title: Interplay between the cancer genome and epigenome.
abstract: Cancer arises as a consequence of cumulative disruptions to cellular growth control with Darwinian selection for those heritable changes that provide the greatest clonal advantage. These traits can be acquired and stably maintained by either genetic or epigenetic means. Here, we explore the ways in which alterations in the genome and epigenome influence each other and cooperate to promote oncogenic transformation. Disruption of epigenomic control is pervasive in malignancy and can be classified as an enabling characteristic of cancer cells, akin to genome instability and mutation.
authors.affiliation: USC Epigenome Center, University of Southern California, Room G511B, 1450 Biggy Street, Los Angeles, CA 90089-9061, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Shen
authors.forename: Peter W
authors.initials: PW
authors.lastname: Laird
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D019175:DNA Methylation; D047108:Embryonic Development; D044127:Epigenesis, Genetic; D006801:Humans; D009369:Neoplasms / Q000235:genetics*
references.citation: Oncogene. 2008 Apr 3;27(15):2237-42
references.pmid: 17934517
references.citation: Genome Res. 2010 Apr;20(4):440-6
references.pmid: 20219944
references.citation: Science. 2012 Sep 21;337(6101):1541-6
references.pmid: 22878500
references.citation: Nat Rev Cancer. 2011 Sep 23;11(10):726-34
references.pmid: 21941284
references.citation: Blood. 2012 Nov 1;120(18):e83-92
references.pmid: 22976956
references.citation: Adv Genet. 2010;70:309-23
references.pmid: 20920753
references.citation: Mol Cell. 2012 Mar 30;45(6):814-25
references.pmid: 22387027
references.citation: Nat Rev Cancer. 2006 Jan;6(1):38-51
references.pmid: 16397526
references.citation: Blood. 2009 Jul 2;114(1):144-7
references.pmid: 19420352
references.citation: Nature. 2012 Aug 23;488(7412):504-7
references.pmid: 22820252
references.citation: Nat Biotechnol. 2012 Mar 07;30(3):224-6
references.pmid: 22398613
references.citation: Nat Rev Genet. 2002 Jun;3(6):415-28
references.pmid: 12042769
references.citation: Cell. 2012 Aug 31;150(5):922-33
references.pmid: 22921915
references.citation: N Engl J Med. 2010 Oct 14;363(16):1532-43
references.pmid: 20942669
references.citation: Oncogene. 2009 Dec 17;28(50):4491-500
references.pmid: 19784073
references.citation: Genome Res. 2012 May;22(5):837-49
references.pmid: 22391556
references.citation: Nat Genet. 2013 Mar;45(3):295-8
references.pmid: 23377182
references.citation: Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6870-5
references.pmid: 9618505
references.citation: Nat Rev Genet. 2009 Nov;10(11):805-11
references.pmid: 19789556
references.citation: Cancer Cell. 2012 Nov 13;22(5):698-698.e1
references.pmid: 23153541
references.citation: Hum Mol Genet. 1999 Apr;8(4):661-6
references.pmid: 10072435
references.citation: J Neurooncol. 2013 Mar;112(1):67-72
references.pmid: 23354654
references.citation: Genome Res. 2012 Dec;22(12):2399-408
references.pmid: 23100115
references.citation: Cell. 2012 Jul 6;150(1):12-27
references.pmid: 22770212
references.citation: Nat Genet. 2000 Mar;24(3):300-3
references.pmid: 10700188
references.citation: PLoS Genet. 2012;8(12):e1003146
references.pmid: 23284304
references.citation: Cell. 2011 Dec 23;147(7):1628-39
references.pmid: 22196736
references.citation: PLoS One. 2009 Dec 21;4(12):e8357
references.pmid: 20027224
references.citation: Cancer Cell. 2008 Jul 8;14(1):36-46
references.pmid: 18598942
