577
Views
108
CrossRef citations to date
0
Altmetric
Review

DNA methylation as a universal biomarker

Pages 481-488 | Published online: 09 Jan 2014

References

  • Dworkin AM, Huang TH, Toland AE. Epigenetic alterations in the breast: implications for breast cancer detection, prognosis and treatment. Semin. Cancer Biol.19(3), 165–171 (2009).
  • Hoque MO. DNA methylation changes in prostate cancer: current developments and future clinical implementation. Expert Rev. Mol. Diagn.9(3), 243–257 (2009).
  • Anglim PP, Alonzo TA, Laird-Offringa IA. DNA methylation-based biomarkers for early detection of non-small cell lung cancer: an update. Mol. Cancer7, 81 (2008).
  • Urdinguio RG, Sanchez-Mut JV, Esteller M. Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies. Lancet Neurol.8(11), 1056–1072 (2009).
  • Zawia NH, Lahiri DK, Cardozo-Pelaez F. Epigenetics, oxidative stress, and Alzheimer disease. Free Radic. Biol. Med.46(9), 1241–1249 (2009).
  • Sananbenesi F, Fischer A. The epigenetic bottleneck of neurodegenerative and psychiatric diseases. Biol. Chem.390(11), 1145–1153 (2009).
  • Dehan P, Kustermans G, Guenin S et al. DNA methylation and cancer diagnosis: new methods and applications. Expert Rev. Mol. Diagn.9(7), 651–657 (2009).
  • Evertts AG, Zee BM, Garcia BA. Modern approaches for investigating epigenetic signaling pathways. J. Appl. Physiol. DOI: 00007.2010v1 (2010) (Epub ahead of print).
  • Hurd PJ, Nelson CJ. Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct. Genomic Proteomic8(3), 174–183 (2009).
  • Weng YI, Huang TH, Yan PS. Methylated DNA immunoprecipitation and microarray-based analysis: detection of DNA methylation in breast cancer cell lines. Methods Mol. Biol.590, 165–176 (2009).
  • Balch C, Fang F, Matei DE, Huang TH, Nephew KP. Minireview: epigenetic changes in ovarian cancer. Endocrinology150(9), 4003–4011 (2009).
  • Frommer M, McDonald LE, Millar DS et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl Acad. Sci. USA89(5), 1827–1831 (1992).
  • Reeben M, Prydz H. An improved method for detection of 5-methylcytosine by PCR-based genomic sequencing. Biotechniques16(3), 416–417 (1994).
  • Grunau C, Clark SJ, Rosenthal A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res.29(13), E65–E65 (2001).
  • Munson K, Clark J, Lamparska-Kupsik K, Smith SS. Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR. Nucleic Acids Res.35(9), 2893–2903 (2007).
  • Rein T, DePamphilis ML, Zorbas H. Identifying 5-methylcytosine and related modifications in DNA genomes. Nucleic Acids Res.26(10), 2255–2264 (1998).
  • Harrison J, Stirzaker C, Clark SJ. Cytosines adjacent to methylated CpG sites can be partially resistant to conversion in genomic bisulfite sequencing leading to methylation artifacts. Anal. Biochem.264(1), 129–132 (1998).
  • Warnecke PM, Stirzaker C, Melki JR et al. Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res.25(21), 4422–4426 (1997).
  • Eads CA, Danenberg KD, Kawakami K et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res.28(8), E32 (2000).
  • Umbricht CB, Evron E, Gabrielson E et al. Hypermethylation of 14–13–3 sigma (stratifin) is an early event in breast cancer. Oncogene20(26), 3348–3353 (2001).
  • Fackler MJ, McVeigh M, Mehrotra J et al. Quantitative multiplex methylation-specific PCR assay for the detection of promoter hypermethylation in multiple genes in breast cancer. Cancer Res.64(13), 4442–4452 (2004).
  • Givens V, Mitchell GE, Harraway-Smith C, Reddy A, Maness DL. Diagnosis and management of adnexal masses. Am. Fam. Physician80(8), 815–820 (2009).
  • Klimstra DS, Pitman MB, Hruban RH. An algorithmic approach to the diagnosis of pancreatic neoplasms. Arch. Pathol. Lab. Med.133(3), 454–464 (2009).
