1932

Abstract

In this review, we explore the current landscape of preclinical and clinical therapeutics targeting epigenetic complexes in cancer, focusing on targets with enzymatic inhibitors, degraders, or ligands capable of disrupting protein–protein interactions. Current strategies face challenges such as limited single-agent clinical efficacy due to insufficient disruption of chromatin complexes and incomplete dissociation from chromatin. Further complications arise from the adaptability of cancer cell chromatin and, in some cases, dose-limiting toxicity. The advent of targeted protein degradation (TPD) through degrader compounds such as proteolysis-targeting chimeras provides a promising approach. These innovative molecules exploit the endogenous ubiquitin–proteasome system to catalytically degrade target proteins and disrupt complexes, potentially amplifying the efficacy of existing epigenetic binders. We highlight the status of TPD-harnessing moieties in clinical and preclinical development, as these compounds may prove crucial for unlocking the potential of epigenetic complex modulation in cancer therapeutics.

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2024-06-12
2024-06-18
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Literature Cited

  1. Abou El Hassan M, Huang K, Eswara MBK, Zhao M, Song L, et al. 2015.. Cancer cells hijack PRC2 to modify multiple cytokine pathways. . PLOS ONE 10:(6):e0126466
    [Crossref] [Google Scholar]
  2. Alabert C, Loos C, Voelker-Albert M, Graziano S, Forné I, et al. 2020.. Domain model explains propagation dynamics and stability of histone H3K27 and H3K36 methylation landscapes. . Cell Rep. 30:(4):122334.e8
    [Crossref] [Google Scholar]
  3. Albrecht BK, Cote A, Crawford T, Duplessis M, Good AC, et al. 2016.. Therapeutic pyridazine compounds and uses thereof. WO Patent 2016/138114A1
    [Google Scholar]
  4. Alendar A, Berns A. 2021.. Sentinels of chromatin: chromodomain helicase DNA-binding proteins in development and disease. . Genes Dev. 35:(21–22):140330
    [Crossref] [Google Scholar]
  5. Alpsoy A, Dykhuizen EC. 2018.. Glioma tumor suppressor candidate region gene 1 (GLTSCR1) and its paralog GLTSCR1-like form SWI/SNF chromatin remodeling subcomplexes. . J. Biol. Chem. 293:(11):3892903
    [Crossref] [Google Scholar]
  6. Armstrong SA, Staunton JE, Silverman LB, Pieters R, Den Boer ML, et al. 2002.. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. . Nat. Genet. 30:(1):4147
    [Crossref] [Google Scholar]
  7. Assimon VA, Tang Y, Vargas JD, Lee GJ, Wu ZY, et al. 2019.. CB-6644 is a selective inhibitor of the RUVBL1/2 complex with anticancer activity. . ACS Chem. Biol. 14:(2):23644
    [Crossref] [Google Scholar]
  8. Barghout SH, Machado RAC, Barsyte-Lovejoy D. 2022.. Chemical biology and pharmacology of histone lysine methylation inhibitors. . Biochim. Biophys. Acta Gene Regul. Mech. 1865:(6):194840
    [Crossref] [Google Scholar]
  9. Basta J, Rauchman M. 2015.. The nucleosome remodeling and deacetylase complex in development and disease. . Transl. Res. 165:(1):3647
    [Crossref] [Google Scholar]
  10. Bennett RL, Licht JD. 2018.. Targeting epigenetics in cancer. . Annu. Rev. Pharmacol. Toxicol. 58::187207
    [Crossref] [Google Scholar]
  11. Bernt KM, Zhu N, Sinha AU, Vempati S, Faber J, et al. 2011.. MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L. . Cancer Cell 20:(1):6678
    [Crossref] [Google Scholar]
  12. Bevill SM, Olivares-Quintero JF, Sciaky N, Golitz BT, Singh D, et al. 2019.. GSK2801, a BAZ2/BRD9 bromodomain inhibitor, synergizes with BET inhibitors to induce apoptosis in triple-negative breast cancer. . Mol. Cancer Res. 17:(7):150318
    [Crossref] [Google Scholar]
  13. Bhat KP, Ümit Kaniskan H, Jin J, Gozani O. 2021.. Epigenetics and beyond: targeting writers of protein lysine methylation to treat disease. . Nat. Rev. Drug Discov. 20:(4):26586
    [Crossref] [Google Scholar]
  14. Biegel JA, Zhou JY, Rorke LB, Stenstrom C, Wainwright LM, Fogelgren B. 1999.. Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors. . Cancer Res. 59:(1):7479
    [Google Scholar]
  15. Bitler BG, Aird KM, Garipov A, Li H, Amatangelo M, et al. 2015.. Synthetic lethality by targeting EZH2 methyltransferase activity in ARID1A-mutated cancers. . Nat. Med. 21:(3):23138
    [Crossref] [Google Scholar]
  16. Blake RA. 2019.. GNE-0011, a novel monovalent BRD4 degrader. . Cancer Res. 79:(13_Suppl.):445252
    [Crossref] [Google Scholar]
  17. Brien GL, Remillard D, Shi J, Hemming ML, Chabon J, et al. 2018.. Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma. . eLife 7::e41305
