161
Views
0
CrossRef citations to date
0
Altmetric
Review

Genome-Wide Screening for Understanding the Role of DNA Methylation in Colorectal Cancer

, , , , , , & show all
Pages 569-581 | Published online: 24 Sep 2013

References

  • Wood LD , ParsonsDW, JonesS et al. The genomic landscapes of human breast and colorectal cancers. Science 318(5853) , 1108–1113 (2007).
  • Laird PW . Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet.11(3) , 191–203 (2010).
  • Laird PW . The power and the promise of DNA methylation markers. Nat. Rev. Cancer3(4) , 253–266 (2003).
  • Schones DE , ZhaoK. Genome-wide approaches to studying chromatin modifications. Nat. Rev. Genet.9(3) , 179–191 (2008).
  • Fraga MF , EstellerM. DNA methylation: a profile of methods and applications. Biotechniques33(3) , 632–649 (2002).
  • Pomraning KR , SmithKM, FreitagM. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods47(3) , 142–150 (2009).
  • Fouse SD , NagarajanRO, CostelloJF. Genome-scale DNA methylation analysis. Epigenomics2(1) , 105–117 (2010).
  • Huang YW , HuangTH, WangLS. Profiling DNA methylomes from microarray to genome-scale sequencing. Technol. Cancer Res. Treat.9(2) , 139–147 (2010).
  • Estecio MR , YanPS, IbrahimAE et al. High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res. 17(10) , 1529–1536 (2007).
  • Weber M , DaviesJJ, WittigD et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37(8) , 853–862 (2005).
  • Taiwo O , WilsonGA, MorrisT et al. Methylome analysis using MeDIP-seq with low DNA concentrations. Nat. Protoc. 7(4) , 617–636 (2012).
  • Jacinto FV , BallestarE, EstellerM. Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques44(1) , 35, 37, 39 passim (2008).
  • Meehan RR , LewisJD, BirdAP. Characterization of MeCP2, a vertebrate DNA binding protein with affinity for methylated DNA. Nucleic Acids Res.20(19) , 5085–5092 (1992).
  • Down TA , RakyanVK, TurnerDJ et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26(7) , 779–785 (2008).
  • Rauch T , LiH, WuX, PfeiferGP. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res.66(16) , 7939–7947 (2006).
  • Serre D , LeeBH, TingAH. MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res.38(2) , 391–399 (2010).
  • De Meyer T , MampaeyE, VlemmixM et al. Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing. PLoS One 8(3) , e59068 (2013).
  • Brinkman AB , SimmerF, MaK, KaanA, ZhuJ, StunnenbergHG. Whole-genome DNA methylation profiling using MethylCap-seq. Methods52(3) , 232–236 (2010).
  • Simmer F , BrinkmanAB, AssenovY et al. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics 7(12) , 1355–1367 (2012).
  • Touleimat N , TostJ. Complete pipeline for Infinium® human methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics4(3) , 325–341 (2012).
  • Bibikova M , LinZ, ZhouL et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16(3) , 383–393 (2006).
  • Jasmine F , RahamanR, RoyS et al. Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue. BMC Res. Notes 5 , 117 (2012).
  • Bibikova M , LeJ, BarnesB et al. Genome-wide DNA methylation profiling using Infinium assay. Epigenomics 1(1) , 177–200 (2009).
  • Meissner A , GnirkeA, BellGW, RamsahoyeB, LanderES, JaenischR. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res.33(18) , 5868–5877 (2005).
  • Gu H , SmithZD, BockC, BoyleP, GnirkeA, MeissnerA. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat. Protoc.6(4) , 468–481 (2011).
  • Schillebeeckx M , SchradeA, LöbsAK, PihlajokiM, WilsonDB, MitraRD. Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Nucleic Acids. Res.41(11) , 116 (2013).
  • Boyle P , ClementK, GuH et al. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol. 13(10) , R92 (2012).
