Super-enhancers (SEs), which are composed of large clusters of enhancers densely loaded with the Mediator complex, transcription factors and chromatin regulators, drive high expression of genes implicated in cell identity and disease, such as lineage-controlling transcription factors and oncogenes1,2. BRD4 and CDK7 are positive regulators of SE-mediated transcription3,4,5. By contrast, negative regulators of SE-associated genes have not been well described. Here we show that the Mediator-associated kinases cyclin-dependent kinase 8 (CDK8) and CDK19 restrain increased activation of key SE-associated genes in acute myeloid leukaemia (AML) cells. We report that the natural product cortistatin A (CA) selectively inhibits Mediator kinases, has anti-leukaemic activity in vitro and in vivo, and disproportionately induces upregulation of SE-associated genes in CA-sensitive AML cell lines but not in CA-insensitive cell lines. In AML cells, CA upregulated SE-associated genes with tumour suppressor and lineage-controlling functions, including the transcription factors CEBPA, IRF8, IRF1 and ETV6 (refs 6, 7, 8). The BRD4 inhibitor I-BET151 downregulated these SE-associated genes, yet also has anti-leukaemic activity. Individually increasing or decreasing the expression of these transcription factors suppressed AML cell growth, providing evidence that leukaemia cells are sensitive to the dosage of SE-associated genes. Our results demonstrate that Mediator kinases can negatively regulate SE-associated gene expression in specific cell types, and can be pharmacologically targeted as a therapeutic approach to AML.

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Gene Expression Omnibus

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Data deposits

The atomic coordinates of CDK8–CCNC in complex with cortistatin A have been deposited in the Protein Data Bank (PDB) with accession number 4CRL. MIAME-compliant microarray data as well as aligned and raw ChIP-seq data were deposited to the Gene Expression Omnibus (GEO) with accession GSE65161.


  1. 1.

    et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013)

  2. 2.

    et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013)

  3. 3.

    et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320–334 (2013)

  4. 4.

    et al. Recurrent mutations, including NPM1c, activate a BRD4-dependent core transcriptional program in acute myeloid leukemia. Leukemia 28, 311–320 (2013)

  5. 5.

    et al. Targeting transcription regulation in cancer with a covalent CDK7 inhibitor. Nature 511, 616–620 (2014)

  6. 6.

    , & The genome-wide molecular signature of transcription factors in leukemia. Exp. Hematol. 42, 637–650 (2014)

  7. 7.

    , & Genetic and epigenetic regulation of interferon regulatory factor expression: implications in human malignancies. J. Genet. Syndr. Gene Ther. 4, 205 (2013)

  8. 8.

    et al. ETV6 fusion genes in hematological malignancies: a review. Leuk. Res. 36, 945–961 (2012)

  9. 9.

    & The Mediator complex: a central integrator of transcription. Nature Rev. Mol. Cell Biol. 16, 155–166 (2015)

  10. 10.

    , , & Cortistatin A is a high-affinity ligand of protein kinases ROCK, CDK8, and CDK11. Angew. Chem. Int. Edn Engl. 48, 8952–8957 (2009)

  11. 11.

    , & Enantioselective synthesis of (+)-cortistatin A, a potent and selective inhibitor of endothelial cell proliferation. J. Am. Chem. Soc. 130, 16864–16866 (2008)

  12. 12.

    , & Synthesis of cortistatins A, J, K and L. Nature Chem. 2, 886–892 (2010)

  13. 13.

    et al. CDK8 kinase phosphorylates transcription factor STAT1 to selectively regulate the interferon response. Immunity 38, 250–262 (2013)

  14. 14.

    et al. Nuclear CDKs drive Smad transcriptional activation and turnover in BMP and TGF-β pathways. Cell 139, 757–769 (2009)

  15. 15.

    et al. In situ kinase profiling reveals functionally relevant properties of native kinases. Chem. Biol. 18, 699–710 (2011)

  16. 16.

    , & Kinase inhibitors and the case for CH...O hydrogen bonds in protein-ligand binding. Proteins 49, 567–576 (2002)

  17. 17.

    & Cation-π interactions in ligand recognition and catalysis. Trends Pharmacol. Sci. 23, 281–287 (2002)

  18. 18.

