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- Nachgewiesen in: MEDLINE
- Sprachen: English
- Publication Type: Journal Article
- Language: English
- [Nature] 2024 Apr; Vol. 628 (8007), pp. 442-449. <i>Date of Electronic Publication: </i>2024 Mar 27.
- MeSH Terms: Mutation* ; Neoplasms* / genetics ; Neoplasms* / metabolism ; SMARCB1 Protein* / deficiency ; SMARCB1 Protein* / genetics ; SMARCB1 Protein* / metabolism ; Multiprotein Complexes* / chemistry ; Multiprotein Complexes* / metabolism ; Animals ; Female ; Humans ; Male ; Mice ; Cell Line, Tumor ; CRISPR-Cas Systems ; Gene Editing ; Tumor Suppressor Proteins / deficiency ; Tumor Suppressor Proteins / genetics ; Tumor Suppressor Proteins / metabolism ; Proteolysis ; Ubiquitin / metabolism
- Comments: Erratum in: Nature. 2024 Apr 29;:. (PMID: 38684813)
- References: Dharia, N. V. et al. A first-generation pediatric cancer dependency map. Nat. Genet. 53, 529–538 (2021). (PMID: 33753930804951710.1038/s41588-021-00819-w) ; Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016). (PMID: 26780180474412510.1038/nbt.3437) ; Meyers, R. M. et al. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat. Genet. 49, 1779–1784 (2017). (PMID: 29083409570919310.1038/ng.3984) ; Mittal, P. & Roberts, C. W. M. The SWI/SNF complex in cancer—biology, biomarkers and therapy. Nat. Rev. Clin. Oncol. 17, 435–448 (2020). (PMID: 32303701872379210.1038/s41571-020-0357-3) ; Zhu, Z. et al. Mitotic bookmarking by SWI/SNF subunits. Nature 618, 180–187 (2023). (PMID: 372259801030308310.1038/s41586-023-06085-6) ; Wang, X. et al. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nat. Genet. 49, 289–295 (2017). (PMID: 2794179710.1038/ng.3746) ; Nakayama, R. T. et al. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nat. Genet. 49, 1613–1623 (2017). (PMID: 28945250580308010.1038/ng.3958) ; Alver, B. H. et al. The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers. Nat. Commun. 8, 14648 (2017). (PMID: 28262751534348210.1038/ncomms14648) ; Valencia, A. M. et al. Recurrent SMARCB1 mutations reveal a nucleosome acidic patch interaction site that potentiates mSWI/SNF complex chromatin remodeling. Cell 179, 1342–1356 (2019). (PMID: 31759698717541110.1016/j.cell.2019.10.044) ; Versteege, I. et al. Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer. Nature 394, 203–206 (1998). (PMID: 967130710.1038/28212) ; Lee, R. S. et al. A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers. J. Clin. Invest. 122, 2983–2988 (2012). (PMID: 22797305340875410.1172/JCI64400) ; Le Loarer, F. et al. Consistent SMARCB1 homozygous deletions in epithelioid sarcoma and in a subset of myoepithelial carcinomas can be reliably detected by FISH in archival material. Genes Chromosomes Cancer 53, 475–486 (2014). (PMID: 24585572422665010.1002/gcc.22159) ; Roberts, C. W. M., Leroux, M. M., Fleming, M. D. & Orkin, S. H. Highly penetrant, rapid tumorigenesis through conditional inversion of the tumor suppressor gene Snf5. Cancer Cell 2, 415–425 (2002). (PMID: 1245079610.1016/S1535-6108(02)00185-X) ; Leng, F. et al. Methylated DNMT1 and E2F1 are targeted for proteolysis by L3MBTL3 and CRL4 DCAF5 ubiquitin ligase. Nat. Commun. 9, 1641 (2018). (PMID: 29691401591560010.1038/s41467-018-04019-9) ; Zhang, C. X. et al. Proteolysis of methylated SOX2 protein is regulated by L3MBTL3 and CRL4 DCAF5 ubiquitin ligase. J. Biol. Chem. 294, 476–489 (2019). (PMID: 3044271310.1074/jbc.RA118.005336) ; He, Y. Z. J., McCall, C. M., Hu, J., Zeng, Y. X. & Xiong, Y. DDB1 functions as a linker to recruit receptor WD40 proteins to CUL4-ROC1 ubiquitin ligases. Genes Dev. 20, 2949–2954 (2006). (PMID: 17079684162002510.1101/gad.1483206) ; Lee, J. & Zhou, P. DCAFs, the missing link of the CUL4-DDB1 ubiquitin ligase. Mol. Cell 26, 775–780 (2007). (PMID: 1758851310.1016/j.molcel.2007.06.001) ; Ahn, J. et al. The cullin-RING E3 ubiquitin ligase CRL4-DCAF1 complex dimerizes via a short helical region in DCAF1. Biochemistry 50, 1359–1367 (2011). (PMID: 2122647910.1021/bi101749s) ; Angers, S. et al. Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery. Nature 443, 590–593 (2006). (PMID: 1696424010.1038/nature05175) ; Wang, X. et al. BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. Nat. Commun. 10, 1881 (2019). (PMID: 31015438647905010.1038/s41467-019-09891-7) ; Shabek, N. et al. Structural insights into DDA1 function as a core component of the CRL4-DDB1 ubiquitin ligase. Cell Discov. 4, 67 (2018). (PMID: 30564455628812610.1038/s41421-018-0064-8) ; Li, T., Robert, E. I., van Breugel, P. C., Strubin, M. & Zheng, N. A promiscuous α-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery. Nat. Struct. Mol. Biol. 17, 105–111 (2010). (PMID: 1996679910.1038/nsmb.1719) ; Wang, X. F. et al. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Cancer. Res. https://doi.org/10.1158/1538-7445.Am2017-Lb-096 (2017). ; Alpsoy, A. & Dykhuizen, E. C. Glioma tumor suppressor candidate region gene 1 (GLTSCR1) and its paralog GLTSCR1-like form SWI/SNF chromatin remodeling subcomplexes. J. Biol. Chem. 293, 3892–3903 (2018). (PMID: 29374058585800310.1074/jbc.RA117.001065) ; Michel, B. C. et al. A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. Nat. Cell Biol. 20, 1410–1420 (2018). (PMID: 30397315669838610.1038/s41556-018-0221-1) ; Guo, P. et al. The assembly of mammalian SWI/SNF chromatin remodeling complexes is regulated by lysine-methylation dependent proteolysis. Nat. Commun. 13, 6696 (2022). (PMID: 36335117963715810.1038/s41467-022-34348-9) ; Nabet, B. et al. Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules. Nat. Commun. 11, 4687 (2020). (PMID: 32948771750129610.1038/s41467-020-18377-w) ; Nabet, B. et al. The dTAG system for immediate and target-specific protein degradation. Nat. Chem. Biol. 14, 431–441 (2018). (PMID: 29581585629591310.1038/s41589-018-0021-8) ; Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes. Cell 175, 1272–1288 (2018). (PMID: 30343899679182410.1016/j.cell.2018.09.032) ; Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. Preprint at bioRxiv https://doi.org/10.1101/2021.10.04.463034 (2022). ; Peng, J. et al. A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21, 921–926 (2003). (PMID: 1287213110.1038/nbt849) ; Langer, L. F., Ward, J. M. & Archer, T. K. Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination. eLife 8, e45672 (2019). (PMID: 31033435653837410.7554/eLife.45672) ; Huang, Z. Q., Li, J., Sachs, L. M., Cole, P. A. & Wong, J. A role for cofactor-cofactor and cofactor-histone interactions in targeting p300, SWI/SNF and Mediator for transcription. EMBO J. 22, 2146–2155 (2003). (PMID: 1272788115609110.1093/emboj/cdg219) ; Schick, S. et al. Acute BAF perturbation causes immediate changes in chromatin accessibility. Nat. Genet. 53, 269–278 (2021). (PMID: 33558760761408210.1038/s41588-021-00777-3) ; Mashtalir, N. et al. A structural model of the endogenous human BAF complex informs disease mechanisms. Cell 183, 802–817 (2020). (PMID: 33053319771717710.1016/j.cell.2020.09.051) ; Phelan, M. L., Sif, S., Narlikar, G. J. & Kingston, R. E. Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. Mol. Cell 3, 247–253 (1999). (PMID: 1007820710.1016/S1097-2765(00)80315-9) ; Wolf, B. K. et al. Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Nat. Struct. Mol. Biol. 30, 10–21 (2023). (PMID: 3652242610.1038/s41594-022-00880-x) ; Vierbuchen, T. et al. AP-1 transcription factors and the BAF complex mediate signal-dependent enhancer selection. Mol. Cell 68, 1067–1082 (2017). (PMID: 29272704574488110.1016/j.molcel.2017.11.026) ; Schapira, M., Tyers, M., Torrent, M. & Arrowsmith, C. H. WD40 repeat domain proteins: a novel target class? Nat. Rev. Drug Discov. 