  • Steinberg W. The clinical utility of the CA 19–19 tumor-associated antigen. Am. J. Gastroenterol.85(4), 350–355 (1990).
  • Moore RG, McMeekin DS, Brown AK et al. A novel multiple marker bioassay utilizing HE4 and CA125 for the prediction of ovarian cancer in patients with a pelvic mass. Gynecol. Oncol.112(1), 40–46 (2009).
  • Leman ES, Getzenberg RH. Biomarkers for prostate cancer. J. Cell. Biochem.108(1), 3–9 (2009).
  • Chatterjee M, Wojciechowski J, Tainsky MA. Discovery of antibody biomarkers using protein microarrays of tumor antigens cloned in high throughput. Methods Mol. Biol.520, 21–38 (2009).
  • Waldman SA, Terzic A. A study of microRNAs in silico and in vivo: diagnostic and therapeutic applications in cancer. FEBS J.276(8), 2157–2164 (2009).
  • Hung EC, Chiu RW, Lo YM. Detection of circulating fetal nucleic acids: a review of methods and applications. J. Clin. Pathol.62(4), 308–313 (2009).
  • Hoque MO, Feng Q, Toure P et al. Detection of aberrant methylation of four genes in plasma DNA for the detection of breast cancer. J. Clin. Oncol.24(26), 4262–4269 (2006).
  • Swarup V, Rajeswari MR. Circulating (cell-free) nucleic acids – a promising, non-invasive tool for early detection of several human diseases. FEBS Lett.581(5), 795–799 (2007).
  • Ellinger J, Albers P, Perabo FG et al. CpG island hypermethylation of cell-free circulating serum DNA in patients with testicular cancer. J. Urol.182(1), 324–329 (2009).
  • Kamat AA, Bischoff FZ, Dang D et al. Circulating cell-free DNA: a novel biomarker for response to therapy in ovarian carcinoma. Cancer Biol. Ther.5(10), 1369–1374 (2006).
  • Wu TL, Zhang D, Chia JH et al. Cell-free DNA: measurement in various carcinomas and establishment of normal reference range. Clin. Chim. Acta321(1–2), 77–87 (2002).
  • Fatouros IG, Destouni A, Margonis K et al. Cell-free plasma DNA as a novel marker of aseptic inflammation severity related to exercise overtraining. Clin. Chem.52(9), 1820–1824 (2006).
  • Taback B, Hoon DS. Circulating nucleic acids in plasma and serum: past, present and future. Curr. Opin. Mol. Ther.6(3), 273–278 (2004).
  • Wong TS, Man MW, Lam AK et al. The study of p16 and p15 gene methylation in head and neck squamous cell carcinoma and their quantitative evaluation in plasma by real-time PCR. Eur. J. Cancer39(13), 1881–1887 (2003).
  • Ramirez JL, Taron M, Balana C et al. Serum DNA as a tool for cancer patient management. Rocz. Akad. Med. Bialymst.48, 34–41 (2003).
  • Melnikov A, Scholtens D, Godwin A, Levenson V. Differential methylation profile of ovarian cancer in tissues and plasma. J. Mol. Diagn.11(1), 60–65 (2009).
  • Illingworth RS, Bird AP. CpG islands – ‘a rough guide’. FEBS Lett.583(11), 1713–1720 (2009).
  • Skvortsova TE, Rykova EY, Tamkovich SN et al. Cell-free and cell-bound circulating DNA in breast tumours: DNA quantification and analysis of tumour-related gene methylation. Br. J. Cancer94(10), 1492–1495 (2006).
  • Benlloch S, Galbis-Caravajal JM, Martin C et al. Potential diagnostic value of methylation profile in pleural fluid and serum from cancer patients with pleural effusion. Cancer107(8), 1859–1865 (2006).
  • Ellinger J, Haan K, Heukamp LC et al. CpG island hypermethylation in cell-free serum DNA identifies patients with localized prostate cancer. Prostate68(1), 42–49 (2008).
  • Goessl C, Muller M, Heicappell R, Krause H, Miller K. DNA-based detection of prostate cancer in blood, urine, and ejaculates. Ann. NY Acad. Sci.945, 51–58 (2001).
