Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Enhancer rewiring in tumors: an opportunity for therapeutic intervention

Abstract

Enhancers are cis-regulatory sequences that fine-tune expression of their target genes in a spatiotemporal manner. They are recognized by sequence-specific transcription factors, which in turn recruit transcriptional coactivators that facilitate transcription by promoting assembly and activation of the basal transcriptional machinery. Their functional importance is underscored by the fact that they are often the target of genetic and nongenetic events in human disease that disrupt their sequence, interactome, activation potential, and/or chromatin environment. Dysregulation of transcription and addiction to transcriptional effectors that interact with and modulate enhancer activity are common features of cancer cells and are amenable to therapeutic intervention. Here, we discuss the current knowledge on enhancer biology, the broad spectrum of mechanisms that lead to their malfunction in tumor cells, and recent progress in developing drugs that efficaciously target their dependencies.

This is a preview of subscription content, access via your institution

Access options

Buy this article

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Distal regulation of promoter activity by enhancers.

Similar content being viewed by others

References

  1. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.

    Article  Google Scholar 

  2. Frankel N, Davis GK, Vargas D, Wang S, Payre F, Stern DL. Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature. 2010;466:490–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010;465:182–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 2010;8:e1000384.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature. 2010;467:430–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Calo E, Wysocka J. Modification of enhancer chromatin: what, how, and why? Mol Cell. 2013;49:825–37.

    Article  CAS  PubMed  Google Scholar 

  7. Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature. 2013;498:516–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Bose DA, Donahue G, Reinberg D, Shiekhattar R, Bonasio R, Berger SL. RNA binding to CBP stimulates histone acetylation and transcription. Cell. 2017;168:135–49.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Spitz F. Gene regulation at a distance: from remote enhancers to 3D regulatory ensembles. Semin Cell Dev Biol. 2016;57:57–67.

    Article  CAS  PubMed  Google Scholar 

  10. Rickels R, Shilatifard A. Enhancer logic and mechanics in development and disease. Trends Cell Biol. 2018;28:608–30.

    Article  CAS  PubMed  Google Scholar 

  11. Esnault C, Ghavi-Helm Y, Brun S, Soutourina J, Van Berkum N, Boschiero C, et al. Mediator-dependent recruitment of TFIIH modules in preinitiation complex. Mol Cell. 2008;31:337–46.

    Article  CAS  PubMed  Google Scholar 

  12. Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H, et al. Structures of transcription pre-initiation complex with TFIIH and Mediator. Nature. 2017;551:204–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kim YJ, Björklund S, Li Y, Sayre MH, Kornberg RD. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell. 1994;77:599–608.

    Article  CAS  PubMed  Google Scholar 

  14. Donner AJ, Ebmeier CC, Taatjes DJ, Espinosa JM. CDK8 is a positive regulator of transcriptional elongation within the serum response network. Nat Struct Mol Biol. 2010;17:194–201.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Takahashi H, Parmely TJ, Sato S, Tomomori-Sato C, Banks CA, Kong SE, et al. Human mediator subunit MED26 functions as a docking site for transcription elongation factors. Cell. 2011;146:92–104.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Madsen JGS, Madsen MS, Rauch A, Traynor S, Van Hauwaert EL, Haakonsson AK, et al. Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells. Nat Genet. 2020;52:1227–38.

    Article  CAS  PubMed  Google Scholar 

  17. Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P. Long-range chromatin regulatory interactions in vivo. Nat Genet. 2002;32:623–6.

    Article  CAS  PubMed  Google Scholar 

  18. Deng W, Rupon JW, Krivega I, Breda L, Motta I, Jahn KS, et al. Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell. 2014;158:849–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012;485:381–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159:1665–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Sanborn AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc Natl Acad Sci U S A. 2015;112:E6456.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell. 2013;153:1281–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. El Khattabi L, Zhao H, Kalchschmidt J, Young N, Jung S, Van Blerkom P, et al. A pliable mediator acts as a functional rather than an architectural bridge between promoters and enhancers. Cell. 2019;178:1145–58.

    Article  CAS  PubMed  Google Scholar 

  25. Fulco CP, Nasser J, Jones TR, Munson G, Bergman DT, Subramanian V, et al. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Nat Genet. 2019;51:1664–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Butler JE, Kadonaga JT. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev. 2001;15:2515–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. van Arensbergen J, van Steensel B, Bussemaker HJ. In search of the determinants of enhancer-promoter interaction specificity. Trends Cell Biol. 2014;24:695–702.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Catarino RR, Stark A. Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. Genes Dev. 2018;32:202–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Benabdallah NS, Williamson I, Illingworth RS, Kane L, Boyle S, Sengupta D, et al. Decreased enhancer-promoter proximity accompanying enhancer activation. Mol Cell. 2019;76:473–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Benabdallah NS, Bickmore WA. Regulatory domains and their mechanisms. Cold Spring Harb Symp Quant Biol. 2015;80:45–51.

    Article  PubMed  Google Scholar 

  31. Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA. A phase separation model for transcriptional control. Cell. 2017;169:13–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Boija A, Klein IA, Sabari BR, Dall’Agnese A, Coffey EL, Zamudio AV, et al. Transcription factors activate genes through the phase-separation capacity of their activation domains. Cell. 2018;175:1842–55.

    Article  CAS  PubMed  Google Scholar 

  33. Cho WK, Spille JH, Hecht M, Lee C, Li C, Grube V, et al. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science. 2018;361:412–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Sabari BR, Dall’Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018;361:eaar3958.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Mir M, Bickmore W, Furlong EEM, Narlikar G. Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase? Development. 2019;146:1–6.

    Article  Google Scholar 

  36. Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013;153:307–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, et al. Super-enhancers in the control of cell identity and disease. Cell. 2013;155:934–47.

    Article  CAS  PubMed  Google Scholar 

  38. Lovén J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell. 2013;153:320–34.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012;337:1190–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014;42:D1001–D1006.