  • Oda M , GlassJL, ThompsonRF et al. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res. 37(12) , 3829–3839 (2009).
  • Bock C , TomazouEM, BrinkmanAB et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat. Biotechnol. 28(10) , 1106–1114 (2010).
  • Li N , YeM, LiY et al. Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods 52(3) , 203–212 (2010).
  • Nair SS , CoolenMW, StirzakerC et al. Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 6(1) , 34–44 (2011).
  • Clark C , PaltaP, JoyceCJ et al. A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the infinium human methylation450 BeadChip® for methylome profiling. PLoS One 7(11) , e50233 (2012).
  • Pedersen IS , KrarupHB, Thorlacius-UssingO, MadsenPH. High recovery of cell-free methylated DNA based on a rapid bisulfite-treatment protocol. BMC Mol. Biol.13 , 12 (2012).
  • Yokoyama S , KitamotoS, YamadaN et al. The application of methylation specific electrophoresis (MSE) to DNA methylation analysis of the 5´ CpG island of mucin in cancer cells. BMC Cancer 12 , 67 (2012).
  • Tierling S , SchusterM, TetznerR, WalterJ. A combined HM-PCR/SNuPE method for high sensitive detection of rare DNA methylation. Epigenetics Chromatin3(1) , 12 (2010).
  • Kneip C , SchmidtB, FleischhackerM et al. A novel method for sensitive and specific detection of DNA methylation biomarkers based on DNA restriction during PCR cycling. Biotechniques 47(3) , 737–744 (2009).
  • Bock C , LengauerT. Computational epigenetics. Bioinformatics24(1) , 1–10 (2008).
  • Lister R , PelizzolaM, DowenRH et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271) , 315–322 (2009).
  • Ferlay J , ParkinDM, Steliarova-FoucherE. Estimates of cancer incidence and mortality in Europe in 2008. Eur. J. Cancer46(4) , 765–781 (2010).
  • Remo A , PancioneM, ZanellaC, VendraminelliR. Molecular pathology of colorectal carcinoma. A systematic review centred on the new role of the pathologist. Pathologica104(6) , 432–441 (2012).
  • Di L ena M, Travaglio E, Altomare DF. New strategies for colorectal cancer screening. World J. Gastroenterol.19(12) , 1855–1860 (2013).
  • Jones PA , BaylinSB. The epigenomics of cancer. Cell128(4) , 683–692 (2007).
  • Wong NC , CraigJM. Epigenetics: A Reference Manual. Caister Academic Press, Norfolk, England (2011).
  • Cadieux B , ChingTT, VandenBergSR, CostelloJF. Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation. Cancer Res.66(17) , 8469–8476 (2006).
  • Toyota M , AhujaN, Ohe-ToyotaM, HermanJG, BaylinSB, IssaJP. CpG island methylator phenotype in colorectal cancer. Proc. Natl Acad. Sci. USA96(15) , 8681–8686 (1999).
  • Fernandez-Rozadilla C , CazierJB, TomlinsonIP et al. A colorectal cancer genome-wide association study in a Spanish cohort identifies two variants associated with colorectal cancer risk at 1p33 and 8p12. BMC Genomics 14 , 55 (2013).
  • Jiao S , HsuL, BerndtS et al. Genome-wide search for gene–gene interactions in colorectal cancer. PLoS One 7(12) , e52535 (2012).
  • Jia WH , ZhangB, MatsuoK et al. Genome-wide association analyses in East Asians identify new susceptibility loci for colorectal cancer. Nat Genet. 45(2) , 191–196 (2013).
  • Wang HM , ChangTH, LinFM et al. A new method for post genome-wide association study (GWAS) analysis of colorectal cancer in Taiwan. Gene 518(1) , 107–113 (2013).
  • Chen W , XiangJ, ChenDF et al. Screening for differentially methylated genes among human colorectal cancer tissues and normal mucosa by microarray chip. Mol. Biol.Rep. 40(5) , 3457–3464 (2013).