    [Crossref] [Google Scholar]
  18. Buchi F, Masala E, Rossi A, Valencia A, Spinelli E, et al. 2014.. Redistribution of H3K27me3 and acetylated histone H4 upon exposure to azacitidine and decitabine results in de-repression of the AML1/ETO target gene IL3. . Epigenetics 9:(3):38795
    [Crossref] [Google Scholar]
  19. Cantley J, Ye X, Rousseau E, Januario T, Hamman BD, et al. 2022.. Selective PROTAC-mediated degradation of SMARCA2 is efficacious in SMARCA4 mutant cancers. . Nat. Commun. 13:(1):6814
    [Crossref] [Google Scholar]
  20. Cavalié F, Kelley G, Strain B, Vitzthum H. 2021.. Foghorn Therapeutics announces first patient dosed in first-in-human clinical trial of FHD-609. Press Release, Aug. 23. https://ir.foghorntx.com/news-releases/news-release-details/foghorn-therapeutics-announces-first-patient-dosed-first-human
    [Google Scholar]
  21. Centore RC, Sandoval GJ, Soares LMM, Kadoch C, Chan HM. 2020.. Mammalian SWI/SNF chromatin remodeling complexes: emerging mechanisms and therapeutic strategies. . Trends Genet. 36:(12):93650
    [Crossref] [Google Scholar]
  22. Chen P, Chaikuad A, Bamborough P, Bantscheff M, Bountra C, et al. 2016.. Discovery and characterization of GSK2801, a selective chemical probe for the bromodomains BAZ2A and BAZ2B. . J. Med. Chem. 59:(4):141024
    [Crossref] [Google Scholar]
  23. Chirnomas D, Hornberger KR, Crews CM. 2023.. Protein degraders enter the clinic – a new approach to cancer therapy. . Nat. Rev. Clin. Oncol. 20:(4):26578
    [Crossref] [Google Scholar]
  24. Chu X, Guo X, Jiang Y, Yu H, Liu L, et al. 2017.. Genotranscriptomic meta-analysis of the CHD family chromatin remodelers in human cancers – initial evidence of an oncogenic role for CHD7. . Mol. Oncol. 11:(10):134860
    [Crossref] [Google Scholar]
  25. Cidado J, Boiko S, Proia T, Ferguson D, Criscione SW, et al. 2020.. AZD4573 is a highly selective CDK9 inhibitor that suppresses MCL-1 and induces apoptosis in hematologic cancer cells. . Clin. Cancer Res. 26:(4):92234
    [Crossref] [Google Scholar]
  26. Clapier CR, Cairns BR. 2009.. The biology of chromatin remodeling complexes. . Annu. Rev. Biochem. 78::273304
    [Crossref] [Google Scholar]
  27. Clark PGK, Vieira LCC, Tallant C, Fedorov O, Singleton DC, et al. 2015.. LP99: discovery and synthesis of the first selective BRD7/9 bromodomain inhibitor. . Angew. Chem. Int. Ed. Engl. 54:(21):621721
    [Crossref] [Google Scholar]
  28. Conrad RJ, Fozouni P, Thomas S, Sy H, Zhang Q, et al. 2017.. The short isoform of BRD4 promotes HIV-1 latency by engaging repressive SWI/SNF chromatin-remodeling complexes. . Mol. Cell 67:(6):100112.e6
    [Crossref] [Google Scholar]
  29. Côté J, Quinn J, Workman JL, Peterson CL. 1994.. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. . Science 265:(5168):5360
    [Crossref] [Google Scholar]
  30. Crawford TD, Vartanian S, Côté A, Bellon S, Duplessis M, et al. 2017.. Inhibition of bromodomain-containing protein 9 for the prevention of epigenetically-defined drug resistance. . Bioorg. Med. Chem. Lett. 27:(15):353441
    [Crossref] [Google Scholar]
  31. de Dieuleveult M, Yen K, Hmitou I, Depaux A, Boussouar F, et al. 2016.. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. . Nature 530:(7588):11316
    [Crossref] [Google Scholar]
  32. Delmore JE, Issa GC, Lemieux ME, Rahl PB, Shi J, et al. 2011.. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. . Cell 146:(6):90417
    [Crossref] [Google Scholar]
  33. Deshmukh S, Ptack A, Krug B, Jabado N. 2022.. Oncohistones: a roadmap to stalled development. . FEBS J. 289:(5):131528
    [Crossref] [Google Scholar]
  34. Diamond JR, Boni V, Lim E, Nowakowski G, Cordoba R, et al. 2022.. First-in-human dose-escalation study of cyclin-dependent kinase 9 inhibitor VIP152 in patients with advanced malignancies shows early signs of clinical efficacy. . Clin. Cancer Res. 28:(7):128593
    [Crossref] [Google Scholar]
  35. Dilworth D, Hanley RP, Ferreira de Freitas R, Allali-Hassani A, Zhou M, et al. 2022.. A chemical probe targeting the PWWP domain alters NSD2 nucleolar localization. . Nat. Chem. Biol. 18:(1):5663
    [Crossref] [Google Scholar]
  36. Dölle A, Adhikari B, Krämer A, Weckesser J, Berner N, et al. 2021.. Design, synthesis, and evaluation of WD-repeat-containing protein 5 (WDR5) degraders. . J. Med. Chem. 64:(15):10682710
    [Crossref] [Google Scholar]
  37. Durbin AD, Wang T, Wimalasena VK, Zimmerman MW, Li D, et al. 2022.. EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma. . Cancer Discov. 12:(3):73051