    Article  CAS  PubMed  Google Scholar 

  41. Nott A, Holtman IR, Coufal NG, Schlachetzki JCM, Yu M, Hu R, et al. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science. 2019;366:1134–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, et al. Genetic control of chromatin states in humans involves local and distal chromosomal interactions. Cell. 2015;162:1051–65.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Dang CV. MYC on the path to cancer. Cell. 2012;149:22–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Sur I, Taipale J. The role of enhancers in cancer. Nat Rev Cancer. 2016;16:483–93.

    Article  CAS  PubMed  Google Scholar 

  45. Dave K, Sur I, Yan J, Zhang J, Kaasinen E, Zhong F, et al. Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. Elife. 2017;6:e23382.

    Article  PubMed  PubMed Central  Google Scholar 

  46. Bahr C, von Paleske L, Uslu VV, Remeseiro S, Takayama N, Ng SW, et al. A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Nature. 2018;553:515–20.

    Article  CAS  PubMed  Google Scholar 

  47. Taub R, Kirsch I, Morton C, Lenoir G, Swan D, Tronick S, et al. Translocation of the c-myc gene into the immunoglobulin heavy chain locus in human Burkitt lymphoma and murine plasmacytoma cells. Proc Natl Acad Sci U S A. 1982;79:7837–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Affer M, Chesi M, Chen WG, Keats JJ, Demchenko YN, Roschke AV, et al. Promiscuous MYC locus rearrangements hijack enhancers but mostly super-enhancers to dysregulate MYC expression in multiple myeloma. Leukemia. 2014;28:1725–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell. 2000;100:57–70.

    Article  CAS  PubMed  Google Scholar 

  50. Bradner JE, Hnisz D, Young RA. Transcriptional addiction in cancer. Cell. 2017;168:629–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, Saiakhova A, Bartels CF, Balasubramanian D, et al. Epigenomic enhancer profiling defines a signature of colon cancer. Science. 2012;336:736–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Chen H, Li C, Peng X, Zhou Z, Weinstein JN, Cancer Genome Atlas Research Network, et al. A pan-cancer analysis of enhancer expression in nearly 9000 patient samples. Cell. 2018;173:386–99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Puente XS, Beà S, Valdés-Mas R, Villamor N, Gutiérrez-Abril J, Martín-Subero JI, et al. Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature. 2015;526:519–24.

    Article  CAS  PubMed  Google Scholar 

  54. Zhou S, Hawley JR, Soares F, Grillo G, Teng M, Madani Tonekaboni SA, et al. Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer. Nat Commun. 2020;11:441.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Zhang X, Choi PS, Francis JM, Imielinski M, Watanabe H, Cherniack AD, et al. Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers. Nat Genet. 2016;48:176–82.

    Article  CAS  PubMed  Google Scholar 

  56. Zimmerman MW, Liu Y, He S, Durbin AD, Abraham BJ, Easton J, et al. MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification. Cancer Discov. 2018;8:320–35.

    Article  CAS  PubMed  Google Scholar 

  57. Gröschel S, Sanders MA, Hoogenboezem R, de Wit E, Bouwman BAM, Erpelinck C, et al. A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukaemia. Cell. 2014;157:369–81.

    Article  PubMed  Google Scholar 

  58. Drier Y, Cotton MJ, Williamson KE, Gillespie SM, Ryan RJ, Kluk MJ, et al. An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. Nat Genet. 2016;48:265–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Northcott PA, Buchhalter I, Morrissy AS, Hovestadt V, Weischenfeldt J, Ehrenberger T, et al. The whole-genome landscape of medulloblastoma subtypes. Nature. 2017;547:311–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Haller F, Bieg M, Will R, Körner C, Weichenhan D, Bott A, et al. Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. Nat Commun. 2019;10:368.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Müller M, Hermann PC, Liebau S, Weidgang C, Seufferlein T, Kleger A, et al. The role of pluripotency factors to drive stemness in gastrointestinal cancer. Stem Cell Res. 2016;16:349–57.

    Article  PubMed  Google Scholar 

  62. Shivdasani RA, Mayer EL, Orkin SH. Absence of blood formation in mice lacking the T-cell leukaemia oncoprotein tal-1/SCL. Nature. 1995;373:432–4.

    Article  CAS  PubMed  Google Scholar 

  63. Hnisz D, Schuijers J, Lin CY, Weintraub AS, Abraham BJ, Lee TI, et al. Convergence of developmental and oncogenic signalling pathways at transcriptional super-enhancers. Mol Cell. 2015;58:362–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Nabet B, Ó Broin P, Reyes JM, Shieh K, Lin CY, Will CM, et al. Deregulation of the Ras-Erk signaling axis modulates the enhancer landscape. Cell Rep. 2015;12:1300–13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Stevens JL, Cantin GT, Wang G, Shevchenko A, Shevchenko A, Berk AJ. Transcription control by E1A and MAP kinase pathway via Sur2 mediator subunit. Science. 2002;296:755–8.

    Article  CAS  PubMed  Google Scholar 

  66. Yang X, Zhao M, Xia M, Liu Y, Yan J, Ji H, et al. Selective requirement for Mediator MED23 in Ras-active lung cancer. Proc Natl Acad Sci U S A. 2012;109:E2813–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Pandey PK, Udayakumar TS, Lin X, Sharma D, Shapiro PS, Fondell JD. Activation of TRAP/mediator subunit TRAP220/Med1 is regulated by mitogen-activated protein kinase-dependent phosphorylation. Mol Cell Biol. 2005;25:10695–710.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Belakavadi M, Pandey PK, Vijayvargia R, Fondell JD. MED1 phosphorylation promotes its association with mediator: implications for nuclear receptor signalling. Mol Cell Biol. 2008;28:3932–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Hamilton WB, Mosesson Y, Monteiro RS, Emdal KB, Knudsen TE, Francavilla C, et al. Dynamic lineage priming is driven via direct enhancer regulation by ERK. Nature. 2019;575:355–60.

