SHANK3 depletion leads to ERK signalling overdose and cell death in KRAS-mutant cancers.
Animals
Proto-Oncogene Proteins p21(ras)
/ genetics
Humans
Mice
Cell Line, Tumor
Female
Nerve Tissue Proteins
/ metabolism
MAP Kinase Signaling System
/ genetics
Mutation
Cell Death
/ genetics
Neoplasms
/ genetics
Extracellular Signal-Regulated MAP Kinases
/ metabolism
Mice, Nude
Microfilament Proteins
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
12 Sep 2024
12 Sep 2024
Historique:
received:
09
12
2022
accepted:
03
09
2024
medline:
13
9
2024
pubmed:
13
9
2024
entrez:
12
9
2024
Statut:
epublish
Résumé
The KRAS oncogene drives many common and highly fatal malignancies. These include pancreatic, lung, and colorectal cancer, where various activating KRAS mutations have made the development of KRAS inhibitors difficult. Here we identify the scaffold protein SH3 and multiple ankyrin repeat domain 3 (SHANK3) as a RAS interactor that binds active KRAS, including mutant forms, competes with RAF and limits oncogenic KRAS downstream signalling, maintaining mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) activity at an optimal level. SHANK3 depletion breaches this threshold, triggering MAPK/ERK signalling hyperactivation and MAPK/ERK-dependent cell death in KRAS-mutant cancers. Targeting this vulnerability through RNA interference or nanobody-mediated disruption of the SHANK3-KRAS interaction constrains tumour growth in vivo in female mice. Thus, inhibition of SHANK3-KRAS interaction represents an alternative strategy for selective killing of KRAS-mutant cancer cells through excessive signalling.
Identifiants
pubmed: 39266533
doi: 10.1038/s41467-024-52326-1
pii: 10.1038/s41467-024-52326-1
doi:
Substances chimiques
Proto-Oncogene Proteins p21(ras)
EC 3.6.5.2
Nerve Tissue Proteins
0
KRAS protein, human
0
Shank3 protein, mouse
0
Extracellular Signal-Regulated MAP Kinases
EC 2.7.11.24
Microfilament Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
8002Subventions
Organisme : EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
ID : 615258
Organisme : Academy of Finland (Suomen Akatemia)
ID : 364182
Informations de copyright
© 2024. The Author(s).
Références
Prior, I. A., Hood, F. E. & Hartley, J. L. The frequency of ras mutations in cancer. Cancer Res. 80, 2969–2974 (2020).
pubmed: 32209560
pmcid: 7367715
doi: 10.1158/0008-5472.CAN-19-3682
Simanshu, D. K., Nissley, D. V. & McCormick, F. RAS proteins and their regulators in human disease. Cell 170, 17–33 (2017).
pubmed: 28666118
pmcid: 5555610
doi: 10.1016/j.cell.2017.06.009
DeStefanis, R. A., Kratz, J. D., Emmerich, P. B. & Deming, D. A. Targeted therapy in metastatic colorectal cancer: current standards and novel agents in review. Curr. Colorectal Cancer Rep. 15, 61–69 (2019).
pubmed: 31130830
pmcid: 6528813
doi: 10.1007/s11888-019-00430-6
Waters, A. M. & Der, C. J. KRAS: The critical driver and therapeutic target for pancreatic cancer. Cold Spring Harb. Perspect. Med. 8, a031435 (2018).
pubmed: 29229669
pmcid: 5995645
doi: 10.1101/cshperspect.a031435
Salgia, R., Pharaon, R., Mambetsariev, I., Nam, A. & Sattler, M. The improbable targeted therapy: KRAS as an emerging target in non-small cell lung cancer (NSCLC). Cell Rep. Med. 2, 100186 (2021).
pubmed: 33521700
pmcid: 7817862
doi: 10.1016/j.xcrm.2020.100186
Siegel, R. L., Miller, K. D., Fuchs, H. E. & Jemal, A. Cancer Statistics, 2021. CA Cancer J. Clin. 71, 7–33 (2021).
pubmed: 33433946
doi: 10.3322/caac.21654
Vetter, I. R. & Wittinghofer, A. The guanine nucleotide-binding switch in three dimensions. Science 294, 1299–1304 (2001).