    [Crossref] [Google Scholar]
  38. Ebbert R, Birkmann A, Schüller HJ. 1999.. The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecular-weight protein complex. . Mol. Microbiol. 32:(4):74151
    [Crossref] [Google Scholar]
  39. Erdel F, Rippe K. 2011.. Chromatin remodelling in mammalian cells by ISWI-type complexes–where, when and why?. FEBS J. 278:(19):360818
    [Crossref] [Google Scholar]
  40. Fan Z, Devlin JR, Hogg SJ, Doyle MA, Harrison PF, et al. 2020.. CDK13 cooperates with CDK12 to control global RNA polymerase II processivity. . Sci. Adv. 6:(18):eaaz5041
    [Crossref] [Google Scholar]
  41. Farnaby W, Koegl M, Roy MJ, Whitworth C, Diers E, et al. 2019.. BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. . Nat. Chem. Biol. 15:(7):67280
    [Crossref] [Google Scholar]
  42. Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, et al. 2010.. Selective inhibition of BET bromodomains. . Nature 468:(7327):106773
    [Crossref] [Google Scholar]
  43. Freire PR, Cutler JA, Armstrong SA. 2024.. Therapeutic targeting of the menin–KMT2A interaction. . Annu. Rev. Cancer Biol. 8::291307
    [Crossref] [Google Scholar]
  44. Ganesan A, Arimondo PB, Rots MG, Jeronimo C, Berdasco M. 2019.. The timeline of epigenetic drug discovery: from reality to dreams. . Clin. Epigenet. 11:(1):174
    [Crossref] [Google Scholar]
  45. Gerstenberger BS, Trzupek JD, Tallant C, Fedorov O, Filippakopoulos P, et al. 2016.. Identification of a chemical probe for family VIII bromodomains through optimization of a fragment hit. . J. Med. Chem. 59:(10):480011
    [Crossref] [Google Scholar]
  46. Gibaja V, Shen F, Harari J, Korn J, Ruddy D, et al. 2016.. Development of secondary mutations in wild-type and mutant EZH2 alleles cooperates to confer resistance to EZH2 inhibitors. . Oncogene 35:(5):55866
    [Crossref] [Google Scholar]
  47. Giles F, Witcher M, Brown B. 2018.. NEO2734: a novel potent oral dual BET and P300/CBP inhibitor. . Ann. Oncol. 29::viii14041
    [Crossref] [Google Scholar]
  48. Grebien F, Vedadi M, Getlik M, Giambruno R, Grover A, et al. 2015.. Pharmacological targeting of the Wdr5-MLL interaction in C/EBPα N-terminal leukemia. . Nat. Chem. Biol. 11:(8):57178
    [Crossref] [Google Scholar]
  49. Hanahan D. 2022.. Hallmarks of cancer: new dimensions. . Cancer Discov. 12:(1):3146
    [Crossref] [Google Scholar]
  50. Hanahan D, Coussens LM. 2012.. Accessories to the crime: functions of cells recruited to the tumor microenvironment. . Cancer Cell 21:(3):30922
    [Crossref] [Google Scholar]
  51. Hanley RP, Nie DY, Tabor JR, Li F, Sobh A, et al. 2023.. Discovery of a potent and selective targeted NSD2 degrader for the reduction of H3K36me2. . J. Am. Chem. Soc. 145:(14):817688
    [Crossref] [Google Scholar]
  52. Hargreaves DC, Horng T, Medzhitov R. 2009.. Control of inducible gene expression by signal-dependent transcriptional elongation. . Cell 138:(1):12945
    [Crossref] [Google Scholar]
  53. Harling JD, Tinworth CP. 2023.. A two-faced selectivity solution to target SMARCA2 for cancer therapy. . Nat. Commun. 14:(1):515
    [Crossref] [Google Scholar]
  54. Hay DA, Rogers CM, Fedorov O, Tallant C, Martin S, et al. 2015.. Design and synthesis of potent and selective inhibitors of BRD7 and BRD9 bromodomains. . MedChemComm 6:(7):138186
    [Crossref] [Google Scholar]
  55. He Y, Selvaraju S, Curtin ML, Jakob CG, Zhu H, et al. 2017.. The EED protein-protein interaction inhibitor A-. 395 inactivates the PRC2 complex. . Nat. Chem. Biol. 13:(4):38995
    [Crossref] [Google Scholar]
  56. Helming KC, Wang X, Wilson BG, Vazquez F, Haswell JR, et al. 2014.. ARID1B is a specific vulnerability in ARID1A-mutant cancers. . Nat. Med. 20:(3):25154
    [Crossref] [Google Scholar]
  57. Hoffman GR, Rahal R, Buxton F, Xiang K, McAllister G, et al. 2014.. Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers. . PNAS 111:(8):312833
    [Crossref] [Google Scholar]
  58. Hogg SJ, Motorna O, Cluse LA, Johanson TM, Coughlan HD, et al. 2021.. Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition. . Mol. Cell 81:(10):2183200.e13
    [Crossref] [Google Scholar]
  59. Hsu JH-R, Rasmusson T, Robinson J, Pachl F, Read J, et al. 2020.. EED-targeted PROTACs degrade EED, EZH2, and SUZ12 in the PRC2 complex. . Cell Chem. Biol. 27:(1):4146.e17
    [Crossref] [Google Scholar]
  60. Hu C-K, Wang W, Brind'Amour J, Singh PP, Reeves GA, et al. 2020.. Vertebrate diapause preserves organisms long term through Polycomb complex members. . Science 367:(6480):87074
    [Crossref] [Google Scholar]