    Article  CAS  PubMed  Google Scholar 

  70. French CA, Ramirez CL, Kolmakova J, Hickman TT, Cameron MJ, Thyne ME, et al. BRD-NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and maintain the growth of carcinoma cells. Oncogene. 2008;27:2237–42.

    Article  CAS  PubMed  Google Scholar 

  71. Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, et al. The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. Genes Dev. 2015;29:1507–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Sze CC, Shilatifard A. MLL3/MLL4/COMPASS family on epigenetic regulation of enhancer function and cancer. Cold Spring Harb Perspect Med. 2016;6:a026427.

    Article  PubMed  PubMed Central  Google Scholar 

  73. Fagan RJ, Dingwall AK. COMPASS ascending: emerging clues regarding the roles of MLL3/KMT2C and MLL2/KMT2D proteins in cancer. Cancer Lett. 2019;458:56–65.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Ortega-Molina A, Boss IW, Canela A, Pan H, Jiang Y, Zhao C, et al. The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development. Nat Med. 2015;21:1199–208.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Andricovich J, Perkail S, Kai Y, Casasanta N, Peng W, Tzatsos A. Loss of KDM6A activates super-enhancers to induce gender-specific squamous-like pancreatic cancer and confers sensitivity to BET inhibitors. Cancer Cell. 2018;33:512–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet. 2010;42:181–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Harms PW, Hristov AC, Kim DS, Anens T, Quist MJ, Siddiqui J, et al. Activating mutations of the oncogene EZH2 in cutaneous melanoma revealed by next generation sequencing. Hum Pathol: Case Rep. 2014;1:21–8.

    Google Scholar 

  78. Calebiro D, Grassi ES, Eszlinger M, Ronchi CL, Godbole A, Bathon K, et al. Recurrent EZH1 mutations are a second hit in autonomous thyroid adenomas. J Clin Invest. 2016;126:3383–8.

    Article  PubMed  PubMed Central  Google Scholar 

  79. Hnisz D, Schuijers J, Li CH, Young RA. Regulation and dysregulation of chromosome structure in cancer. Annu Rev Cancer Biol. 2018;2:21–40.

    Article  Google Scholar 

  80. Rao SSP, Huang S-C, St Hilaire BG, Engreitz JM, Perez EM, Kieffer-Kwon K-R. et al.Cohesin loss eliminates all loop domains. Cell. 2017;171:305–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Katainen R, Dave K, Pitkänen E, Palin K, Kivioja T, Välimäki N, et al. CTCF/cohesin-binding sites are frequently mutated in cancer. Nat Genet. 2015;47:818–21.

    Article  CAS  PubMed  Google Scholar 

  82. Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, et al. Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs. Nature. 2019;575:229–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Flavahan WA, Drier Y, Liau BB, Gillespie SM, Venteicher AS, Stemmer-Rachamimov AO, et al. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. 2016;529:110–4.

    Article  CAS  PubMed  Google Scholar 

  84. De Koninck M, Losada A. Cohesin mutations in cancer. Cold Spring Harb Perspect Med. 2016;6:a026476.

    Article  PubMed  PubMed Central  Google Scholar 

  85. Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, et al. The origin and evolution of mutations in acute myeloid leukaemia. Cell. 2012;150:264–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Balbás-Martínez C, Sagrera A, Carrillo-de-Santa-Pau E, Earl J, Márquez M, Vazquez M, et al. Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy. Nat Genet. 2013;45:1464–9.

    Article  PubMed  PubMed Central  Google Scholar 

  87. Guo G, Sun X, Chen C, Wu S, Huang P, Li Z, et al. Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nat Genet. 2013;45:1459–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Kojic A, Cuadrado A, De Koninck M, Giménez-Llorente D, Rodríguez-Corsino M, Gómez-López G, et al. Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization. Nat Struct Mol Biol. 2018;25:496–504.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Tothova Z, Valton AL, Gorelov R, Vallurupalli M, Krill-Burger JM, Holmes A, et al. Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML. JCI Insight. 2020;6:e142149.

    Article  Google Scholar 

  90. Casa V, Moronta Gines M, Gade Gusmao E, Slotman JA, Zirkel A, Josipovic N, et al. Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control. Genome Res. 2020;30:515–27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Debruyne DN, Dries R, Sengupta S, Seruggia D, Gao Y, Sharma B, et al. BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells. Nature. 2019;572:676–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O, et al. Selective inhibition of BET bromodomains. Nature. 2010;468:1067–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Nicodeme E, Jeffrey KL, Schaefer U, Beinke S, Dewell S, Chung C-W, et al. Suppression of inflammation by a synthetic histone mimic. Nature. 2010;468:1119–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Chapuy B, McKeown MR, Lin CY, Monti S, Roemer MG, Qi J, et al. Discovery and characterization of super-enhancer -associated dependencies in diffuse large B cell lymphoma. Cancer Cell. 2013;24:777–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Delmore JE, Issa GC, Lemieux ME, Rahl PB, Shi J, Jacobs HM, et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell. 2011;146:904–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Mertz JA, Conery AR, Bryant BM, Sandy P, Balasubramanian S, Mele DA, et al. Targeting MYC dependence in cancer by inhibiting BET bromodomains. Proc Natl Acad Sci U S A. 2011;108:16669–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Cromm PM, Crews CM. Targeted protein degradation: from chemical biology to drug discovery. Cell Chem Biol. 2017;24:1181–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Zengerle M, Chan KH, Ciulli A. Selective small molecule induced degradation of the BET bromodomain protein BRD4. ACS Chem Biol. 2015;10:1770–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Lu J, Qian Y, Altieri M, Dong H, Wang J, Raina K, et al. Hijacking the E3 ubiquitin ligase cereblon to efficiently target BRD4. Chem Biol. 2015;22:755–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Stathis A, Zucca E, Bekradda M, Gomez-Roca C, Delord JP, de La Motte Rouge T, et al. Clinical response of carcinomas harboring the BRD4-NUT oncoprotein to the targeted bromodomain inhibitor OTX015/MK-8628. Cancer Discov. 2016;6:492–500.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Lewin J, Soria JC, Stathis A, Delord JP, Peters S, Awada A, et al. Phase Ib trial with Birabresib, a small-molecule inhibitor of bromodomain and extraterminal proteins, in patients with selected advanced solid tumors. J Clin Oncol. 2018;36:3007–14.