pubmed: 11701921
doi: 10.1126/science.1062023
Cox, A. D. & Der, C. J. Ras history: the saga continues. Small GTPases 1, 2–27 (2010).
pubmed: 21686117
pmcid: 3109476
doi: 10.4161/sgtp.1.1.12178
Drosten, M. & Barbacid, M. Targeting the MAPK pathway in KRAS-driven tumors. Cancer Cell 37, 543–550 (2020).
pubmed: 32289276
doi: 10.1016/j.ccell.2020.03.013
Stalnecker, C. A. & Der, C. J. RAS, wanted dead or alive: advances in targeting RAS mutant cancers. Sci. Signal 13, eaay6013 (2020).
pubmed: 32209699
pmcid: 7393681
doi: 10.1126/scisignal.aay6013
Ostrem, J. M., Peters, U., Sos, M. L., Wells, J. A. & Shokat, K. M. K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature 503, 548–551 (2013).
pubmed: 24256730
pmcid: 4274051
doi: 10.1038/nature12796
Fell, J. B. et al. Identification of the clinical development candidate MRTX849, a covalent KRASG12C inhibitor for the treatment of cancer. J. Med. Chem. 63, 6679–6693 (2020).
pubmed: 32250617
doi: 10.1021/acs.jmedchem.9b02052
Hong, D. S. et al. KRASG12C inhibition with sotorasib in advanced solid tumors. N. Engl. J. Med. 383, 1207–1217 (2020).
pubmed: 32955176
pmcid: 7571518
doi: 10.1056/NEJMoa1917239
Canon, J. et al. The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity. Nature 575, 217–223 (2019).
pubmed: 31666701
doi: 10.1038/s41586-019-1694-1
Lanman, B. A. et al. Discovery of a covalent Inhibitor of KRASG12C (AMG 510) for the treatment of solid tumors. J. Med. Chem. 63, 52–65 (2020).
pubmed: 31820981
doi: 10.1021/acs.jmedchem.9b01180
Janes, M. R. et al. Targeting KRAS mutant cancers with a covalent G12C-specific inhibitor. Cell 172, 578–589.e17 (2018).
pubmed: 29373830
doi: 10.1016/j.cell.2018.01.006
Mao, Z. et al. KRAS(G12D) can be targeted by potent inhibitors via formation of salt bridge. Cell Discov. 8, 5 (2022).
pubmed: 35075146
pmcid: 8786924
doi: 10.1038/s41421-021-00368-w
Zhang, Z. et al. GTP-state-selective cyclic peptide ligands of K-ras(G12D) block its interaction with Raf. ACS Cent. Sci. 6, 1753–1761 (2020).
pubmed: 33145412
pmcid: 7596874
doi: 10.1021/acscentsci.0c00514
Molina-Arcas, M., Samani, A. & Downward, J. Drugging the undruggable: advances on RAS targeting in cancer. Genes (Basel) 12, 899 (2021).
pubmed: 34200676
doi: 10.3390/genes12060899
Di Nicolantonio, F. et al. Precision oncology in metastatic colorectal cancer - from biology to medicine. Nat. Rev. Clin. Oncol. 18, 506–525 (2021).
pubmed: 33864051
doi: 10.1038/s41571-021-00495-z
Awad, M. M. et al. Acquired resistance to KRASG12C inhibition in cancer. N. Engl. J. Med. 384, 2382–2393 (2021).
pubmed: 34161704
pmcid: 8864540
doi: 10.1056/NEJMoa2105281
Tanaka, N. et al. Clinical acquired resistance to KRASG12C inhibition through a novel KRAS switch-II pocket mutation and polyclonal alterations converging on RAS-MAPK reactivation. Cancer Discov. 11, 1913–1922 (2021).
pubmed: 33824136
pmcid: 8338755
doi: 10.1158/2159-8290.CD-21-0365
Zhao, Y. et al. Diverse alterations associated with resistance to KRAS(G12C) inhibition. Nature 599, 679–683 (2021).
pubmed: 34759319
pmcid: 8887821
doi: 10.1038/s41586-021-04065-2
Hofmann, M. H., Gerlach, D., Misale, S., Petronczki, M. & Kraut, N. Expanding the reach of precision oncology by drugging All KRAS mutants. Cancer Discov. 12, 924–937 (2022).
pubmed: 35046095
pmcid: 9394389
doi: 10.1158/2159-8290.CD-21-1331
Kim, D. et al. Pan-KRAS inhibitor disables oncogenic signalling and tumour growth. Nature 619, 160–166 (2023).
pubmed: 37258666
pmcid: 10322706
doi: 10.1038/s41586-023-06123-3
Hofmann, M. H. et al. BI-3406, a potent and selective SOS1-KRAS interaction inhibitor, is effective in KRAS-driven cancers through combined MEK inhibition. Cancer Discov. 11, 142–157 (2021).
pubmed: 32816843
doi: 10.1158/2159-8290.CD-20-0142
Kerr, D. L., Haderk, F. & Bivona, T. G. Allosteric SHP2 inhibitors in cancer: targeting the intersection of RAS, resistance, and the immune microenvironment. Curr. Opin. Chem. Biol. 62, 1–12 (2021).
pubmed: 33418513
doi: 10.1016/j.cbpa.2020.11.007
Nichols, R. J. et al. RAS nucleotide cycling underlies the SHP2 phosphatase dependence of mutant BRAF-, NF1- and RAS-driven cancers. Nat. Cell Biol. 20, 1064–1073 (2018).
pubmed: 30104724
pmcid: 6115280
doi: 10.1038/s41556-018-0169-1
Bery, N., Miller, A. & Rabbitts, T. A potent KRAS macromolecule degrader specifically targeting tumours with mutant KRAS. Nat. Commun. 11, 3233 (2020).
pubmed: 32591521
pmcid: 7319959
doi: 10.1038/s41467-020-17022-w
Gutierrez-Prat, N. et al. DUSP4 protects BRAF- and NRAS-mutant melanoma from oncogene overdose through modulation of MITF. Life Sci. Alliance 5, e202101235 (2022).
pubmed: 35580987
pmcid: 9113946
doi: 10.26508/lsa.202101235
Ito, T. et al. Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers. Nat. Genet 53, 1664–1672 (2021).
pubmed: 34857952
doi: 10.1038/s41588-021-00967-z
Leung, G. P. et al. Hyperactivation of MAPK Signaling Is Deleterious to RAS/RAF-mutant Melanoma. Mol. Cancer Res. 17, 199–211 (2019).
pubmed: 30201825
doi: 10.1158/1541-7786.MCR-18-0327
Chang, L. et al. Systematic profiling of conditional pathway activation identifies context-dependent synthetic lethalities. Nat. Genet 55, 1709–1720 (2023).
pubmed: 37749246
doi: 10.1038/s41588-023-01515-7
Lilja, J. et al. SHANK proteins limit integrin activation by directly interacting with Rap1 and R-Ras. Nat. Cell Biol. 19, 292–305 (2017).
pubmed: 28263956
pmcid: 5386136
doi: 10.1038/ncb3487
Cai, Q., Hosokawa, T., Zeng, M., Hayashi, Y. & Zhang, M. Shank3 binds to and stabilizes the active form of Rap1 and HRas GTPases via its NTD-ANK tandem with distinct mechanisms. Structure 28, 290–300.e4 (2020).
pubmed: 31879129
doi: 10.1016/j.str.2019.11.018
Sheng, M. & Kim, E. The Shank family of scaffold proteins. J. Cell Sci. 113, 1851–1856 (2000).
pubmed: 10806096
doi: 10.1242/jcs.113.11.1851
Salomaa, S. I. et al. SHANK3 conformation regulates direct actin binding and crosstalk with Rap1 signaling. Curr. Biol. 31, 4956–4970.e9 (2021).
pubmed: 34610274
doi: 10.1016/j.cub.2021.09.022
Dempster, J. M. et al. Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets. Nat. Commun. 10, 5817 (2019).
pubmed: 31862961
pmcid: 6925302
doi: 10.1038/s41467-019-13805-y
Cowley, G. S. et al. Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies. Sci. Data 1, 140035 (2014).
pubmed: 25984343
pmcid: 4432652
doi: 10.1038/sdata.2014.35
Rezaei Adariani, S. et al. A comprehensive analysis of RAS-effector interactions reveals interaction hotspots and new binding partners. J. Biol. Chem. 296, 100626 (2021).
pubmed: 33930461
pmcid: 8163975
doi: 10.1016/j.jbc.2021.100626
Nassar, N. et al. Ras/Rap effector specificity determined by charge reversal. Nat. Struct. Biol. 3, 723–729 (1996).
pubmed: 8756332
doi: 10.1038/nsb0896-723
Hancock, J. F., Paterson, H. & Marshall, C. J. A polybasic domain or palmitoylation is required in addition to the CAAX motif to localize p21ras to the plasma membrane. Cell 63, 133–139 (1990).
pubmed: 2208277
doi: 10.1016/0092-8674(90)90294-O
Fang, Z. et al. Multivalent assembly of KRAS with the RAS-binding and cysteine-rich domains of CRAF on the membrane. Proc. Natl Acad. Sci. USA 117, 12101–12108 (2020).
pubmed: 32414921
pmcid: 7275734
doi: 10.1073/pnas.1914076117
Guzmán, C. et al. The efficacy of raf kinase recruitment to the GTPase H-ras depends on H-ras membrane conformer-specific nanoclustering. J. Biol. Chem. 289, 9519–9533 (2014).
pubmed: 24569991
pmcid: 3975003
doi: 10.1074/jbc.M113.537001
Unni, A. M. et al. Hyperactivation of ERK by multiple mechanisms is toxic to RTK-RAS mutation-driven lung adenocarcinoma cells. Elife 7, e33718 (2018).
pubmed: 30475204
pmcid: 6298772
doi: 10.7554/eLife.33718
Cho, E., Lou, H. J., Kuruvilla, L., Calderwood, D. A. & Turk, B. E. PPP6C negatively regulates oncogenic ERK signaling through dephosphorylation of MEK. Cell Rep. 34, 108928 (2021).
pubmed: 33789117
pmcid: 8068315
doi: 10.1016/j.celrep.2021.108928
Timofeev, O., Giron, P., Lawo, S., Pichler, M. & Noeparast, M. ERK pathway agonism for cancer therapy: evidence, insights, and a target discovery framework. npj Precis. Onc. 8, 1–16 (2024).
doi: 10.1038/s41698-024-00554-5
Kudo, T. et al. Live-cell measurements of kinase activity in single cells using translocation reporters. Nat. Protoc. 13, 155–169 (2018).
pubmed: 29266096
doi: 10.1038/nprot.2017.128
Wang, L. et al. A kinome-wide RNAi screen identifies ERK2 as a druggable regulator of Shank3 stability. Mol. Psychiatry 25, 2504–2516 (2020).
pubmed: 30696942
doi: 10.1038/s41380-018-0325-9
Hayes, T. K. et al. Long-term ERK inhibition in KRAS-mutant pancreatic cancer is associated with MYC degradation and senescence-like growth suppression. Cancer Cell 29, 75–89 (2016).
pubmed: 26725216
doi: 10.1016/j.ccell.2015.11.011
Dias, M. H. & Bernards, R. Playing cancer at its own game: activating mitogenic signaling as a paradoxical intervention. Mol. Oncol. 15, 1975–1985 (2021).
pubmed: 33955157
pmcid: 8333773
doi: 10.1002/1878-0261.12979
Wood, K. C. Hyperactivation of oncogenic driver pathways as a precision therapeutic strategy. Nat. Genet. 55, 1613–1614 (2023).
pubmed: 37749245
doi: 10.1038/s41588-023-01493-w
Nakajima, E. C. et al. FDA approval summary: sotorasib for KRAS G12C-mutated metastatic NSCLC. Clin. Cancer Res. 28, 1482–1486 (2022).
pubmed: 34903582
pmcid: 9012672
doi: 10.1158/1078-0432.CCR-21-3074
Jovčevska, I. & Muyldermans, S. The therapeutic potential of nanobodies. BioDrugs 34, 11–26 (2020).
pubmed: 31686399
doi: 10.1007/s40259-019-00392-z
Jameson, K. L. et al. IQGAP1 scaffold-kinase interaction blockade selectively targets RAS-MAP kinase-driven tumors. Nat. Med. 19, 626–630 (2013).
pubmed: 23603816
pmcid: 4190012
doi: 10.1038/nm.3165
Diepstraten, S. T. et al. The manipulation of apoptosis for cancer therapy using BH3-mimetic drugs. Nat. Rev. Cancer 22, 45–64 (2022).
pubmed: 34663943
doi: 10.1038/s41568-021-00407-4
Ledford, H. Gene-silencing technology gets first drug approval after 20 year wait. Nature 560, 291–292 (2018).
pubmed: 30108348
doi: 10.1038/d41586-018-05867-7
Honor, A., Rudnick, S. R. & Bonkovsky, H. L. Givosiran to treat acute porphyria. Drugs Today (Barc.) 57, 47–59 (2021).
pubmed: 33594389
doi: 10.1358/dot.2021.57.1.3230207
Shah, V. N. & Pyle, L. Lumasiran, an RNAi therapeutic for primary hyperoxaluria type 1. N. Engl. J. Med. 385, e69 (2021).
pubmed: 34758264
Kreienkamp, H.-J. Scaffolding proteins at the postsynaptic density: shank as the architectural framework. Handb Exp. Pharmacol. 186, 365–380 (2008).
Abankwa, D. et al. A novel switch region regulates H-ras membrane orientation and signal output. EMBO J. 27, 727–735 (2008).
pubmed: 18273062
pmcid: 2265749
doi: 10.1038/emboj.2008.10
Najumudeen, A. K. et al. Cancer stem cell drugs target K-ras signaling in a stemness context. Oncogene 35, 5248–5262 (2016).
pubmed: 26973241
pmcid: 5057041
doi: 10.1038/onc.2016.59
Vuoriluoto, K. et al. Vimentin regulates EMT induction by slug and oncogenic H-Ras and migration by governing Axl expression in breast cancer. Oncogene 30, 1436–1448 (2011).
pubmed: 21057535
doi: 10.1038/onc.2010.509
Härmä, V. et al. A comprehensive panel of three-dimensional models for studies of prostate cancer growth, invasion and drug responses. PLoS ONE 5, e10431 (2010).
pubmed: 20454659
pmcid: 2862707
doi: 10.1371/journal.pone.0010431
Guzmán, C., Bagga, M., Kaur, A., Westermarck, J. & Abankwa, D. ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays. PLoS ONE 9, e92444 (2014).
pubmed: 24647355
pmcid: 3960247
doi: 10.1371/journal.pone.0092444
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
pubmed: 22743772
doi: 10.1038/nmeth.2019
John, J. et al. Kinetics of interaction of nucleotides with nucleotide-free H-ras p21. Biochemistry 29, 6058–6065 (1990).
pubmed: 2200519
doi: 10.1021/bi00477a025
Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).
doi: 10.1016/j.softx.2015.06.001
Huang, J. et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods 14, 71–73 (2017).
pubmed: 27819658
doi: 10.1038/nmeth.4067
Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 29, 1859–1865 (2008).
pubmed: 18351591
doi: 10.1002/jcc.20945
Wu, E. L. et al. CHARMM-GUI membrane builder toward realistic biological membrane simulations. J. Comput. Chem. 35, 1997–2004 (2014).
pubmed: 25130509
pmcid: 4165794
doi: 10.1002/jcc.23702
Lee, J. et al. CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. J. Chem. Theory Comput. 12, 405–413 (2016).
pubmed: 26631602
doi: 10.1021/acs.jctc.5b00935
Mark, P. & Nilsson, L. Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298. K. J. Phys. Chem. A 105, 9954–9960 (2001).
doi: 10.1021/jp003020w
Van Gunsteren, W. F. & Berendsen, H. J. C. A leap-frog algorithm for stochastic dynamics. Mol. Simul. 1, 173–185 (1988).
doi: 10.1080/08927028808080941
Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472 (1997).
doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 52, 7182–7190 (1981).
doi: 10.1063/1.328693
Goedhart, J. SuperPlotsOfData-a web app for the transparent display and quantitative comparison of continuous data from different conditions. Mol. Biol. Cell 32, 470–474 (2021).
pubmed: 33476183
pmcid: 8101441
doi: 10.1091/mbc.E20-09-0583