Transcriptional Amplification in Tumor Cells with Elevated c-Myc

Cell - Tập 151 - Trang 56-67 - 2012
Charles Y. Lin1,2, Jakob Lovén1, Peter B. Rahl1, Ronald M. Paranal3, Christopher B. Burge4, James E. Bradner3,5, Tong Ihn Lee1, Richard A. Young1,4
1Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142 USA
2Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
3Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
4Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
5Department of Medicine, Harvard Medical School 25 Shattuck Street, Boston, MA 02115, USA

Tài liệu tham khảo

Amati, 1998, Myc and the cell cycle, Front. Biosci., 3, d250, 10.2741/A239 Amati, 2001, Function of the c-Myc oncoprotein in chromatin remodeling and transcription, Biochim. Biophys. Acta, 1471, M135 Arabi, 2005, c-Myc associates with ribosomal DNA and activates RNA polymerase I transcription, Nat. Cell Biol., 7, 303, 10.1038/ncb1225 Beroukhim, 2010, The landscape of somatic copy-number alteration across human cancers, Nature, 463, 899, 10.1038/nature08822 Blackwood, 1991, Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc, Science, 251, 1211, 10.1126/science.2006410 Blackwood, 1992, Myc and Max associate in vivo, Genes Dev., 6, 71, 10.1101/gad.6.1.71 Bouchard, 2004, Myc-induced proliferation and transformation require Akt-mediated phosphorylation of FoxO proteins, EMBO J., 23, 2830, 10.1038/sj.emboj.7600279 Brès, 2009, SKIP interacts with c-Myc and Menin to promote HIV-1 Tat transactivation, Mol. Cell, 36, 75, 10.1016/j.molcel.2009.08.015 Bulger, 2011, Functional and mechanistic diversity of distal transcription enhancers, Cell, 144, 327, 10.1016/j.cell.2011.01.024 Campbell, 2008, Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing, Nat. Genet., 40, 722, 10.1038/ng.128 Chandriani, 2009, A core MYC gene expression signature is prominent in basal-like breast cancer but only partially overlaps the core serum response, PLoS ONE, 4, e6693, 10.1371/journal.pone.0006693 Chen, 2008, Integration of external signaling pathways with the core transcriptional network in embryonic stem cells, Cell, 133, 1106, 10.1016/j.cell.2008.04.043 Cole, 2008, Transcription-independent functions of MYC: regulation of translation and DNA replication, Nat. Rev. Mol. Cell Biol., 9, 810, 10.1038/nrm2467 Cowling, 2010, Myc Regulation of mRNA Cap Methylation, Genes Cancer, 1, 576, 10.1177/1947601910378025 Dai, 2008, Crosstalk between c-Myc and ribosome in ribosomal biogenesis and cancer, J. Cell. Biochem., 105, 670, 10.1002/jcb.21895 Dang, 2010, Rethinking the Warburg effect with Myc micromanaging glutamine metabolism, Cancer Res., 70, 859, 10.1158/0008-5472.CAN-09-3556 Dang, 2012, MYC on the path to cancer, Cell, 149, 22, 10.1016/j.cell.2012.03.003 Dang, 2006, The c-Myc target gene network, Semin. Cancer Biol., 16, 253, 10.1016/j.semcancer.2006.07.014 Eberhardy, 2001, c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism, J. Biol. Chem., 276, 48562, 10.1074/jbc.M109014200 Eberhardy, 2002, Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter, J. Biol. Chem., 277, 40156, 10.1074/jbc.M207441200 Ecevit, 2010, Kinetic analysis of the interaction of b/HLH/Z transcription factors Myc, Max, and Mad with cognate DNA, Biochemistry, 49, 2627, 10.1021/bi901913a Eilers, 2008, Myc’s broad reach, Genes Dev., 22, 2755, 10.1101/gad.1712408 Facchini, 1998, The molecular role of Myc in growth and transformation: recent discoveries lead to new insights, FASEB J., 12, 633, 10.1096/fasebj.12.9.633 Farina, 