    Article  CAS  PubMed  Google Scholar 

  102. Amorim S, Stathis A, Gleeson M, Iyengar S, Magarotto V, Leleu X, et al. Bromodomain inhibitor OTX015 in patients with lymphoma or multiple myeloma: a dose-escalation, open-label, pharmacokinetic, phase 1 study. Lancet Haematol. 2016;3:e196–204.

    Article  PubMed  Google Scholar 

  103. Berthon C, Raffoux E, Thomas X, Vey N, Gomez-Roca C, Yee K, et al. Bromodomain inhibitor OTX015 in patients with acute leukaemia: a dose-escalation, phase 1 study. Lancet Haematol. 2016;3:e186–95.

    Article  PubMed  Google Scholar 

  104. Piha-Paul SA, Hann CL, French CA, Cousin S, Braña I, Cassier PA, et al. Phase 1 study of Molibresib (GSK525762), a Bromodomain and Extra-Terminal Domain Protein Inhibitor, in NUT carcinoma and other solid tumors. JNCI Cancer Spectr. 2019;4:pkz093.

    Article  PubMed  PubMed Central  Google Scholar 

  105. Moreno V, Sepulveda JM, Vieito M, Hernández-Guerrero T, Doger B, Saavedra O. et al. Phase I study of CC-90010, a reversible, oral BET inhibitor in patients with advanced solid tumors and relapsed/refractory non-Hodgkin lymphoma. Ann Oncol. 2020;31:780–8.

    Article  CAS  PubMed  Google Scholar 

  106. Rathert P, Roth M, Neumann T, Muerdter F, Roe JS, Muhar M, et al. Transcriptional plasticity promotes primary and acquired resistance to BET inhibition. Nature. 2015;525:543–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Fong CY, Gilan O, Lam EY, Rubin AF, Ftouni S, Tyler D, et al. BET inhibitor resistance emerges from leukaemia stem cells. Nature. 2015;525:538–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Liao S, Maertens O, Cichowski K, Elledge SJ. Genetic modifiers of the BRD4-NUT dependency of NUT midline carcinoma uncovers a synergism between BETis and CDK4/6is. Genes Dev. 2018;32:1188–200.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Guo L, Li J, Zeng H, Guzman AG, Li T, Lee M, et al. A combination strategy targeting enhancer plasticity exerts synergistic lethality against BETi-resistant leukaemia cells. Nat Commun. 2020;11:740.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Jin X, Yan Y, Wang D, Ding D, Ma T, Ye Z, et al. DUB3 promotes BET inhibitor resistance and cancer progression by deubiquitinating BRD4. Mol Cell. 2018;71:592–605.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Dai X, Gan W, Li X, Wang S, Zhang W, Huang L, et al. Prostate cancer-associated SPOP mutations confer resistance to BET inhibitors through stabilization of BRD4. Nat Med. 2017;23:1063–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Kurimchak AM, Shelton C, Duncan KE, Johnson KJ, Brown J, O’Brien S, et al. Resistance to BET bromodomain inhibitors is mediated by kinome reprogramming in ovarian cancer. Cell Rep. 2016;16:1273–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Iniguez AB, Alexe G, Wang EJ, Roti G, Patel S, Chen L, et al. Resistance to epigenetic-targeted therapy engenders tumor cell vulnerabilities associated with enhancer remodeling. Cancer Cell. 2018;34:922–38.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Ambrosini G, Do C, Tycko B, Realubit RB, Karan C, Musi E, et al. Inhibition of NF-κB-dependent signaling enhances sensitivity and overcomes resistance to BET inhibition in uveal melanoma. Cancer Res. 2019;79:2415–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Chua V, Orloff M, Teh JL, Sugase T, Liao C, Purwin TJ, et al. Stromal fibroblast growth factor 2 reduces the efficacy of bromodomain inhibitors in uveal melanoma. EMBO Mol Med. 2019;11:e9081.

    Article  PubMed  PubMed Central  Google Scholar 

  116. Han X, Yu D, Gu R, Jia Y, Wang Q, Jaganathan A, et al. Roles of the BRD4 short isoform in phase separation and active gene transcription. Nat Struct Mol Biol. 2020;27:333–41.

    Article  CAS  PubMed  Google Scholar 

  117. Wu SY, Lee CF, Lai HT, Yu CT, Lee JE, Zuo H, et al. Opposing functions of BRD4 isoforms in breast cancer. Mol Cell. 2020;78:1114–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Faivre EJ, McDaniel KF, Albert DH, Mantena SR, Plotnik JP, Wilcox D, et al. Selective inhibition of the BD2 bromodomain of BET proteins in prostate cancer. Nature. 2020;578:306–10.

    Article  CAS  PubMed  Google Scholar 

  119. Gilan O, Rioja I, Knezevic K, Bell MJ, Yeung MM, Harker NR, et al. Selective targeting of BD1 and BD2 of the BET proteins in cancer and immunoinflammation. Science. 2020;368:387–94.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Waring MJ, Chen H, Rabow AA, Walker G, Bobby R, Boiko S, et al. Potent and selective bivalent inhibitors of BET bromodomains. Nat Chem Biol. 2016;12:1097–104.

