Onco-condensates: formation, multi-component organization, and biological functions
Tài liệu tham khảo
Mao, 2011, Biogenesis and function of nuclear bodies, Trends Genet., 27, 295, 10.1016/j.tig.2011.05.006
Decker, 2012, P-bodies and stress granules: possible roles in the control of translation and mRNA degradation, Cold Spring Harb. Perspect. Biol., 4, 10.1101/cshperspect.a012286
Lamond, 2003, Nuclear speckles: a model for nuclear organelles, Nat. Rev. Mol. Cell Biol., 4, 605, 10.1038/nrm1172
Nott, 2015, Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles, Mol. Cell, 57, 936, 10.1016/j.molcel.2015.01.013
Brangwynne, 2009, Germline P granules are liquid droplets that localize by controlled dissolution/condensation, Science, 324, 1729, 10.1126/science.1172046
Banani, 2017, Biomolecular condensates: organizers of cellular biochemistry, Nat. Rev. Mol. Cell Biol., 18, 285, 10.1038/nrm.2017.7
Forman-Kay, 2018, Phase separation in biology and disease, J. Mol. Biol., 430, 4603, 10.1016/j.jmb.2018.09.006
Elbaum-Garfinkle, 2021, Phase separation in biology & disease: the next chapter, J. Mol. Biol., 433, 10.1016/j.jmb.2021.166990
Boija, 2021, Biomolecular condensates and cancer, Cancer Cell, 39, 174, 10.1016/j.ccell.2020.12.003
Shin, 2017, Liquid phase condensation in cell physiology and disease, Science, 357, 10.1126/science.aaf4382
Wang, 2018, A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins, Cell, 174, 688, 10.1016/j.cell.2018.06.006
Lin, 2017, Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs, J. Biol. Chem., 292, 19110, 10.1074/jbc.M117.800466
Quiroga, 2022, Oncogenic fusion proteins and their role in three-dimensional chromatin structure, phase separation, and cancer, Curr. Opin. Genet. Dev., 74, 10.1016/j.gde.2022.101901
Boulay, 2017, Cancer-specific retargeting of BAF complexes by a prion-like domain, Cell, 171, 163, 10.1016/j.cell.2017.07.036
Zuo, 2021, Loci-specific phase separation of FET fusion oncoproteins promotes gene transcription, Nat. Commun., 12, 1491, 10.1038/s41467-021-21690-7
Ahn, 2021, Phase separation drives aberrant chromatin looping and cancer development, Nature, 595, 591, 10.1038/s41586-021-03662-5
Terlecki-Zaniewicz, 2021, Biomolecular condensation of NUP98 fusion proteins drives leukemogenic gene expression, Nat. Struct. Mol. Biol., 28, 190, 10.1038/s41594-020-00550-w
Chandra, 2022, Phase separation mediates NUP98 fusion oncoprotein leukemic transformation, Cancer Discov., 12, 1152, 10.1158/2159-8290.CD-21-0674
Jevtic, 2022, SMARCA5 interacts with NUP98-NSD1 oncofusion protein and sustains hematopoietic cells transformation, J. Exp. Clin. Cancer Res., 41, 34, 10.1186/s13046-022-02248-x
Lyons, 2022, Functional partitioning of transcriptional regulators by patterned charge blocks, Cell, 186, 327, 10.1016/j.cell.2022.12.013
Chong, 2022, Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription, Mol. Cell, 82, 2084, 10.1016/j.molcel.2022.04.007
Hu, 2023, Nuclear condensates of YAP fusion proteins alter transcription to drive ependymoma tumourigenesis, Nat. Cell Biol., 25, 323
Cheng, 2022, Phase transition and remodeling complex assembly are important for SS18-SSX oncogenic activity in synovial sarcomas, Nat. Commun., 13, 2724, 10.1038/s41467-022-30447-9
Tulpule, 2021, Kinase-mediated RAS signaling via membraneless cytoplasmic protein granules, Cell, 184, 2649, 10.1016/j.cell.2021.03.031
Gerbich, 2021, Moving beyond disease to function: physiological roles for polyglutamine-rich sequences in cell decisions, Curr. Opin. Cell Biol., 69, 120, 10.1016/j.ceb.2021.01.003
Jain, 2017, RNA phase transitions in repeat expansion disorders, Nature, 546, 243, 10.1038/nature22386