2004, Reconstitution of an E box-binding Myc:Max complex with recombinant full-length proteins expressed in Escherichia coli, Protein Expr. Purif., 34, 215, 10.1016/j.pep.2003.11.021 Felsher, 1999, Reversible tumorigenesis by MYC in hematopoietic lineages, Mol. Cell, 4, 199, 10.1016/S1097-2765(00)80367-6 Fernandez, 2003, Genomic targets of the human c-Myc protein, Genes Dev., 17, 1115, 10.1101/gad.1067003 Flores, 2004, Defining the temporal requirements for Myc in the progression and maintenance of skin neoplasia, Oncogene, 23, 5923, 10.1038/sj.onc.1207796 Gallant, 2005, Myc, cell competition, and compensatory proliferation, Cancer Res., 65, 6485, 10.1158/0008-5472.CAN-05-1101 Gargano, 2007, P-TEFb is a crucial co-factor for Myc transactivation, Cell Cycle, 6, 2031, 10.4161/cc.6.16.4554 Geiss, 2008, Direct multiplexed measurement of gene expression with color-coded probe pairs, Nat. Biotechnol., 26, 317, 10.1038/nbt1385 Gomez-Roman, 2003, Direct activation of RNA polymerase III transcription by c-Myc, Nature, 421, 290, 10.1038/nature01327 Göndör, 2009, Chromosome crosstalk in three dimensions, Nature, 461, 212, 10.1038/nature08453 Graf, 2009, Forcing cells to change lineages, Nature, 462, 587, 10.1038/nature08533 Grandori, 2005, c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I, Nat. Cell Biol., 7, 311, 10.1038/ncb1224 Guccione, 2006, Myc-binding-site recognition in the human genome is determined by chromatin context, Nat. Cell Biol., 8, 764, 10.1038/ncb1434 Hanahan, 2011, Hallmarks of cancer: the next generation, Cell, 144, 646, 10.1016/j.cell.2011.02.013 Herold, 2009, Facilitating replication under stress: an oncogenic function of MYC?, Nat. Rev. Cancer, 9, 441, 10.1038/nrc2640 Hirvonen, 1994, Differential expression of myc, max and RB1 genes in human gliomas and glioma cell lines, Br. J. Cancer, 69, 16, 10.1038/bjc.1994.3 Hoffman, 2008, Apoptotic signaling by c-MYC, Oncogene, 27, 6462, 10.1038/onc.2008.312 Hurlin, 2004, Functions of myc:max in the control of cell proliferation and tumorigenesis, Int. Rev. Cytol., 238, 183, 10.1016/S0074-7696(04)38004-6 Jain, 2002, Sustained loss of a neoplastic phenotype by brief inactivation of MYC, Science, 297, 102, 10.1126/science.1071489 Ji, 2011, Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation, PLoS ONE, 6, e26057, 10.1371/journal.pone.0026057 Johnson, 1987, myc family oncogene amplification in tumor cell lines established from small cell lung cancer patients and its relationship to clinical status and course, J. Clin. Invest., 79, 1629, 10.1172/JCI112999 Kagey, 2010, Mediator and cohesin connect gene expression and chromatin architecture, Nature, 467, 430, 10.1038/nature09380 Kanazawa, 2003, c-Myc recruits P-TEFb for transcription, cellular proliferation and apoptosis, Oncogene, 22, 5707, 10.1038/sj.onc.1206800 Kidder, 2008, Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells, PLoS ONE, 3, e3932, 10.1371/journal.pone.0003932 Kim, 2006, Combined microarray analysis of small cell lung cancer reveals altered apoptotic balance and distinct expression signatures of MYC family gene amplification, Oncogene, 25, 130, 10.1038/sj.onc.1208997 Kuttler, 2006, c-Myc, Genomic Instability and Disease, Genome Dyn., 1, 171, 10.1159/000092507 Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25 Li, 2003, A global transcriptional regulatory role for c-Myc in Burkitt’s lymphoma cells, Proc. Natl. Acad. Sci. USA, 100, 8164, 10.1073/pnas.1332764100 Lin, 2009, c-Myc and eIF4F constitute a feedforward loop that regulates