references.citation: J Biol Chem. 2000 Jan 28;275(4):2727-32
references.pmid: 10644736
references.citation: Nat Genet. 2005 Apr;37(4):391-400
references.pmid: 15765097
references.citation: PLoS Genet. 2012;8(5):e1002692
references.pmid: 22615578
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5521-6
references.pmid: 17376869
references.citation: Cell. 2011 Mar 4;144(5):646-74
references.pmid: 21376230
references.citation: Genes Chromosomes Cancer. 1998 May;22(1):26-36
references.pmid: 9591631
references.citation: Nucleic Acids Res. 2004 Feb 11;32(3):959-76
references.pmid: 14960713
references.citation: Nat Genet. 2009 Aug;41(8):941-5
references.pmid: 19633671
references.citation: Science. 2011 Aug 26;333(6046):1157-60
references.pmid: 21798893
references.citation: Science. 2012 Dec 14;338(6113):1435-9
references.pmid: 23239728
references.citation: Nat Rev Genet. 2010 Mar;11(3):191-203
references.pmid: 20125086
references.citation: Nature. 2011 Jul 27;476(7360):298-303
references.pmid: 21796119
references.citation: Nat Genet. 2011 Dec 04;44(1):23-31
references.pmid: 22138693
references.citation: Science. 2011 Mar 4;331(6021):1199-203
references.pmid: 21252315
references.citation: Cancer Cell. 2010 May 18;17(5):510-22
references.pmid: 20399149
references.citation: Cancer Res. 2000 May 1;60(9):2368-71
references.pmid: 10811111
references.citation: Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8681-6
references.pmid: 10411935
references.citation: Genome Biol. 2012 Oct 03;13(10):R84
references.pmid: 23034185
references.citation: Nat Genet. 1999 Feb;21(2):163-7
references.pmid: 9988266
references.citation: Nat Genet. 2003 Jun;34(2):145-7
references.pmid: 12730693
references.citation: N Engl J Med. 2000 Nov 9;343(19):1350-4
references.pmid: 11070098
references.citation: Proc Natl Acad Sci U S A. 2005 Jun 21;102(25):8905-9
references.pmid: 15956212
references.citation: Nucleic Acids Res. 1982 Apr 24;10(8):2709-21
references.pmid: 7079182
references.citation: Nature. 2011 Jun 29;474(7353):609-15
references.pmid: 21720365
references.citation: N Engl J Med. 2010 Dec 16;363(25):2424-33
references.pmid: 21067377
references.citation: Nat Genet. 2010 Aug;42(8):665-7
references.pmid: 20601954
references.citation: Nat Genet. 2009 Feb;41(2):178-186
references.pmid: 19151715
references.citation: Nat Cell Biol. 2010 Mar;12(3):235-46
references.pmid: 20173741
references.citation: Nucleic Acids Res. 2004 Oct 27;32(19):5742-9
references.pmid: 15509869
references.citation: Nat Rev Genet. 2012 Jan 31;13(3):153-62
references.pmid: 22290458
references.citation: Genome Res. 2013 Feb;23(2):270-80
references.pmid: 23124521
references.citation: N Engl J Med. 2012 Mar 8;366(10):883-892
references.pmid: 22397650
references.citation: N Engl J Med. 2005 Mar 10;352(10):997-1003
references.pmid: 15758010
references.citation: Nat Genet. 2008 Jul;40(7):904-8
references.pmid: 18568024
references.citation: N Engl J Med. 2012 Jan 5;366(1):95-6
references.pmid: 22216861
references.citation: Epigenetics. 2013 Jan;8(1):92-104
references.pmid: 23249680
references.citation: Am J Pathol. 2012 Nov;181(5):1847-61
references.pmid: 22995252
references.citation: Nat Genet. 2012 Dec;44(12):1321-5
references.pmid: 23143597
references.citation: EMBO Rep. 2011 Dec 23;13(1):28-35
references.pmid: 22157888
references.citation: Hum Mol Genet. 2011 Aug 15;20(16):3241-55
references.pmid: 21636528
references.citation: Nature. 2012 Oct 4;490(7418):61-70
references.pmid: 23000897
references.citation: Leukemia. 2012 Aug;26(8):1797-803
references.pmid: 22388726