16, 773–786 (2017). (PMID: 29026209597595710.1038/nrd.2017.179) ; Grebien, F. et al. Pharmacological targeting of the Wdr5-MLL interaction in C/EBPα N-terminal leukemia. Nat. Chem. Biol. 11, 571–578 (2015). (PMID: 26167872451183310.1038/nchembio.1859) ; He, Y. P. et al. The EED protein-protein interaction inhibitor A-395 inactivates the PRC2 complex. Nat. Chem. Biol. 13, 922–922 (2017). (PMID: 2885373810.1038/nchembio0817-922b) ; Qi, W. et al. An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of EED. Cancer Res. https://doi.org/10.1158/1538-7445.Am2017-Lb-288 (2017). ; Stewart, E. et al. Targeting the DNA repair pathway in Ewing sarcoma. Cell Rep. 9, 829–840 (2014). (PMID: 25437539438666910.1016/j.celrep.2014.09.028) ; Lord, C. J. & Ashworth, A. PARP inhibitors: Synthetic lethality in the clinic. Science 355, 1152–1158 (2017). (PMID: 28302823617505010.1126/science.aam7344) ; Brien, G. L. et al. Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma. eLife 7, e41305 (2018). (PMID: 30431433627719710.7554/eLife.41305) ; Padovani, C., Jevtic, P. & Rape, M. Quality control of protein complex composition. Mol. Cell 82, 1439–1450 (2022). (PMID: 3531666010.1016/j.molcel.2022.02.029) ; Mena, E. L. et al. Dimerization quality control ensures neuronal development and survival. Science 362, eaap8236 (2018). (PMID: 3019031010.1126/science.aap8236) ; Hong, A. L. et al. Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition. eLife 8, e44161 (2019). (PMID: 30860482643689510.7554/eLife.44161) ; Helming, K. C. et al. ARID1B is a specific vulnerability in ARID1A-mutant cancers. Nat. Med. 20, 251–254 (2014). (PMID: 24562383395470410.1038/nm.3480) ; Wilson, B. G. et al. Residual complexes containing SMARCA2 (BRM) underlie the oncogenic drive of SMARCA4 (BRG1) mutation. Mol. Cell. Biol. 34, 1136–1144 (2014). (PMID: 24421395395803410.1128/MCB.01372-13) ; Wang, L., Li, L. R. & Young, K. H. New agents and regimens for diffuse large B cell lymphoma. J. Hematol. Oncol. 13, 175 (2020). (PMID: 33317571773486210.1186/s13045-020-01011-z) ; Stewart, E. et al. Targeting the DNA repair pathway in Ewing sarcoma. Cell Rep. 9, 829–841 (2014). (PMID: 25437539438666910.1016/j.celrep.2014.09.028) ; Zheng, M. et al. Caspase-6 promotes activation of the caspase-11-NLRP3 inflammasome during Gram-negative bacterial infections. J. Biol. Chem. 297, 101379 (2021). (PMID: 34740613863368710.1016/j.jbc.2021.101379) ; Sidoli, S. et al. One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry. Genome Res. 29, 978–987 (2019). (PMID: 31123082658105110.1101/gr.247353.118) ; Drosos, Y. et al. NSD1 mediates antagonism between SWI/SNF and polycomb complexes and is required for transcriptional activation upon EZH2 inhibition. Mol. Cell 82, 2472–2489 (2022). (PMID: 35537449952060710.1016/j.molcel.2022.04.015) ; Connelly, J. P. & Pruett-Miller, S. M. CRIS.py: a versatile and high-throughput analysis program for CRISPR-based genome editing. Sci. Rep. 9, 4194 (2019). (PMID: 30862905641449610.1038/s41598-019-40896-w) ; McAlister, G. C. et al. MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes. Anal. Chem. 86, 7150–7158 (2014). ; Rose, C. M. et al. Highly multiplexed quantitative mass spectrometry analysis of ubiquitylomes. Cell Syst. 3, 395–403 (2016). (PMID: 27667366524107910.1016/j.cels.2016.08.009) ; Yu, K. et al. High-throughput profiling of proteome and posttranslational modifications by 16-plex TMT labeling and mass spectrometry. Methods Mol. Biol. 2228, 205–224 (2021). (PMID: 33950493845800910.1007/978-1-0716-1024-4_15) ; Faust, T. B. et al. Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15. Nat. Chem. Biol. 16, 7–14 (2020). (PMID: 3168603110.1038/s41589-019-0378-3) ; Abdulrahman, W. et al. A set of baculovirus transfer vectors for screening of affinity tags and parallel expression strategies. Anal. Biochem. 385, 383–385 (2009). (PMID: 1906185310.1016/j.ab.2008.10.044) ; He, S. et al. Structure of nucleosome-bound human BAF complex. Science 367, 875–881 (2020). (PMID: 3200152610.1126/science.aaz9761) ; Schorb, M., Haberbosch, I., Hagen, W. J. H., Schwab, Y. & Mastronarde, D. N. Software tools for automated transmission electron microscopy. Nat. Methods 16, 471–477 (2019). (PMID: 31086343700023810.1038/s41592-019-0396-9) ; Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017). (PMID: 2816547310.1038/nmeth.4169) ; Scheres, S. H. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012). (PMID: 22842542491203310.1038/nmeth.2115) ; Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003). (PMID: 1456853310.1016/j.jmb.2003.07.013) ; Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019). (PMID: 31591578685854510.1038/s41592-019-0575-8) ; Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021). (PMID: 34267316828284710.1038/s42003-021-02399-1) ; Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010). (PMID: 20383002285231310.1107/S0907444910007493) ; Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021). (PMID: 34282049761221310.1126/science.abj8754) ; Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018). (PMID: 2871077410.1002/pro.3235) ; Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018). (PMID: 10.1107/S2059798318002425) ; Leman, J. K. et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat. Methods 17, 665–680 (2020). (PMID: 3248333310.1038/s41592-020-0848-2) ; Wang, R. Y. et al. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5, e17219 (2016). (PMID: 27669148511586810.7554/eLife.17219) ; Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010). (PMID: 20124702281567010.1107/S0907444909052925) ; Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D 74, 531–544 (2018). (PMID: 10.1107/S2059798318006551) ; Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007). (PMID: 1768153710.1016/j.jmb.2007.05.022) ; Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D 60, 2256–2268 (2004). (PMID: 1557277910.1107/S0907444904026460) ; Armon, A., Graur, D. & Ben-Tal, N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol. 307, 447–463 (2001). (PMID: 1124383010.1006/jmbi.2000.4474) ; Cardone, G., Heymann, J. B. & Steven, A. C. One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. J. Struct. Biol. 184, 226–236 (2013). (PMID: 2395465310.1016/j.jsb.2013.08.002) ; Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017). (PMID: 28671674553364910.1038/nmeth.4347) ; Morin, A. et al. Collaboration gets the most out of software. eLife 2, e01456 (2013). (PMID: 24040512377156310.7554/eLife.01456) ; Duda, D. M. et al. Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Cell 134, 995–1006 (2008). (PMID: 18805092262863110.1016/j.cell.2008.07.022) ; Fischer, E. S. et al. Structure of the DDB1-CRBN E3 ubiquitin ligase in complex with thalidomide. Nature 512, 49–53 (2014). (PMID: 25043012442381910.1038/nature13527) ; Radko-Juettner, S. et al. Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF. GitHub https://github.com/jamyers2358/SWISNF.DCAF5.Dependency (2024).
- Substance Nomenclature: 0 (SMARCB1 Protein) ; 0 (SMARCB1 protein, human) ; 0 (Tumor Suppressor Proteins) ; 0 (Multiprotein Complexes) ; 0 (Ubiquitin)
- Entry Date(s): Date Created: 20240328 Date Completed: 20240412 Latest Revision: 20240429
- Update Code: 20240430
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