title: Integrated epigenetics of human breast cancer: synoptic investigation of targeted genes, microRNAs and proteins upon demethylation treatment.
abstract: BACKGROUND
  The contribution of aberrant DNA methylation in silencing of tumor suppressor genes (TSGs) and microRNAs has been investigated. Since these epigenetic alterations are reversible, it became of interest to determine the effects of the 5-aza-2'-deoxycytidine (DAC) demethylation therapy in breast cancer at different molecular levels.
  
  
  RESULTS
  Here we investigate a synoptic model to predict complete DAC treatment effects at the level of genes, microRNAs and proteins for several human breast cancer lines. The present study assessed an effective treatment dosage based on the cell viability, cytotoxicity, apoptosis and methylation assays for the investigated cell lines. A highly aggressive and a non-aggressive cell line were investigated using omics approaches such as MALDI-TOF MS, mRNA- and microRNA expression arrays, 2-D gel electrophoresis and LC-MS-MS. Complete molecular profiles including the biological interaction and possible early and late systematic stable or transient effects of the methylation inhibition were determined. Beside the activation of several epigenetically suppressed TSGs, we also showed significant dysregulation of some important oncogenes, oncomiRs and oncosuppressors miRNAs as well as drug tolerance genes/miRNAs/proteins.
  
  
  CONCLUSIONS
  In the present study, the results denote some new molecular DAC targets and pathways based on the chemical modification of DNA methylation in breast cancer. The outlined approach might prove to be useful as an epigenetic treatment model also for other human solid tumors in the management of cancer patients.
authors.affiliation: Laboratory for Gynecological Oncology, Department of Biomedicine/Women's Hospital, University of Basel, Basel, Switzerland.
authors.forename: Ramin
authors.initials: R
authors.lastname: Radpour
authors.forename: Zeinab
authors.initials: Z
authors.lastname: Barekati
authors.forename: Corina
authors.initials: C
authors.lastname: Kohler
authors.forename: Martin M
authors.initials: MM
authors.lastname: Schumacher
authors.forename: Thomas
authors.initials: T
authors.lastname: Grussenmeyer
authors.forename: Paul
authors.initials: P
authors.lastname: Jenoe
authors.forename: Nicole
authors.initials: N
authors.lastname: Hartmann
authors.forename: Suzette
authors.initials: S
authors.lastname: Moes
authors.forename: Martin
authors.initials: M
authors.lastname: Letzkus
authors.forename: Johannes
authors.initials: J
authors.lastname: Bitzer
authors.forename: Ivan
authors.initials: I
authors.lastname: Lefkovits
authors.forename: Frank
authors.initials: F
authors.lastname: Staedtler
authors.forename: Xiao Yan
authors.initials: XY
authors.lastname: Zhong
mesh_terms: D000964:Antimetabolites, Antineoplastic / Q000494:pharmacology; D017209:Apoptosis; D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D014408:Biomarkers, Tumor / Q000235:genetics* / Q000378:metabolism*; D015153:Blotting, Western; D001943:Breast Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism*; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D019175:DNA Methylation; D000077209:Decitabine; D015180:Electrophoresis, Gel, Two-Dimensional; D044127:Epigenesis, Genetic; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D020868:Gene Silencing; D006801:Humans; D035683:MicroRNAs / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D000964:Antimetabolites, Antineoplastic; D014408:Biomarkers, Tumor; D035683:MicroRNAs; D012333:RNA, Messenger; D000077209:Decitabine; D001374:Azacitidine
references.citation: Proc Natl Acad Sci U S A. 2007 Apr 17;104(16):6696-701
references.pmid: 17420453
references.citation: Nat Rev Cancer. 2006 Apr;6(4):259-69
references.pmid: 16557279
references.citation: Int J Cancer. 1995 Nov 15;63(4):584-91
references.pmid: 7591270
references.citation: Front Biosci. 2008 May 01;13:5138-54
references.pmid: 18508576
references.citation: Clin Cancer Res. 2010 Jun 1;16(11):2927-31
references.pmid: 20484021
references.citation: Cytokine. 2006 Jun;34(5-6):271-7
references.pmid: 16870466
references.citation: Oncogene. 2009 Aug 20;28(33):2969-78
references.pmid: 19503099
references.citation: Lancet Oncol. 2009 Mar;10(3):223-32
references.pmid: 19230772
references.citation: Nature. 2007 Oct 11;449(7163):682-8
references.pmid: 17898713
references.citation: Cancer Res. 2005 Aug 15;65(16):7065-70
references.pmid: 16103053
references.citation: PLoS One. 2011 Jan 24;6(1):e16080
references.pmid: 21283676
references.citation: Cancer Res. 1979 Mar;39(3):870-80
references.pmid: 427776
references.citation: J Clin Invest. 2007 Dec;117(12):3660-3
references.pmid: 18060028
references.citation: J Biol Chem. 2002 Feb 15;277(7):5484-9