references.citation: Nat Rev Cancer. 2011 Jun 09;11(7):481-92
references.pmid: 21654818
references.citation: PLoS Genet. 2011 Feb 03;7(2):e1001286
references.pmid: 21304883
references.citation: Nat Genet. 2007 Feb;39(2):237-42
references.pmid: 17211412
references.citation: Nat Rev Genet. 2013 Jan;14(1):62-75
references.pmid: 23247436
references.citation: PLoS Genet. 2011 Aug;7(8):e1002228
references.pmid: 21852959
references.citation: PLoS Genet. 2008 Oct;4(10):e1000242
references.pmid: 18974828
references.citation: Cancer Cell. 2003 Aug;4(2):121-31
references.pmid: 12957287
references.citation: Biochem Biophys Res Commun. 1982 Jul 16;107(1):19-26
references.pmid: 6289818
references.citation: Mol Cell. 2008 Jun 20;30(6):755-66
references.pmid: 18514006
references.citation: Cancer Res. 2001 Jun 15;61(12):4689-92
references.pmid: 11406538
references.citation: Nature. 2010 Dec 9;468(7325):839-43
references.pmid: 21057493
references.citation: Cell. 2006 Apr 21;125(2):315-26
references.pmid: 16630819
references.citation: Cell. 1999 Oct 29;99(3):247-57
references.pmid: 10555141
references.citation: Nature. 2012 Aug 2;488(7409):100-5
references.pmid: 22832583
references.citation: Nature. 1983 Jan 6;301(5895):89-92
references.pmid: 6185846
references.citation: Cell. 1995 Apr 21;81(2):197-205
references.pmid: 7537636
references.citation: Cell. 1985 Jan;40(1):91-9
references.pmid: 2981636
references.citation: Genome Res. 2012 Feb;22(2):271-82
references.pmid: 21659424
references.citation: Nat Genet. 2009 May;41(5):521-3
references.pmid: 19330029
references.citation: Hum Mol Genet. 2007 Apr 15;16 Spec No 1:R88-95
references.pmid: 17613553
references.citation: Cell. 2013 Feb 14;152(4):685-9
references.pmid: 23375745
references.citation: Nat Genet. 2011 Jul 31;43(9):830-7
references.pmid: 21804550
references.citation: Nat Genet. 2012 Jan 29;44(3):251-3
references.pmid: 22286216
references.citation: Cancer Cell. 2012 Oct 16;22(4):425-37
references.pmid: 23079654
references.citation: Nat Genet. 2011 Aug 28;43(10):1022-5
references.pmid: 21874000
references.citation: Nat Genet. 2010 Apr;42(4):338-42
references.pmid: 20228800
references.citation: Nat Genet. 2007 Feb;39(2):232-6
references.pmid: 17200670
references.citation: Nat Struct Mol Biol. 2011 Jul 03;18(8):950-5
references.pmid: 21725294
references.citation: Nat Cell Biol. 2006 Apr;8(4):416-24
references.pmid: 16565708
references.citation: Nature. 2006 Jul 20;442(7100):307-11
references.pmid: 16732293
references.citation: Cancer Cell. 2010 Dec 14;18(6):553-67
references.pmid: 21130701
references.citation: Blood. 2008 Mar 1;111(5):2505-15
references.pmid: 18299451
references.citation: Nature. 2012 Aug 2;488(7409):43-8
references.pmid: 22722829
references.citation: Nature. 2004 Jun 24;429(6994):891-5
references.pmid: 15215866
references.citation: Nature. 2012 Sep 6;489(7414):57-74
references.pmid: 22955616
references.citation: Science. 2012 Dec 14;338(6113):1465-9
references.pmid: 23239736
references.citation: Cell. 2012 Jun 22;149(7):1474-87
references.pmid: 22726435
references.citation: Nature. 1998 Jul 9;394(6689):203-6
references.pmid: 9671307
references.citation: Cancer Res. 2002 Jan 1;62(1):48-52
references.pmid: 11782357
references.citation: Nature. 2009 Nov 19;462(7271):315-22
references.pmid: 19829295
references.citation: Nat Rev Cancer. 2010 Oct;10(10):669-82
references.pmid: 20865010
references.citation: Cancer Cell. 2012 Jul 10;22(1):9-20
references.pmid: 22789535
references.citation: Cancer Res. 1986 Jun;46(6):2917-22
