A Myc Network Accounts for Similarities between Embryonic Stem and Cancer Cell Transcription Programs

Cell

Volumn 143, Issue 2, 2010, Pages 313-324

  Kim, Jonghwan ^a,b,c   Woo, Andrew J ^a,c   Chu, Jianlin ^a,b,c   Snow, Jonathan W ^a,b,c   Fujiwara, Yuko ^a,b,c,d   Kim, Chul Geun ^e   Cantor, Alan B ^a,c   Orkin, Stuart H ^a,b,c,d  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD STEM CELL INSTITUTE   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^e Hanyang University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CORE PROTEIN; DNA; MYC PROTEIN; POLYCOMB GROUP PROTEIN; PROTEIN; HISTONE; HISTONE ACETYLTRANSFERASE; TRANSCRIPTION FACTOR;

ANIMAL CELL; ARTICLE; CANCER CELL; CANCER STEM CELL; CELL TYPE; COMPLEX FORMATION; CONTROLLED STUDY; DNA PROTEIN COMPLEX; EMBRYONIC STEM CELL; GENE REGULATORY NETWORK; HUMAN; HUMAN CELL; HYPOTHESIS; NEOPLASM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; TRANSCRIPTION REGULATION; ACETYLATION; ANIMAL; CELL LINE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOUSE; PLURIPOTENT STEM CELL;

ACETYLATION; ANIMALS; CELL LINE; EMBRYONIC STEM CELLS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HISTONE ACETYLTRANSFERASES; HISTONES; HUMANS; INDUCED PLURIPOTENT STEM CELLS; MICE; NEOPLASMS; PROTO-ONCOGENE PROTEINS C-MYC; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 77957757417     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2010.09.010     Document Type: Article

References (52)