    & Lineage dependency and lineage-survival oncogenes in human cancer. Nature Rev. Cancer 6, 593–602 (2006)

  19. 19.

    et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005)

  20. 20.

    & Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nature Rev. Genet. 13, 720–731 (2012)

  21. 21.

    et al. Antileukemic activity of nuclear export inhibitors that spare normal hematopoietic cells. Leukemia 27, 66–74 (2013)

  22. 22.

    et al. CDK8-Mediated STAT1–S727 phosphorylation restrains NK cell cytotoxicity and tumor surveillance. Cell Rep. 4, 437–444 (2013)

  23. 23.

    et al. Crystal structure of HIV-1 Tat complexed with human P-TEFb. Nature 465, 747–751 (2010)

  24. 24.

    , , , & The human CDK8 subcomplex is a histone kinase that requires Med12 for activity and can function independently of mediator. Mol. Cell. Biol. 29, 650–661 (2009)

  25. 25.

    et al. Profiling native kinases by immuno-assisted activity-based profiling. Curr Protoc Chem Biol 5, 213–226 (2013)

  26. 26.

    et al. A novel CDK7 inhibitor of the pyrazolotriazine class exerts broad-spectrum antiviral activity at nanomolar concentrations. Antimicrob. Agents Chemother. 59, 2062–2071 (2015)

  27. 27.

    et al. The structure of CDK8/CycC implicates specificity in the CDK/Cyclin family and reveals interaction with a deep pocket binder. J. Mol. Biol. 412, 251–266 (2011)

  28. 28.

    Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr. D 66, 133–144 (2010)

  29. 29.

    & Molecular replacement with MOLREP. Acta Crystallogr. D 66, 22–25 (2010)

  30. 30.

    & Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

  31. 31.

    , & Collaborative computational project, number 4. Providing programs for protein crystallography. Methods Enzymol. 277, 620–633 (1997)

  32. 32.

    et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr. D 60, 2184–2195 (2004)

  33. 33.

    The PyMOL molecular graphics system v. 1.3r1 (Schrödinger, LLC, 2010)

  34. 34.

    et al. CDK8 is a colorectal cancer oncogene that regulates β-catenin activity. Nature 455, 547–551 (2008)

  35. 35.

    et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004)

  36. 36.

    et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15 (2003)

  37. 37.

    , & Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118–127 (2007)

  38. 38.

    & Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289–300 (1995)

  39. 39.

    et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013)

  40. 40.

    & Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009)

  41. 41.

    , & HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015)

  42. 42.

    & Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010)

  43. 43.

    , , & voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15, R29 (2014)

  44. 44.

    , & Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44–57 (2009)

  45. 45.

    , , & Genome Biol. 10, R25 (2009)

  46. 46.

    , & Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nature Biotechnol. 26, 1351–1359 (2008)

  47. 47.

    et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008)

  48. 48.

    et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813–1831 (2012)

  49. 49.

    & BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010)

  50. 50.

    et al. c-Myc regulates transcriptional pause release. Cell 141, 432–445 (2010)

  51. 51.

    , , & ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 15, 284 (2014)

  52. 52.

    , , & Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat. 5, 1752–1779 (2011)

  53. 53.

    et al. HIF1A employs Cdk8-mediator to stimulate RNAPII elongation in response to hypoxia. Cell 153, 1327–1339 (2013)

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We thank R. Levine, R. King, B. Ebert, B. Bernstein, S. Gillespie, M. Galbraith, M. Patricelli and T. Nomanbhoy for discussions. Lentiviral packaging was completed at the University of Massachusetts Medical School RNAi core facility. Microarray data collection was performed at DFCI MicroArray Core Facility and UMass Medical School Genomics Core Facility. Formulation was performed at VivoPath. In-vivo portions of pharmacokinetic, natural killer and SET-2 studies were performed at Charles River. We thank S. Trauger and G. Byrd of Harvard FAS Small Molecule Mass Spectrometry for PK data acquisition and Harvard FAS Center for Systems Biology for flow sorting and high-throughput sequencing. Recombinant expression of CDK8 module subunits was completed at the Tissue Culture Shared Resource at the University of Colorado Cancer Center, supported by the NCI (P30 CA046934). HCT116 RNA-seq was carried out at the Genomics Shared Resource at the University of Colorado Cancer Center and supported by grant P30-CA046934. We thank A. Odell and R. Dowell for HCT116 RNA-seq data analysis, the R. Levine laboratory (MSKCC) for carrying out the SET-2 RNA-seq acquisition, the M. Geyer laboratory for purified CDK12–CCNK and CDK13–CCNK complexes, and P. Kovarik for STAT1 plasmids. This work was supported by NIH grant CA66996 (S.A.A.), NCI grants R01 CA170741 (D.J.T.) and F31 CA180419 (Z.C.P.), NIH T32 GM08759 (Z.C.P.), a Leukemia and Lymphoma Society Translational Research Program Grant (M.D.S.), the Blavatnik Biomedical Accelerator Program at Harvard (M.D.S.) and the Starr Cancer Consortium (M.D.S.).

