Sensitive and selective amplification of methylated DNA sequences using helper-dependent chain reaction in combination with a methylation-dependent restriction enzymes

Nucleic Acids Research

Volumn 41, Issue 1, 2013, Pages

  Rand, Keith N ^a   Young, Graeme P ^b   Ho, Thu ^a   Molloy, Peter L ^a  

^a CSIRO   (Australia)

^b FLINDERS UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; OLIGONUCLEOTIDE; RESTRICTION ENDONUCLEASE; RESTRICTION ENDONUCLEASE GLAL; SEPTIN; SEPTIN 9; UNCLASSIFIED DRUG;

AMPLICON; ARTICLE; CONTROLLED STUDY; DNA METHYLATION; DNA SEQUENCE; GENE AMPLIFICATION; HELPER DEPENDENT CHAIN REACTION; HUMAN; HUMAN CELL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN DEGRADATION; SENSITIVITY ANALYSIS;

BASE SEQUENCE; COLORECTAL NEOPLASMS; DNA METHYLATION; DNA RESTRICTION ENZYMES; HUMANS; K562 CELLS; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEPTINS;

EID: 84871790438     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks831     Document Type: Article

References (45)

1. Estecio, M.R. and Issa, J.P. (2011) Dissecting DNA hypermethylation in cancer. FEBS Lett., 585, 2078-2086.
2. van Vlodrop, I.J.H., Niessen, H.E.C., Derks, S., Baldewijns, M., van Criekinge, W., Herman, J.G. and van Engeland, M. (2011) Analysis of Promoter CpG Island Hypermethylation in Cancer: Location, Location, Location! Clin. Cancer Res., 17, 4225-4231.
3. Rodriguez-Paredes, M. and Esteller, M. (2011) Cancer epigenetics reaches mainstream oncology. Nat. Med., 17, 330-339.
4. Hashad, D.I., Hashad, M.M., Talaat, I.M. and Ibrahim, M.A. (2011) Role of glutathione-S-yransferase P1 hypermethylation in molecular detection of prostate cancer. Genet. Test Mol. Biomarkers., 15, 667-670.
5. Hoque, M.O., Topaloglu, O., Begum, S., Henrique, R., Rosenbaum, E., Van Criekinge, W., Westra, W.H. and Sidransky, D. (2005) Quantitative methylation-specific polymerase chain reaction gene patterns in urine sediment distinguish prostate cancer patients from control subjects. J. Clin. Oncol., 23, 6569-6575.
6. Bastian, P.J., Palapattu, G.S., Yegnasubramanian, S., Rogers, C.G., Lin, X., Mangold, L.A., Trock, B., Eisenberger, M.A., Partin, A.W. and Nelson, W.G. (2008) CpG island hypermethylation profile in the serum of men with clinically localized and hormone refractory metastatic prostate cancer. J. Urol., 179, 529-534; discussion 534-525.
7. Baek, Y.H., Chang, E., Kim, Y.J., Kim, B.K., Sohn, J.H. and Park, D.I. (2009) Stool methylation-specific polymerase chain reaction assay for the detection of colorectal neoplasia in Korean patients. Dis. Colon Rectum, 52, 1452-1459; discussion 1459-1463.
8. Chen, W.D., Han, Z.J., Skoletsky, J., Olson, J., Sah, J., Myeroff, L., Platzer, P., Lu, S., Dawson, D., Willis, J. et al. (2005) Detection in fecal DNA of colon cancer-specific methylation of the nonexpressed vimentin gene. J. Natl Cancer Inst., 97, 1124-1132.
9. deVos, T., Tetzner, R., Model, F., Weiss, G., Schuster, M., Distler, J., Grutzmann, R., Pilarsky, C., Habermann, J.K., Fleshner, P. et al. (2009) Circulating Methylated Septin 9 DNA in Plasma Is a Biomarker for Colorectal Cancer. Gastroenterology, 136, A623-A623.
10. Begum, S., Brait, M., Dasgupta, S., Ostrow, K.L., Zahurak, M., Carvalho, A.L., Califano, J.A., Goodman, S.N., Westra, W.H., Hoque, M.O. et al. (2011) An epigenetic marker panel for detection of lung cancer using cell-free serum DNA. Clin. Cancer Res., 17, 4494-4503.
11. Hsu, H.S., Chen, T.P., Hung, C.H., Wen, C.K., Lin, R.K., Lee, H.C. and Wang, Y.C. (2007) Characterization of a multiple epigenetic marker panel for lung cancer detection and risk assessment in plasma. Cancer, 110, 2019-2026.
