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Review

The potential of DNA modifications as biomarkers and therapeutic targets in oncology

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References

  • Costello JF, Plass C. Methylation matters. J Med Genet 2001;38(5):285-303
  • Baylin SB, Jones PA. A decade of exploring the cancer epigenome — biological and translational implications. Nat Rev Cancer 2011;11(10):726-34
  • Esteller M. Epigenetics in cancer. N Engl J Med 2008;358(11):1148-59
  • Robertson KD. DNA methylation and human disease. Nat Rev Genet 2005;6(8):597-610
  • Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002;16(1):6-21
  • Razin A, Riggs AD. DNA methylation and gene function. Science 1980;210(4470):604-10
  • Tahiliani M, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009;324(5929):930-5
  • He YF, Li BZ, Li Z, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 2011;333(6047):1303-7
  • Ito S, Shen L, Dai Q, et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011;333(6047):1300-3
  • 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(6):341-56
  • Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008;9(6):465-76
  • Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 2003;33(Suppl):245-54
  • Jirtle RL, Skinner MK. Environmental epigenomics and disease susceptibility. Nat Rev Genet 2007;8(4):253-62
  • Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet 2006;7(1):21-33
  • Teschendorff AE, West J, Beck S. Age-associated epigenetic drift: implications, and a case of epigenetic thrift? Hum Mol Genet 2013;22(R1):R7-R15
  • Issa JP. Aging and epigenetic drift: a vicious cycle. J Clin Invest 2014;124(1):24-9
  • Issa JP, Ottaviano YL, Celano P, et al. Methylation of the oestrogen receptor CpG island links ageing and neoplasia in human colon. Nat Genet 1994;7(4):536-40
  • Toyota M, Ahuja N, Ohe-Toyota M, et al. CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci USA 1999;96(15):8681-6
  • Ahuja N, Issa JP. Aging, methylation and cancer. Histol Histopathol 2000;15:835-42
  • Bjornsson HT, Sigurdsson MI, Fallin MD, et al. Intra-individual change over time in DNA methylation with familial clustering. JAMA 2008;299:2877-83
  • Fraga MF, Ballestar E, Paz MF, et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 2005;102(30):10604-9
  • Christensen BC, Houseman EA, Marsit CJ, et al. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet 2009;5(8):e1000602
  • Maegawa S, Hinkal G, Kim HS, et al. Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res 2010;20(3):332-40
  • Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 2013;368(22):2059-74
  • Talens RP, Christensen K, Putter H, et al. Epigenetic variation during the adult lifespan: cross-sectional and longitudinal data on monozygotic twin pairs. Aging Cell 2012;11(4):694-703
  • Sandoval J, Esteller M. Cancer epigenomics: beyond genomics. Curr Opin Genet Dev 2012;22(1):50-5
  • You JS, Jones PA. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 2012;22(1):9-20
  • Esteller M. Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum Mol Genet 2007;16(Spec No 1):R50-9
  • Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet 2012;13(10):679-92
  • Esteller M. Relevance of DNA methylation in the management of cancer. Lancet Oncol 2003;4(6):351-8
  • Plass C, Pfister SM, Lindroth AM, et al. Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nat Rev Genet 2013;14(11):765-80
  • Nestor CE, Ottaviano R, Reddington J, et al. Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res 2012;22(3):467-77
  • Ko M, Huang Y, Jankowska AM, et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 2010;468(7325):839-43
  • Laird A, Thomson JP, Harrison DJ, Meehan RR. 5-hydroxymethylcytosine profiling as an indicator of cellular state. Epigenomics 2013;5(6):655-69
  • Ficz G, Branco MR, Seisenberger S, et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 2011;473(7347):398-402
  • Ficz G, Gribben JG. Loss of 5-hydroxymethylcytosine in cancer: cause or consequence? Genomics 2014;104(5):352-7
  • Xu Y, Wu F, Tan L, et al. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell 2011;42(4):451-64
  • Kinney SM, Chin HG, Vaisvila R, et al. Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomes. J Biol Chem 2011;286(28):24685-93