Author information

Author notes

    • Henry E. Pelish
    •  & Brian B. Liau

    These authors contributed equally to this work.


  1. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA

    • Henry E. Pelish
    • , Brian B. Liau
    • , Ioana I. Nitulescu
    • , Anupong Tangpeerachaikul
    • , Diogo H. Da Silva
    • , Brittany T. Caruso
    • , Alexander Arefolov
    • , Olugbeminiyi Fadeyi
    • , Karrie Du
    • , Ge Zou
    • , Chong Si
    • , Andrew G. Myers
    •  & Matthew D. Shair
  2. Department of Chemistry and Biochemistry, University of Colorado, Campus Box 596, Boulder, Colorado 80303, USA

    • Zachary C. Poss
    • , Christopher C. Ebmeier
    •  & Dylan J. Taatjes
  3. Lurie Family Imaging Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA

    • Amanda L. Christie
    •  & Nancy E. Kohl
  4. Division of Hematology/Oncology, Children's Hospital, Boston, Massachusetts 02215, USA

    • Deepti Banka
  5. Proteros Biostructures GmbH, Bunsenstrasse 7a, D-82152 Martinsried, Germany

    • Elisabeth V. Schneider
    •  & Anja Jestel
  6. Max-Planck-Institut für Biochemie, Am Kloperspitz 18, D-82152 Martinsried, Germany

    • Elisabeth V. Schneider
  7. Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA

    • Roderick T. Bronson
  8. Cancer Biology and Genetics Program and Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA

    • Andrei V. Krivtsov
    •  & Scott A. Armstrong
  9. Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA

    • Andrew L. Kung
  10. Bioinfo, Plantagenet, Ontario K0B 1L0, Canada

    • Madeleine E. Lemieux


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H.E.P., B.B.L. and M.D.S. designed the research and analysed data. H.E.P., B.B.L., I.I.N., A.T., D.H.D., B.T.C. and K.D. performed cell-based and biochemical experiments not otherwise specified, and analysed data under guidance from M.D.S. Z.C.P. and C.C.E. performed in vitro kinase assays and HCT116 gene expression under guidance from D.J.T. A.A. and O.F. synthesized CA under guidance from M.D.S. C.S. and G.Z. synthesized CA under guidance from A.G.M. A.L.C. performed MV4;11 in vivo efficacy and safety studies under guidance from N.E.K. D.B. performed early MOLM-14 cell growth assays under guidance of S.A.A. E.V.S. and A.J. performed X-ray crystallography. R.T.B. performed mouse histopathology. A.L.K. advised on in vivo studies. S.A.A. and A.V.K. advised on AML studies. M.E.L. performed computational biology studies. H.E.P., B.B.L., D.J.T. and M.D.S. wrote the manuscript. M.D.S. supervised the research.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Matthew D. Shair.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Text with an additional reference and Supplementary Figure 1, which shows the un-cropped scans for Figure 2 and Extended Data Figures 2, 4, 5, 6, 7, 8.

Excel files

  1. 1.

    Supplementary Table 1

    This table shows Super-Enhancer mapping in AML cell lines and Gene Ontology analysis on Super-Enhancer associated genes in MOLM-14 cells.

  2. 2.

    Supplementary Table 2

    This table shows Kinome profiling of cortistatin A in MOLM-14 cell lysate and in vitro with recombinant kinases.

  3. 3.

    Supplementary Table 3

    This table shows Genes differentially expressed in MOLM-14 cells upon 3h or 24h treatment with cortistatin A.

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