1. Ard P.G., Chatterjee C., Kunjibettu S., Adside L.R., Gralinski L.E., McMahon S.B. Transcriptional regulation of the mdm2 oncogene by p53 requires TRRAP acetyltransferase complexes. Mol. Cell. Biol. 2002, 22:5650-5661.
2. Ben-Porath I., Thomson M.W., Carey V.J., Ge R., Bell G.W., Regev A., Weinberg R.A. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat. Genet. 2008, 40:499-507.
3. Bild A.H., Yao G., Chang J.T., Wang Q., Potti A., Chasse D., Joshi M.B., Harpole D., Lancaster J.M., Berchuck A., et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2006, 439:353-357.
4. Boyer L.A., Lee T.I., Cole M.F., Johnstone S.E., Levine S.S., Zucker J.P., Guenther M.G., Kumar R.M., Murray H.L., Jenner R.G., et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005, 122:947-956.
5. Boyer L.A., Plath K., Zeitlinger J., Brambrink T., Medeiros L.A., Lee T.I., Levine S.S., Wernig M., Tajonar A., Ray M.K., et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 2006, 441:349-353.
6. Cai Y., Jin J., Tomomori-Sato C., Sato S., Sorokina I., Parmely T.J., Conaway R.C., Conaway J.W. Identification of new subunits of the multiprotein mammalian TRRAP/TIP60-containing histone acetyltransferase complex. J. Biol. Chem. 2003, 278:42733-42736.
7. Chen X., Xu H., Yuan P., Fang F., Huss M., Vega V.B., Wong E., Orlov Y.L., Zhang W., Jiang J., et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-1117.
8. Clarke M.F., Fuller M. Stem cells and cancer: two faces of eve. Cell 2006, 124:1111-1115.
9. Cole M.D., Henriksson M. 25 years of the c-Myc oncogene. Semin. Cancer Biol. 2006, 16:241.
10. de Boer E., Rodriguez P., Bonte E., Krijgsveld J., Katsantoni E., Heck A., Grosveld F., Strouboulis J. Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc. Natl. Acad. Sci. USA 2003, 100:7480-7485.
11. Dennis G., Sherman B.T., Hosack D.A., Yang J., Gao W., Lane H.C., Lempicki R.A. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. 2003, 4:3.
12. Ding L., Paszkowski-Rogacz M., Nitzsche A., Slabicki M.M., Heninger A.K., de Vries I., Kittler R., Junqueira M., Shevchenko A., Schulz H., et al. A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Cell Stem Cell 2009, 4:403-415.
13. Doyon Y., Côté J. The highly conserved and multifunctional NuA4 HAT complex. Curr. Opin. Genet. Dev. 2004, 14:147-154.
14. Fazzio T.G., Huff J.T., Panning B. An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identity. Cell 2008, 134:162-174.
15. Frank S.R., Parisi T., Taubert S., Fernandez P., Fuchs M., Chan H.M., Livingston D.M., Amati B. MYC recruits the TIP60 histone acetyltransferase complex to chromatin. EMBO Rep. 2003, 4:575-580.
16. Frank S.R., Schroeder M., Fernandez P., Taubert S., Amati B. Binding of c-Myc to chromatin mediates mitogen-induced acetylation of histone H4 and gene activation. Genes Dev. 2001, 15:2069-2082.
17. Fuchs M., Gerber J., Drapkin R., Sif S., Ikura T., Ogryzko V., Lane W.S., Nakatani Y., Livingston D.M. The p400 complex is an essential E1A transformation target. Cell 2001, 106:297-307.
18. Graf T., Enver T. Forcing cells to change lineages. Nature 2009, 462:587-594.
19. Hu G., Kim J., Xu Q., Leng Y., Orkin S.H., Elledge S.J. A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev. 2009, 23:837-848.
20. Huangfu D., Maehr R., Guo W., Eijkelenboom A., Snitow M., Chen A.E., Melton D.A. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat. Biotechnol. 2008, 26:795-797.
21. Ikura T., Ogryzko V.V., Grigoriev M., Groisman R., Wang J., Horikoshi M., Scully R., Qin J., Nakatani Y. Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 2000, 102:463-473.
22. Kang J., Shakya A., Tantin D. Stem cells, stress, metabolism and cancer: a drama in two Octs. Trends Biochem. Sci. 2009, 34:491-499.
23. Kim J., Cantor A.B., Orkin S.H., Wang J. Use of in vivo biotinylation to study protein-protein and protein-DNA interactions in mouse embryonic stem cells. Nat. Protoc. 2009, 4:506-517.
24. Kim J., Chu J., Shen X., Wang J., Orkin S.H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 2008, 132:1049-1061.
25. Krivtsov A.V., Twomey D., Feng Z., Stubbs M.C., Wang Y., Faber J., Levine J.E., Wang J., Hahn W.C., Gilliland D.G., et al. Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature 2006, 442:818-822.
26. Lee T.I., Jenner R.G., Boyer L.A., Guenther M.G., Levine S.S., Kumar R.M., Chevalier B., Johnstone S.E., Cole M.F., Isono K., et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006, 125:301-313.