  • Jin SG, Jiang Y, Qiu R, et al. 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. Cancer Res 2011;71(24):7360-5
  • Haffner MC, Chaux A, Meeker AK, et al. Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers. Oncotarget 2011;2(8):627-37
  • Bhattacharyya S, Yu Y, Suzuki M, et al. Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer. Nucleic Acids Res 2013;41(16):e157
  • Lian CG, Xu Y, Ceol C, et al. Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 2012;150(6):1135-46
  • Shi H, Wang MX, Caldwell CW. CpG islands: their potential as biomarkers for cancer. Expert Rev Mol Diagn 2007;7(5):519-31
  • Olkhov-Mitsel E, Bapat B. Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers. Cancer Med 2012;1(2):237-60
  • Rivera CM, Ren B. Mapping human epigenomes. Cell 2013;155(1):39-55
  • 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(6):692-702
  • Bibikova M, Lin Z, Zhou L, et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res 2006;16(3):383-93
  • Harris RA, Wang T, Coarfa C, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010;28(10):1097-105
  • Hirotsune S, Hatada I, Komatsubara H, et al. New approach for detection of amplification in cancer DNA using restriction landmark genomic scanning. Cancer Res 1992;52(13):3642-7
  • Huang TH, Perry MR, Laux DE. Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 1999;8(3):459-70
  • Gebhard C, Schwarzfischer L, Pham TH, et al. Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. Cancer Res 2006;66(12):6118-28
  • Weber M, Davies JJ, Wittig D, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005;37(8):853-62
  • Meissner A, Gnirke A, Bell GW, et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 2005;33(18):5868-77
  • Lister R, Pelizzola M, Dowen RH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009;462(7271):315-22
  • Adey A, Shendure J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Res 2012;22(6):1139-43
  • Tost J, Schatz P, Schuster M, et al. Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry. Nucleic Acids Res 2003;31(9):e50
  • Liu L, Kron KJ, Pethe VV, et al. Association of tissue promoter methylation levels of APC, TGFβ2, HOXD3 and RASSF1A with prostate cancer progression. Int J Cancer 2011;129(10):2454-62
  • Rawson JB, Manno M, Mrkonjic M, et al. Promoter methylation of Wnt antagonists DKK1 and SFRP1 is associated with opposing tumor subtypes in two large populations of colorectal cancer patients. Carcinogenesis 2011;32(5):741-7
  • Pastor WA, Pape UJ, Huang Y, et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011;473(7347):394-7
  • Robertson AB, Dahl JA, Vagbø CB, et al. A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res 2011;39(8):e55
  • Song CX, Szulwach KE, Fu Y, et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 2011;29(1):68-72
  • Williams K, Christensen J, Pedersen MT, et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011;473(7347):343-8
  • Booth MJ, Branco MR, Ficz G, et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 2012;336(6083):934-7
  • Yu M, Hon GC, Szulwach KE, et al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 2012;149(6):1368-80
  • Mikeska T, Bock C, Do H, et al. DNA methylation biomarkers in cancer: progress towards clinical implementation. Expert Rev Mol Diagn 2012;12(5):473-87
  • Kristensen LS, Mikeska T, Krypuy M, et al. Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection. Nucleic Acids Res 2008;36(7):e42
  • Mikeska T, Felsberg J, Hewitt CA, et al. Analysing DNA methylation using bisulphite pyrosequencing. Methods Mol Biol 2011;791:33-53
  • Wojdacz TK, Dobrovic A. Methylationsensitive high resolution melting (MSHRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res 2007;35(6):e41
  • Li M, Chen WD, Papadopoulos N, et al. Sensitive digital quantification of DNA methylation in clinical samples. Nat Biotechnol 2009;27(9):858-63
  • Laird PW. The power and the promise of DNA methylation markers. Nat Rev Cancer 2003;3(4):253-66
  • Shivapurkar N, Gazdar AF. DNA methylation based biomarkers in non-invasive cancer screening. Curr Mol Med 2010;10(2):123-32
  • Esteller M, Corn PG, Baylin SB, et al. A gene hypermethylation profile of human cancer. Cancer Res 2001;61(8):3225-9
  • Issa JP, Ahuja N, Toyota M, et al. Accelerated age-related CpG island methylation in ulcerative colitis. Cancer Res 2001;61(9):3573-7
