WRN inhibition leads to its chromatin-associated degradation via the PIAS4-RNF4-p97/VCP axis.
Werner Syndrome Helicase
/ metabolism
Humans
Animals
Chromatin
/ metabolism
Valosin Containing Protein
/ metabolism
Protein Inhibitors of Activated STAT
/ metabolism
Mice
Cell Line, Tumor
Nuclear Proteins
/ metabolism
Microsatellite Instability
Proteolysis
/ drug effects
Sumoylation
/ drug effects
Transcription Factors
/ metabolism
Xenograft Model Antitumor Assays
Female
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
18 Jul 2024
18 Jul 2024
Historique:
received:
19
12
2023
accepted:
01
07
2024
medline:
19
7
2024
pubmed:
19
7
2024
entrez:
18
7
2024
Statut:
epublish
Résumé
Synthetic lethality provides an attractive strategy for developing targeted cancer therapies. For example, cancer cells with high levels of microsatellite instability (MSI-H) are dependent on the Werner (WRN) helicase for survival. However, the mechanisms that regulate WRN spatiotemporal dynamics remain poorly understood. Here, we used single-molecule tracking (SMT) in combination with a WRN inhibitor to examine WRN dynamics within the nuclei of living cancer cells. WRN inhibition traps the helicase on chromatin, requiring p97/VCP for extraction and proteasomal degradation in a MSI-H dependent manner. Using a phenotypic screen, we identify the PIAS4-RNF4 axis as the pathway responsible for WRN degradation. Finally, we show that co-inhibition of WRN and SUMOylation has an additive toxic effect in MSI-H cells and confirm the in vivo activity of WRN inhibition using an MSI-H mouse xenograft model. This work elucidates a regulatory mechanism for WRN that may facilitate identification of new therapeutic modalities, and highlights the use of SMT as a tool for drug discovery and mechanism-of-action studies.
Identifiants
pubmed: 39025847
doi: 10.1038/s41467-024-50178-3
pii: 10.1038/s41467-024-50178-3
doi:
Substances chimiques
Werner Syndrome Helicase
EC 3.6.4.12
WRN protein, human
EC 3.6.4.12
Chromatin
0
Valosin Containing Protein
EC 3.6.4.6
Protein Inhibitors of Activated STAT
0
VCP protein, human
EC 3.6.4.6
Nuclear Proteins
0
Transcription Factors
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
6059Informations de copyright
© 2024. The Author(s).
Références
Opresko, P. L., Cheng, W. H., von Kobbe, C., Harrigan, J. A. & Bohr, V. A. Werner syndrome and the function of the Werner protein; what they can teach us about the molecular aging process. Carcinogenesis 24, 791–802 (2003).
pubmed: 12771022
doi: 10.1093/carcin/bgg034
Croteau, D. L., Popuri, V., Opresko, P. L. & Bohr, V. A. Human RecQ helicases in DNA repair, recombination, and replication. Annu. Rev. Biochem. 83, 519–552 (2014).
pubmed: 24606147
pmcid: 4586249
doi: 10.1146/annurev-biochem-060713-035428
Constantinou, A. et al. Werner’s syndrome protein (WRN) migrates Holliday junctions and co-localizes with RPA upon replication arrest. EMBO Rep. 1, 80–84 (2000).
pubmed: 11256630
pmcid: 1083680
doi: 10.1093/embo-reports/kvd004
Bendtsen, K. M. et al. Dynamics of the DNA repair proteins WRN and BLM in the nucleoplasm and nucleoli. Eur. Biophys. J. 43, 509–516 (2014).
pubmed: 25119658
pmcid: 5576897
doi: 10.1007/s00249-014-0981-x
von Kobbe, C. & Bohr, V. A. A nucleolar targeting sequence in the Werner syndrome protein resides within residues 949-1092. J. Cell Sci. 115, 3901–3907 (2002).
doi: 10.1242/jcs.00076
Shen, J. & Loeb, L. A. Unwinding the molecular basis of the Werner syndrome. Mech. Ageing Dev. 122, 921–944 (2001).
pubmed: 11348659
doi: 10.1016/S0047-6374(01)00248-2
O’Neil, N. J., Bailey, M. L. & Hieter, P. Synthetic lethality and cancer. Nat. Rev. Genet. 18, 613–623 (2017).
pubmed: 28649135
doi: 10.1038/nrg.2017.47
Chan, E. M. et al. WRN helicase is a synthetic lethal target in microsatellite unstable cancers. Nature 568, 551–556 (2019).