  • Papadopoulou E, Davilas E, Sotiriou V et al. Cell-free DNA and RNA in plasma as a new molecular marker for prostate and breast cancer. Ann. NY Acad. Sci.1075, 235–243 (2006).
  • Tani N, Ichikawa D, Ikoma D et al. Circulating cell-free mRNA in plasma as a tumor marker for patients with primary and recurrent gastric cancer. Anticancer Res.27(2), 1207–1212 (2007).
  • Ellinger J, El Kassem N, Heukamp LC et al. Hypermethylation of cell-free serum DNA indicates worse outcome in patients with bladder cancer. J. Urol.179(1), 346–352 (2008).
  • Koyanagi K, Mori T, O’Day SJ et al. Association of circulating tumor cells with serum tumor-related methylated DNA in peripheral blood of melanoma patients. Cancer Res.66(12), 6111–6117 (2006).
  • Wei SH, Balch C, Paik HH et al. Prognostic DNA methylation biomarkers in ovarian cancer. Clin. Cancer Res.12(9), 2788–2794 (2006).
  • Liggett TE, Melnikov AA, Yi Q-L et al. Differential methylation of cell-free circulating DNA among patients with pancreatic cancer versus chronic pancreatitis. Cancer116(7), 1674–1680. (2010).
  • Lindenmeyer MT, Kern C, Sparna T et al. Microarray analysis reveals influence of the sesquiterpene lactone parthenolide on gene transcription profiles in human epithelial cells. Life Sci.80(17), 1608–1618 (2007).
  • Stewart DJ, Issa JP, Kurzrock R et al. Decitabine effect on tumor global DNA methylation and other parameters in a Phase I trial in refractory solid tumors and lymphomas. Clin. Cancer Res.15(11), 3881–3888 (2009).
  • Hegi ME, Diserens AC, Godard S et al. Clinical trial substantiates the predictive value of O-6-methylguanine-DNA methyltransferase promoter methylation in glioblastoma patients treated with temozolomide. Clin. Cancer Res.10(6), 1871–1874 (2004).
  • Paz MF, Yaya-Tur R, Rojas-Marcos I et al. CpG island hypermethylation of the DNA repair enzyme methyltransferase predicts response to temozolomide in primary gliomas. Clin. Cancer Res.10(15), 4933–4938 (2004).
  • Dunn J, Baborie A, Alam F et al. Extent of MGMT promoter methylation correlates with outcome in glioblastomas given temozolomide and radiotherapy. Br. J. Cancer101(1), 124–131 (2009).
  • Wei SH, Brown R, Huang TH. Aberrant DNA methylation in ovarian cancer: is there an epigenetic predisposition to drug response? Ann. NY Acad. Sci.983, 243–250 (2003).
  • Chaudhry P, Srinivasan R, Patel FD. Utility of gene promoter methylation in prediction of response to platinum-based chemotherapy in epithelial ovarian cancer (EOC). Cancer Invest.27(8), 877–884 (2009).
  • Martens JW, Nimmrich I, Koenig T et al. Association of DNA methylation of phosphoserine aminotransferase with response to endocrine therapy in patients with recurrent breast cancer. Cancer Res.65(10), 4101–4117 (2005).
  • Hartmann O, Spyratos F, Harbeck N et al. DNA methylation markers predict outcome in node-positive, estrogen receptor-positive breast cancer with adjuvant anthracycline-based chemotherapy. Clin. Cancer Res.15(1), 315–323 (2009).
  • Suzuki T, Yoshida K, Wada Y et al. Melanoma-associated antigen-A1 expression predicts resistance to docetaxel and paclitaxel in advanced and recurrent gastric cancer. Oncol. Rep.18(2), 329–336 (2007).
  • Brabender J, Arbab D, Huan X et al. Death-associated protein kinase (DAPK) promoter methylation and response to neoadjuvant radiochemotherapy in esophageal cancer. Ann. Surg. Oncol.16(5), 1378–1383 (2009).
  • Augustine CK, Yoo JS, Potti A et al. Genomic and molecular profiling predicts response to temozolomide in melanoma. Clin. Cancer Res.15(2), 502–510 (2009).
  • Wei SH, Chen CM, Strathdee G et al. Methylation microarray analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers. Clin. Cancer Res.8(7), 2246–2252 (2002).