Shi, 2021, UTX condensation underlies its tumour-suppressive activity, Nature, 597, 726, 10.1038/s41586-021-03903-7
Gibson, 2019, Organization of chromatin by intrinsic and regulated phase separation, Cell, 179, 470, 10.1016/j.cell.2019.08.037
Reynoird, 2010, Oncogenesis by sequestration of CBP/p300 in transcriptionally inactive hyperacetylated chromatin domains, EMBO J., 29, 2943, 10.1038/emboj.2010.176
Alekseyenko, 2015, The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains, Genes Dev., 29, 1507, 10.1101/gad.267583.115
Zee, 2016, The oncoprotein BRD4-NUT generates aberrant histone modification patterns, PLoS ONE, 11, 10.1371/journal.pone.0163820
Rosencrance, 2020, Chromatin hyperacetylation impacts chromosome folding by forming a nuclear subcompartment, Mol. Cell, 78, 112, 10.1016/j.molcel.2020.03.018
Ibrahim, 2022, Structural insights into p300 regulation and acetylation-dependent genome organisation, Nat. Commun., 13, 7759, 10.1038/s41467-022-35375-2
Yu, 2023, Structural mechanism of BRD4-NUT and p300 bipartite interaction in propagating aberrant gene transcription in chromatin in NUT carcinoma, Nat. Commun., 14, 378, 10.1038/s41467-023-36063-5
Han, 2020, Roles of the BRD4 short isoform in phase separation and active gene transcription, Nat. Struct. Mol. Biol., 27, 333, 10.1038/s41594-020-0394-8
Alekseyenko, 2017, Ectopic protein interactions within BRD4-chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma, Proc. Natl. Acad. Sci. U. S. A., 114, E4184, 10.1073/pnas.1702086114
Wang, 2020, The diverse roles of SPOP in prostate cancer and kidney cancer, Nat. Rev. Urol., 17, 339, 10.1038/s41585-020-0314-z
Bouchard, 2018, Cancer mutations of the tumor suppressor SPOP disrupt the formation of active, phase-separated compartments, Mol. Cell, 72, 19, 10.1016/j.molcel.2018.08.027
Yang, 2022, Phase separation of Myc differentially regulates gene transcription, bioRxiv
Zhu, 2020, Phase separation of disease-associated SHP2 mutants underlies MAPK hyperactivation, Cell, 183, 490, 10.1016/j.cell.2020.09.002
Song, 2022, Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer, Mol. Cell, 82, 4080, 10.1016/j.molcel.2022.09.034
Wan, 2020, Impaired cell fate through gain-of-function mutations in a chromatin reader, Nature, 577, 121, 10.1038/s41586-019-1842-7
Eppert, 2022, Context is key: modulated protein multivalency in disease, Mol. Cell, 82, 3965, 10.1016/j.molcel.2022.10.011
Falini, 2020, NPM1-mutated acute myeloid leukemia: from bench to bedside, Blood, 136, 1707, 10.1182/blood.2019004226
Wang, 2023, Mutant NPM1 hijacks transcriptional hubs to maintain pathogenic gene programs in acute myeloid leukemia, Cancer Discov., 13, 724, 10.1158/2159-8290.CD-22-0424
Mitrea, 2018, Self-interaction of NPM1 modulates multiple mechanisms of liquid-liquid phase separation, Nat. Commun., 9, 842, 10.1038/s41467-018-03255-3
Boeynaems, 2018, Protein phase separation: a new phase in cell biology, Trends Cell Biol., 28, 420, 10.1016/j.tcb.2018.02.004
Boija, 2018, Transcription factors activate genes through the phase-separation capacity of their activation domains, Cell, 175, 1842, 10.1016/j.cell.2018.10.042
Dunford, 2017, Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias, Nat. Genet., 49, 10, 10.1038/ng.3726
Showpnil, 2022, EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma, Nucleic Acids Res., 50, 9814, 10.1093/nar/gkac747
Wang, 2009, Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger, Nature, 459, 847, 10.1038/nature08036
Sengupta, 2017, Super-enhancer-driven transcriptional dependencies in cancer, Trends Cancer, 3, 269, 10.1016/j.trecan.2017.03.006
