WRN inhibition leads to its chromatin-associated degradation via the PIAS4-RNF4-p97/VCP axis.


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
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

6059

Informations 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

Auteurs

Fernando Rodríguez Pérez (F)

Eikon Therapeutics, Hayward, CA, 94545, USA. perezf@eikontx.com.

Dean Natwick (D)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Lauren Schiff (L)

Eikon Therapeutics, Hayward, CA, 94545, USA.

David McSwiggen (D)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Alec Heckert (A)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Melina Huey (M)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Huntly Morrison (H)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Mandy Loo (M)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Rafael G Miranda (RG)

Eikon Therapeutics, Hayward, CA, 94545, USA.

John Filbin (J)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Jose Ortega (J)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Kayla Van Buren (K)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Danny Murnock (D)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Arnold Tao (A)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Renee Butler (R)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Kylie Cheng (K)

Eikon Therapeutics, Hayward, CA, 94545, USA.

William Tarvestad (W)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Zhengjian Zhang (Z)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Eric Gonzalez (E)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Rand M Miller (RM)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Marcus Kelly (M)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Yangzhong Tang (Y)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Jaclyn Ho (J)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Daniel Anderson (D)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Charlene Bashore (C)

Eikon Therapeutics, Hayward, CA, 94545, USA.

Stephen Basham (S)

Eikon Therapeutics, Hayward, CA, 94545, USA. bashams@eikontx.com.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH