K128 ubiquitination constrains RAS activity by expanding its binding interface with GAP proteins.
NF1
RAS Interactome
RAS Signaling
Senescence-Associated Secretory Phenotype
Ubiquitination
Journal
The EMBO journal
ISSN: 1460-2075
Titre abrégé: EMBO J
Pays: England
ID NLM: 8208664
Informations de publication
Date de publication:
10 Jun 2024
10 Jun 2024
Historique:
received:
17
10
2023
accepted:
29
05
2024
revised:
13
05
2024
medline:
11
6
2024
pubmed:
11
6
2024
entrez:
10
6
2024
Statut:
aheadofprint
Résumé
The RAS pathway is among the most frequently activated signaling nodes in cancer. However, the mechanisms that alter RAS activity in human pathologies are not entirely understood. The most prevalent post-translational modification within the GTPase core domain of NRAS and KRAS is ubiquitination at lysine 128 (K128), which is significantly decreased in cancer samples compared to normal tissue. Here, we found that K128 ubiquitination creates an additional binding interface for RAS GTPase-activating proteins (GAPs), NF1 and RASA1, thus increasing RAS binding to GAP proteins and promoting GAP-mediated GTP hydrolysis. Stimulation of cultured cancer cells with growth factors or cytokines transiently induces K128 ubiquitination and restricts the extent of wild-type RAS activation in a GAP-dependent manner. In KRAS mutant cells, K128 ubiquitination limits tumor growth by restricting RAL/ TBK1 signaling and negatively regulating the autocrine circuit induced by mutant KRAS. Reduction of K128 ubiquitination activates both wild-type and mutant RAS signaling and elicits a senescence-associated secretory phenotype, promoting RAS-driven pancreatic tumorigenesis.
Identifiants
pubmed: 38858602
doi: 10.1038/s44318-024-00146-w
pii: 10.1038/s44318-024-00146-w
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : EC | Horizon 2020 Framework Programme (H2020)
ID : ub-RASDisease,ID: 772649
Organisme : NCI NIH HHS
ID : HHSN261201500003I
Pays : United States
Organisme : Israel Cancer Research Fund (ICRF)
ID : 940283
Organisme : Technologická Agentura České Republiky (Czech Technological Agency)
ID : GA CR 22-26981S
Organisme : Israel Science Foundation (ISF)
ID : 1440/21
Informations de copyright
© 2024. The Author(s).
Références
Baietti MF, Simicek M, Abbasi Asbagh L, Radaelli E, Lievens S, Crowther J, Steklov M, Aushev VN, Martinez Garcia D, Tavernier J et al (2016) OTUB1 triggers lung cancer development by inhibiting RAS monoubiquitination. EMBO Mol Med 8:288–303
pubmed: 26881969
pmcid: 4772950
doi: 10.15252/emmm.201505972
Baker R, Lewis SM, Sasaki AT, Wilkerson EM, Locasale JW, Cantley LC, Kuhlman B, Dohlman HG, Campbell SL (2013a) Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function. Nat Struct Mol Biol 20:46–52
pubmed: 23178454
doi: 10.1038/nsmb.2430
Baker R, Wilkerson EM, Sumita K, Isom DG, Sasaki AT, Dohlman HG, Campbell SL (2013b) Differences in the regulation of K-Ras and H-Ras isoforms by monoubiquitination. J Biol Chem 288:36856–36862
pubmed: 24247240
pmcid: 3873545
doi: 10.1074/jbc.C113.525691
Birch J, Gil J (2020) Senescence and the SASP: many therapeutic avenues. Genes Dev 34:1565–1576
pubmed: 33262144
pmcid: 7706700
doi: 10.1101/gad.343129.120
Campbell SL, Philips MR (2021) Post-translational modification of RAS proteins. Curr Opin Struct Biol 71:180–192
pubmed: 34365229
pmcid: 8649064
doi: 10.1016/j.sbi.2021.06.015
Chaker-Margot M, Werten S, Dunzendorfer-Matt T, Lechner S, Ruepp A, Scheffzek K, Maier T (2022) Structural basis of activation of the tumor suppressor protein neurofibromin. Mol Cell 82:1288–1296.e1285
pubmed: 35353986
doi: 10.1016/j.molcel.2022.03.011
Courtois-Cox S, Genther Williams SM, Reczek EE, Johnson BW, McGillicuddy LT, Johannessen CM, Hollstein PE, MacCollin M, Cichowski K (2006) A negative feedback signaling network underlies oncogene-induced senescence. Cancer Cell 10:459–472
pubmed: 17157787
pmcid: 2692661
doi: 10.1016/j.ccr.2006.10.003
Cruz VH, Arner EN, Du W, Bremauntz AE, Brekken RA (2019) Axl-mediated activation of TBK1 drives epithelial plasticity in pancreatic cancer. JCI Insight 5:e126117
pubmed: 30938713
doi: 10.1172/jci.insight.126117
Dybas JM, O’Leary CE, Ding H, Spruce LA, Seeholzer SH, Oliver PM (2019) Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4(+) T cells. Nat Immunol 20:747–755
pubmed: 31061531
pmcid: 7007700
doi: 10.1038/s41590-019-0381-6
Edwards NJ, Oberti M, Thangudu RR, Cai S, McGarvey PB, Jacob S, Madhavan S, Ketchum KA (2015) The CPTAC data portal: a resource for cancer proteomics research. J Proteome Res 14:2707–2713
pubmed: 25873244
doi: 10.1021/pr501254j
Fridman AL, Tainsky MA (2008) Critical pathways in cellular senescence and immortalization revealed by gene expression profiling. Oncogene 27:5975–5987
pubmed: 18711403
doi: 10.1038/onc.2008.213
Grudzien P, Jang H, Leschinsky N, Nussinov R, Gaponenko V (2022) Conformational dynamics allows sampling of an “active-like” state by oncogenic K-Ras-GDP. J Mol Biol 434:167695
pubmed: 35752212
doi: 10.1016/j.jmb.2022.167695
Hobbs GA, Bonini MG, Gunawardena HP, Chen X, Campbell SL (2013) Glutathiolated Ras: characterization and implications for Ras activation. Free Radic Biol Med 57:221–229
pubmed: 23123410
doi: 10.1016/j.freeradbiomed.2012.10.531
Jang H, Smith IN, Eng C, Nussinov R (2021) The mechanism of full activation of tumor suppressor PTEN at the phosphoinositide-enriched membrane. iScience 24:102438
pubmed: 34113810
pmcid: 8169795
doi: 10.1016/j.isci.2021.102438
Jang H, Zhang M, Nussinov R (2020) The quaternary assembly of KRas4B with Raf-1 at the membrane. Comput Struct Biotechnol J 18:737–748
pubmed: 32257057
pmcid: 7125320
doi: 10.1016/j.csbj.2020.03.018
Jura N, Scotto-Lavino E, Sobczyk A, Bar-Sagi D (2006) Differential modification of Ras proteins by ubiquitination. Mol Cell 21:679–687
pubmed: 16507365
doi: 10.1016/j.molcel.2006.02.011
Kikuchi A, Demo SD, Ye ZH, Chen YW, Williams LT (1994) ralGDS family members interact with the effector loop of ras p21. Mol Cell Biol 14:7483–7491
pubmed: 7935463
pmcid: 359284
Levin-Kravets O, Kordonsky A, Shusterman A, Biswas S, Persaud A, Elias S, Langut Y, Florentin A, Simpson-Lavy KJ, Yariv E et al (2021) Split chloramphenicol acetyl-transferase assay reveals self-ubiquitylation-dependent regulation of UBE3B. J Mol Biol 433:167276
pubmed: 34599943
doi: 10.1016/j.jmb.2021.167276
Levin-Kravets O, Tanner N, Shohat N, Attali I, Keren-Kaplan T, Shusterman A, Artzi S, Varvak A, Reshef Y, Shi X et al (2016) A bacterial genetic selection system for ubiquitylation cascade discovery. Nat Methods 13:945–952
pubmed: 27694912
doi: 10.1038/nmeth.4003
Liu Y, Zhang M, Jang H, Nussinov R (2023) Higher-order interactions of Bcr-Abl can broaden chronic myeloid leukemia (CML) drug repertoire. Protein Sci 32:e4504
pubmed: 36369657
pmcid: 9795542
doi: 10.1002/pro.4504
Magits W, Sablina AA (2022) The regulation of the protein interaction network by monoubiquitination. Curr Opin Struct Biol 73:102333
pubmed: 35176591
doi: 10.1016/j.sbi.2022.102333
Miller AL, Perurena N, Gardner A, Hinoue T, Loi P, Laird PW, Cichowski K (2023) DAB2IP is a bifunctional tumor suppressor that regulates wild-type RAS and inflammatory cascades in KRAS mutant colon cancer. Cancer Res 83:1800–1814
pubmed: 36939385
pmcid: 10236151
doi: 10.1158/0008-5472.CAN-22-0370
Mondal S, Hsiao K, Goueli SA (2015) A homogenous bioluminescent system for measuring GTPase, GTPase activating protein, and guanine nucleotide exchange factor activities. Assay Drug Dev Technol 13:444–455
pubmed: 26167953
pmcid: 4605356
doi: 10.1089/adt.2015.643
Najm P, Zhao P, Steklov M, Sewduth RN, Baietti MF, Pandolfi S, Criem N, Lechat B, Maia TM, Van Haver D et al (2021) Loss-of-function mutations in TRAF7 and KLF4 cooperatively activate RAS-like GTPase signaling and promote meningioma development. Cancer Res 81:4218–4229
pubmed: 34215617
doi: 10.1158/0008-5472.CAN-20-3669
Ni S, Liu Q, Chen X, Ding L, Cai L, Mao F, Shi D, Hoffman RM, Li J, Jia L (2022) Pro-senescence neddylation inhibitor combined with a senescence activated beta-galactosidase prodrug to selectively target cancer cells. Signal Transduct Target Ther 7:313
pubmed: 36075909
pmcid: 9458665
doi: 10.1038/s41392-022-01128-2
Ovaa H, Vertegaal ACO (2018) Probing ubiquitin and SUMO conjugation and deconjugation. Biochem Soc Trans 46:423–436
pubmed: 29588386
doi: 10.1042/BST20170086
Prag G, Misra S, Jones EA, Ghirlando R, Davies BA, Horazdovsky BF, Hurley JH (2003) Mechanism of ubiquitin recognition by the CUE domain of Vps9p. Cell 113:609–620
pubmed: 12787502
doi: 10.1016/S0092-8674(03)00364-7
Punekar SR, Velcheti V, Neel BG, Wong KK (2022) The current state of the art and future trends in RAS-targeted cancer therapies. Nat Rev Clin Oncol 19:637–655
pubmed: 36028717
pmcid: 9412785
doi: 10.1038/s41571-022-00671-9
Ramakrishnan G, Parajuli P, Singh P, Friend C, Hurwitz E, Prunier C, Razzaque MS, Xu K, Atfi A (2022) NF1 loss of function as an alternative initiating event in pancreatic ductal adenocarcinoma. Cell Rep 41:111623
pubmed: 36351408
pmcid: 9716579
doi: 10.1016/j.celrep.2022.111623
Reilly SM, Chiang SH, Decker SJ, Chang L, Uhm M, Larsen MJ, Rubin JR, Mowers J, White NM, Hochberg I et al (2013) An inhibitor of the protein kinases TBK1 and IKK-varepsilon improves obesity-related metabolic dysfunctions in mice. Nat Med 19:313–321
pubmed: 23396211
pmcid: 3594079
doi: 10.1038/nm.3082
Rielland M, Cantor DJ, Graveline R, Hajdu C, Mara L, Diaz Bde D, Miller G, David G (2014) Senescence-associated SIN3B promotes inflammation and pancreatic cancer progression. J Clin Invest 124:2125–2135
pubmed: 24691445
pmcid: 4001548
doi: 10.1172/JCI72619
Sapmaz A, Berlin I, Bos E, Wijdeven RH, Janssen H, Konietzny R, Akkermans JJ, Erson-Bensan AE, Koning RI, Kessler BM et al (2019) USP32 regulates late endosomal transport and recycling through deubiquitylation of Rab7. Nat Commun 10:1454
pubmed: 30926795
pmcid: 6440979
doi: 10.1038/s41467-019-09437-x
Sasaki AT, Carracedo A, Locasale JW, Anastasiou D, Takeuchi K, Kahoud ER, Haviv S, Asara JM, Pandolfi PP, Cantley LC (2011) Ubiquitination of K-Ras enhances activation and facilitates binding to select downstream effectors. Sci Signal 4:ra13
pubmed: 21386094
pmcid: 3437993
doi: 10.1126/scisignal.2001518
Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC et al (2021) A proteogenomic portrait of lung squamous cell carcinoma. Cell 184:4348–4371.e4340
pubmed: 34358469
pmcid: 8475722
doi: 10.1016/j.cell.2021.07.016
Satpathy S, Wagner SA, Beli P, Gupta R, Kristiansen TA, Malinova D, Francavilla C, Tolar P, Bishop GA, Hostager BS et al (2015) Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation. Mol Syst Biol 11:810
pubmed: 26038114
pmcid: 4501846
doi: 10.15252/msb.20145880
Saul D, Kosinsky RL, Atkinson EJ, Doolittle ML, Zhang X, LeBrasseur NK, Pignolo RJ, Robbins PD, Niedernhofer LJ, Ikeno Y et al (2022) A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues. Nat Commun 13:4827
pubmed: 35974106
pmcid: 9381717
doi: 10.1038/s41467-022-32552-1
Sewduth RN, Carai P, Ivanisevic T, Zhang M, Jang H, Lechat B, Van Haver D, Impens F, Nussinov R, Jones E et al (2023) Spatial mechano-signaling regulation of GTPases through non-degradative ubiquitination. Adv Sci 10:e2303367
doi: 10.1002/advs.202303367
Shin D, Na W, Lee JH, Kim G, Baek J, Park SH, Choi CY, Lee S (2017) Site-specific monoubiquitination downregulates Rab5 by disrupting effector binding and guanine nucleotide conversion. Elife 6:e29154
pubmed: 28968219
pmcid: 5624781
doi: 10.7554/eLife.29154
Simanshu DK, Nissley DV, McCormick F (2017) RAS proteins and their regulators in human disease. Cell 170:17–33
pubmed: 28666118
pmcid: 5555610
doi: 10.1016/j.cell.2017.06.009
Simicek M, Lievens S, Laga M, Guzenko D, Aushev VN, Kalev P, Baietti MF, Strelkov SV, Gevaert K, Tavernier J et al (2013) The deubiquitylase USP33 discriminates between RALB functions in autophagy and innate immune response. Nat Cell Biol 15:1220–1230
pubmed: 24056301
doi: 10.1038/ncb2847
Steklov M, Pandolfi S, Baietti MF, Batiuk A, Carai P, Najm P, Zhang M, Jang H, Renzi F, Cai Y et al (2018) Mutations in LZTR1 drive human disease by dysregulating RAS ubiquitination. Science 362:1177–1182
pubmed: 30442762
pmcid: 8058620
doi: 10.1126/science.aap7607
Thakur VS, Welford SM (2020) Generation of a conditional mutant knock-in under the control of the natural promoter using CRISPR-Cas9 and Cre-Lox systems. PLoS ONE 15:e0240256
pubmed: 33007045
pmcid: 7531807
doi: 10.1371/journal.pone.0240256
Wang X, Min S, Liu H, Wu N, Liu X, Wang T, Li W, Shen Y, Wang H, Qian Z et al (2019) Nf1 loss promotes Kras-driven lung adenocarcinoma and results in Psat1-mediated glutamate dependence. EMBO Mol Med 11:e9856
pubmed: 31036704
pmcid: 6554671
doi: 10.15252/emmm.201809856
Williams JG, Pappu K, Campbell SL (2003) Structural and biochemical studies of p21Ras S-nitrosylation and nitric oxide-mediated guanine nucleotide exchange. Proc Natl Acad Sci USA 100:6376–6381
pubmed: 12740440
pmcid: 164454
doi: 10.1073/pnas.1037299100
Xu L, Lubkov V, Taylor LJ, Bar-Sagi D (2010) Feedback regulation of Ras signaling by Rabex-5-mediated ubiquitination. Curr Biol 20:1372–1377
pubmed: 20655225
pmcid: 3436604
doi: 10.1016/j.cub.2010.06.051
Yen HC, Xu Q, Chou DM, Zhao Z, Elledge SJ (2008) Global protein stability profiling in mammalian cells. Science 322:918–923
pubmed: 18988847
doi: 10.1126/science.1160489
Yin G, Zhang J, Nair V, Truong V, Chaia A, Petela J, Harrison J, Gorfe AA, Campbell SL (2020) KRAS ubiquitination at lysine 104 retains exchange factor regulation by dynamically modulating the conformation of the interface. iScience 23:101448
pubmed: 32882514
pmcid: 7479270
doi: 10.1016/j.isci.2020.101448
Zhu Z, Aref AR, Cohoon TJ, Barbie TU, Imamura Y, Yang S, Moody SE, Shen RR, Schinzel AC, Thai TC et al (2014) Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit. Cancer Discov 4:452–465
pubmed: 24444711
pmcid: 3980023
doi: 10.1158/2159-8290.CD-13-0646