chou-Talalay method. Cancer Res. 70, 440–446 (2010).
Acknowledgements
We sincerely thank J. Klekota for bioinformatics support and K. Galvin, P. Veiby, C. Lou, M. Manfredi and C. Claiborne for insightful comments. We thank R. Hay (University of Dundee) for p300 cells.
Author information
Authors and Affiliations
Contributions
X.H., E.S.L., N.B. and S.M.P. conceived and designed the experiments. X.H., J.R., M.G., H.B., C.R., K.X., Z.Y. and J.B. performed cell biology experiments. T.S. and J.M. performed in vitro enzymatic assays. X.Y. and H.L. performed mass spectrometry analysis. M.S. provided structural prediction. H.X., M.D., D.E., H.M., Z.H., J.G., R.C. and S.L. designed chemical compounds and/or performed chemical synthesis. E.K., P.S. and E.S.L. performed RNA-seq analysis. All authors discussed the data and provided scientific input. X.H., T.S., E.K., L.R.D., J.E.B., J.N., S.L., E.S.L., N.B. and S.M.P. wrote and/or edited the paper.
Corresponding authors
Ethics declarations
Competing interests
Takeda Pharmaceuticals International Co. provided complete financial support for the study design, data collection and analysis, decision to publish, preparation of the manuscript and salaries for authors X.H., J.R., T.S., E.K., J.M., M.G., H.B., X.Y., H.L., C.R., P.S., K.X., Z.Y., M.S., J.B., H.X., M.D., D.E., H.M., Z.H., J.G., R.C., L.R.D., J.E.B., J.N., S.L., E.S.L., N.B. and S.M.P. during the time when studies were conducted. Patent application WO2015/002994 has been filed for compound ML-792.
Supplementary information
Supplementary Text and Figures
Supplementary Results, Supplementary Figures 1–22. (PDF 3242 kb)
Supplementary Table 1
ML-792 activity against a panel of 366 ATP-utilizing enzymes. (XLSX 34 kb)
Supplementary Table 2
RNAseq analysis on HCT116 cells harboring UBA2 shRNA s or treated with ML-792. (XLSX 111 kb)
Supplementary Table 3
quantitative proteomic profiling in HCT116 cells treated with DMSO or ML-792. (XLSX 1405 kb)
Supplementary Note 1
Synthesis and Characterization of ML-792. (PDF 451 kb)
Rights and permissions
About this article
Cite this article
He, X., Riceberg, J., Soucy, T. et al. Probing the roles of SUMOylation in cancer cell biology by using a selective SAE inhibitor. Nat Chem Biol 13, 1164–1171 (2017). https://doi.org/10.1038/nchembio.2463
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nchembio.2463
This article is cited by
-
Circ-RAPGEF5 promotes intrahepatic cholangiocarcinoma progression by stabilizing SAE1 to facilitate SUMOylation
Journal of Experimental & Clinical Cancer Research (2023)
-
The emerging roles of SUMOylation in the tumor microenvironment and therapeutic implications
Experimental Hematology & Oncology (2023)
-
Inflammasome activity is controlled by ZBTB16-dependent SUMOylation of ASC
Nature Communications (2023)
-
A novel prognostic signature for hepatocellular carcinoma based on SUMOylation-related genes
Scientific Reports (2023)
-
The essential functions of protein SUMOylation in cell proliferation
Nature Structural & Molecular Biology (2023)