    Article  CAS  PubMed  Google Scholar 

  121. Lambert JP, Picaud S, Fujisawa T, Hou H, Savitsky P, Uusküla-Reimand L, et al. Interactome rewiring following pharmacological targeting of BET bromodomains. Mol Cell. 2019;73:621–38.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Shu S, Lin CY, He HH, Witwicki RM, Tabassum DP, Roberts JM, et al. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. Nature. 2016;529:413–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Dawson MA, Prinjha RK, Dittmann A, Giotopoulos G, Bantscheff M, Chan WI, et al. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature. 2011;478:529–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Akhtar MS, Heidemann M, Tietjen JR, Zhang DW, Chapman RD, Eick D, et al. TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II. Mol Cell. 2009;34:387–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Larochelle S, Amat R, Glover-Cutter K, Sansó M, Zhang C, Allen JJ, et al. Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II. Nat Struct Mol Biol. 2012;19:1108–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Edmondson SD, Yang B, Fallan C. Proteolysis targeting chimeras (PROTACs) in ‘beyond rule-of-five’ chemical space: Recent progress and future challenges. Bioorg Med Chem Lett. 2019;29:1555–64.

    Article  CAS  PubMed  Google Scholar 

  127. Galbraith MD, Bender H, Espinosa JM. Therapeutic targeting of transcriptional cyclin-dependent kinases. Transcription. 2019;10:118–36.

    Article  CAS  PubMed  Google Scholar 

  128. Fant CB, Taatjes DJ. Regulatory functions of the mediator kinases CDK8 and CDK19. Transcription. 2019;10:76–90.

    Article  PubMed  Google Scholar 

  129. Iniguez AB, Stolte B, Wang EJ, Conway AS, Alexe G, Dharia NV, et al. EWS/FLI confers tumor cell synthetic lethality to CDK12 inhibition in ewing sarcoma. Cancer Cell. 2018;33:202–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Quereda V, Bayle S, Vena F, Frydman SM, Monastyrskyi A, Roush WR, et al. Therapeutic targeting of CDK12/CDK13 in triple-negative breast cancer. Cancer Cell. 2019;36:545–58.

    Article  CAS  PubMed  Google Scholar 

  131. Chipumuro E, Marco E, Christensen CL, Kwiatkowski N, Zhang T, Hatheway CM, et al. CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer. Cell. 2014;159:1126–39.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Christensen CL, Kwiatkowski N, Abraham BJ, Carretero J, Al-Shahrour F, Zhang T, et al. Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor. Cancer Cell. 2014;26:909–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Kwiatkowski N, Zhang T, Rahl PB, Abraham BJ, Reddy J, Ficarro SB, et al. Targeting transcription regulation in cancer with a covalent CDK7 inhibitor. Nature. 2014;511:616–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Wang Y, Zhang T, Kwiatkowski N, Abraham BJ, Lee TI, Xie S, et al. CDK7-dependent transcriptional addiction in triple-negative breast cancer. Cell. 2015;163:174–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Zhang X, Lee HC, Shirazi F, Baladandayuthapani V, Lin H, Kuiatse I, et al. Protein targeting chimeric molecules specific for bromodomain and extra-terminal motif family proteins are active against pre-clinical models of multiple myeloma. Leukemia. 2018;32:2224–39.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Firestein R, Bass AJ, Kim SY, Dunn IF, Silver SJ, Guney I, et al. CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity. Nature. 2008;455:547–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Kapoor A, Goldberg MS, Cumberland LK, Ratnakumar K, Segura MF, Emanuel PO, et al. The histone variant macroH2A suppresses melanoma progression through regulation of CDK8. Nature. 2010;468:1105–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Gu W, Wang C, Li W, Hsu FN, Tian L, Zhou J, et al. Tumor-suppressive effects of CDK8 in endometrial cancer cells. Cell Cycle. 2013;12:987–99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Pelish HE, Liau BB, Nitulescu II, Tangpeerachaikul A, Poss ZC, Da Silva DH, et al. Mediator kinase inhibition further activates super-enhancer-associated genes in AML. Nature. 2015;526:273–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Clarke PA, Ortiz-Ruiz MJ, TePoele R, Adeniji-Popoola O, Box G, et al. Assessing the mechanism and therapeutic potential of modulators of the human Mediator complex-associated protein kinases. Elife. 2016;5:e20722.

    Article  PubMed  PubMed Central  Google Scholar 

  141. Cayrol F, Praditsuktavorn P, Fernando TM, Kwiatkowski N, Marullo R, Calvo-Vidal MN, et al. THZ1 targeting CDK7 suppresses STAT transcriptional activity and sensitizes T-cell lymphomas to BCL2 inhibitors. Nat Commun. 2017;8:14290.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Zhang H, Pandey S, Travers M, Sun H, Morton G, Madzo J, et al. Targeting CDK9 reactivates epigenetically silenced genes in cancer. Cell. 2018;175:1244–58.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Lu H, Xue Y, Yu GK, Arias C, Lin J, Fong S, et al. Compensatory induction of MYC expression by sustained CDK9 inhibition via a BRD4-dependent mechanism. Elife. 2015;4:e06535.

    Article  PubMed  PubMed Central  Google Scholar 

  144. Zhang W, Ge H, Jiang Y, Huang R, Wu Y, Wang D, et al. Combinational therapeutic targeting of BRD4 and CDK7 synergistically induces anticancer effects in head and neck squamous cell carcinoma. Cancer Lett. 2020;469:510–23.

    Article  CAS  PubMed  Google Scholar 

  145. Klein IA, Boija A, Afeyan LK, Hawken SW, Fan M, Dall’Agnese A, et al. Partitioning of cancer therapeutics in nuclear condensates. Science. 2020;368:1386–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Sharko AC, Lim CU, McDermott MSJ, Hennes C, Philavong KP, Aiken T, et al. The inhibition of CDK8/19 mediator kinases prevents the development of resistance to EGFR-targeting drugs. Cells. 2021;10:E144.

    Article  Google Scholar 

  147. Rusan M, Li K, Li Y, Christensen CL, Abraham BJ, Kwiatkowski N, et al. Suppression of adaptive responses to targeted cancer therapy by transcriptional repression. Cancer Discov. 2018;8:59–73.