references.pmid: 3009002
references.citation: Cancer Res. 2013 Jan 15;73(2):473-7
references.pmid: 23316035
references.citation: Nat Genet. 2011 Mar 13;43(4):309-15
references.pmid: 21399634
references.citation: Nature. 2012 Jul 12;487(7406):239-43
references.pmid: 22722839
references.citation: Nat Rev Genet. 2011 Oct 04;12(11):756-66
references.pmid: 21969038
references.citation: Science. 2003 Apr 18;300(5618):455
references.pmid: 12702868
references.citation: Cancer Cell. 2010 Dec 14;18(6):590-605
references.pmid: 21156283
references.citation: Nature. 2010 Dec 23;468(7327):1067-73
references.pmid: 20871596
references.citation: Adv Genet. 2010;70:87-99
references.pmid: 20920746
references.citation: Science. 2010 Oct 8;330(6001):228-31
references.pmid: 20826764
references.citation: Curr Opin Genet Dev. 2012 Feb;22(1):50-5
references.pmid: 22402447
references.citation: Cancer Cell. 2012 Aug 14;22(2):180-93
references.pmid: 22897849
references.citation: Nat Genet. 2012 Dec;44(12):1310-5
references.pmid: 23104009
references.citation: Nature. 2011 Mar 10;471(7337):235-9
references.pmid: 21390130
references.citation: Nature. 2011 Feb 10;470(7333):214-20
references.pmid: 21307934
references.citation: Cancer Cell. 2012 May 15;21(5):655-667
references.pmid: 22624715
references.citation: Genome Res. 2010 Oct;20(10):1369-82
references.pmid: 20716667
references.citation: Nat Rev Cancer. 2013 Feb;13(2):97-110
references.pmid: 23344542
references.citation: Nat Genet. 2011 Aug 28;43(10):1018-21
references.pmid: 21874003
references.citation: Annu Rev Biochem. 2012;81:97-117
references.pmid: 22404632
references.citation: Nat Genet. 2013 Mar;45(3):242-52
references.pmid: 23334668
references.citation: Genes Dev. 2012 Apr 1;26(7):651-6
references.pmid: 22431509
references.citation: Leukemia. 2011 Jan;25(1):130-4
references.pmid: 21030981
references.citation: Nature. 2012 Feb 15;483(7390):479-83
references.pmid: 22343889
references.citation: Nat Med. 2012 Feb 06;18(2):298-301
references.pmid: 22237151
references.citation: Cancer Cell. 2011 Jan 18;19(1):17-30
references.pmid: 21251613
references.citation: Leukemia. 2012 May;26(5):934-42
references.pmid: 22116554
references.citation: Science. 2011 Jul 22;333(6041):425
references.pmid: 21719641
references.citation: Nat Genet. 2011 Nov 27;44(1):40-6
references.pmid: 22120008
references.citation: Cancer Cell. 2011 Jul 12;20(1):25-38
references.pmid: 21723201
references.citation: Cold Spring Harb Perspect Biol. 2010 Jan;2(1):a001008
references.pmid: 20182602
references.citation: Cell. 2012 Jul 20;150(2):251-63
references.pmid: 22817889
references.citation: Genes Dev. 2005 Feb 1;19(3):295-310
references.pmid: 15687254
references.citation: Nat Genet. 2011 Oct 02;43(11):1091-7
references.pmid: 21964573
references.citation: Am J Hum Genet. 2010 Feb 12;86(2):279-84
references.pmid: 20137775
references.citation: Nat Genet. 2007 Feb;39(2):157-8
references.pmid: 17200673
references.citation: Nature. 2012 Jul 18;487(7407):330-7
references.pmid: 22810696
references.citation: Nature. 2011 May 5;473(7345):43-9
references.pmid: 21441907
references.citation: Curr Opin Cell Biol. 2011 Jun;23(3):266-76
references.pmid: 21470840
references.citation: Nat Genet. 2012 May 27;44(7):760-4
references.pmid: 22634756
references.citation: Cell. 2011 Sep 16;146(6):1016-28
references.pmid: 21925322
references.citation: Science. 2011 Jan 28;331(6016):435-9
references.pmid: 21163964
references.citation: Nat Struct Mol Biol. 2012 Dec;19(12):1218-27
references.pmid: 23211769