  61. Hulse M, Agarwal A, Wang M, Carter J, Sivakumar M, et al. 2022.. Preclinical characterization of PRT3789, a potent and selective SMARCA2 targeted degrader. . Cancer Res. 82:(12_Suppl.):3263
    [Crossref] [Google Scholar]
  62. Husmann D, Gozani O. 2019.. Histone lysine methyltransferases in biology and disease. . Nat. Struct. Mol. Biol. 26:(10):88089
    [Crossref] [Google Scholar]
  63. Italiano A, Soria JC, Toulmonde M, Michot JM, Lucchesi C, et al. 2018.. Tazemetostat, an EZH2 inhibitor, in relapsed or refractory B-cell non-Hodgkin lymphoma and advanced solid tumours: a first-in-human, open-label, phase 1 study. . Lancet Oncol. 19:(5):64959
    [Crossref] [Google Scholar]
  64. Izutsu K, Ando K, Nishikori M, Shibayama H, Teshima T, et al. 2021.. Phase II study of tazemetostat for relapsed or refractory B-cell non-Hodgkin lymphoma with EZH2 mutation in Japan. . Cancer Sci. 112:(9):362735
    [Crossref] [Google Scholar]
  65. Jackson KL, Agafonov RV, Carlson MW, Chaturvedi P, Cocozziello D, et al. 2022.. The discovery and characterization of CFT8634: a potent and selective degrader of BRD9 for the treatment of SMARCB1-perturbed cancers. . Cancer Res. 82:(12_Suppl.):ND09
    [Crossref] [Google Scholar]
  66. Jang MK, Mochizuki K, Zhou M, Jeong HS, Brady JN, Ozato K. 2005.. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. . Mol. Cell 19:(4):52334
    [Crossref] [Google Scholar]
  67. Janssen SM, Lorincz MC. 2021.. Interplay between chromatin marks in development and disease. . Nat. Rev. Genet. 23:(3):13753
    [Crossref] [Google Scholar]
  68. Jiang B, Gao Y, Che J, Lu W, Kaltheuner IH, et al. 2021.. Discovery and resistance mechanism of a selective CDK12 degrader. . Nat. Chem. Biol. 17:(6):67583
    [Crossref] [Google Scholar]
  69. Jin B, Ernst J, Tiedemann RL, Xu H, Sureshchandra S, et al. 2012.. Linking DNA methyltransferases to epigenetic marks and nucleosome structure genome-wide in human tumor cells. . Cell Rep. 2:(5):141124
    [Crossref] [Google Scholar]
  70. Kadoch C, Crabtree GR. 2013.. Reversible disruption of mSWI/SNF (BAF) complexes by the SS18-SSX oncogenic fusion in synovial sarcoma. . Cell 153:(1):7185
    [Crossref] [Google Scholar]
  71. Kadoch C, Hargreaves DC, Hodges C, Elias L, Ho L, et al. 2013.. Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. . Nat. Genet. 45:(6):592601
    [Crossref] [Google Scholar]
  72. Kawano S, Grassian AR, Tsuda M, Knutson SK, Warholic NM, et al. 2016.. Preclinical evidence of anti-tumor activity induced by EZH2 inhibition in human models of synovial sarcoma. . PLOS ONE 11:(7):e0158888
    [Crossref] [Google Scholar]
  73. Kim KH, Roberts CWM. 2016.. Targeting EZH2 in cancer. . Nat. Med. 22:(2):12834
    [Crossref] [Google Scholar]
  74. Kishtagari A, Ng KP, Jarman C, Tiwari AD, Phillips JG, et al. 2018.. A first-in-class inhibitor of ISWI-mediated (ATP-dependent) transcription repression releases terminal-differentiation in AML cells while sparing normal hematopoiesis. . Blood 132:(Suppl. 1):216
    [Crossref] [Google Scholar]
  75. Kofink C, Trainor N, Mair B, Wöhrle S, Wurm M, et al. 2022.. A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo. . Nat. Commun. 13:(1):5969
    [Crossref] [Google Scholar]
  76. Krämer KF, Moreno N, Frühwald MC, Kerl K. 2017.. BRD9 inhibition, alone or in combination with cytostatic compounds as a therapeutic approach in rhabdoid tumors. . Int. J. Mol. Sci. 18:(7):1537
    [Crossref] [Google Scholar]
  77. Krivtsov AV, Armstrong SA. 2007.. MLL translocations, histone modifications and leukaemia stem-cell development. . Nat. Rev. Cancer 7:(11):82333
    [Crossref] [Google Scholar]
  78. Krivtsov AV, Twomey D, Feng Z, Stubbs MC, Wang Y, et al. 2006.. Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. . Nature 442:(7104):81822
    [Crossref] [Google Scholar]
  79. Kwon H, Imbalzano AN, Khavari PA, Kingston RE, Green MR. 1994.. Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex. . Nature 370:(6489):47781
    [Crossref] [Google Scholar]
  80. Lai AY, Wade PA. 2011.. Cancer biology and NuRD: a multifaceted chromatin remodelling complex. . Nat. Rev. Cancer 11:(8):58896
    [Crossref] [Google Scholar]
  81. Lasko LM, Jakob CG, Edalji RP, Qiu W, Montgomery D, et al. 2017.. Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours. . Nature 550:(7674):12832
    [Crossref] [Google Scholar]
  82. Lemon B, Inouye C, King DS, Tjian R. 2001.. Selectivity of chromatin-remodelling cofactors for ligand-activated transcription. . Nature 414:(6866):92428
    [Crossref] [Google Scholar]