  • Kim YH , LeeHC, KimSY et al. Epigenomic analysis of aberrantly methylated genes in colorectal cancer identifies genes commonly affected by epigenetic alterations. Ann. Surg. Oncol. 18(8) , 2338–2347 (2011).
  • Schuebel KE , ChenW, CopeL et al. Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet. 3(9) , 1709–1723 (2007).
  • Mori Y , CaiK, ChengY et al. A genome-wide search identifies epigenetic silencing of somatostatin, tachykinin-1, and 5 other genes in colon cancer. Gastroenterology 131(3) , 797–808 (2006).
  • Cancer Genome Atlas Network: Comprehensive molecular characterization of human colon and rectal cancer . Nature487(7407) , 330–337 (2012).
  • Davis CD , UthusEO. DNA methylation, cancer susceptibility, and nutrient interactions. Exp. Biol. Med. (Maywood)229(10) , 988–995 (2004).
  • Delgado-Plasencia L , Medina-AranaV, Bravo-GutiérrezA et al. Impact of the MTHFR C677T polymorphism on colorectal cancer in a population with low genetic variability. Int. J. Colorectal. Dis. 28(9) , 1187–1193 (2013).
  • Kibriya MG , RazaM, JasmineF et al. A genome-wide DNA methylation study in colorectal carcinoma. BMC Med. Genomics 4 , 50 (2011).
  • van Rijnsoever M , GrieuF, ElsalehH, JosephD, IacopettaB. Characterisation of colorectal cancers showing hypermethylation at multiple CpG islands. Gut51(6) , 797–802 (2002).
  • Beggs AD , JonesA, El-BahwaryM, AbulafiM, HodgsonSV, TomlinsonIP. Whole-genome methylation analysis of benign and malignant colorectal tumours. J. Pathol.229(5) , 697–704 (2013).
  • Ju HX , AnB, OkamotoY et al. Distinct profiles of epigenetic evolution between colorectal cancers with and without metastasis. Am. J. Pathol. 178(4) , 1835–1846 (2011).
  • Yi JM , DhirM, Van Neste L et al. Genomic and epigenomic integration identifies a prognostic signature in colon cancer. Clin. Cancer Res.17(6) , 1535–1545 (2011).
  • Kim JC , LeeHC, ChoDH et al. Genome-wide identification of possible methylation markers chemosensitive to targeted regimens in colorectal cancers. J. Cancer Res. Clin. Oncol. 137(10) , 1571–1580 (2011).
  • Chen B , DodgeME, TangW et al. Small molecule-mediated disruption of Wnt-dependent signaling in tissue regeneration and cancer. Nat. Chem. Biol. 5(2) , 100–107 (2009).
  • Sack U , WaltherW, ScudieroD et al. S100A4-induced cell motility and metastasis is restricted by the Wnt/β-catenin pathway inhibitor calcimycin in colon cancer cells. Mol. Biol. Cell 22(18) , 3344–3354 (2011).
  • Hinoue T , WeisenbergerDJ, LangeCP et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res. 22(2) , 271–282 (2012).
  • Weisenberger DJ , SiegmundKD, CampanM et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat. Genet. 38(7) , 787–793 (2006).
  • Shen L , ToyotaM, KondoY et al. Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proc. Natl Acad. Sci. USA 104(47) , 18654–18659 (2007).
  • Yagi K , AkagiK, HayashiH et al. Three DNA methylation epigenotypes in human colorectal cancer. Clin. Cancer Res. 16(1) , 21–33 (2010).
  • Nosho K , IraharaN, ShimaK et al. Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample. PLoS One 3(11) , e3698 (2008).
  • Patai AV , MolnárB, TulassayZ, SiposF. Serrated pathway: alternative route to colorectal cancer. World J. Gastroenterol.19(5) , 607–615 (2013).