pubmed: 30971823
pmcid: 6580861
doi: 10.1038/s41586-019-1102-x
Kategaya, L., Perumal, S. K., Hager, J. H. & Belmont, L. D. Werner syndrome helicase is required for the survival of cancer cells with microsatellite instability. iScience 13, 488–497 (2019).
pubmed: 30898619
pmcid: 6441948
doi: 10.1016/j.isci.2019.02.006
Lou, K., Gilbert, L. A. & Shokat, K. M. A bounty of new challenging targets in oncology for chemical discovery. Biochemistry 58, 3328–3330 (2019).
pubmed: 31343870
doi: 10.1021/acs.biochem.9b00570
Picco, G. et al. Werner helicase is a synthetic-lethal vulnerability in mismatch repair-deficient colorectal cancer refractory to targeted therapies, chemotherapy, and immunotherapy. Cancer Discov. 11, 1923–1937 (2021).
pubmed: 33837064
doi: 10.1158/2159-8290.CD-20-1508
Lieb, S. et al. Werner syndrome helicase is a selective vulnerability of microsatellite instability-high tumor cells. eLife 8, e43333 (2019).
pubmed: 30910006
pmcid: 6435321
doi: 10.7554/eLife.43333
Bordas, V. et al. Triazolo-pyrimidine analogues for treating diseases connected to the inhibiton of werner syndrome recq helicase (wrn). WO 2022/249060 A1 (2022).
Ferretti, S. et al. Discovery of WRN inhibitor HRO761 with synthetic lethality in MSI cancers. Nature 629, 443–449 (2024).
pubmed: 38658754
pmcid: 11078746
doi: 10.1038/s41586-024-07350-y
McSwiggen, D. T. et al. A high-throughput platform for single-molecule tracking identifies drug interaction and cellular mechanisms. eLife 12, RP93183 (2023).
Marciniak, R. A., Lombard, D. B., Johnson, F. B. & Guarente, L. Nucleolar localization of the Werner syndrome protein in human cells. Proc. Natl Acad. Sci. USA 95, 6887–6892 (1998).
pubmed: 9618508
pmcid: 22674
doi: 10.1073/pnas.95.12.6887
Zhu, M. et al. HERC2 inactivation abrogates nucleolar localization of RecQ helicases BLM and WRN. Sci. Rep. 11, 360 (2021).
pubmed: 33432007
pmcid: 7801386
doi: 10.1038/s41598-020-79715-y
Kamath-Loeb, A. S. et al. Homozygosity for the WRN Helicase-Inactivating Variant, R834C, does not confer a Werner syndrome clinical phenotype. Sci. Rep. 7, 44081 (2017).
pubmed: 28276523
pmcid: 5343477
doi: 10.1038/srep44081
Driouchi, A. et al. Oblique Line Scan Illumination Enables Expansive, Accurate and Sensitive Single Protein Measurements in Solution and in Living Cells. Preprint at bioRxiv 2023.2012.2021.571765 (2023).
Lord, C. J. & Ashworth, A. PARP inhibitors: synthetic lethality in the clinic. Science 355, 1152–1158 (2017).
pubmed: 28302823
pmcid: 6175050
doi: 10.1126/science.aam7344
Helleday, T. The underlying mechanism for the PARP and BRCA synthetic lethality: clearing up the misunderstandings. Mol. Oncol. 5, 387–393 (2011).
pubmed: 21821475
pmcid: 5528309
doi: 10.1016/j.molonc.2011.07.001
Illuzzi, G. et al. Preclinical characterization of AZD5305, a next-generation, highly selective PARP1 inhibitor and trapper. Clin. Cancer Res. 28, 4724–4736 (2022).
pubmed: 35929986
pmcid: 9623235
doi: 10.1158/1078-0432.CCR-22-0301
Edenberg, E. R., Downey, M. & Toczyski, D. Polymerase stalling during replication, transcription and translation. Curr. Biol. 24, R445–R452 (2014).
pubmed: 24845677
doi: 10.1016/j.cub.2014.03.060
Le, T. T. et al. Etoposide promotes DNA loop trapping and barrier formation by topoisomerase II. Nat. Chem. Biol. 19, 641–650 (2023).
pubmed: 36717711
pmcid: 10154222
doi: 10.1038/s41589-022-01235-9
Challa, K. et al. Damage-induced chromatome dynamics link Ubiquitin ligase and proteasome recruitment to histone loss and efficient DNA repair. Mol. Cell 81, 811–829.e816 (2021).
pubmed: 33529595
doi: 10.1016/j.molcel.2020.12.021
Meyer, H., Bug, M. & Bremer, S. Emerging functions of the VCP/p97 AAA-ATPase in the ubiquitin system. Nat. Cell Biol. 14, 117–123 (2012).
