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Research Papers

DNA methylation reprogramming of human cancer cells by expression of a plant 5-methylcytosine DNA glycosylase

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Pages 95-107 | Received 11 Oct 2017, Accepted 29 Nov 2017, Published online: 07 Feb 2018

References

  • Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010;11:204–220. doi:10.1038/nrg2719. PMID:20142834
  • Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet. 2013;14:204–220. doi:10.1038/nrg3354. PMID:23400093
  • Rodriguez-Cortez VC, Hernando H, de la Rica L, et al. Epigenomic deregulation in the immune system. Epigenomics. 2011;3:697–713. doi:10.2217/epi.11.99. PMID:22126290
  • Robertson KD. DNA methylation and human disease. Nat Rev Genet. 2005;6:597–610. doi:10.1038/nrg1655. PMID:16136652
  • Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet. 2007;8:286–298. doi:10.1038/nrg2005. PMID:17339880
  • Sandoval J, Esteller M. Cancer epigenomics: beyond genomics. Curr Opin Genet Dev. 2012;22:50–55. doi:10.1016/j.gde.2012.02.008. PMID:22402447
  • Baylin SB, Jones PA. Epigenetic determinants of cancer. Cold Spring Harbor Symp Quant Biol. 2016;8.
  • Issa JP, Kantarjian HM. Targeting DNA methylation. Clin Cancer Res. 2009;15:3938–3946. doi:10.1158/1078-0432.CCR-08-2783. PMID:19509174
  • Bell JS, Kagey JD, Barwick BG, et al. Factors affecting the persistence of drug-induced reprogramming of the cancer methylome. Epigenetics. 2016;11:273–287. doi:10.1080/15592294.2016.1158364. PMID:27082926
  • Tahiliani M, Koh KP, Shen Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009;324:930–935. doi:10.1126/science.1170116. PMID:19372391
  • Ito S, Shen L, Dai Q, et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. 2011;333:1300–1303. doi:10.1126/science.1210597. PMID:21778364
  • Wu H, Zhang Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell. 2014;156:45–68. doi:10.1016/j.cell.2013.12.019. PMID:24439369
  • Kohli RM, Zhang Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature. 2013;502:472–479. doi:10.1038/nature12750. PMID:24153300
  • Pastor WA, Aravind L, Rao A. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol. 2013;14:341–356. doi:10.1038/nrm3589. PMID:23698584
  • Spruijt CG, Gnerlich F, Smits AH, et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell. 2013;152:1146–1159. doi:10.1016/j.cell.2013.02.004. PMID:23434322
  • Hashimoto H, Olanrewaju YO, Zheng Y, et al. Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence. Genes Dev. 2014;28:2304–2313. doi:10.1101/gad.250746.114. PMID:25258363
  • Wang D, Hashimoto H, Zhang X, et al. MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma. Nucleic Acids Res. 2017;45:2396–2407. doi:10.1093/nar/gkw1184. PMID:27903915
  • Choi Y, Gehring M, Johnson L, et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell. 2002;110:33–42. doi:10.1016/S0092-8674(02)00807-3. PMID:12150995
  • Gong Z, Morales-Ruiz T, Ariza RR, et al. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell. 2002;111:803–814. doi:10.1016/S0092-8674(02)01133-9. PMID:12526807
  • Morales-Ruiz T, Ortega-Galisteo AP, Ponferrada-Marin MI, et al. DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc Natl Acad Sci USA. 2006;103:6853–6858. doi:10.1073/pnas.0601109103. PMID:16624880
  • Gehring M, Huh JH, Hsieh TF, et al. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell. 2006;124:495–506. doi:10.1016/j.cell.2005.12.034. PMID:16469697
  • Penterman J, Zilberman D, Huh JH, et al. DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA. 2007;104:6752–6757. doi:10.1073/pnas.0701861104. PMID:17409185
  • Ortega-Galisteo AP, Morales-Ruiz T, Ariza RR, et al. Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. Plant Mol Biol. 2008;67:671–681. doi:10.1007/s11103-008-9346-0. PMID:18493721
  • Parrilla-Doblas JT, Ariza RR, Roldan-Arjona T. Targeted DNA demethylation in human cells by fusion of a plant 5-methylcytosine DNA glycosylase to a sequence-specific DNA binding domain. Epigenetics. 2017;12:296–303. doi:10.1080/15592294.2017.1294306. PMID:28277978
  • Lara E, Calvanese V, Huidobro C, et al. Epigenetic repression of ROR2 has a Wnt-mediated, pro-tumourigenic role in colon cancer. Mol Cancer. 2010;9:170. doi:10.1186/1476-4598-9-170. PMID:20591152
  • Esteller M, Tortola S, Toyota M, et al. Hypermethylation-associated inactivation of p14(ARF) is independent of p16(INK4a) methylation and p53 mutational status. Cancer Res. 2000;60:129–133. PMID:10646864