    Article  CAS  PubMed  Google Scholar 

  148. Yokoyama Y, Zhu H, Lee JH, Kossenkov AV, Wu SY, Wickramasinghe JM, et al. BET inhibitors suppress ALDH activity by targeting ALDH1A1 super-enhancer in ovarian cancer. Cancer Res. 2016;76:6320–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Zawistowski JS, Bevill SM, Goulet DR, Stuhlmiller TJ, Beltran AS, Olivares-Quintero JF, et al. Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complex. Cancer Discov. 2017;7:302–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Mazur PK, Herner A, Mello SS, Wirth M, Hausmann S, Sánchez-Rivera FJ, et al. Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma. Nat Med. 2015;21:1163–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Leal AS, Williams CR, Royce DB, Pioli PA, Sporn MB, Liby KT. Bromodomain inhibitors, JQ1 and I-BET 762, as potential therapies for pancreatic cancer. Cancer Lett. 2017;394:76–87.

    Article  CAS  PubMed  Google Scholar 

  152. Piunti A, Hashizume R, Morgan MA, Bartom ET, Horbinski CM, Marshall SA, et al. Therapeutic targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas. Nat Med. 2017;23:493–500.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Sin-Chan P, Mumal I, Suwal T, Ho B, Fan X, Singh I, et al. A C19MC-LIN28A-MYCN oncogenic circuit driven by hijacked super-enhancers is a distinct therapeutic vulnerability in ETMRs: a lethal brain tumor. Cancer Cell. 2019;36:51–67.

    Article  CAS  PubMed  Google Scholar 

  154. Gollavilli PN, Pawar A, Wilder-Romans K, Natesan R, Engelke CG, Dommeti VL, et al. EWS/ETS-driven Ewing sarcoma requires BET bromodomain proteins. Cancer Res. 2018;78:4760–73.

    Article  CAS  PubMed  Google Scholar 

  155. Welti J, Sharp A, Yuan W, Dolling D, Nava Rodrigues D, Figueiredo I, et al. Targeting Bromodomain and Extra-Terminal (BET) Family Proteins in Castration-Resistant Prostate Cancer (CRPC). Clin Cancer Res. 2018;24:3149–62.

    Article  CAS  PubMed  Google Scholar 

  156. Mahe M, Dufour F, Neyret-Kahn H, Moreno-Vega A, Beraud C, Shi M, et al. An FGFR3/MYC positive feedback loop provides new opportunities for targeted therapies in bladder cancers. EMBO Mol Med. 2018;10:e8163.

    Article  PubMed  PubMed Central  Google Scholar 

  157. Camero S, Camicia L, Marampon F, Ceccarelli S, Shukla R, Mannarino O, et al. BET inhibition therapy counteracts cancer cell survival, clonogenic potential and radioresistance mechanisms in rhabdomyosarcoma cells. Cancer Lett. 2020;479:71–88.

    Article  CAS  PubMed  Google Scholar 

  158. Chaidos A, Caputo V, Gouvedenou K, Liu B, Marigo I, Chaudhry MS, et al. Potent antimyeloma activity of the novel bromodomain inhibitors I-BET151 and I-BET762. Blood. 2014;123:697–705.

    Article  CAS  PubMed  Google Scholar 

  159. Zhang G, Plotnikov AN, Rusinova E, Shen T, Morohashi K, Joshua J, et al. Structure-guided design of potent diazobenzene inhibitors for the BET bromodomains. J Med Chem. 2013;56:9251–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Segura MF, Fontanals-Cirera B, Gaziel-Sovran A, Guijarro MV, Hanniford D, Zhang G, et al. BRD4 sustains melanoma proliferation and represents a new target for epigenetic therapy. Cancer Res. 2013;73:6264–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Siu KT, Ramachandran J, Yee AJ, Eda H, Santo L, Panaroni C, et al. Preclinical activity of CPI-0610, a novel small-molecule bromodomain and extra-terminal protein inhibitor in the therapy of multiple myeloma. Leukemia. 2017;31:1760–9.

    Article  CAS  PubMed  Google Scholar 

  162. Albrecht BK, Gehling VS, Hewitt MC, Vaswani RG, Côté A, Leblanc Y, et al. Identification of a Benzoisoxazoloazepine Inhibitor (CPI-0610) of the Bromodomain and Extra-Terminal (BET) Family as a candidate for human clinical trials. J Med Chem. 2016;59:1330–9.

    Article  CAS  PubMed  Google Scholar 

  163. Morrison-Smith CD, Knox TM, Filic I, Soroko KM, Eschle BK, Wilkens MK, et al. Combined targeting of the BRD4-NUT-p300 axis in NUT midline carcinoma by dual selective bromodomain inhibitor, NEO2734. Mol Cancer Ther. 2020;19:1406–14.

    Article  CAS  PubMed  Google Scholar 

  164. Stubbs MC, Burn TC, Sparks R, Maduskuie T, Diamond S, Rupar M, et al. The novel bromodomain and extraterminal domain inhibitor INCB054329 induces vulnerabilities in myeloma cells that inform rational combination strategies. Clin Cancer Res. 2019;25:300–11.

    Article  CAS  PubMed  Google Scholar 

  165. Ozer HG, El-Gamal D, Powell B, Hing ZA, Blachly JS, Harrington B, et al. BRD4 profiling identifies critical chronic lymphocytic leukemia oncogenic circuits and reveals sensitivity to PLX51107, a novel structurally distinct BET inhibitor. Cancer Discov. 2018;8:458–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Noblejas-López MDM, Nieto-Jimenez C, Burgos M, Gómez-Juárez M, Montero JC, Esparís-Ogando A, et al. Activity of BET-proteolysis targeting chimeric (PROTAC) compounds in triple negative breast cancer. J Exp Clin Cancer Res. 2019;38:383.