  83. Li D, Yu X, Kottur J, Gong W, Zhang Z, et al. 2022.. Discovery of a dual WDR5 and Ikaros PROTAC degrader as an anti-cancer therapeutic. . Oncogene 41:(24):332840
    [Crossref] [Google Scholar]
  84. Li J, Liu T, Song Y, Wang M, Liu L, et al. 2022.. Discovery of small-molecule degraders of the CDK9-cyclin T1 complex for targeting transcriptional addiction in prostate cancer. . J. Med. Chem. 65:(16):1103457
    [Crossref] [Google Scholar]
  85. Li N, Yang H, Liu K, Zhou L, Huang Y, et al. 2022.. Structure-based discovery of a series of NSD2-PWWP1 inhibitors. . J. Med. Chem. 65:(13):945977
    [Crossref] [Google Scholar]
  86. Li Y, Gong H, Wang P, Zhu Y, Peng H, et al. 2021.. The emerging role of ISWI chromatin remodeling complexes in cancer. . J. Exp. Clin. Cancer Res. 40:(1):346
    [Crossref] [Google Scholar]
  87. Liu Z, Hu X, Wang Q, Wu X, Zhang Q, et al. 2021.. Design and synthesis of EZH2-based PROTACs to degrade the PRC2 complex for targeting the noncatalytic activity of EZH2. . J. Med. Chem. 64:(5):282948
    [Crossref] [Google Scholar]
  88. Lovén J, Hoke HA, Lin CY, Lau A, Orlando DA, et al. 2013.. Selective inhibition of tumor oncogenes by disruption of super-enhancers. . Cell 153:(2):32034
    [Crossref] [Google Scholar]
  89. Lu J, Qian Y, Altieri M, Dong H, Wang J, et al. 2015.. Hijacking the E3 ubiquitin ligase cereblon to efficiently target BRD4. . Chem. Biol. 22:(6):75563
    [Crossref] [Google Scholar]
  90. Lücking U, Kosemund D, Böhnke N, Lienau P, Siemeister G, et al. 2021.. Changing for the better: discovery of the highly potent and selective CDK9 inhibitor VIP152 suitable for once weekly intravenous dosing for the treatment of cancer. . J. Med. Chem. 64:(15):1165174
    [Crossref] [Google Scholar]
  91. Ma A, Stratikopoulos E, Park KS, Wei J, Martin TC, et al. 2020.. Discovery of a first-in-class EZH2 selective degrader. . Nat. Chem. Biol. 16:(2):21422
    [Crossref] [Google Scholar]
  92. Maneiro M, Forte N, Shchepinova MM, Kounde CS, Chudasama V, et al. 2020.. Antibody–PROTAC conjugates enable HER2-dependent targeted protein degradation of BRD4. . ACS Chem. Biol. 15:(6):130612
    [Crossref] [Google Scholar]
  93. Marineau JJ, Hammas KB, Hu S, Alnemy S, Mihalich J, et al. 2022.. Discovery of SY-5609: a selective, noncovalent inhibitor of CDK7. . J. Med. Chem. 65:(2):145880
    [Crossref] [Google Scholar]
  94. Martin LJ, Koegl M, Bader G, Cockcroft X-L, Fedorov O, et al. 2016.. Structure-based design of an in vivo active selective BRD9 inhibitor. . J. Med. Chem. 59:(10):446275
    [Crossref] [Google Scholar]
  95. Michel BC, D'Avino AR, Cassel SH, Mashtalir N, McKenzie ZM, et al. 2018.. A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. . Nat. Cell Biol. 20:(12):141020
    [Crossref] [Google Scholar]
  96. Molteni E, Baldan F, Damante G, Allegri L. 2023.. GSK2801 reverses paclitaxel resistance in anaplastic thyroid cancer cell lines through MYCN downregulation. . Int. J. Mol. Sci. 24:(6):5993
    [Crossref] [Google Scholar]
  97. Morschhauser F, Tilly H, Chaidos A, McKay P, Phillips T, et al. 2020.. Tazemetostat for patients with relapsed or refractory follicular lymphoma: an open-label, single-arm, multicentre, phase 2 trial. . Lancet Oncol. 21:(11):143342
    [Crossref] [Google Scholar]
  98. Myrianthopoulos V, Gaboriaud-Kolar N, Tallant C, Hall M-L, Grigoriou S, et al. 2016.. Discovery and optimization of a selective ligand for the switch/sucrose nonfermenting-related bromodomains of polybromo protein-1 by the use of virtual screening and hydration analysis. . J. Med. Chem. 59:(19):8787803
    [Crossref] [Google Scholar]
  99. Narita T, Ito S, Higashijima Y, Chu WK, Neumann K, et al. 2021.. Enhancers are activated by p300/CBP activity-dependent PIC assembly, RNAPII recruitment, and pause release. . Mol. Cell 81:(10):216682.e6
    [Crossref] [Google Scholar]
  100. Navada SC, Steinmann J, Lübbert M, Silverman LR. 2014.. Clinical development of demethylating agents in hematology. . J. Clin. Investig. 124:(1):4046
    [Crossref] [Google Scholar]
  101. Nicolson GL, Nawa A, Toh Y, Taniguchi S, Nishimori K, Moustafa A. 2003.. Tumor metastasis-associated human MTA1 gene and its MTA1 protein product: role in epithelial cancer cell invasion, proliferation and nuclear regulation. . Clin. Exp. Metastasis 20:(1):1924
    [Crossref] [Google Scholar]
  102. Noblejas-López MDM, Gandullo-Sánchez L, Galán-Moya EM, López-Rosa R, Tébar-García D, et al. 2022.. Antitumoral activity of a CDK9 PROTAC compound in HER2-positive breast cancer. . Int. J. Mol. Sci. 23:(10):5476
    [Crossref] [Google Scholar]