  • Merlo A, Herman JG, Mao L, et al. 5' CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers. Nat Med. 1995;1:686–692. doi:10.1038/nm0795-686. PMID:7585152
  • Wiederhold L, Leppard JB, Kedar P, et al. AP endonuclease-independent DNA base excision repair in human cells. Mol Cell. 2004;15:209–220. doi:10.1016/j.molcel.2004.06.003. PMID:15260972
  • Noren Hooten N, Fitzpatrick M, Kompaniez K, et al. Coordination of DNA repair by NEIL1 and PARP-1: a possible link to aging. Aging. 2012;4:674–685. doi:10.18632/aging.100492. PMID:23104860
  • Huidobro C, Urdinguio RG, Rodriguez RM, et al. A DNA methylation signature associated with aberrant promoter DNA hypermethylation of DNMT3B in human colorectal cancer. Eur J Cancer. 2012;48:2270–2281. doi:10.1016/j.ejca.2011.12.019. PMID:22244828
  • Urdinguio RG, Fernandez AF, Moncada-Pazos A, et al. Immune-dependent and independent antitumor activity of GM-CSF aberrantly expressed by mouse and human colorectal tumors. Cancer Res. 2013;73:395–405. doi:10.1158/0008-5472.CAN-12-0806. PMID:23108143
  • Rodriguez RM, Huidobro C, Urdinguio RG, et al. Aberrant epigenetic regulation of bromodomain BRD4 in human colon cancer. J Mol Med (Berl). 2012;90:587–595. doi:10.1007/s00109-011-0837-0. PMID:22120039
  • Gu Y, Rosenblatt J, Morgan DO. Cell cycle regulation of CDK2 activity by phosphorylation of Thr160 and Tyr15. EMBO J. 1992;11:3995–4005. PMID:1396589
  • Visvader JE.. Cells of origin in cancer. Nature. 2011;469:314–322. doi:10.1038/nature09781. PMID:21248838
  • Visvader JE, Lindeman GJ. Cancer stem cells: current status and evolving complexities. Cell Stem Cell. 2012;10:717–728. doi:10.1016/j.stem.2012.05.007. PMID:22704512
  • Shaheen S, Ahmed M, Lorenzi F, et al. Spheroid-Formation (Colonosphere) Assay for in Vitro Assessment and Expansion of Stem Cells in Colon Cancer. Stem Cell Rev. 2016;12:492–499. doi:10.1007/s12015-016-9664-6. PMID:27207017
  • Jin C, Lu Y, Jelinek J, et al. TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells. Nucleic Acids Res. 2014;42:6956–6971. doi:10.1093/nar/gku372. PMID:24875481
  • Kong L, Tan L, Lv R, et al. A primary role of TET proteins in establishment and maintenance of De Novo bivalency at CpG islands. Nucleic Acids Res. 2016;44:8682–8692. doi:10.1093/nar/gkw529. PMID:27288448
  • Yang X, Han H, De Carvalho DD, et al. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell. 2014;26:577–590. doi:10.1016/j.ccr.2014.07.028. PMID:25263941
  • Berman BP, Weisenberger DJ, Aman JF, et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet. 2011;44:40–46. doi:10.1038/ng.969. PMID:22120008
  • Sandoval J, Heyn H, Moran S, et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics. 2011;6:692–702. doi:10.4161/epi.6.6.16196. PMID:21593595
  • Miyoshi N, Ishii H, Nagai K, et al. Defined factors induce reprogramming of gastrointestinal cancer cells. Proc Natl Acad Sci U S A. 2010;107:40–45. doi:10.1073/pnas.0912407107. PMID:20018687
  • Morita R, Hirohashi Y, Suzuki H, et al. DNA methyltransferase 1 is essential for initiation of the colon cancers. Exp Mol Pathol. 2013;94:322–329. doi:10.1016/j.yexmp.2012.10.004. PMID:23064049
  • Neri F, Dettori D, Incarnato D, et al. TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway. Oncogene. 2015;34:4168–4176. doi:10.1038/onc.2014.356. PMID:25362856
  • Ford CE, Qian Ma SS, Quadir A, et al. The dual role of the novel Wnt receptor tyrosine kinase, ROR2, in human carcinogenesis. Int J Cancer. 2013;133:779–787. doi:10.1002/ijc.27984. PMID:23233346
  • Ying Y, Tao Q. Epigenetic disruption of the WNT/beta-catenin signaling pathway in human cancers. Epigenetics. 2009;4:307–312. doi:10.4161/epi.4.5.9371.
  • Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT Method. Methods. 2001;25:402–408. doi:10.1006/meth.2001.1262. PMID:11846609
  • Le T, Kim KP, Fan G, et al. A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal Biochem. 2011;412:203–209. doi:10.1016/j.ab.2011.01.026. PMID:21272560
  • Maksimovic J, Gordon L, Oshlack A. SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol. 2012;13:R44. doi:10.1186/gb-2012-13-6-r44. PMID:22703947
  • Lopez-Sanchez LM, Jimenez C, Valverde A, et al. CoCl2, a mimic of hypoxia, induces formation of polyploid giant cells with stem characteristics in colon cancer. PLoS One. 2014;9:e99143. doi:10.1371/journal.pone.0099143. PMID:24932611

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