cell growth: implications for anticancer therapy, Cancer Res., 69, 7491, 10.1158/0008-5472.CAN-09-0813 Little, 1983, Amplification and expression of the c-myc oncogene in human lung cancer cell lines, Nature, 306, 194, 10.1038/306194a0 Meyer, 2008, Reflecting on 25 years with MYC, Nat. Rev. Cancer, 8, 976, 10.1038/nrc2231 Nesbit, 1999, MYC oncogenes and human neoplastic disease, Oncogene, 18, 3004, 10.1038/sj.onc.1202746 Nie, 2012, c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells, Cell, 151, 68, 10.1016/j.cell.2012.08.033 Nieminen, 2007, c-Myc blazing a trail of death: coupling of the mitochondrial and death receptor apoptosis pathways by c-Myc, Cell Cycle, 6, 2464, 10.4161/cc.6.20.4917 Nilsson, 2003, Myc pathways provoking cell suicide and cancer, Oncogene, 22, 9007, 10.1038/sj.onc.1207261 Ong, 2011, Enhancer function: new insights into the regulation of tissue-specific gene expression, Nat. Rev. Genet., 12, 283, 10.1038/nrg2957 Pajic, 2000, Cell cycle activation by c-myc in a burkitt lymphoma model cell line, Int. J. Cancer, 87, 787, 10.1002/1097-0215(20000915)87:6<787::AID-IJC4>3.0.CO;2-6 Pelengaris, 1999, Reversible activation of c-Myc in skin: induction of a complex neoplastic phenotype by a single oncogenic lesion, Mol. Cell, 3, 565, 10.1016/S1097-2765(00)80350-0 Peterson, 2011, An extended Myc network contributes to glucose homeostasis in cancer and diabetes, Front. Biosci., 16, 2206, 10.2741/3848 Pomerantz, 2009, The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer, Nat. Genet., 41, 882, 10.1038/ng.403 Prendergast, 1991, Association of Myn, the murine homolog of max, with c-Myc stimulates methylation-sensitive DNA binding and ras cotransformation, Cell, 65, 395, 10.1016/0092-8674(91)90457-A Prochownik, 2008, c-Myc: linking transformation and genomic instability, Curr. Mol. Med., 8, 446, 10.2174/156652408785747988 Rahl, 2010, c-Myc regulates transcriptional pause release, Cell, 141, 432, 10.1016/j.cell.2010.03.030 Rudolph, 1999, Determination of copy number of c-Myc protein per cell by quantitative Western blotting, Anal. Biochem., 269, 66, 10.1006/abio.1999.3095 Ruggero, 2009, The role of Myc-induced protein synthesis in cancer, Cancer Res., 69, 8839, 10.1158/0008-5472.CAN-09-1970 Schlosser, 2005, Dissection of transcriptional programmes in response to serum and c-Myc in a human B-cell line, Oncogene, 24, 520, 10.1038/sj.onc.1208198 Schuhmacher, 1999, Control of cell growth by c-Myc in the absence of cell division, Curr. Biol., 9, 1255, 10.1016/S0960-9822(99)80507-7 Schuhmacher, 2001, The transcriptional program of a human B cell line in response to Myc, Nucleic Acids Res., 29, 397, 10.1093/nar/29.2.397 Secombe, 2004, Myc: a weapon of mass destruction, Cell, 117, 153, 10.1016/S0092-8674(04)00336-8 Shchors, 2007, Tumor angiogenesis: cause or consequence of cancer?, Cancer Res., 67, 7059, 10.1158/0008-5472.CAN-07-2053 Shou, 2000, Diverse karyotypic abnormalities of the c-myc locus associated with c-myc dysregulation and tumor progression in multiple myeloma, Proc. Natl. Acad. Sci. USA, 97, 228, 10.1073/pnas.97.1.228 Singh, 2009, The cell cycle and Myc intersect with mechanisms that regulate pluripotency and reprogramming, Cell Stem Cell, 5, 141, 10.1016/j.stem.2009.07.003 Sodir, 2011, Endogenous Myc maintains the tumor microenvironment, Genes Dev., 25, 907, 10.1101/gad.2038411 Soucek, 2008, Modelling Myc inhibition as a cancer therapy, Nature, 455, 679, 10.1038/nature07260 van Riggelen, 2010, MYC as a regulator of ribosome biogenesis