  103. Nowak RP, Deangelo SL, Buckley D, He Z, Donovan KA, et al. 2018.. Plasticity in binding confers selectivity in ligand-induced protein degradation. . Nat. Chem. Biol. 14:(7):70614
    [Crossref] [Google Scholar]
  104. O'Brien Laramy MN, Luthra S, Brown MF, Bartlett DW. 2023.. Delivering on the promise of protein degraders. . Nat. Rev. Drug Discov. 22:(5):41027
    [Crossref] [Google Scholar]
  105. Olson CM, Jiang B, Erb MA, Liang Y, Doctor ZM, et al. 2018.. Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation. . Nat. Chem. Biol. 14:(2):16370
    [Crossref] [Google Scholar]
  106. O'Neil NJ, Bailey ML, Hieter P. 2017.. Synthetic lethality and cancer. . Nat. Rev. Genet. 18:(10):61323
    [Crossref] [Google Scholar]
  107. Oppikofer M, Bai T, Gan Y, Haley B, Liu P, et al. 2017.. Expansion of the ISWI chromatin remodeler family with new active complexes. . EMBO Rep. 18:(10):1697706
    [Crossref] [Google Scholar]
  108. Oudelaar AM, Higgs DR. 2021.. The relationship between genome structure and function. . Nat. Rev. Genet. 22:(3):15468
    [Crossref] [Google Scholar]
  109. Papillon JPN, Nakajima K, Adair CD, Hempel J, Jouk AO, et al. 2018.. Discovery of orally active inhibitors of Brahma homolog (BRM)/SMARCA2 ATPase activity for the treatment of brahma related gene 1 (BRG1)/SMARCA4-mutant cancers. . J. Med. Chem. 61:(22):1015572
    [Crossref] [Google Scholar]
  110. Pawel BR. 2018.. SMARCB1-deficient tumors of childhood: a practical guide. . Pediatr. Dev. Pathol. 21:(1):628
    [Crossref] [Google Scholar]
  111. Perner F, Armstrong SA. 2020.. Targeting chromatin complexes in myeloid malignancies and beyond: from basic mechanisms to clinical innovation. . Cells 9:(12):2721
    [Crossref] [Google Scholar]
  112. Pfaff P, Samarasinghe KTG, Crews CM, Carreira EM. 2019.. Reversible spatiotemporal control of induced protein degradation by bistable PhotoPROTACs. . ACS Cent. Sci. 5:(10):168290
    [Crossref] [Google Scholar]
  113. Piunti A, Shilatifard A. 2021.. The roles of Polycomb repressive complexes in mammalian development and cancer. . Nat. Rev. Mol. Cell Biol. 22:(5):32645
    [Crossref] [Google Scholar]
  114. Postow MA, Callahan MK, Wolchok JD. 2015.. Immune checkpoint blockade in cancer therapy. . J. Clin. Oncol. 33:(17):197482
    [Crossref] [Google Scholar]
  115. Potjewyd F, Turner AMW, Beri J, Rectenwald JM, Norris-Drouin JL, et al. 2020.. Degradation of Polycomb repressive complex 2 with an EED-targeted bivalent chemical degrader. . Cell Chem. Biol. 27:(1):4756.e15
    [Crossref] [Google Scholar]
  116. Qi W, Zhao K, Gu J, Huang Y, Wang Y, et al. 2017.. An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of EED. . Nat. Chem. Biol. 13:(4):38188
    [Crossref] [Google Scholar]
  117. Rafati H, Parra M, Hakre S, Moshkin Y, Verdin E, Mahmoudi T. 2011.. Repressive LTR nucleosome positioning by the BAF complex is required for HIV latency. . PLOS Biol. 9:(11):e1001206
    [Crossref] [Google Scholar]
  118. Rahman S, Sowa ME, Ottinger M, Smith JA, Shi Y, et al. 2011.. The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3. . Mol. Cell. Biol. 31:(13):264152
    [Crossref] [Google Scholar]
  119. Raisner R, Kharbanda S, Jin L, Jeng E, Chan E, et al. 2018.. Enhancer activity requires CBP/P300 bromodomain-dependent histone H3K27 acetylation. . Cell Rep. 24:(7):172229
    [Crossref] [Google Scholar]
  120. Rehman SK, Haynes J, Collignon E, Brown KR, Wang Y, et al. 2021.. Colorectal cancer cells enter a diapause-like DTP state to survive chemotherapy. . Cell 184:(1):22642.e21
    [Crossref] [Google Scholar]
  121. Richters A, Doyle SK, Freeman DB, Lee C, Leifer BS, et al. 2021.. Modulating androgen receptor-driven transcription in prostate cancer with selective CDK9 inhibitors. . Cell Chem. Biol. 28:(2):13447.e14
    [Crossref] [Google Scholar]
  122. Romero FA, Murray J, Lai KW, Tsui V, Albrecht BK, et al. 2017.. GNE-781, a highly advanced potent and selective bromodomain inhibitor of cyclic adenosine monophosphate response element binding protein, binding protein (CBP). . J. Med. Chem. 60:(22):916283
    [Crossref] [Google Scholar]
  123. Sahu RK, Singh S, Tomar RS. 2020.. The mechanisms of action of chromatin remodelers and implications in development and disease. . Biochem. Pharmacol. 180::114200
    [Crossref] [Google Scholar]
  124. Sava GP, Fan H, Coombes RC, Buluwela L, Ali S. 2020.. CDK7 inhibitors as anticancer drugs. . Cancer Metastasis Rev. 39:(3):80523
    [Crossref] [Google Scholar]
  125. Schwalm MP, Knapp S. 2022.. BET bromodomain inhibitors. . Curr. Opin. Chem. Biol. 68::102148