  • Ogino S , KawasakiT, KirknerGJ, LodaM, FuchsCS. CpG island methylator phenotype-low (CIMP-low) in colorectal cancer: possible associations with male sex and KRAS mutations. J. Mol. Diagn.8(5) , 582–588 (2006).
  • Ogino S , KawasakiT, KirknerGJ, OhnishiM, FuchsCS. 18q loss of heterozygosity in microsatellite stable colorectal cancer is correlated with CpG island methylator phenotype-negative (CIMP-0) and inversely with CIMP-low and CIMP-high. BMC Cancer7 , 72 (2007).
  • Goel A , NagasakaT, ArnoldCN et al. The CpG island methylator phenotype and chromosomal instability are inversely correlated in sporadic colorectal cancer. Gastroenterology 132(1) , 127–138 (2007).
  • Barault L , Charon-BarraC, JoosteV et al. Hypermethylator phenotype in sporadic colon cancer: study on a population-based series of 582 cases. Cancer Res. 68(20) , 8541–8546 (2008).
  • Dahlin AM , PalmqvistR, HenrikssonML et al. The role of the CpG island methylator phenotype in colorectal cancer prognosis depends on microsatellite instability screening status. Clin. Cancer Res. 16(6) , 1845–1855 (2010).
  • Kim JH , ShinSH, KwonHJ, ChoNY, KangGH. Prognostic implications of CpG island hypermethylator phenotype in colorectal cancers. Virchows Arch.455(6) , 485–494 (2009).
  • Zlobec I , BihlM, FoersterA, RufleA, LugliA. Comprehensive analysis of CpG island methylator phenotype (CIMP)-high, -low, and -negative colorectal cancers based on protein marker expression and molecular features. J. Pathol.225(3) , 336–343 (2011).
  • Yagi K , AkagiK, HayashiH et al. Three DNA methylation epigenotypes in human colorectal cancer. Clin. Cancer Res. 16(1) , 21–33 (2010).
  • Ang PW , LohM, LiemN et al. Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features. BMC Cancer 10 , 227 (2010).
  • Yamauchi M , MorikawaT, KuchibaA et al. Assessment of colorectal cancer molecular features along bowel subsites challenges the conception of distinct dichotomy of proximal versus distal colorectum. Gut 61(6) , 847–854 (2012).
  • Teodoridis JM , HardieC, BrownR. CpG island methylator phenotype (CIMP) in cancer: causes and implications. Cancer Lett.268(2) , 177–186 (2008).
  • Balkwill F , MantovaniA. Inflammation and cancer: back to Virchow? Lancet357(9255) , 539–545 (2001).
  • Olaru AV , ChengY, AgarwalR et al. Unique patterns of CpG island methylation in inflammatory bowel disease-associated colorectal cancers. Inflamm. Bowel Dis. 18(4) , 641–648 (2012).
  • Patai AV , MolnárB, KalmárA, SchöllerA, TóthK, TulassayZ. Role of DNA methylation in colorectal carcinogenesis. Dig. Dis.30(3) , 310–315 (2012).
  • Tang D , LiuJ, WangDR, YuHF, LiYK, ZhangJQ. Diagnostic and prognostic value of the methylation status of secreted frizzled-related protein 2 in colorectal cancer. Clin. Invest. Med.34(2) , e88–e95 (2011).
  • Lange CP , CampanM, HinoueT et al. Genome-scale discovery of DNA-methylation biomarkers for blood-based detection of colorectal cancer. PLoS One 7(11) , e50266 (2012).
  • Tóth K , SiposF, KalmárA et al. Detection of methylated SEPT9 in plasma is a reliable screening method for both left- and right-sided colon cancers. PLoS One 7(9) , e46000 (2012).
  • Bennett KL , KarpenkoM, LinMT et al. Frequently methylated tumor suppressor genes in head and neck squamous cell carcinoma. Cancer Res. 68(12) , 4494–4499 (2008).