  • Fujiwara K, Fujimoto N, Tabata M, et al. Identification of epigenetic aberrant promoter methylation in serum DNA is useful for early detection of lung cancer. Clin Cancer Res 2005;11(3):1219-25
  • Belinsky SA, Klinge DM, Dekker JD, et al. Gene promoter methylation in plasma and sputum increases with lung cancer risk. Clin Cancer Res 2005;11(18):6505-11
  • Schmidt B, Liebenberg V, Dietrich D, et al. SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer based on bronchial aspirates. BMC Cancer 2010;10:600
  • Kneip C, Schmidt B, Seegebarth A, et al. SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer in plasma. J Thorac Oncol 2011;6(10):1632-8
  • Ahmed H, Cappello F, Rodolico V, Vasta GR. Evidence of heavy methylation in the galectin 3 promoter in early stages of prostate adenocarcinoma: development and validation of a methylated marker for early diagnosis of prostate cancer. Transl Oncol 2009;2(3):146-56
  • Goessl C, Krause H, Muller M, et al. Fluorescent methylation-specific polymerase chain reaction for DNA-based detection of prostate cancer in bodily fluids. Cancer Res 2000;60(21):5941-5
  • Goessl C, Muller M, Heicappell R, et al. DNA-based detection of prostate cancer in urine after prostatic massage. Urology 2001;58(3):335-8
  • Steenbergen RD, Snijders PJ, Heideman DA, et al. Clinical implications of (epi)genetic changes in HPV-induced cervical precancerous lesions. Nat Rev Cancer 2014;14(6):395-405
  • Diehl F, Li M, Dressman D, et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci USA 2005;102(45):16368-73
  • Jung K, Fleischhacker M, Rabien A. Cell-free DNA in the blood as a solid tumor biomarker-A critical appraisal of the literature. Clin Chim Acta 2010;411(21–22):1611-24
  • Schwarzenbach H, Hoon DSB, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer 2011;11(6):426-37
  • Li L, Choi JY, Lee KM, et al. DNA methylation in peripheral blood: a potential biomarker for cancer molecular epidemiology. J Epidemiol 2012;22(5):384-94
  • Maier S, Nimmrich I, Koenig T, et al. DNA-methylation of the homeodomain transcription factor PITX2 reliably predicts risk of distant disease recurrence in tamoxifen-treated, node-negative breast cancer patients – technical and clinical validation in a multi-centre setting in collaboration with the European organisation for research and treatment of cancer (EORTC) pathobiology group. Eur J Cancer 2007;43:1679-86
  • Strand SH, Orntoft TF, Sorensen KD. Prognostic DNA methylation markers for prostate cancer. Int J Mol Sci 2014;15(9):16544-76
  • Brock MV, Hooker CM, Ota-Machida E, et al. DNA methylation markers and early recurrence in stage I lung cancer. N Engl J Med 2008;358:1118-28
  • Balgkouranidou I, Liloglou T, Lianidou ES. Lung cancer epigenetics: emerging biomarkers. Biomark Med 2013;7(1):49-58
  • Esteller M, Garcia-Foncillas J, Andion E, et al. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med 2000;343:1350-4
  • Fernandez AF, Assenov Y, Martin-Subero JI. et al. A DNA methylation fingerprint of 1628 human samples. Genome Res 2011;22(2):407-19
  • Kelly TK, De Carvalho DD, Jones PA. Epigenetic modifications as therapeutic targets. Nature biotechnology 2010;28:1069-78
  • Fenaux P, Mufti GJ, Hellstrom-Lindberg E, et al. Low-dose decitabine versus best supportive care in elderly patients with intermediate- or high-risk myelodysplastic syndrome (MDS) ineligible for intensive chemotherapy: final results of the randomized phase III study of the European Organisation for Research and Treatment of Cancer Leukemia Group and the German MDS Study Group. J Clin Oncol 2011;29(15):1987-96
  • Hatzimichael E, Crook T. Cancer epigenetics: new therapies and new challenges. J Drug Deliv 2013;2013:529312
  • Chung CW, Witherington J. Progress in the discovery of small-molecule inhibitors of bromodomain-histone interactions. J Biomol Screen 2011;16(10):1170-85
  • Filippakopoulos P, Qi J, Picaud S, et al. Selective inhibition of BET bromodomains. Nature 2010;468(7327):1067-73
  • Rohle D, Popovici-Muller J, Palaskas N, et al. An inhibitor of mutant IDH1 delays growth and promotes differentiation of glioma cells. Science 2013;340(6132):626-30

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