references.pmid: 11729185
references.citation: Biochim Biophys Acta. 1998 Oct 14;1378(2):F115-77
references.pmid: 9823374
references.citation: J Biol Chem. 2007 Jan 12;282(2):1479-86
references.pmid: 17110380
references.citation: Carcinogenesis. 2008 Apr;29(4):779-89
references.pmid: 17999991
references.citation: Anal Chem. 2000 Feb 15;72(4):757-63
references.pmid: 10701260
references.citation: Curr Treat Options Oncol. 2005 Mar;6(2):147-59
references.pmid: 15717996
references.citation: Science. 2010 Nov 19;330(6007):1066-71
references.pmid: 20929726
references.citation: Nucleic Acids Res. 2005 Nov 10;33(20):e175
references.pmid: 16284200
references.citation: Semin Oncol. 2005 Oct;32(5):443-51
references.pmid: 16210084
references.citation: Expert Opin Biol Ther. 2007 Jul;7(7):1009-19
references.pmid: 17665990
references.citation: Hum Mol Genet. 2010 Aug 1;19(15):2936-46
references.pmid: 20466735
references.citation: Nature. 2008 Mar 13;452(7184):187-93
references.pmid: 18337816
references.citation: Cancer. 2006 Apr 15;106(8):1794-803
references.pmid: 16532500
references.citation: Cell Res. 2008 Mar;18(3):350-9
references.pmid: 18270520
references.citation: Lung Cancer. 2007 Feb;55(2):205-13
references.pmid: 17140695
references.citation: RNA. 2008 Nov;14(11):2348-60
references.pmid: 18812439
references.citation: J Cell Sci. 1994 Dec;107 ( Pt 12):3557-68
references.pmid: 7535787
references.citation: Curr Opin Oncol. 2003 Nov;15(6):446-51
references.pmid: 14624227
references.citation: Nature. 2008 Mar 6;452(7183):112-5
references.pmid: 18322535
references.citation: Cancer Res. 2006 Sep 15;66(18):9090-8
references.pmid: 16982751
references.citation: J Clin Invest. 2010 Jan;120(1):41-50
references.pmid: 20051635
references.citation: Oncogene. 2011 Apr 7;30(14):1681-92
references.pmid: 21151177
references.citation: Cell. 2005 Jul 15;122(1):6-7
references.pmid: 16009126
references.citation: Exp Mol Pathol. 2007 Oct;83(2):188-97
references.pmid: 17540367
references.citation: Ann Oncol. 2001;12 Suppl 1:S3-8
references.pmid: 11521719
references.citation: Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15805-10
references.pmid: 17890317
references.citation: Nat Rev Cancer. 2003 Apr;3(4):253-66
references.pmid: 12671664
references.citation: Annu Rev Immunol. 2005;23:1-21
references.pmid: 15771564
references.citation: J Natl Cancer Inst. 1979 Feb;62(2):225-30
references.pmid: 283258
references.citation: Cancer. 2007 Nov 1;110(9):1911-28
references.pmid: 17849470
references.citation: Cancer Gene Ther. 2010 Aug;17(8):523-31
references.pmid: 20467450
references.citation: Cancer Res. 1997 Dec 1;57(23):5386-90
references.pmid: 9393764
references.citation: Genet Test Mol Biomarkers. 2009 Oct;13(5):565-71
references.pmid: 19814613
references.citation: BMC Cancer. 2010 Jul 06;10:354
references.pmid: 20602797
references.citation: PLoS One. 2008 Mar 26;3(3):e1864
references.pmid: 18365017
references.citation: Nature. 2008 Mar 6;452(7183):45-50
references.pmid: 18322525
references.citation: J Biol Chem. 2008 Jan 11;283(2):1026-33
references.pmid: 17991735
references.citation: Nat Biotechnol. 2010 Aug;28(8):827-38
references.pmid: 20676074
references.citation: Oncogene. 2008 Jul 17;27(31):4373-9
references.pmid: 18372920
references.citation: Arch Gynecol Obstet. 2005 Jun;272(1):48-52
references.pmid: 15682318
references.citation: J Natl Cancer Inst. 1981 Jun;66(6):1003-12
references.pmid: 7017212
references.citation: Nat Rev Drug Discov. 2006 Jan;5(1):37-50
references.pmid: 16485345
references.citation: Exp Biol Med (Maywood). 2003 Oct;228(9):995-1003
references.pmid: 14530507
references.citation: Blood. 2009 Jun 18;113(25):6411-8
references.pmid: 19211935
references.citation: Nat Cell Biol. 2001 Nov;3(11):973-82
references.pmid: 11715018
references.citation: Nat Rev Genet. 2008 Jun;9(6):465-76
references.pmid: 18463664
references.citation: Cancer Res. 2005 Jul 15;65(14):6029-33
references.pmid: 16024602
references.citation: Cancer Res. 2007 Feb 15;67(4):1424-9
references.pmid: 17308079
references.citation: Cell. 2004 Jan 23;116(2):281-97
references.pmid: 14744438
references.citation: Nature. 2001 Mar 1;410(6824):50-6
references.pmid: 11242036
references.citation: J Proteome Res. 2009 Nov;8(11):5264-74
references.pmid: 19780627
references.citation: Nature. 2000 Nov 16;408(6810):307-10
references.pmid: 11099028
references.citation: Toxicol Appl Pharmacol. 2004 May 1;196(3):422-30
references.pmid: 15094313
references.citation: Genes Dev. 2009 Nov 15;23(22):2625-38
references.pmid: 19933152
references.citation: Cancer Res. 2007 Nov 15;67(22):11001-11
references.pmid: 18006846
references.citation: Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7263-8
references.pmid: 8692980
references.citation: Genes Dev. 2002 Jan 1;16(1):6-21
references.pmid: 11782440