SPOP mutation induces replication over-firing by impairing Geminin ubiquitination and triggers replication catastrophe upon ATR inhibition

Ma, Jian; Shi, Qing; Cui, Gaofeng; Sheng, Haoyue; Botuyan, Maria Victoria; Zhou, Yingke; Yan, Yuqian; He, Yundong; Wang, Liguo; Wang, Yuzhuo; Mer, Georges; Ye, Dingwei; Wang, Chenji; Huang, Haojie

doi:10.1038/s41467-021-26049-6

SPOP mutation induces replication over-firing by impairing Geminin ubiquitination and triggers replication catastrophe upon ATR inhibition

Journal Article · Fri Oct 01 00:00:00 EDT 2021 · Nature Communications

DOI:https://doi.org/10.1038/s41467-021-26049-6· OSTI ID:1839716

Ma, Jian ^[1]; Shi, Qing ^[2]; Cui, Gaofeng ^[3]; Sheng, Haoyue ^[1]; ^[4]; Zhou, Yingke ^[3]; Yan, Yuqian ^[3]; He, Yundong ^[3]; ^[3]; ^[5]; ^[4]; Ye, Dingwei ^[6]; ^[2]; ^[4]

Fudan Univ. Shanghai Cancer Center (China); Fudan Univ., Shanghai (China). Shanghai Medical College; Mayo Clinic College of Medicine and Science, Rochester, MN (United States)
Fudan Univ., Shanghai (China). MOE Engineering Research Center of Gene Technology, State Key Lab. of Genetic Engineering
Mayo Clinic College of Medicine and Science, Rochester, MN (United States)
Mayo Clinic College of Medicine and Science, Rochester, MN (United States); Mayo Clinic College of Medicine and Science, Rochester, MN (United States). Mayo Clinic Cancer Center
BC Cancer Research Center, Vancouver, BC (Canada)
Fudan Univ. Shanghai Cancer Center (China); Fudan Univ., Shanghai (China). Shanghai Medical College

Geminin and its binding partner Cdt1 are essential for the regulation of DNA replication. Here we show that the CULLIN3 E3 ubiquitin ligase adaptor protein SPOP binds Geminin at endogenous level and regulates DNA replication. SPOP promotes K27-linked non-degradative poly-ubiquitination of Geminin at lysine residues 100 and 127. This poly-ubiquitination of Geminin prevents DNA replication over-firing by indirectly blocking the association of Cdt1 with the MCM protein complex, an interaction required for DNA unwinding and replication. SPOP is frequently mutated in certain human cancer types and implicated in tumorigenesis. We show that cancer-associated SPOP mutations impair Geminin K27-linked poly-ubiquitination and induce replication origin over-firing and re-replication. The replication stress caused by SPOP mutations triggers replication catastrophe and cell death upon ATR inhibition. Our results reveal a tumor suppressor role of SPOP in preventing DNA replication over-firing and genome instability and suggest that SPOP-mutated tumors may be susceptible to ATR inhibitor therapy.

View Accepted Manuscript (DOE)

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: Mayo Clinic Foundation; National Institutes of Health (NIH); National Natural Science Foundation of China (NSFC); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1839716

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 12; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (72)