pubmed: 22298039
doi: 10.1038/ncb2407
Wojcik, C., Yano, M. & DeMartino, G. N. RNA interference of valosin-containing protein (VCP/p97) reveals multiple cellular roles linked to ubiquitin/proteasome-dependent proteolysis. J. Cell Sci. 117, 281–292 (2004).
pubmed: 14657277
doi: 10.1242/jcs.00841
Jarosch, E. et al. Protein dislocation from the ER requires polyubiquitination and the AAA-ATPase Cdc48. Nat. Cell Biol. 4, 134–139 (2002).
pubmed: 11813000
doi: 10.1038/ncb746
Rape, M. et al. Mobilization of processed, membrane-tethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone. Cell 107, 667–677 (2001).
pubmed: 11733065
doi: 10.1016/S0092-8674(01)00595-5
Anderson, D. J. et al. Targeting the AAA ATPase p97 as an Approach to Treat Cancer through Disruption of Protein Homeostasis. Cancer Cell 28, 653–665 (2015).
pubmed: 26555175
pmcid: 4941640
doi: 10.1016/j.ccell.2015.10.002
Kim, K. B. & Crews, C. M. From epoxomicin to carfilzomib: chemistry, biology, and medical outcomes. Nat. Prod. Rep. 30, 600–604 (2013).
pubmed: 23575525
pmcid: 3815659
doi: 10.1039/c3np20126k
Li, M. et al. MIB1-mediated degradation of WRN promotes cellular senescence in response to camptothecin treatment. FASEB J. 34, 11488–11497 (2020).
pubmed: 32652764
doi: 10.1096/fj.202000268RRR
Liu, B. et al. MDM2-mediated degradation of WRN promotes cellular senescence in a p53-independent manner. Oncogene 38, 2501–2515 (2019).
pubmed: 30532073
doi: 10.1038/s41388-018-0605-5
Roman-Trufero, M. & Dillon, N. The UBE2D ubiquitin conjugating enzymes: potential regulatory hubs in development, disease and evolution. Front. Cell Dev. Biol. 10, 1058751 (2022).
pubmed: 36578786
pmcid: 9790923
doi: 10.3389/fcell.2022.1058751
DiBello, A., Datta, A. B., Zhang, X. & Wolberger, C. Role of E2-RING interactions in governing RNF4-mediated substrate ubiquitination. J. Mol. Biol. 428, 4639–4650 (2016).
pubmed: 27678051
pmcid: 5115946
doi: 10.1016/j.jmb.2016.09.018
Ward, C. C. et al. Covalent ligand screening uncovers a RNF4 E3 ligase recruiter for targeted protein degradation applications. ACS Chem. Biol. 14, 2430–2440 (2019).
pubmed: 31059647
pmcid: 7422721
doi: 10.1021/acschembio.8b01083
Kaiser, F. J., Moroy, T., Chang, G. T., Horsthemke, B. & Ludecke, H. J. The RING finger protein RNF4, a co-regulator of transcription, interacts with the TRPS1 transcription factor. J. Biol. Chem. 278, 38780–38785 (2003).
pubmed: 12885770
doi: 10.1074/jbc.M306259200
Tatham, M. H. et al. RNF4 is a poly-SUMO-specific E3 ubiquitin ligase required for arsenic-induced PML degradation. Nat. Cell Biol. 10, 538–546 (2008).
pubmed: 18408734
doi: 10.1038/ncb1716
Hyer, M. L. et al. A small-molecule inhibitor of the ubiquitin activating enzyme for cancer treatment. Nat. Med. 24, 186–193 (2018).
pubmed: 29334375
doi: 10.1038/nm.4474
Rodriguez-Perez, F. et al. Ubiquitin-dependent remodeling of the actin cytoskeleton drives cell fusion. Dev. Cell 56, 588–601.e589 (2021).
pubmed: 33609460
doi: 10.1016/j.devcel.2021.01.016
Manford, A. G. et al. A cellular mechanism to detect and alleviate reductive stress. Cell 183, 46–61.e21 (2020).
pubmed: 32941802
doi: 10.1016/j.cell.2020.08.034
Padovani, C., Jevtic, P. & Rape, M. Quality control of protein complex composition. Mol. Cell 82, 1439–1450 (2022).
pubmed: 35316660
doi: 10.1016/j.molcel.2022.02.029
Krastev, D. B. et al. The ubiquitin-dependent ATPase p97 removes cytotoxic trapped PARP1 from chromatin. Nat. Cell Biol. 24, 62–73 (2022).