27. Loh Y.H., Wu Q., Chew J.L., Vega V.B., Zhang W., Chen X., Bourque G., George J., Leong B., Liu J., et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet. 2006, 38:431-440.
28. Maherali N., Sridharan R., Xie W., Utikal J., Eminli S., Arnold K., Stadtfeld M., Yachechko R., Tchieu J., Jaenisch R., et al. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell 2007, 1:55-70.
29. Marson A., Levine S.S., Cole M.F., Frampton G.M., Brambrink T., Johnstone S., Guenther M.G., Johnston W.K., Wernig M., Newman J., et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008, 134:521-533.
30. McMahon S.B., Van Buskirk H.A., Dugan K.A., Copeland T.D., Cole M.D. The novel ATM-related protein TRRAP is an essential cofactor for the c-Myc and E2F oncoproteins. Cell 1998, 94:363-374.
31. McMahon S.B., Wood M.A., Cole M.D. The essential cofactor TRRAP recruits the histone acetyltransferase hGCN5 to c-Myc. Mol. Cell. Biol. 2000, 20:556-562.
32. Melton C., Judson R.L., Blelloch R. Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature 2010, 463:621-626.
33. Meshorer E., Yellajoshula D., George E., Scambler P.J., Brown D.T., Misteli T. Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev. Cell 2006, 10:105-116.
34. Niwa H., Burdon T., Chambers I., Smith A. Self-renewal of pluripotent embryonic stem cells is mediated via activation of STAT3. Genes Dev. 1998, 12:2048-2060.
35. Ogata H., Goto S., Sato K., Fujibuchi W., Bono H., Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999, 27:29-34.
36. Park I.H., Zhao R., West J.A., Yabuuchi A., Huo H., Ince T.A., Lerou P.H., Lensch M.W., Daley G.Q. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 2008, 451:141-146.
37. Reya T., Morrison S.J., Clarke M.F., Weissman I.L. Stem cells, cancer, and cancer stem cells. Nature 2001, 414:105-111.
38. Sanchez-Carbayo M., Socci N.D., Lozano J., Saint F., Cordon-Cardo C. Defining molecular profiles of poor outcome in patients with invasive bladder cancer using oligonucleotide microarrays. J. Clin. Oncol. 2006, 24:778-789.
39. Sato N., Meijer L., Skaltsounis L., Greengard P., Brivanlou A.H. Maintenance of pluripotency in human and mouse embryonic stem cells through activation of Wnt signaling by a pharmacological GSK-3-specific inhibitor. Nat. Med. 2004, 10:55-63.
40. Schoenhals M., Kassambara A., De Vos J., Hose D., Moreaux J., Klein B. Embryonic stem cell markers expression in cancers. Biochem. Biophys. Res. Commun. 2009, 383:157-162.
41. Shen X., Liu Y., Hsu Y.J., Fujiwara Y., Kim J., Mao X., Yuan G.C., Orkin S.H. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol. Cell 2008, 32:491-502.
42. Somervaille T.C., Matheny C.J., Spencer G.J., Iwasaki M., Rinn J.L., Witten D.M., Chang H.Y., Shurtleff S.A., Downing J.R., Cleary M.L. Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells. Cell Stem Cell 2009, 4:129-140.
43. Sridharan R., Tchieu J., Mason M.J., Yachechko R., Kuoy E., Horvath S., Zhou Q., Plath K. Role of the murine reprogramming factors in the induction of pluripotency. Cell 2009, 136:364-377.
44. Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., Paulovich A., Pomeroy S.L., Golub T.R., Lander E.S., Mesirov J.P. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 2005, 102:15545-15550.
45. Takahashi K., Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126:663-676.
46. van't Veer L.J., Dai H., van de Vijver M.J., He Y.D., Hart A.A., Mao M., Peterse H.L., van der Kooy K., Marton M.J., Witteveen A.T., et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536.
47. Wang J., Rao S., Chu J., Shen X., Levasseur D.N., Theunissen T.W., Orkin S.H. A protein interaction network for pluripotency of embryonic stem cells. Nature 2006, 444:364-368.
48. Wolfer A., Wittner B.S., Irimia D., Flavin R.J., Lupien M., Gunawardane R.N., Meyer C.A., Lightcap E.S., Tamayo P., Mesirov J.P., et al. MYC regulation of a " poor-prognosis" metastatic cancer cell state. Proc. Natl. Acad. Sci. USA 2010, 107:3698-3703.
49. Wong D.J., Liu H., Ridky T.W., Cassarino D., Segal E., Chang H.Y. Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell 2008, 2:333-344.
50. Wong D.J., Segal E., Chang H.Y. Stemness, cancer and cancer stem cells. Cell Cycle 2008, 7:3622-3624.
51. Xu X., Bieda M., Jin V.X., Rabinovich A., Oberley M.J., Green R., Farnham P.J. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res. 2007, 17:1550-1561.
52. Yu J., Vodyanik M.A., Smuga-Otto K., Antosiewicz-Bourget J., Frane J.L., Tian S., Nie J., Jonsdottir G.A., Ruotti V., Stewart R., et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 2007, 318:1917-1920.