12. Belinsky, S.A., Klinge, D.M., Dekker, J.D., Smith, M.W., Bocklage, T.J., Gilliland, F.D., Crowell, R.E., Karp, D.D., Stidley, C.A. and Picchi, M.A. (2005) Gene promoter methylation in plasma and sputum increases with lung cancer risk. Clin. Cancer Res., 11, 6505-6511.
13. Brock, M.V., Hooker, C.M., Ota-Machida, E., Han, Y., Guo, M., Ames, S., Glockner, S., Piantadosi, S., Gabrielson, E., Pridham, G. et al. (2008) DNA methylation markers and early recurrence in stage I lung cancer. N. Engl. J. Med., 358, 1118-1128.
14. von Deimling, A., Korshunov, A. and Hartmann, C. (2011) The next generation of glioma biomarkers: MGMT methylation, BRAF fusions and IDH1 mutations. Brain Pathol., 21, 74-87.
15. Hegi, M.E., Diserens, A.C., Godard, S., Dietrich, P.Y., Regli, L., Ostermann, S., Otten, P., Van Melle, G., de Tribolet, N. and Stupp, R. (2004) Clinical trial substantiates the predictive value of O-6-methylguanine-DNA methyltransferase promoter methylation in glioblastoma patients treated with temozolomide. Clin. Cancer Res., 10, 1871-1874.
16. Weller, M., Felsberg, J., Hartmann, C., Berger, H., Steinbach, J.P., Schramm, J., Westphal, M., Schackert, G., Simon, M., Tonn, J.C. et al. (2009) Molecular predictors of progression-free and overall survival in patients with newly diagnosed glioblastoma: a prospective translational study of the German Glioma Network. J. Clin. Oncol., 27, 5743-5750.
17. Brandes, A.A., Franceschi, E., Tosoni, A., Bartolini, S., Bacci, A., Agati, R., Ghimenton, C., Turazzi, S., Talacchi, A., Skrap, M. et al. (2010) O(6)-methylguanine DNA-methyltransferase methylation status can change between first surgery for newly diagnosed glioblastoma and second surgery for recurrence: clinical implications. Neuro. Oncol., 12, 283-288.
18. Brandes, A.A., Franceschi, E., Tosoni, A., Blatt, V., Pession, A., Tallini, G., Bertorelle, R., Bartolini, S., Calbucci, F., Andreoli, A. et al. (2008) MGMT promoter methylation status can predict the incidence and outcome of pseudoprogression after concomitant radiochemotherapy in newly diagnosed glioblastoma patients. J. Clin. Oncol., 26, 2192-2197.
19. Brandes, A.A., Tosoni, A., Franceschi, E., Sotti, G., Frezza, G., Amista, P., Morandi, L., Spagnolli, F. and Ermani, M. (2009) Recurrence pattern after temozolomide concomitant with and adjuvant to radiotherapy in newly diagnosed patients with glioblastoma: correlation With MGMT promoter methylation status. J. Clin. Oncol., 27, 1275-1279.
20. Shivapurkar, N. and Gazdar, A.F. (2010) DNA methylation based biomarkers in non-invasive cancer screening. Curr. Mol. Med., 10, 123-132.
21. Diehl, F., Li, M., Dressman, D., He, Y., Shen, D., Szabo, S., Diaz, L.A. Jr, Goodman, S.N., David, K.A., Juhl, H. et al. (2005) Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc. Natl Acad. Sci. USA, 102, 16368-16373.
22. Clark, S.J., Harrison, J., Paul, C.L. and Frommer, M. (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res., 22, 2990-2997.
23. Herman, J.G., Graff, J.R., Myohanen, S., Nelkin, B.D. and Baylin, S.B. (1996) Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl Acad. Sci. USA, 93, 9821-9826.
24. Kristensen, L.S., Mikeska, T., Krypuy, M. and Dobrovic, A. (2008) Sensitive melting analysis after real time-methylation specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection. Nucleic Acids Res., 36, e42.
25. Rand, K.N., Mitchell, S.M., Clark, S.J. and Molloy, P.L. (2006) Bisulphite differential denaturation PCR for analysis of DNA methylation. Epigenetics, 1, 94-100.
26. Cottrell, S.E., Distler, J., Goodman, N.S., Mooney, S.H., Kluth, A., Olek, A., Schwope, I., Tetzner, R., Ziebarth, H. and Berlin, K. (2004) A real-time PCR assay for DNA-methylation using methylation-specific blockers. Nucleic Acids Res., 32, e10.