  • Grady WM , RajputA, LutterbaughJD, MarkowitzSD. Detection of aberrantly methylated hMLH1 promoter DNA in the serum of patients with microsatellite unstable colon cancer. Cancer Res.61(3) , 900–902 (2001).
  • Leung WK , ToKF, ManEP et al. Quantitative detection of promoter hypermethylation in multiple genes in the serum of patients with colorectal cancer. Am. J. Gastroenterol. 100(10) , 2274–2279 (2005).
  • Nakayama H , HibiK, TakaseT et al. Molecular detection of p16 promoter methylation in the serum of recurrent colorectal cancer patients. Int. J. Camcer 105(4) , 491–493 (2003).
  • Zou HZ , YuBM, WangZW et al. Detection of aberrant p16 methylation in the serum of colorectal cancer patients. Clin. Cancer Res. 8(1) , 188–191 (2002).
  • Müller HM , WidschwendterM. Methylated DNA as a possible screening marker for neoplastic disease in several body fluids. Expert Rev. Mol. Diagn.3(4) , 443–458 (2003).
  • deVos T , TetznerR, ModelF et al. Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer. Clin. Chem. 55(7) , 1337–1346 (2009).
  • Lofton-Day C , ModelF, DevosT et al. DNA methylation biomarkers for blood-based colorectal cancer screening. Clin. Chem. 54(2) , 414–423 (2008).
  • Wallner M , HerbstA, BehrensA et al. Methylation of serum DNA is an independent prognostic marker in colorectal cancer. Clin. Cancer Res. 12(24) , 7347–7352 (2006).
  • Herbst A , WallnerM, RahmigK et al. Methylation of helicase-like transcription factor in serum of patients with colorectal cancer is an independent predictor of disease recurrence. Eur. J. Gastroenterol. Hepatol. 21(5) , 565–569 (2009).
  • Tang D , LiuJ, WangDR, YuHF, LiYK, ZhangJQ. Diagnostic and prognostic value of the methylation status of secreted frizzled related protein 2 in colorectal cancer. Clin. Invest. Med.34(2) , e88–e95 (2011).
  • Herbst A , RahmigK, StieberP et al. Methylation of NEUROG1 in serum is a sensitive marker for the detection of early colorectal cancer. Am. J. Gastroenterol. 106(6) , 1110–1118 (2011).
  • Ahlquist DA , TaylorWR, MahoneyDW et al. The stool DNA test is more accurate than the plasma septin 9 test in detecting colorectal neoplasia. Clin. Gastroenterol. Hepatol. 10(3) , 272–277 (2012).
  • Tänzer M , BalluffB, DistlerJ et al. Performance of epigenetic markers SEPT9 and ALX4 in plasma for detection of colorectal precancerous lesions. PLoS One 5(2) , e9061 (2010).
  • Li M , ChenWD, PapadopoulosN et al. Sensitive digital quantification of DNA methylation in clinical samples. Nat. Biotechnol. 27(9) , 858–863 (2009).
  • Kim TO , ParkJ, KangMJ et al. DNA hypermethylation of a selective gene panel as a risk marker for colon cancer in patients with ulcerative colitis. Int. J. Mol. Med. 31(5) , 1255–1261 (2013).
  • Balasubramanyam K , VarierRA, AltafM et al. Curcumin, a novel p300/CREB-binding protein-specific inhibitor of acetyltransferase, represses the acetylation of histone/nonhistone proteins and histone acetyltransferase-dependent chromatin transcription. J. Biol. Chem. 279(49) , 51163–51171 (2004).
  • Liu Z , XieZ, JonesW et al. Curcumin is a potent DNA hypomethylation agent. Bioorg. Med. Chem. Lett. 19(3) , 706–709 (2009).
  • Link A , BalaguerF, ShenY et al. Curcumin modulates DNA methylation in colorectal cancer cells. PLoS One 8(2) , e57709 (2013).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.