    [Crossref] [Google Scholar]
  126. Shain AH, Pollack JR. 2013.. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. . PLOS ONE 8:(1):e55119
    [Crossref] [Google Scholar]
  127. Shen J, Ju Z, Zhao W, Wang L, Peng Y, et al. 2018.. ARID1A deficiency promotes mutability and potentiates therapeutic antitumor immunity unleashed by immune checkpoint blockade. . Nat. Med. 24:(5):55662
    [Crossref] [Google Scholar]
  128. Shen X, Mizuguchi G, Hamiche A, Wu C. 2000.. A chromatin remodelling complex involved in transcription and DNA processing. . Nature 406:(6795):54144
    [Crossref] [Google Scholar]
  129. Shu S, Lin CY, He HH, Witwicki RM, Tabassum DP, et al. 2016.. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. . Nature 529:(7586):41317
    [Crossref] [Google Scholar]
  130. Sims JK, Wade PA. 2011.. SnapShot: chromatin remodeling: CHD. . Cell 144:(4):626.e1
    [Crossref] [Google Scholar]
  131. Stein EM, Garcia-Manero G, Rizzieri DA, Tibes R, Berdeja JG, et al. 2018.. The DOT1L inhibitor pinometostat reduces H3K79 methylation and has modest clinical activity in adult acute leukemia. . Blood 131:(24):266269
    [Crossref] [Google Scholar]
  132. Strain B, Hellsvik K, Lampe M, Vitzthum H. 2023.. Foghorn Therapeutics announces FDA has lifted clinical hold on phase 1 study of FHD-286 in relapsed and/or refractory AML/MDS patients. Press Release, June 5. https://ir.foghorntx.com/news-releases/news-release-details/foghorn-therapeutics-announces-fda-has-lifted-clinical-hold/
    [Google Scholar]
  133. Sutherell CL, Tallant C, Monteiro OP, Yapp C, Fuchs JE, et al. 2016.. Identification and development of 2,3-dihydropyrrolo[1,2-a]quinazolin-5(1H)-one inhibitors targeting bromodomains within the switch/sucrose nonfermenting complex. . J. Med. Chem. 59:(10):5095101
    [Crossref] [Google Scholar]
  134. Theodoulou NH, Bamborough P, Bannister AJ, Becher I, Bit RA, et al. 2016.. Discovery of I-BRD9, a selective cell active chemical probe for bromodomain containing protein 9 inhibition. . J. Med. Chem. 59:(4):142539
    [Crossref] [Google Scholar]
  135. Trojer P. 2022.. Targeting BET bromodomains in cancer. . Annu. Rev. Cancer Biol. 6::31336
    [Crossref] [Google Scholar]
  136. Urick AK, Hawk LML, Cassel MK, Mishra NK, Liu S, et al. 2015.. Dual screening of BPTF and Brd4 using protein-observed fluorine NMR uncovers new bromodomain probe molecules. . ACS Chem. Biol. 10:(10):224656
    [Crossref] [Google Scholar]
  137. Valencia AM, Kadoch C. 2019.. Chromatin regulatory mechanisms and therapeutic opportunities in cancer. . Nat. Cell Biol. 21:(2):15261
    [Crossref] [Google Scholar]
  138. Vangamudi B, Paul TA, Shah PK, Kost-Alimova M, Nottebaum L, et al. 2015.. The SMARCA2/4 ATPase domain surpasses the bromodomain as a drug target in SWI/SNF-mutant cancers: insights from cDNA rescue and PFI-3 inhibitor studies. . Cancer Res. 75:(18):386578
    [Crossref] [Google Scholar]
  139. Vannam R, Sayilgan J, Ojeda S, Karakyriakou B, Hu E, et al. 2021.. Targeted degradation of the enhancer lysine acetyltransferases CBP and p300. . Cell Chem. Biol. 28:(4):50314.e12
    [Crossref] [Google Scholar]
  140. Versteege I, Sévenet N, Lange J, Rousseau-Merck MF, Ambros P, et al. 1998.. Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer. . Nature 394:(6689):2036
    [Crossref] [Google Scholar]
  141. Vervoort SJ, Devlin JR, Kwiatkowski N, Teng M, Gray NS, Johnstone RW. 2022.. Targeting transcription cycles in cancer. . Nat. Rev. Cancer 22:(1):524
    [Crossref] [Google Scholar]
  142. Wang D, Quiros J, Mahuron K, Pai C-C, Ranzani V, et al. 2018.. Targeting EZH2 reprograms intratumoral regulatory T cells to enhance cancer immunity. . Cell Rep. 23:(11):326274
    [Crossref] [Google Scholar]
  143. Wang H, Li B, Zuo L, Wang B, Yan Y, et al. 2022.. The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors. . Nat. Commun. 13:(1):5703
    [Crossref] [Google Scholar]
  144. Wang W, Côté J, Xue Y, Zhou S, Khavari PA, et al. 1996.. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. . EMBO J. 15:(19):537082
    [Crossref] [Google Scholar]
  145. Wang X, Wang S, Troisi EC, Howard TP, Haswell JR, et al. 2019.. BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. . Nat. Commun. 10:(1):1881
    [Crossref] [Google Scholar]
  146. Weinberg DN, Papillon-Cavanagh S, Chen H, Yue Y, Chen X, et al. 2019.. The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape. . Nature 573:(7773):28186
    [Crossref] [Google Scholar]
  147. Welti J, Sharp A, Brooks N, Yuan W, McNair C, et al. 2021.. Targeting the p300/CBP axis in lethal prostate cancer. . Cancer Discov. 11:(5):111837