    Article  PubMed  PubMed Central  Google Scholar 

  167. Raina K, Lu J, Qian Y, Altieri M, Gordon D, Rossi AM, et al. PROTAC-induced BET protein degradation as a therapy for castration-resistant prostate cancer. Proc Natl Acad Sci U S A. 2016;113:7124–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Sun B, Fiskus W, Qian Y, Rajapakshe K, Raina K, Coleman KG, et al. BET protein proteolysis targeting chimera (PROTAC) exerts potent lethal activity against mantle cell lymphoma cells. Leukemia. 2018;32:343–52.

    Article  CAS  PubMed  Google Scholar 

  169. Piya S, Mu H, Bhattacharya S, Lorenzi PL, Davis RE, McQueen T, et al. BETP degradation simultaneously targets acute myelogenous leukaemia stem cells and the microenvironment. J Clin Invest. 2019;129:1878–94.

    Article  PubMed  PubMed Central  Google Scholar 

  170. Abramson JS, Blum KA, Flinn IW, Gutierrez M, Goy A, Maris M, et al. BET inhibitor CPI-0610 is well tolerated and induces responses in diffuse large B-cell lymphoma and follicular lymphoma: preliminary analysis of an ongoing phase 1 study. Blood. 2015;126:1491.

    Article  Google Scholar 

  171. Pulikkan JA, Hegde M, Ahmad HM, Belaghzal H, Illendula A, Yu J, et al. CBFβ-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia. Cell. 2018;174:172–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Bagratuni T, Mavrianou N, Gavalas NG, Tzannis K, Arapinis C, Liontos M, et al. JQ1 inhibits tumour growth in combination with cisplatin and suppresses JAK/STAT signalling pathway in ovarian cancer. Eur J Cancer. 2020;126:125–35.

    Article  CAS  PubMed  Google Scholar 

  173. Lam FC, Morton SW, Wyckoff J, Vu Han TL, Hwang MK, Maffa A, et al. Enhanced efficacy of combined temozolomide and bromodomain inhibitor therapy for gliomas using targeted nanoparticles. Nat Commun. 2018;9:1991.

    Article  PubMed  PubMed Central  Google Scholar 

  174. Fehling SC, Miller AL, Garcia PL, Vance RB, Yoon KJ. The combination of BET and PARP inhibitors is synergistic in models of cholangiocarcinoma. Cancer Lett. 2020;468:48–58.

    Article  CAS  PubMed  Google Scholar 

  175. Yang L, Zhang Y, Shan W, Hu Z, Yuan J, Pi J, et al. Repression of BET activity sensitizes homologous recombination-proficient cancers to PARP inhibition. Sci Transl Med. 2017;9:eaal1645.

    Article  PubMed  PubMed Central  Google Scholar 

  176. Ge JY, Shu S, Kwon M, Jovanović B, Murphy K, Gulvady A, et al. Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer. Nat Commun. 2020;11:2350.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Bandopadhayay P, Piccioni F, O’Rourke R, Ho P, Gonzalez EM, Buchan G, et al. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun. 2019;10:2400.

    Article  PubMed  PubMed Central  Google Scholar 

  178. Bolin S, Borgenvik A, Persson CU, Sundström A, Qi J, Bradner JE, et al. Combined BET bromodomain and CDK2 inhibition in MYC-driven medulloblastoma. Oncogene. 2018;37:2850–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  179. Chen J, Nelson C, Wong M, Tee AE, Liu PY, La T, et al. Targeted therapy of TERT-rearranged neuroblastoma with BET bromodomain inhibitor and proteasome inhibitor combination therapy. Clin Cancer Res J Am Assoc Cancer Res. 2021;27:1438–51.

    Article  CAS  Google Scholar 

  180. Walsh L, Haley KE, Moran B, Mooney B, Tarrant F, Madden SF, et al. BET inhibition as a rational therapeutic strategy for invasive lobular breast cancer. Clin Cancer Res. 2019;25:7139–50.

    Article  CAS  PubMed  Google Scholar 

  181. Li W, Gupta SK, Han W, Kundson RA, Nelson S, Knutson D, et al. Targeting MYC activity in double-hit lymphoma with MYC and BCL2 and/or BCL6 rearrangements with epigenetic bromodomain inhibitors. J Hematol Oncol. 2019;12:73.

    Article  PubMed  PubMed Central  Google Scholar 

  182. Fiskus W, Mill CP, Perera D, Birdwell C, Deng Q, Yang H et al. BET proteolysis targeted chimera-based therapy of novel models of Richter transformation-diffuse large B-cell lymphoma. Leukemia. 2021. https://doi.org/10.1038/s41375-021-01181-w.

  183. Latif A-L, Newcombe A, Li S, Gilroy K, Robertson NA, Lei X, et al. BRD4-mediated repression of p53 is a target for combination therapy in AML. Nat Commun. 2021;12:241.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Risom T, Langer EM, Chapman MP, Rantala J, Fields AJ, Boniface C, et al. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nat Commun. 2018;9:3815.

    Article  PubMed  PubMed Central  Google Scholar 

  185. Stratikopoulos EE, Dendy M, Szabolcs M, Khaykin AJ, Lefebvre C, Zhou M-M, et al. Kinase and BET inhibitors together clamp inhibition of PI3K signaling and overcome resistance to therapy. Cancer Cell. 2015;27:837–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Boedicker C, Hussong M, Grimm C, Dolgikh N, Meister MT, Enßle JC, et al. Co-inhibition of BET proteins and PI3Kα triggers mitochondrial apoptosis in rhabdomyosarcoma cells. Oncogene 2020;39:3837–52.

    Article  CAS  PubMed  Google Scholar 

  187. Guerra SL, Maertens O, Kuzmickas R, De Raedt T, Adeyemi RO, Guild CJ, et al. A deregulated HOX gene axis confers an epigenetic vulnerability in KRAS-mutant lung cancers. Cancer Cell. 2020;37:705–19.

