Mediator kinase inhibition further activates super-enhancer-associated genes in AML

Nature

Volumn 526, Issue 7572, 2015, Pages 273-276

  Pelish, Henry E ^a   Liau, Brian B ^a   Nitulescu, Ioana I ^a   Tangpeerachaikul, Anupong ^a   Poss, Zachary C ^b   Da Silva, Diogo H ^a   Caruso, Brittany T ^a   Arefolov, Alexander ^a   Fadeyi, Olugbeminiyi ^a   Christie, Amanda L ^c   Du, Karrie ^a   Banka, Deepti ^d   Schneider, Elisabeth V ^e,f   Jestel, Anja ^e   Zou, Ge ^a   Si, Chong ^a   Ebmeier, Christopher C ^b   Bronson, Roderick T ^c   Krivtsov, Andrei V ^g   Myers, Andrew G ^a   Kohl, Nancy E ^c   Kung, Andrew L ^h   Armstrong, Scott A ^g   Lemieux, Madeleine E ⁱ   Taatjes, Dylan J ^b   Shair, Matthew D ^a   more..

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d BOSTON CHILDREN S HOSPITAL   (United States)

^e PROTEROS BIOSTRUCTURES GMBH   (Germany)

^f MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^g MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^h New York Presbyterian Morgan Stanley Children's Hospital   (United States)

ⁱ Bioinfo   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

7 (3,5 DIMETHYL 4 ISOXAZOLYL) 1,3 DIHYDRO 8 METHOXY 1 [1 (2 PYRIDINYL)ETHYL] 2H IMIDAZO[4,5 C]QUINOLIN 2 ONE; ANTILEUKEMIC AGENT; CCAAT ENHANCER BINDING PROTEIN ALPHA; CORTISTATIN; CORTISTATIN A; CYCLIN DEPENDENT KINASE; CYCLIN DEPENDENT KINASE 19; CYCLIN DEPENDENT KINASE 8; DOXORUBICIN; INTERFERON CONSENSUS SEQUENCE BINDING PROTEIN; INTERFERON REGULATORY FACTOR 1; PACLITAXEL; RNA POLYMERASE II; STAT1 PROTEIN; TRANSCRIPTION FACTOR ETV6; UNCLASSIFIED DRUG; BRD4 PROTEIN, HUMAN; CDK19 PROTEIN, HUMAN; CDK8 PROTEIN, HUMAN; FUSED HETEROCYCLIC RINGS; NUCLEAR PROTEIN; POLYCYCLIC HYDROCARBON; TRANSCRIPTION FACTOR;

CANCER; CELLS AND CELL COMPONENTS; ENZYME ACTIVITY; GENE EXPRESSION; PROTEIN; TUMOR;

ACUTE MYELOBLASTIC LEUKEMIA; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ANTINEOPLASTIC ACTIVITY; ANTIPROLIFERATIVE ACTIVITY; ARTICLE; CANCER INHIBITION; CELL GROWTH; CELL LINEAGE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DOWN REGULATION; DRUG EFFICACY; DRUG SAFETY; DRUG SENSITIVITY; ENHANCER REGION; ENZYME INHIBITION; ENZYME INHIBITOR INTERACTION; FEMALE; GENE ACTIVATION; GENE EXPRESSION REGULATION; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; LEUKEMIA CELL; MALE; MEDIATOR; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; SUPER ENHANCER; TUMOR SUPPRESSOR GENE; UPREGULATION; ANIMAL; ANTAGONISTS AND INHIBITORS; BIOSYNTHESIS; CELL DIVISION; DISEASE COURSE; DRUG EFFECTS; ENZYMOLOGY; GENETICS; INBRED MOUSE STRAIN; LEUKEMIA, MYELOID, ACUTE; METABOLISM; PATHOLOGY; SCID MOUSE; TUMOR CELL LINE; TUMOR GENE;

ANIMALS; CELL DIVISION; CELL LINE, TUMOR; CELL LINEAGE; CYCLIN-DEPENDENT KINASE 8; CYCLIN-DEPENDENT KINASES; DISEASE PROGRESSION; DOWN-REGULATION; ENHANCER ELEMENTS, GENETIC; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; GENES, TUMOR SUPPRESSOR; HETEROCYCLIC COMPOUNDS, 4 OR MORE RINGS; HUMANS; LEUKEMIA, MYELOID, ACUTE; MALE; MICE; MICE, INBRED STRAINS; MICE, SCID; NUCLEAR PROTEINS; POLYCYCLIC COMPOUNDS; TRANSCRIPTION FACTORS; UP-REGULATION;

EID: 84944257870     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature14904     Document Type: Article

References (53)

1. Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934-947 (2013)
2. Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307-319(2013)
3. Loven, J. et al. Selective inhibition of tumor oncogenes bydisruption of super-enhancers. Cell 153, 320-334 (2013)
4. Dawson, M.A. et al. Recurrent mutations, including NPM1c, activate a BRD4-dependent core transcriptional program in acute myeloid leukemia. Leukemia 28, 311-320 (2013)
5. Kwiatkowski, N. et al. Targeting transcription regulation in cancer with a covalent CDK7 inhibitor. Nature 511, 616-620 (2014)
6. Prange, K. H. M., Singh, A. A. & Martens, J. H. A. The genome-wide molecular signature of transcription factors in leukemia. Exp. Hematol. 42, 637-650(2014)
7. Fragale, A., Marsili, G. & Battistini, A. Genetic and epigenetic regulation of interferon regulatory factor expression: implications in human malignancies. J. Genet Syndr. Gene Ther. 4, 205 (2013)
8. de Braekeleer, E. et al. ETV6 fusion genes in hematological malignancies: a review. Leuk. Res. 36, 945-961 (2012)
9. Allen, B. L. & Taatjes, D. J. The Mediator complex: a central integrator of transcription. Nature Rev. Mol. Cell Biol. 16, 155-166 (2015)
10. Cee, V. J., Chen, D. Y.-K., Lee, M. R. & Nicolaou, K. C. Cortistatin A is a high-affinity ligand of protein kinases ROCK, CDK8, and CDK11. Angew. Chem. Int. Edn Engl. 48, 8952-8957 (2009)
11. Lee, H. M., Nieto-Oberhuber, C. & Shair, M. D. Enantioselective synthesis of (+)-cortistatin A, a potent and selective inhibitor of endothelial cell proliferation. J.Am. Chem. Soc. 130, 16864-16866 (2008)
12. Flyer, A. N., Si, C. & Myers, A. G. Synthesis of cortistatins A, J, K and L. Nature Chem. 2, 886-892 (2010)
13. Bancerek, J. et al. CDK8 kinase phosphorylates transcription factorSTAT1 to selectively regulate the interferon response. Immunity 38, 250-262 (2013)
14. Alarcon, C. et al. Nuclear CDKs drive Smad transcriptional activation and turnover in BMP and TGF-b pathways. Cell 139, 757-769 (2009)
15. Patricelli, M. P. et al. In situ kinase profiling reveals functionally relevant properties of native kinases. Chem. Biol. 18, 699-710 (2011)
16. Pierce, A. C., Sandretto, K. L. & Bemis, G. W. Kinase inhibitors and the case for CH...O hydrogen bonds in protein-ligand binding. Proteins 49, 567-576 (2002)
17. Zacharias, N. & Dougherty, D. A. Cation-p interactions in ligand recognition and catalysis. Trends Pharmacol. Sci. 23, 281-287 (2002)
18. Garraway, L. A. & Sellers, W. R. Lineage dependency and lineage-survival oncogenes in human cancer. Nature Rev. Cancer 6, 593-602 (2006)
19. Subramanian, A. 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. Adelman, K. & Lis, J. T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nature Rev. Genet 13, 720-731 (2012)
21. Etchin, J. et al. Antileukemic activity of nuclear export inhibitors that spare normal hematopoietic cells. Leukemia 27, 66-74 (2013)
22. Putz, E. M. et al. CDK8-Mediated STAT1-S727 phosphorylation restrains NKcell cytotoxicity and tumor surveillance. Cell Rep. 4, 437-444 (2013)
23. Tahirov, T. H. et al. Crystal structure of HIV-1 Tat complexed with human P-TEFb. Nature 465, 747-751 (2010)
24. Knuesel, M.T., Meyer, K. D., Donner, A. J., Espinosa, J. M. & Taatjes, D.J. 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. Okerberg, E. et al. Profiling native kinases by immuno-assisted activity-based profiling. CurrProtoc Chem Biol5, 213-226(2013)
26. Hutterer, C. 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. Schneider, E. V. 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. Kabsch, W. Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr. D 66, 133-144 (2010)
29. Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D 66, 22-25 (2010)
30. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004)
31. Dodson, E. J., Winn, M. & Ralph, A. Collaborative computational project, number4. Providing programs for protein crystallography. Methods Enzymol. 277, 620-633 (1997)
32. Vagin, A. A. et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr. D 60, 2184-2195 (2004)
33. The PyMOL moleculargraphics system v. 1.3r1 (Schrodinger, LLC, 2010)
34. Firestein, R. et al. CDK8 is a colorectal cancer oncogene that regulates p-catenin activity. Nature 455, 547-551 (2008)
35. Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004)
36. Rafael, R. A. et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15(2003)
37. Johnson, W. E., Li, C. & Rabinovic, A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118-127 (2007)
38. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat Soc. B 57, 289-300 (1995)
39. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics29, 15-21 (2013)
40. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009)
41. Anders, S., Pyl, P. T. & Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015)
42. Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010)
43. Law, C. W., Chen, Y., Shi, W. & Smyth, G. K. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15, R29 (2014)
44. da Huang, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44-57 (2009)
45. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Genome Biol. 10, R25 (2009)
46. Kharchenko, P. V., Tolstorukov, M. Y. & Park, P.J. Design and analysis of ChlP-seq experimentsforDNA-binding proteins. Nature Biotechnol. 26, 1351-1359(2008)
47. Zhang, Y. et al. Model-based analysis of ChlP-Seq (MACS). Genome Biol. 9, R137 (2008)
48. Landt, S. G. et al. ChlP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813-1831 (2012)
49. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics26, 841-842 (2010)
50. Rahl, P. B. et al. c-Myc regulates transcriptional pause release. Cell 141, 432-445 (2010)
51. Shen, L., Shao, N., Liu, X. & Nestler, E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 15, 284 (2014)
52. Li, Q., Brown, J. B., Huang, H. & Bickel, P. J. Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat 5, 1752-1779 (2011)
53. Galbraith, M. D. et al. HIF1A employs Cdk8-mediator to stimulate RNAPII elongation in response to hypoxia. Cell 153, 1327-1339 (2013)