pubmed: 35013556
pmcid: 8760077
doi: 10.1038/s41556-021-00807-6
Liu, J. C. Y. et al. Mechanism and function of DNA replication-independent DNA-protein crosslink repair via the SUMO-RNF4 pathway. EMBO J. 40, e107413 (2021).
pubmed: 34346517
pmcid: 8441304
doi: 10.15252/embj.2020107413
Sun, Y. et al. A conserved SUMO pathway repairs topoisomerase DNA-protein cross-links by engaging ubiquitin-mediated proteasomal degradation. Sci. Adv. 6, eaba6290 (2020).
pubmed: 33188014
pmcid: 7673754
doi: 10.1126/sciadv.aba6290
He, X. et al. Probing the roles of SUMOylation in cancer cell biology by using a selective SAE inhibitor. Nat. Chem. Biol. 13, 1164–1171 (2017).
pubmed: 28892090
doi: 10.1038/nchembio.2463
Hande, K. R. Etoposide: four decades of development of a topoisomerase II inhibitor. Eur. J. Cancer 34, 1514–1521 (1998).
pubmed: 9893622
doi: 10.1016/S0959-8049(98)00228-7
Bailly, C. Irinotecan: 25 years of cancer treatment. Pharm. Res. 148, 104398 (2019).
doi: 10.1016/j.phrs.2019.104398
Shen, Y., Aoyagi-Scharber, M. & Wang, B. Trapping poly(ADP-Ribose) polymerase. J. Pharmacol. Exp. Therap. 353, 446–457 (2015).
doi: 10.1124/jpet.114.222448
Hopkins, T. A. et al. PARP1 trapping by PARP inhibitors drives cytotoxicity in both cancer cells and healthy bone marrow. Mol. Cancer Res. 17, 409–419 (2019).
pubmed: 30429212
doi: 10.1158/1541-7786.MCR-18-0138
Rose, M., Burgess, J. T., O’Byrne, K., Richard, D. J. & Bolderson, E. PARP inhibitors: clinical relevance, mechanisms of action and tumor resistance. Front. Cell Dev. Biol. 8, 564601 (2020).
pubmed: 33015058
pmcid: 7509090
doi: 10.3389/fcell.2020.564601
Ianevski, A., Giri, A. K. & Aittokallio, T. SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples. Nucleic Acids Res. 50, W739–W743 (2022).
pubmed: 35580060
pmcid: 9252834
doi: 10.1093/nar/gkac382
Chen, X. et al. Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein. eLife 10, e65339 (2021).
pubmed: 33647232
pmcid: 7924943
doi: 10.7554/eLife.65339
Sergé, A., Bertaux, N., Rigneault, H. & Marguet, D. Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes. Nat. Methods 5, 687–694 (2008).
pubmed: 18604216
doi: 10.1038/nmeth.1233
Levenberg, K. A method for the solution of certain non-linear problems in least squares. Q. Appl. Math. 2, 164–168 (1944).
doi: 10.1090/qam/10666
Marquardt, D. W. An algorithm for least-squares estimation of nonlinear parameters. J. Soc. Ind. Appl. Math. 11, 431–441 (1963).
doi: 10.1137/0111030
Laurence, T. A. & Chromy, B. A. Efficient maximum likelihood estimator fitting of histograms. Nat. Methods 7, 338–339 (2010).
pubmed: 20431544
doi: 10.1038/nmeth0510-338
Smith, C. S., Joseph, N., Rieger, B. & Lidke, K. A. Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat. Methods 7, 373–375 (2010).
pubmed: 20364146
pmcid: 2862147
doi: 10.1038/nmeth.1449
Parthasarathy, R. Rapid, accurate particle tracking by calculation of radial symmetry centers. Nat. Methods 9, 724–726 (2012).
pubmed: 22688415
doi: 10.1038/nmeth.2071
Chenouard, N. et al. Objective comparison of particle tracking methods. Nat. Methods 11, 281–289 (2014).
pubmed: 24441936
pmcid: 4131736
doi: 10.1038/nmeth.2808
Sbalzarini, I. F. & Koumoutsakos, P. Feature point tracking and trajectory analysis for video imaging in cell biology. J. Struct. Biol. 151, 182–195 (2005).
pubmed: 16043363
doi: 10.1016/j.jsb.2005.06.002
Ronneberger, O., Fischer, P. & Brox, T. in Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015. (eds Navab, N., Hornegger, J., Wells,W. M. & Frangi, A. F.) (Springer International Publishing, 2015).
Heckert, A., Dahal, L., Tjian, R. & Darzacq, X. Recovering mixtures of fast-diffusing states from short single-particle trajectories. eLife 11, e70169 (2022).
pubmed: 36066004
pmcid: 9451534
doi: 10.7554/eLife.70169