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data Huang, Jing; MacKerell, Alexander D. Journal of Computational Chemistry, Vol. 34, Issue 25 https://doi.org/10.1002/jcc.23354	journal	July 2013
PyXlinkViewer : A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system Schiffrin, Bob; Radford, Sheena E.; Brockwell, David J. Protein Science, Vol. 29, Issue 8 https://doi.org/10.1002/pro.3902	journal	July 2020
NMRPipe: A multidimensional spectral processing system based on UNIX pipes Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW. Journal of Biomolecular NMR, Vol. 6, Issue 3 https://doi.org/10.1007/BF00197809	journal	November 1995
Structure of ubiquitin refined at 1.8 Å resolution Vijay-kumar, Senadhi; Bugg, Charles E.; Cook, William J. Journal of Molecular Biology, Vol. 194, Issue 3 https://doi.org/10.1016/0022-2836(87)90679-6	journal	April 1987
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Geminin, an Inhibitor of DNA Replication, Is Degraded during Mitosis McGarry, Thomas J.; Kirschner, Marc W. Cell, Vol. 93, Issue 6 https://doi.org/10.1016/S0092-8674(00)81209-X	journal	June 1998
TRIM24 Is an Oncogenic Transcriptional Activator in Prostate Cancer Groner, Anna C.; Cato, Laura; de Tribolet-Hardy, Jonas Cancer Cell, Vol. 29, Issue 6 https://doi.org/10.1016/j.ccell.2016.04.012	journal	June 2016
SPOP Mutation Drives Prostate Tumorigenesis In Vivo through Coordinate Regulation of PI3K/mTOR and AR Signaling Blattner, Mirjam; Liu, Deli; Robinson, Brian D. Cancer Cell, Vol. 31, Issue 3 https://doi.org/10.1016/j.ccell.2017.02.004	journal	March 2017
ATR Prohibits Replication Catastrophe by Preventing Global Exhaustion of RPA Toledo, Luis Ignacio; Altmeyer, Matthias; Rask, Maj-Britt Cell, Vol. 155, Issue 5 https://doi.org/10.1016/j.cell.2013.10.043	journal	November 2013
Single-Molecule Studies of Origin Licensing Reveal Mechanisms Ensuring Bidirectional Helicase Loading Ticau, Simina; Friedman, Larry J.; Ivica, Nikola A. Cell, Vol. 161, Issue 3 https://doi.org/10.1016/j.cell.2015.03.012	journal	April 2015
The Molecular Taxonomy of Primary Prostate Cancer Abeshouse, Adam; Ahn, Jaeil; Akbani, Rehan Cell, Vol. 163, Issue 4 https://doi.org/10.1016/j.cell.2015.10.025	journal	November 2015
Destruction of Full-Length Androgen Receptor by Wild-Type SPOP, but Not Prostate-Cancer-Associated Mutants An, Jian; Wang, Chenji; Deng, Yibin Cell Reports, Vol. 6, Issue 4 https://doi.org/10.1016/j.celrep.2014.01.013	journal	February 2014
Whole-genome and Transcriptome Sequencing of Prostate Cancer Identify New Genetic Alterations Driving Disease Progression Ren, Shancheng; Wei, Gong-Hong; Liu, Dongbing European Urology, Vol. 73, Issue 3 https://doi.org/10.1016/j.eururo.2017.08.027	journal	March 2018
Control over DNA replication in time and space Symeonidou, Ioanna-Eleni; Taraviras, Stavros; Lygerou, Zoi FEBS Letters, Vol. 586, Issue 18 https://doi.org/10.1016/j.febslet.2012.07.042	journal	July 2012
Crystal Structure of the Coiled-coil Dimerization Motif of Geminin: Structural and Functional Insights on DNA Replication Regulation Thépaut, Michel; Maiorano, Domenico; Guichou, Jean-François Journal of Molecular Biology, Vol. 342, Issue 1 https://doi.org/10.1016/j.jmb.2004.06.065	journal	September 2004
Multiple Weak Linear Motifs Enhance Recruitment and Processivity in SPOP-Mediated Substrate Ubiquitination Pierce, Wendy K.; Grace, Christy R.; Lee, Jihun Journal of Molecular Biology, Vol. 428, Issue 6 https://doi.org/10.1016/j.jmb.2015.10.002	journal	March 2016
A Dimerized Coiled-Coil Domain and an Adjoining Part of Geminin Interact with Two Sites on Cdt1 for Replication Inhibition Saxena, Sandeep; Yuan, Ping; Dhar, Suman Kumar Molecular Cell, Vol. 15, Issue 2 https://doi.org/10.1016/j.molcel.2004.06.045	journal	July 2004
Deregulated Replication Licensing Causes DNA Fragmentation Consistent with Head-to-Tail Fork Collision Davidson, Iain F.; Li, Anatoliy; Blow, J. Julian Molecular Cell, Vol. 24, Issue 3 https://doi.org/10.1016/j.molcel.2006.09.010	journal	November 2006
Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases Zhuang, Min; Calabrese, Matthew F.; Liu, Jiang Molecular Cell, Vol. 36, Issue 1 https://doi.org/10.1016/j.molcel.2009.09.022	journal	October 2009
Truncated ERG Oncoproteins from TMPRSS2-ERG Fusions Are Resistant to SPOP-Mediated Proteasome Degradation An, Jian; Ren, Shancheng; Murphy, Stephen J. Molecular Cell, Vol. 59, Issue 6 https://doi.org/10.1016/j.molcel.2015.07.025	journal	September 2015
The Structure of the SPOP-Pdx1 Interface Reveals Insights into the Phosphorylation-Dependent Binding Regulation Ostertag, Michael Sebastian; Messias, Ana Cristina; Sattler, Michael Structure, Vol. 27, Issue 2 https://doi.org/10.1016/j.str.2018.10.005	journal	February 2019
The DNA fibre technique – tracking helicases at work Nieminuszczy, Jadwiga; Schwab, Rebekka A.; Niedzwiedz, Wojciech Methods, Vol. 108 https://doi.org/10.1016/j.ymeth.2016.04.019	journal	October 2016
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation Hess, Berk Journal of Chemical Theory and Computation, Vol. 4, Issue 1 https://doi.org/10.1021/ct700200b	journal	December 2007
The Cdt1 protein is required to license DNA for replication in fission yeast Nishitani, Hideo; Lygerou, Zoi; Nishimoto, Takeharu Nature, Vol. 404, Issue 6778 https://doi.org/10.1038/35007110	journal	April 2000
Repression of origin assembly in metaphase depends on inhibition of RLF-B/Cdt1 by geminin Tada, Shusuke; Li, Anatoliy; Maiorano, Domenico Nature Cell Biology, Vol. 3, Issue 2 https://doi.org/10.1038/35055000	journal	February 2001
Cyclin-dependent kinases prevent DNA re-replication through multiple mechanisms Nguyen, Van Q.; Co, Carl; Li, Joachim J. Nature, Vol. 411, Issue 6841 https://doi.org/10.1038/35082600	journal	June 2001
Structural basis for inhibition of the replication licensing factor Cdt1 by geminin Lee, Changwook; Hong, BumSoo; Choi, Jung Min Nature, Vol. 430, Issue 7002 https://doi.org/10.1038/nature02813	journal	August 2004
Cyclin D–CDK4 kinase destabilizes PD-L1 via cullin 3–SPOP to control cancer immune surveillance Zhang, Jinfang; Bu, Xia; Wang, Haizhen Nature, Vol. 553, Issue 7686 https://doi.org/10.1038/nature25015	journal	November 2017
PCNA functions as a molecular platform to trigger Cdt1 destruction and prevent re-replication Arias, Emily E.; Walter, Johannes C. Nature Cell Biology, Vol. 8, Issue 1 https://doi.org/10.1038/ncb1346	journal	December 2005
Causes and consequences of replication stress Zeman, Michelle K.; Cimprich, Karlene A. Nature Cell Biology, Vol. 16, Issue 1 https://doi.org/10.1038/ncb2897	journal	December 2013
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer Barbieri, Christopher E.; Baca, Sylvan C.; Lawrence, Michael S. Nature Genetics, Vol. 44, Issue 6 https://doi.org/10.1038/ng.2279	journal	May 2012
Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes Le Gallo, Matthieu; O'Hara, Andrea J.; Rudd, Meghan L. Nature Genetics, Vol. 44, Issue 12 https://doi.org/10.1038/ng.2455	journal	October 2012
Prostate cancer–associated SPOP mutations confer resistance to BET inhibitors through stabilization of BRD4 Dai, Xiangpeng; Gan, Wenjian; Li, Xiaoning Nature Medicine, Vol. 23, Issue 9 https://doi.org/10.1038/nm.4378	journal	August 2017
Intrinsic BET inhibitor resistance in SPOP-mutated prostate cancer is mediated by BET protein stabilization and AKT–mTORC1 activation Zhang, Pingzhao; Wang, Dejie; Zhao, Yu Nature Medicine, Vol. 23, Issue 9 https://doi.org/10.1038/nm.4379	journal	August 2017
Prereplication-complex formation: a molecular double take? Yardimci, Hasan; Walter, Johannes C. Nature Structural & Molecular Biology, Vol. 21, Issue 1 https://doi.org/10.1038/nsmb.2738	journal	January 2014
Open-ringed structure of the Cdt1–Mcm2–7 complex as a precursor of the MCM double hexamer Zhai, Yuanliang; Cheng, Erchao; Wu, Hao Nature Structural & Molecular Biology, Vol. 24, Issue 3 https://doi.org/10.1038/nsmb.3374	journal	February 2017