  • Fiegl H, Millinger S, Mueller-Holzner E et al. Circulating tumor-specific DNA: a marker for monitoring efficacy of adjuvant therapy in cancer patients. Cancer Res.65(4), 1141–1145 (2005).
  • Kim YK, Kim WJ. Epigenetic markers as promising prognosticators for bladder cancer. Int. J. Urol.16(1), 17–22 (2009).
  • de Maat MF, van de Velde CJ, van der Werff MP et al. Quantitative analysis of methylation of genomic loci in early-stage rectal cancer predicts distant recurrence. J. Clin. Oncol.26(14), 2327–2335 (2008).
  • Jarmalaite S, Andrekute R, Scesnaite A et al. Promoter hypermethylation in tumour suppressor genes and response to interleukin-2 treatment in bladder cancer: a pilot study. J. Cancer Res. Clin. Oncol. DOI: 10.1007/s00432-009-0725-y (2009) (Epub ahead of print).
  • Owen CM, Segars JH Jr. Imprinting disorders and assisted reproductive technology. Semin. Reprod. Med.27(5), 417–428 (2009).
  • Hattori M, Torii C, Yagihashi T et al. Diagnosis of Russell–Silver syndrome by the combined bisulfite restriction analysis-denaturing high-performance liquid chromatography assay. Genet. Test Mol. Biomarkers13(5), 623–630 (2009).
  • Bird A. The methyl-CpG-binding protein MeCP2 and neurological disease. Biochem. Soc. Trans.36(Pt 4), 575–583 (2008).
  • Behrens MI, Lendon C, Roe CM. A common biological mechanism in cancer and Alzheimer’s disease? Curr. Alzheimer Res.6(3), 196–204 (2009).
  • Kronenberg G, Colla M, Endres M. Folic acid, neurodegenerative and neuropsychiatric disease. Curr. Mol. Med.9(3), 315–323 (2009).
  • Feng J, Fan G. The role of DNA methylation in the central nervous system and neuropsychiatric disorders. Int. Rev. Neurobiol.89, 67–84 (2009).
  • Mastroeni D, McKee A, Grover A, Rogers J, Coleman PD. Epigenetic differences in cortical neurons from a pair of monozygotic twins discordant for Alzheimer’s disease. PLoS ONE4(8), e6617 (2009).
  • Wang SC, Oelze B, Schumacher A. Age-specific epigenetic drift in late-onset Alzheimer’s disease. PLoS ONE3(7), e2698 (2008).
  • Costa E, Chen Y, Dong E et al. GABAergic promoter hypermethylation as a model to study the neurochemistry of schizophrenia vulnerability. Expert Rev. Neurother.9(1), 87–98 (2009).
  • Deutsch SI, Rosse RB, Mastropaolo J, Long KD, Gaskins BL. Epigenetic therapeutic strategies for the treatment of neuropsychiatric disorders: ready for prime time? Clin. Neuropharmacol.31(2), 104–119 (2008).
  • Mastronardi FG, Noor A, Wood DD, Paton T, Moscarello MA. Peptidyl argininedeiminase 2 CpG island in multiple sclerosis white matter is hypomethylated. J. Neurosci. Res.85(9), 2006–2016 (2007).
  • Kobow K, Jeske I, Hildebrandt M et al. Increased reelin promoter methylation is associated with granule cell dispersion in human temporal lobe epilepsy. J. Neuropathol. Exp. Neurol.68(4), 356–364 (2009).
  • Dion V, Wilson JH. Instability and chromatin structure of expanded trinucleotide repeats. Trends Genet.25(7), 288–297 (2009).
  • Kiran M, Chawla YK, Kaur J. Methylation profiling of tumor suppressor genes and oncogenes in hepatitis virus-related hepatocellular carcinoma in northern India. Cancer Genet. Cytogenet.195(2), 112–119 (2009).
  • Nakajima T, Yamashita S, Maekita T et al. The presence of a methylation fingerprint of Helicobacter pylori infection in human gastric mucosae. Int. J. Cancer124(4), 905–910 (2009).
  • Flatley JE, McNeir K, Balasubramani L et al. Folate status and aberrant DNA methylation are associated with HPV infection and cervical pathogenesis. Cancer Epidemiol. Biomarkers Prev.18(10), 2782–2789 (2009).

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.