    Article  CAS  PubMed  Google Scholar 

  188. Knoechel B, Roderick JE, Williamson KE, Zhu J, Lohr JG, Cotton MJ, et al. An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukaemia. Nat Genet. 2014;46:364–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Arfaoui A, Rioualen C, Azzoni V, Pinna G, Finetti P, Wicinski J, et al. A genome-wide RNAi screen reveals essential therapeutic targets of breast cancer stem cells. EMBO Mol Med. 2019;11:e9930.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  190. Matkar S, Sharma P, Gao S, Gurung B, Katona BW, Liao J, et al. An epigenetic pathway regulates sensitivity of breast cancer cells to HER2 inhibition via FOXO/c-Myc axis. Cancer Cell. 2015;28:472–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Saenz DT, Fiskus W, Mill CP, Perera D, Manshouri T, Lara BH, et al. Mechanistic basis and efficacy of targeting the β-catenin-TCF7L2-JMJD6-c-Myc axis to overcome resistance to BET inhibitors. Blood. 2020;135:1255–69.

    Article  PubMed  PubMed Central  Google Scholar 

  192. Bihani T, Ezell SA, Ladd B, Grosskurth SE, Mazzola AM, Pietras M, et al. Resistance to everolimus driven by epigenetic regulation of MYC in ER+ breast cancers. Oncotarget. 2015;6:2407–20.

    Article  PubMed  Google Scholar 

  193. Vázquez R, Riveiro ME, Astorgues-Xerri L, Odore E, Rezai K, Erba E, et al. The bromodomain inhibitor OTX015 (MK-8628) exerts anti-tumor activity in triple-negative breast cancer models as single agent and in combination with everolimus. Oncotarget. 2017;8:7598–613.

    Article  PubMed  Google Scholar 

  194. Liddicoat BJ, Dawson MA. Place your BETs in combination therapy. Mol Cell. 2020;78:991–3.

    Article  CAS  PubMed  Google Scholar 

  195. Ali S, Heathcote DA, Kroll SH, Jogalekar AS, Scheiper B, Patel H, et al. The development of a selective cyclin-dependent kinase inhibitor that shows antitumor activity. Cancer Res. 2009;69:6208–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Patel H, Periyasamy M, Sava GP, Bondke A, Slafer BW, Kroll SHB, et al. ICEC0942, an orally bioavailable selective inhibitor of CDK7 for cancer treatment. Mol Cancer Ther. 2018;17:1156–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Kelso TW, Baumgart K, Eickhoff J, Albert T, Antrecht C, Lemcke S, et al. Cyclin-dependent kinase 7 controls mRNA synthesis by affecting stability of preinitiation complexes, leading to altered gene expression, cell cycle progression, and survival of tumor cells. Mol Cell Biol. 2014;34:3675–88.

    Article  PubMed  PubMed Central  Google Scholar 

  198. Jiang YY, Lin DC, Mayakonda A, Hazawa M, Ding LW, Chien WW, et al. Targeting super-enhancer-associated oncogenes in oesophageal squamous cell carcinoma. Gut. 2017;66:1358–68.

    Article  CAS  PubMed  Google Scholar 

  199. Li B, Ni Chonghaile T, Fan Y, Madden SF, Klinger R, O’Connor AE, et al. Therapeutic rationale to target highly expressed CDK7 conferring poor outcomes in triple-negative breast cancer. Cancer Res. 2017;77:3834–45.

    Article  CAS  PubMed  Google Scholar 

  200. Zhang J, Liu W, Zou C, Zhao Z, Lai Y, Shi Z, et al. Targeting super-enhancer-associated oncogenes in Osteosarcoma with THZ2, a covalent CDK7 inhibitor. Clin Cancer Res. 2020;26:2681–92.

    Article  CAS  PubMed  Google Scholar 

  201. Lücking U, Scholz A, Lienau P, Siemeister G, Kosemund D, Bohlmann R, et al. Identification of Atuveciclib (BAY 1143572), the first highly selective, clinical PTEFb/CDK9 Inhibitor for the treatment of cancer. ChemMedChem. 2017;12:1776–93.

    Article  PubMed  PubMed Central  Google Scholar 

  202. Beauchamp EM, Abedin SM, Radecki SG, Fischietti M, Arslan AD, Blyth GT, et al. Identification and targeting of novel CDK9 complexes in acute myeloid leukaemia. Blood. 2019;133:1171–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Olson CM, Jiang B, Erb MA, Liang Y, Doctor ZM, Zhang Z, et al. Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation. Nat Chem Biol. 2018;14:163–70.

    Article  CAS  PubMed  Google Scholar 

  204. McDermott MS, Chumanevich AA, Lim CU, Liang J, Chen M, Altilia S, et al. Inhibition of CDK8 mediator kinase suppresses estrogen dependent transcription and the growth of estrogen receptor positive breast cancer. Oncotarget. 2017;8:12558–75.

    Article  PubMed  PubMed Central  Google Scholar 

  205. Dale T, Clarke PA, Esdar C, Waalboer D, Adeniji-Popoola O, Ortiz-Ruiz MJ, et al. A selective chemical probe for exploring the role of CDK8 and CDK19 in human disease. Nat Chem Biol. 2015;11:973–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Zhang T, Kwiatkowski N, Olson CM, Dixon-Clarke SE, Abraham BJ, et al. Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors. Nat Chem Biol. 2016;12:876–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

Work in the lab of RM is supported by the Fondation pour la Recherche Médicale (Equipe FRM EQU202003010312). LR work was partly supported by a research grant from Pfizer. We thank Daniel Holoch and Ming-Kang Lee for their critical review of the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Raphaël Margueron.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Richart, L., Bidard, FC. & Margueron, R. Enhancer rewiring in tumors: an opportunity for therapeutic intervention. Oncogene 40, 3475–3491 (2021). https://doi.org/10.1038/s41388-021-01793-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Version of record:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41388-021-01793-7

This article is cited by

Search

Quick links