references.citation: Nat Rev Cancer. 2011 Jul 07;11(8):588-96
references.pmid: 21734722
references.citation: Nature. 2012 Aug 2;488(7409):106-10
references.pmid: 22820256
references.citation: Nature. 2011 May 22;474(7352):516-20
references.pmid: 21602827
references.citation: Cell. 2012 Sep 14;150(6):1107-20
references.pmid: 22980975
references.citation: Cancer Cell. 2011 Aug 16;20(2):200-13
references.pmid: 21840485
references.citation: Hum Mol Genet. 2008 May 1;17(9):1306-17
references.pmid: 18252747
references.citation: Nature. 2012 Jan 29;482(7384):226-31
references.pmid: 22286061
references.citation: Nature. 2012 Sep 27;489(7417):519-25
references.pmid: 22960745
references.citation: Genes Dev. 2011 Jun 15;25(12):1306-19
references.pmid: 21685365
references.citation: Nat Genet. 2008 Jun;40(6):741-50
references.pmid: 18488029
references.citation: Cell. 2007 Mar 23;128(6):1231-45
references.pmid: 17382889
references.citation: PLoS Genet. 2012;8(11):e1003036
references.pmid: 23166509
references.citation: Biochim Biophys Acta. 1982 Jun 30;697(3):371-7
references.pmid: 7104364
references.citation: Nat Genet. 2011 Jun 26;43(8):768-75
references.pmid: 21706001
references.citation: Genes Chromosomes Cancer. 2005 Jun;43(2):155-61
references.pmid: 15761865
references.citation: Genome Res. 2013 Mar;23(3):419-30
references.pmid: 23222848
references.citation: Nat Genet. 2009 Jul;41(7):838-42
references.pmid: 19483684
references.citation: Nat Rev Genet. 2012 May 29;13(7):484-92
references.pmid: 22641018
references.citation: Mol Cell Biol. 2006 Jan;26(1):199-208
references.pmid: 16354691
references.citation: Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12979-84
references.pmid: 18753622
references.citation: Nat Genet. 2010 Feb;42(2):181-5
references.pmid: 20081860
references.citation: Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84
references.pmid: 22343534
references.citation: Science. 2011 Sep 2;333(6047):1300-3
references.pmid: 21778364
references.citation: Am J Surg Pathol. 2011 May;35(5):625-32
references.pmid: 21412130
references.citation: Genome Res. 2012 Feb;22(2):246-58
references.pmid: 22156296
references.citation: Nat Rev Cancer. 2010 Jul;10(7):457-69
references.pmid: 20574448
references.citation: Nat Genet. 2006 Jul;38(7):787-93
references.pmid: 16804544
references.citation: Nature. 2010 Jan 21;463(7279):360-3
references.pmid: 20054297
references.citation: Nature. 2012 Feb 15;483(7390):474-8
references.pmid: 22343901
references.citation: Cell. 2011 May 27;145(5):773-86
references.pmid: 21620139
references.citation: Science. 2012 Aug 24;337(6097):967-71
references.pmid: 22745252
references.citation: Cancer Cell. 2011 Nov 15;20(5):563-75
references.pmid: 22094252
references.citation: Nat Genet. 2010 Aug;42(8):722-6
references.pmid: 20601953
references.citation: EMBO J. 2003 Oct 15;22(20):5323-35
references.pmid: 14532106
references.citation: Science. 2008 Dec 12;322(5908):1695-9
references.pmid: 19008416
references.citation: Nat Genet. 2011 Aug 07;43(9):875-8
references.pmid: 21822268
references.citation: Science. 1981 Jun 19;212(4501):1350-7
references.pmid: 6262918
references.citation: Nat Genet. 2009 Jan;41(1):112-7
references.pmid: 19098912
references.citation: Nature. 2005 Jun 30;435(7046):1262-6
references.pmid: 15988529
references.citation: Cell. 2013 Jan 31;152(3):642-54
references.pmid: 23333102
references.citation: Nature. 2011 Jan 27;469(7331):539-42
references.pmid: 21248752
references.citation: Nature. 2012 Jan 11;481(7380):157-63
references.pmid: 22237106