Molecular structure of human geminin Okorokov, Andrei L.; Orlova, Elena V.; Kingsbury, Sarah R. Nature Structural & Molecular Biology, Vol. 11, Issue 10 https://doi.org/10.1038/nsmb835	journal	September 2004
The long tail of oncogenic drivers in prostate cancer Armenia, Joshua; Wankowicz, Stephanie A. M.; Liu, David Nature Genetics, Vol. 50, Issue 5 https://doi.org/10.1038/s41588-018-0078-z	journal	April 2018
Human Geminin promotes pre-RC formation and DNA replication by stabilizing CDT1 in mitosis Ballabeni, Andrea; Melixetian, Marina; Zamponi, Raffaella The EMBO Journal, Vol. 23, Issue 15 https://doi.org/10.1038/sj.emboj.7600314	journal	July 2004
Two E3 ubiquitin ligases, SCF-Skp2 and DDB1-Cul4, target human Cdt1 for proteolysis Nishitani, Hideo; Sugimoto, Nozomi; Roukos, Vassilis The EMBO Journal, Vol. 25, Issue 5 https://doi.org/10.1038/sj.emboj.7601002	journal	February 2006
A Cdt1–geminin complex licenses chromatin for DNA replication and prevents rereplication during S phase in Xenopus Lutzmann, Malik; Maiorano, Domenico; Méchali, Marcel The EMBO Journal, Vol. 25, Issue 24 https://doi.org/10.1038/sj.emboj.7601436	journal	November 2006
Canonical sampling through velocity rescaling Bussi, Giovanni; Donadio, Davide; Parrinello, Michele The Journal of Chemical Physics, Vol. 126, Issue 1 https://doi.org/10.1063/1.2408420	journal	January 2007
Quaternary structure of the human Cdt1-Geminin complex regulates DNA replication licensing De Marco, V.; Gillespie, P. J.; Li, A. Proceedings of the National Academy of Sciences, Vol. 106, Issue 47 https://doi.org/10.1073/pnas.0905281106	journal	November 2009
Prostate cancer-associated mutations in speckle-type POZ protein (SPOP) regulate steroid receptor coactivator 3 protein turnover Geng, C.; He, B.; Xu, L. Proceedings of the National Academy of Sciences, Vol. 110, Issue 17 https://doi.org/10.1073/pnas.1304502110	journal	April 2013
Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6 Yuan, Zuanning; Schneider, Sarah; Dodd, Thomas Proceedings of the National Academy of Sciences, Vol. 117, Issue 30 https://doi.org/10.1073/pnas.2006231117	journal	July 2020
The Human Licensing Factor for DNA Replication Cdt1 Accumulates in G1 and Is Destabilized after Initiation of S-phase Nishitani, Hideo; Taraviras, Stavros; Lygerou, Zoi Journal of Biological Chemistry, Vol. 276, Issue 48 https://doi.org/10.1074/jbc.M105406200	journal	November 2001
Geminin Stabilizes Cdt1 during Meiosis in Xenopus Oocytes Narasimhachar, Yadushyla; Coué, Martine Journal of Biological Chemistry, Vol. 284, Issue 40 https://doi.org/10.1074/jbc.M109.008854	journal	October 2009
Geminin Has Dimerization, Cdt1-binding, and Destruction Domains That Are Required for Biological Activity Benjamin, Jacqueline M.; Torke, Susanna J.; Demeler, Borries Journal of Biological Chemistry, Vol. 279, Issue 44 https://doi.org/10.1074/jbc.M407726200	journal	October 2004
PCNA Is a Cofactor for Cdt1 Degradation by CUL4/DDB1-mediated N-terminal Ubiquitination Senga, Takeshi; Sivaprasad, Umasundari; Zhu, Wenge Journal of Biological Chemistry, Vol. 281, Issue 10 https://doi.org/10.1074/jbc.M512705200	journal	March 2006
A Leap-frog Algorithm for Stochastic Dynamics Van Gunsteren, W. F.; Berendsen, H. J. C. Molecular Simulation, Vol. 1, Issue 3 https://doi.org/10.1080/08927028808080941	journal	March 1988
Speckle-type POZ protein, SPOP, is involved in the DNA damage response Zhang, D.; Wang, H.; Sun, M. Carcinogenesis, Vol. 35, Issue 8 https://doi.org/10.1093/carcin/bgu022	journal	January 2014
SPOP promotes transcriptional expression of DNA repair and replication factors to prevent replication stress and genomic instability Hjorth-Jensen, Kim; Maya-Mendoza, Apolinar; Dalgaard, Nanna Nucleic Acids Research, Vol. 46, Issue 18 https://doi.org/10.1093/nar/gky719	journal	August 2018