    [Crossref] [Google Scholar]
  148. Wiley MM, Muthukumar V, Griffin TM, Griffin CT. 2015.. SWI/SNF chromatin-remodeling enzymes Brahma-related gene 1 (BRG1) and Brahma (BRM) are dispensable in multiple models of postnatal angiogenesis but are required for vascular integrity in infant mice. . J. Am. Heart Assoc. 4:(4):e001972
    [Crossref] [Google Scholar]
  149. Wilson BG, Helming KC, Wang X, Kim Y, Vazquez F, et al. 2014.. Residual complexes containing SMARCA2 (BRM) underlie the oncogenic drive of SMARCA4 (BRG1) mutation. . Mol. Cell. Biol. 34:(6):113644
    [Crossref] [Google Scholar]
  150. Winter GE, Buckley DL, Paulk J, Roberts JM, Souza A, et al. 2015.. Phthalimide conjugation as a strategy for in vivo target protein degradation. . Science 348:(6241):137681
    [Crossref] [Google Scholar]
  151. Winter GE, Mayer A, Buckley DL, Erb MA, Roderick JE, et al. 2017.. BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment. . Mol. Cell 67:(1):518.e19
    [Crossref] [Google Scholar]
  152. Wojcik JB, Marchione DM, Sidoli S, Djedid A, Lisby A, et al. 2019.. Epigenomic reordering induced by polycomb loss drives oncogenesis but leads to therapeutic vulnerabilities in malignant peripheral nerve sheath tumors. . Cancer Res. 79:(13):320519
    [Crossref] [Google Scholar]
  153. Xiao L, Parolia A, Qiao Y, Bawa P, Eyunni S, et al. 2022.. Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer. . Nature 601:(7893):43439
    [Crossref] [Google Scholar]
  154. Xu J, Wang Q, Leung ELH, Li Y, Fan X, et al. 2020.. Compound C620-0696, a new potent inhibitor targeting BPTF, the chromatin-remodeling factor in non-small-cell lung cancer. . Front. Med. 14:(1):6067
    [Crossref] [Google Scholar]
  155. Xue Y, Canman JC, Lee CS, Nie Z, Yang D, et al. 2000.. The human SWI/SNF-B chromatin-remodeling complex is related to yeast Rsc and localizes at kinetochores of mitotic chromosomes. . PNAS 97:(24):1301520
    [Crossref] [Google Scholar]
  156. Yang T, Hu Y, Miao J, Chen J, Liu J, et al. 2022.. A BRD4 PROTAC nanodrug for glioma therapy via the intervention of tumor cells proliferation, apoptosis and M2 macrophages polarization. . Acta Pharm. Sin. B 12:(6):265871
    [Crossref] [Google Scholar]
  157. Yang Y, Zhang R, Li Z, Mei L, Wan S, et al. 2020.. Discovery of highly potent, selective, and orally efficacious p300/CBP histone acetyltransferases inhibitors. . J. Med. Chem. 63:(3):133760
    [Crossref] [Google Scholar]
  158. Yellapu NK, Ly T, Sardiu ME, Pei D, Welch DR, et al. 2022.. Synergistic anti-proliferative activity of JQ1 and GSK2801 in triple-negative breast cancer. . BMC Cancer 22:(1):627
    [Crossref] [Google Scholar]
  159. Yokoyama A, Somervaille TCP, Smith KS, Rozenblatt-Rosen O, Meyerson M, Cleary ML. 2005.. The menin tumor suppressor protein is an essential oncogenic cofactor for MLL-associated leukemogenesis. . Cell 123:(2):20718
    [Crossref] [Google Scholar]
  160. Yu H, Wang J, Lackford B, Bennett B, Li J-L, Hu G. 2021.. INO80 promotes H2A.Z occupancy to regulate cell fate transition in pluripotent stem cells. . Nucleic Acids Res. 49:(12):673955
    [Crossref] [Google Scholar]
  161. Zengerle M, Chan KH, Ciulli A. 2015.. Selective small molecule induced degradation of the BET bromodomain protein BRD4. . ACS Chem. Biol. 10:(8):177077
    [Crossref] [Google Scholar]
  162. Zhang S, Zhou B, Wang L, Li P, Bennett BD, et al. 2017.. INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer. . Oncogene 36:(10):143039
    [Crossref] [Google Scholar]
  163. Zhao S, Allis CD, Wang GG. 2021.. The language of chromatin modification in human cancers. . Nat. Rev. Cancer 21:(7):41330
    [Crossref] [Google Scholar]
  164. Zhou B, Wang L, Zhang S, Bennett BD, He F, et al. 2016.. INO80 governs superenhancer-mediated oncogenic transcription and tumor growth in melanoma. . Genes Dev. 30:(12):144053
    [Crossref] [Google Scholar]
  165. Zhou M, Yuan J, Deng Y, Fan X, Shen J. 2021.. Emerging role of SWI/SNF complex deficiency as a target of immune checkpoint blockade in human cancers. . Oncogenesis 10:(1):3
    [Crossref] [Google Scholar]
  166. Zoppi V, Hughes SJ, Maniaci C, Testa A, Gmaschitz T, et al. 2019.. Iterative design and optimization of initially inactive proteolysis targeting chimeras (PROTACs) identify VZ185 as a potent, fast, and selective von Hippel–Lindau (VHL) based dual degrader probe of BRD9 and BRD7. . J. Med. Chem. 62:(2):699726
    [Crossref] [Google Scholar]
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