Sabari, 2018, Coactivator condensation at super-enhancers links phase separation and gene control, Science, 361, 10.1126/science.aar3958
Cho, 2018, Mediator and RNA polymerase II clusters associate in transcription-dependent condensates, Science, 361, 412, 10.1126/science.aar4199
Hnisz, 2017, A phase separation model for transcriptional control, Cell, 169, 13, 10.1016/j.cell.2017.02.007
Sabari, 2020, Biomolecular condensates in the nucleus, Trends Biochem. Sci., 45, 961, 10.1016/j.tibs.2020.06.007
Nair, 2022, Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures, Trends Genet., 38, 1019, 10.1016/j.tig.2022.05.015
Li, 2022, Nuclear protein condensates and their properties in regulation of gene expression, J. Mol. Biol., 434, 10.1016/j.jmb.2021.167151
Lyon, 2021, A framework for understanding the functions of biomolecular condensates across scales, Nat. Rev. Mol. Cell Biol., 22, 215, 10.1038/s41580-020-00303-z
Boyd-Shiwarski, 2022, WNK kinases sense molecular crowding and rescue cell volume via phase separation, Cell, 185, 4488, 10.1016/j.cell.2022.09.042
Fonteneau, 2022, Stress granules determine the development of obesity-associated pancreatic cancer, Cancer Discov., 12, 1984, 10.1158/2159-8290.CD-21-1672
Moya, 2019, Hippo-YAP/TAZ signalling in organ regeneration and regenerative medicine, Nat. Rev. Mol. Cell Biol., 20, 211, 10.1038/s41580-018-0086-y
Panciera, 2017, Mechanobiology of YAP and TAZ in physiology and disease, Nat. Rev. Mol. Cell Biol., 18, 758, 10.1038/nrm.2017.87
Lu, 2020, Phase separation of TAZ compartmentalizes the transcription machinery to promote gene expression, Nat. Cell Biol., 22, 453, 10.1038/s41556-020-0485-0
Cai, 2019, Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression, Nat. Cell Biol., 21, 1578, 10.1038/s41556-019-0433-z
Liu, 2021, Glycogen accumulation and phase separation drives liver tumor initiation, Cell, 184, 5559, 10.1016/j.cell.2021.10.001
Xu, 2011, Gain of function of mutant p53 by coaggregation with multiple tumor suppressors, Nat. Chem. Biol., 7, 285, 10.1038/nchembio.546
Wolfe, 2020, Metabolic compartmentalization at the leading edge of metastatic cancer cells, Front. Oncol., 10, 10.3389/fonc.2020.554272
Altmeyer, 2015, Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose), Nat. Commun., 6, 8088, 10.1038/ncomms9088
Kilic, 2019, Phase separation of 53BP1 determines liquid-like behavior of DNA repair compartments, EMBO J., 38, 10.15252/embj.2018101379
Yamazaki, 2018, Functional domains of NEAT1 architectural lncRNA induce paraspeckle assembly through phase separation, Mol. Cell, 70, 1038, 10.1016/j.molcel.2018.05.019
Lee, 2021, Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation, Mol. Cell, 81, 3368, 10.1016/j.molcel.2021.07.024
Pessina, 2019, Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors, Nat. Cell Biol., 21, 1286, 10.1038/s41556-019-0392-4
Zhao, 2020, Phase separation in membrane biology: the interplay between membrane-bound organelles and membraneless condensates, Dev. Cell, 55, 30, 10.1016/j.devcel.2020.06.033
Conti, 2022, Biomolecular condensates: new opportunities for drug discovery and RNA therapeutics, Trends Pharmacol. Sci., 43, 820, 10.1016/j.tips.2022.07.001
Mitrea, 2022, Modulating biomolecular condensates: a novel approach to drug discovery, Nat. Rev. Drug Discov., 21, 841, 10.1038/s41573-022-00505-4
Klein, 2020, Partitioning of cancer therapeutics in nuclear condensates, Science, 368, 1386, 10.1126/science.aaz4427
Xie, 2022, Targeting androgen receptor phase separation to overcome antiandrogen resistance, Nat. Chem. Biol., 18, 1341, 10.1038/s41589-022-01151-y