iProX: an integrated proteome resource Ma, Jie; Chen, Tao; Wu, Songfeng Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky869	journal	September 2018
ATR phosphorylates SMARCAL1 to prevent replication fork collapse Couch, Frank B.; Bansbach, Carol E.; Driscoll, Robert Genes & Development, Vol. 27, Issue 14 https://doi.org/10.1101/gad.214080.113	journal	July 2013
Deregulated origin licensing leads to chromosomal breaks by rereplication of a gapped DNA template Neelsen, Kai J.; Zanini, Isabella M. Y.; Mijic, Sofija Genes & Development, Vol. 27, Issue 23 https://doi.org/10.1101/gad.226373.113	journal	December 2013
DNA replication origins—where do we begin? Prioleau, Marie-Noëlle; MacAlpine, David M. Genes & Development, Vol. 30, Issue 15 https://doi.org/10.1101/gad.285114.116	journal	August 2016
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Loss of DNA Replication Control Is a Potent Inducer of Gene Amplification Green, Brian M.; Finn, Kenneth J.; Li, Joachim J. Science, Vol. 329, Issue 5994 https://doi.org/10.1126/science.1190966	journal	August 2010
Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer Theurillat, Jean-Philippe P.; Udeshi, Namrata D.; Errington, Wesley J. Science, Vol. 346, Issue 6205 https://doi.org/10.1126/science.1250255	journal	October 2014
Inhibition of Eukaryotic DNA Replication by Geminin Binding to Cdt1 Wohlschlegel, James A.; Dwyer, Brian T.; Dhar, Suman K. Science, Vol. 290, Issue 5500 https://doi.org/10.1126/science.290.5500.2309	journal	December 2000
Stress-Stimulated Mitogen-Activated Protein Kinases Control the Stability and Activity of the Cdt1 DNA Replication Licensing Factor Chandrasekaran, S.; Tan, T. X.; Hall, J. R. Molecular and Cellular Biology, Vol. 31, Issue 22 https://doi.org/10.1128/MCB.06163-11	journal	September 2011
Initiation of dna Replication in Eukaryotic Cells Dutta, Anindya; Bell, Stephen P. Annual Review of Cell and Developmental Biology, Vol. 13, Issue 1 https://doi.org/10.1146/annurev.cellbio.13.1.293	journal	November 1997
SPOP promotes ATF2 ubiquitination and degradation to suppress prostate cancer progression Ma, Jian; Chang, Kun; Peng, Jingtao Journal of Experimental & Clinical Cancer Research, Vol. 37, Issue 1 https://doi.org/10.1186/s13046-018-0809-0	journal	July 2018
Dynamic interactions of high Cdt1 and geminin levels regulate S phase in early Xenopus embryos Kisielewska, Jolanta; Blow, J. Julian Development, Vol. 139, Issue 1 https://doi.org/10.1242/dev.068676	journal	January 2012
Re-replication of a Centromere Induces Chromosomal Instability and Aneuploidy Hanlon, Stacey L.; Li, Joachim J. PLOS Genetics, Vol. 11, Issue 4 https://doi.org/10.1371/journal.pgen.1005039	journal	April 2015
Higher‐order oligomerization promotes localization of SPOP to liquid nuclear speckles Marzahn, Melissa R.; Marada, Suresh; Lee, Jihun The EMBO Journal, Vol. 35, Issue 12 https://doi.org/10.15252/embj.201593169	journal	May 2016
The novel BET‐CBP/p300 dual inhibitor NEO2734 is active in SPOP mutant and wild‐type prostate cancer Yan, Yuqian; Ma, Jian; Wang, Dejie EMBO Molecular Medicine, Vol. 11, Issue 11 https://doi.org/10.15252/emmm.201910659	journal	September 2019
An Inactive Geminin Mutant That Binds Cdt1 Suchyta, Marissa; Miotto, Benoit; McGarry, Thomas Genes, Vol. 6, Issue 2 https://doi.org/10.3390/genes6020252	journal	May 2015
Regulation and Function of Cdt1; A Key Factor in Cell Proliferation and Genome Stability Pozo, Pedro; Cook, Jeanette Genes, Vol. 8, Issue 1 https://doi.org/10.3390/genes8010002	journal	December 2016
SPOP mutation leads to genomic instability in prostate cancer Boysen, Gunther; Barbieri, Christopher E.; Prandi, Davide eLife, Vol. 4 https://doi.org/10.7554/eLife.09207	journal	September 2015

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SPOP mutation induces replication over-firing by impairing Geminin ubiquitination and triggers replication catastrophe upon ATR inhibition

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