and protein synthesis, Nat. Rev. Cancer, 10, 301, 10.1038/nrc2819 Verbeek, 1991, Mice bearing the E mu-myc and E mu-pim-1 transgenes develop pre-B-cell leukemia prenatally, Mol. Cell. Biol., 11, 1176 Wright, 2010, Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells, Mol. Cell. Biol., 30, 1411, 10.1128/MCB.01384-09 Zeller, 2003, An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets, Genome Biol., 4, R69, 10.1186/gb-2003-4-10-r69 Zeller, 2006, Global mapping of c-Myc binding sites and target gene networks in human B cells, Proc. Natl. Acad. Sci. USA, 103, 17834, 10.1073/pnas.0604129103 Zhang, 2008, Model-based analysis of ChIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137 Zhou, 2012, RNA polymerase II elongation control, Annu. Rev. Biochem., 81, 119, 10.1146/annurev-biochem-052610-095910 Bailey, T.L., and Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36. Core, L.J., and Lis, J.T. (2008). Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 319, 1791–1792. Core, L.J., Waterfall, J.J., and Lis, J.T. (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845–1848. Creyghton, M.P., Cheng, A.W., Welstead, G.G., Kooistra, T., Carey, B.W., Steine, E.J., Hanna, J., Lodato, M.A., Frampton, G.M., Sharp, P.A., et al. (2010). Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. USA 107, 21931–21936. Delmore, J.E., Issa, G.C., Lemieux, M.E., Rahl, P.B., Shi, J., Jacobs, H.M., Kastritis, E., Gilpatrick, T., Paranal, R.M., Qi, J., et al. (2011). BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146, 904–917. Ecevit, O., Khan, M.A., and Goss, D.J. (2010). Kinetic analysis of the interaction of b/HLH/Z transcription factors Myc, Max, and Mad with cognate DNA. Biochemistry 49, 2627–2635. Farina, A., Faiola, F., and Martinez, E. (2004). Reconstitution of an E box-binding Myc:Max complex with recombinant full-length proteins expressed in Escherichia coli. Protein Expr. Purif. 34, 215–222. Guenther, M.G., Levine, S.S., Boyer, L.A., Jaenisch, R., and Young, R.A. (2007). A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88. Kagey, M.H., Newman, J.J., Bilodeau, S., Zhan, Y., Orlando, D.A., van Berkum, N.L., Ebmeier, C.C., Goossens, J., Rahl, P.B., Levine, S.S., et al. (2010). Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430–435. Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25. Mourelatos, Z., Dostie, J., Paushkin, S., Sharma, A., Charroux, B., Abel, L., Rappsilber, J., Mann, M., and Dreyfuss, G. (2002). miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 16, 720–728. Pasquinelli, A.E., Reinhart, B.J., Slack, F., Martindale, M.Q., Kuroda, M.I., Maller, B., Hayward, D.C., Ball, E.E., Degnan, B., Müller, P., et al. (2000). Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408, 86–89. Pruitt, K.D., Tatusova, T., and Maglott, D.R. (2007). NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35 (Database issue), D61–D65. Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S.A., Flynn, R.A., and Wysocka, J. (2011). A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283. Rahl, P.B., Lin, C.Y., Seila, A.C., Flynn, R.A., McCuine, S., Burge, C.B., Sharp, P.A., and Young, R.A. (2010). c-Myc regulates transcriptional pause release. Cell 141, 432–445. Rudolph, C., Adam, G., and Simm, A. (1999). Determination of copy number of c-Myc protein per cell by quantitative Western blotting. Anal. Biochem. 269, 66–71. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., and Liu, X.S. (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137.