27. Rand, K.N., Ho, T., Qu, W., Mitchell, S.M., White, R., Clark, S.J. and Molloy, P.L. (2005) Headloop suppression PCR and its application to selective amplification of methylated DNA sequences. Nucleic Acids Res., 33, e127.
28. Lofton-Day, C., Model, F., DeVos, T., Tetzner, R., Distler, J., Schuster, M., Song, X.L., Lesche, R., Liebenberg, V., Ebert, M. et al. (2008) DNA methylation biomarkers for blood-based colorectal cancer screening. Clin. Chem., 54, 414-423.
29. Devos, T., Lofton-Day, C., Model, F., Sledziewski, A., Liebenberg, V. and Day, R. (2007) Methylated Septin 9 DNA: a biomarker found in blood plasma, for the detection of colorectal cancer. Clin. Chem., 53, A109-A109.
30. Tanaka, K. and Okamoto, A. (2007) Degradation of DNA by bisulfite treatment. Bioorg. Med. Chem. Lett., 17, 1912-1915.
31. Grunau, C., Clark, S.J. and Rosenthal, A. (2001) Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res., 29, E65-E65.
32. Tollefsbol, T.O. (2004) Methods of epigenetic analysis. Methods Mol. Biol., 287, 1-8.
33. Rand, K.N. and Molloy, P.L. (2010) Sensitive measurement of unmethylated repeat DNA sequences by end-specific PCR. Biotechniques, 49, XIII-XVII.
34. Chernukhin, V.A., Najakshina, T.N., Abdurashitov, M.A., Tomilova, J.E., Mezentzeva, N.V., Dedkov, V.S., Mikhnenkova, N.A., Gonchar, D.A. and SKh, D. (2006) A novel restriction endonuclease GlaI recognizes methylated sequence 5′-G(m5C) GC-3′. Biotechnologia, 4, 31-35.
35. Tarasova, G.V., Nayakshina, T.N. and Degtyarev, S.K.H. (2008) Substrate specificity of new methyl-directed DNA endonuclease GlaI. BMC Mol. Biol., 9, 7-18.
36. Wagner, I. and Capesius, I. (1981) Determination of 5-methylcytosine from plant DNA by high-performance liquid chromatography. Biochim. Biophys. Acta, 654, 52-56.
37. Wojdacz, T.K., Hansen, L.L. and Dobrovic, A. (2008) A new approach to primer design for the control of PCR bias in methylation studies. BMC Res. Notes, 1, 54-56.
38. Cradic, K.W., Wells, J.E., Allen, L., Kruckeberg, K.E., Singh, R.J. and Grebe, S.K. (2004) Substitution of 3'-phosphate cap with a carbon-based blocker reduces the possibility of fluorescence resonance energy transfer probe failure in real-time PCR assays. Clin. Chem., 50, 1080-1082.
39. Stump, M.D., Cherry, J.L. and Weiss, R.B. (1999) The use of modified primers to eliminate cycle sequencing artifacts. Nucleic Acids Res., 27, 4642-4648.
40. Watkins, N.E. Jr and SantaLucia, J. Jr (2005) Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Res., 33, 6258-6267.
41. Zheng, Y., Cohen-Karni, D., Xu, D., Chin, H.G., Wilson, G., Pradhan, S. and Roberts, R.J. (2010) A unique family of Mrr-like modification-dependent restriction endonucleases. Nucleic Acids Res., 38, 5527-5534.
42. Ehrich, M., Zoll, S., Sur, S. and van den Boom, D. (2007) A new method for accurate assessment of DNA quality after bisulfite treatment. Nucleic Acids Res., 35, e29.
43. Taylor, K.H., Kramer, R.S., Davis, J.W., Guo, J., Duff, D.J., Xu, D., Caldwell, C.W. and Shi, H. (2007) Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res., 67, 8511-8518.
44. Warnecke, P.M., Stirzaker, C., Song, J., Grunau, C., Melki, J.R. and Clark, S.J. (2002) Identification and resolution of artifacts in bisulfite sequencing. Methods, 27, 101-107.
45. Oster, B., Thorsen, K., Lamy, P., Wojdacz, T.K., Hansen, L.L., Birkenkamp-Demtroder, K., Sørensen, K.D., Laurberg, S., Orntoft, T.F. and Andersen, C.L. (2011) Identification and validation of highly frequent CpG island hypermethylation in colorectal adenomas and carcinomas. Int. J. Cancer, 129, 2855-2866.