Hofweber, 2018, Phase separation of FUS is suppressed by its nuclear import receptor and arginine methylation, Cell, 173, 706, 10.1016/j.cell.2018.03.004
Qamar, 2018, FUS phase separation is modulated by a molecular chaperone and methylation of arginine cation-pi interactions, Cell, 173, 720, 10.1016/j.cell.2018.03.056
Ruff, 2021, AlphaFold and implications for intrinsically disordered proteins, J. Mol. Biol., 433, 10.1016/j.jmb.2021.167208
Babinchak, 2020, Small molecules as potent biphasic modulators of protein liquid-liquid phase separation, Nat. Commun., 11, 5574, 10.1038/s41467-020-19211-z
Peran, 2020, Managing hyperosmotic stress through phase separation, Trends Biochem. Sci., 45, 721, 10.1016/j.tibs.2020.05.004
Alberti, 2019, Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates, Cell, 176, 419, 10.1016/j.cell.2018.12.035
Alberti, 2019, Liquid-liquid phase separation in disease, Annu. Rev. Genet., 53, 171, 10.1146/annurev-genet-112618-043527
Alberti, 2017, Phase separation in biology, Curr. Biol., 27, R1097, 10.1016/j.cub.2017.08.069
Hyman, 2014, Liquid-liquid phase separation in biology, Annu. Rev. Cell Dev. Biol., 30, 39, 10.1146/annurev-cellbio-100913-013325
Lee, 2013, Spatial organization of the cell cytoplasm by position-dependent phase separation, Phys. Rev. Lett., 111
Roden, 2021, RNA contributions to the form and function of biomolecular condensates, Nat. Rev. Mol. Cell Biol., 22, 183, 10.1038/s41580-020-0264-6
Alberti, 2021, Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing, Nat. Rev. Mol. Cell Biol., 22, 196, 10.1038/s41580-020-00326-6
Woodruff, 2018, Organization and function of non-dynamic biomolecular condensates, Trends Biochem. Sci., 43, 81, 10.1016/j.tibs.2017.11.005
Kilgore, 2022, Learning the chemical grammar of biomolecular condensates, Nat. Chem. Biol., 18, 1298, 10.1038/s41589-022-01046-y
Ruff, 2018, Advances in understanding stimulus-responsive phase behavior of intrinsically disordered protein polymers, J. Mol. Biol., 430, 4619, 10.1016/j.jmb.2018.06.031
Franzmann, 2019, Prion-like low-complexity sequences: key regulators of protein solubility and phase behavior, J. Biol. Chem., 294, 7128, 10.1074/jbc.TM118.001190
Quiroz, 2020, Liquid-liquid phase separation drives skin barrier formation, Science, 367, 10.1126/science.aax9554
Li, 2012, Phase transitions in the assembly of multivalent signalling proteins, Nature, 483, 336, 10.1038/nature10879
Ditlev, 2018, Who's in and who's out-compositional control of biomolecular condensates, J. Mol. Biol., 430, 4666, 10.1016/j.jmb.2018.08.003
Mittag, 2021, Fusion proteins form onco-condensates, Nat. Struct. Mol. Biol., 28, 543, 10.1038/s41594-021-00608-3
Weber, 2012, Getting RNA and protein in phase, Cell, 149, 1188, 10.1016/j.cell.2012.05.022
Alberti, 2016, Are aberrant phase transitions a driver of cellular aging?, Bioessays, 38, 959, 10.1002/bies.201600042
Feric, 2016, Coexisting liquid phases underlie nucleolar subcompartments, Cell, 165, 1686, 10.1016/j.cell.2016.04.047
Patel, 2015, A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation, Cell, 162, 1066, 10.1016/j.cell.2015.07.047
Murakami, 2015, ALS/FTD mutation-induced phase transition of FUS liquid droplets and reversible hydrogels into irreversible hydrogels impairs RNP granule function, Neuron, 88, 678, 10.1016/j.neuron.2015.10.030
Jawerth, 2020, Protein condensates as aging Maxwell fluids, Science, 370, 1317, 10.1126/science.aaw4951
Alshareedah, 2021, Programmable viscoelasticity in protein-RNA condensates with disordered sticker-spacer polypeptides, Nat. Commun., 12, 6620, 10.1038/s41467-021-26733-7