Novel multiplex methylight protocol for detection of DNA methylation in patient tissues and bodily fluids

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Olkhov Mitsel, Ekaterina ^a,b   Zdravic, Darko ^a,b   Kron, Ken ^c   Van Der Kwast, Theodorus ^b,d   Fleshner, Neil ^d   Bapat, Bharati ^a,b,d  

^a MOUNT SINAI HOSPITAL   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c PRINCESS MARGARET HOSPITAL   (Canada)

^d UNIVERSITY HEALTH NETWORK   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

APC PROTEIN; APC PROTEIN, HUMAN; DNA; HOMEODOMAIN PROTEIN; HOXD3 PROTEIN, HUMAN; PRIMER DNA; TGFB2 PROTEIN, HUMAN; TRANSFORMING GROWTH FACTOR BETA2;

ARTICLE; CHEMISTRY; CPG ISLAND; DNA METHYLATION; GENETICS; HUMAN; MALE; METHODOLOGY; MULTIPLEX POLYMERASE CHAIN REACTION; PROMOTER REGION; PROSTATE TUMOR; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; TUMOR CELL LINE; URINE;

ADENOMATOUS POLYPOSIS COLI PROTEIN; CELL LINE, TUMOR; CPG ISLANDS; DNA METHYLATION; DNA PRIMERS; DNA, NEOPLASM; HOMEODOMAIN PROTEINS; HUMANS; MALE; MULTIPLEX POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; PROSTATIC NEOPLASMS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; TRANSFORMING GROWTH FACTOR BETA2;

EID: 84898902068     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep04432     Document Type: Article

References (44)

1. Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915-926 (1992).
2. Baylin, S. B., Herman, J. G., Graff, J. R., Vertino, P. M. & Issa, J. P. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res 72, 141-196 (1998).
3. Goelz, S. E., Vogelstein, B., Hamilton, S. R. & Feinberg, A. P. Hypomethylation of DNA from benign and malignant human colon neoplasms. Science 228, 187-190 (1985).
4. Jones, P. A. & Laird, P. W. Cancer epigenetics comes of age. Nat Genet 21, 163-167, doi:10.1038/5947 (1999).
5. Fenaux, P. et al. Efficacy of azacitidine compared with that of conventional care regimens in the treatment of higher-risk myelodysplastic syndromes: a randomised, open-label, phase III study. Lancet Oncol 10, 223-232, doi:10.1016/S1470-2045(09)70003-8 (2009).
6. Brock, M. V. et al. DNA methylation markers and early recurrence in stage I lung cancer. N Engl J Med 358, 1118-1128, doi:10.1056/NEJMoa0706550 (2008).
7. Esteller, M. et al. Inactivation of glutathione S-transferase P1 gene by promoter hypermethylation in human neoplasia. Cancer Res 58, 4515-4518 (1998).
8. Esteller, M. et al. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med 343, 1350-1354, doi:10.1056/NEJM200011093431901 (2000).
9. Milani, L. et al. DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia. Blood 115, 1214-1225, doi:10.1182/blood-2009-04-214668 (2010).
10. Muller, H. M. et al. DNA methylation in serum of breast cancer patients: an independent prognostic marker. Cancer Res 63, 7641-7645 (2003).
11. Rawson, J. B. 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 32, 741-747, doi:10.1093/carcin/ bgr020 (2011).
12. Nikolaidis, G. et al. DNA methylation biomarkers offer improved diagnostic efficiency in lung cancer. Cancer Res 72, 5692-5701, doi:10.1158/0008-5472.CAN-12-2309 (2012).
13. Esteller, M., Corn, P. G., Baylin, S. B. & Herman, J. G. A gene hypermethylation profile of human cancer. Cancer Res 61, 3225-3229 (2001).
14. Paluszczak, J. & Baer-Dubowska, W. Epigenetic diagnostics of cancer-the application of DNA methylation markers. J Appl Genet 47, 365-375, doi:10.1007/BF03194647 (2006).
15. Rodriguez-Paredes, M. & Esteller, M. Cancer epigenetics reaches mainstream oncology. Nat Med 17, 330-339, doi:10.1038/nm.2305 (2011).
16. Herman, J. G. & Baylin, S. B. Methylation-specific PCR. Curr Protoc Hum Genet Chapter 10, Unit 10 16; doi:10.1002/0471142905.hg1006s16 (2001).
17. Trinh, B. N., Long, T. I. & Laird, P. W. DNA methylation analysis by Methy Light technology. Methods 25, 456-462, doi:10.1006/meth.2001.1268 (2001).
18. Eads, C. A. et al. Methy Light: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 28, E32 (2000).
19. Kron, K. et al. Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays. PLoS One 4, e4830, doi:10.1371/journal.pone.0004830 (2009).
20. Kron, K. J. et al. DNA methylation of HOXD3 as a marker of prostate cancer progression. Lab Invest 90, 1060-1067, doi:10.1038/labinvest.2010.57 (2010).
21. Liu, L. et al. Association of tissue promoter methylation levels of APC, TGFbeta2, HOXD3 and RASSF1A with prostate cancer progression. Int J Cancer 129, 2454-2462, doi:10.1002/ijc.25908 (2011).
22. Weisenberger, D. J. et al. Analysis of repetitive element DNA methylation by Methy Light. Nucleic Acids Res 33, 6823-6836, doi:10.1093/nar/gki987 (2005).
23. Brownie, J. et al. The elimination of primer-dimer accumulation in PCR. Nucleic Acids Res 25, 3235-3241 (1997).
24. Koshkin, A. A. & Wengel, J. Synthesis of Novel 29,39-Linked Bicyclic Thymine Ribonucleosides. J Org Chem 63, 2778-2781 (1998).
25. Reynisson, E., Josefsen, M. H., Krause, M. & Hoorfar, J. Evaluation of probe chemistries and platforms to improve the detection limit of real-time PCR. J Microbiol Methods 66, 206-216, doi:10.1016/j.mimet.2005.11.006 (2006).
26. Dahl, C.&Guldberg, P. Aligation assay for multiplex analysis of CpG methylation using bisulfite-treated DNA. Nucleic Acids Res 35, e144, doi:10.1093/nar/gkm984 (2007).
27. Hung, C. C. et al. Identification of CpG methylation of the SNRPN gene by methylation-specific multiplex PCR. Electrophoresis 30, 410-416, doi:10.1002/elps.200800225 (2009).
28. Wang, J., Yu, M., Li, K., Xiao, J.&Zhou, Y. Improved PCR-BSP assay for multiplex methylation pattern analysis in minimal amount of DNA. Mol Biotechnol 42, 333-340, doi:10.1007/s12033-009-9169-5 (2009).
29. Shi, X., Tang, C., Zhou, D., Zhao, H. & Lu, Z. Multiplex detection of CpG methylation using microarray combining with target-selection-padlock probe. Clin Chim Acta 411, 1187-1194, doi:10.1016/j.cca.2010.03.026 (2010).
30. Zerilli, F. et al. Methylation-specific loop-mediated isothermal amplification for detecting hypermethylatedDNAin simplex and multiplex formats. Clin Chem 56, 1287-1296, doi:10.1373/clinchem.2010.143545 (2010).
31. Bormann, F. et al. Methylation-specific ligation detection reaction (msLDR): a new approach for multiplex evaluation of methylation patterns. Mol Genet Genomics 286, 279-291, doi:10.1007/s00438-011-0645-9 (2011).
32. Zhang, Z. et al. Development of a non-invasive method, multiplex methylation specific PCR (MMSP), for early diagnosis of nasopharyngeal carcinoma. PLoS One 7, e45908, doi:10.1371/journal.pone.0045908 (2012).
33. Zou, H. et al. Quantification of methylated markers with amultiplex methylationspecific technology. Clin Chem 58, 375-383, doi:10.1373/clinchem. 2011.171264 (2012).
34. Mokany, E., Tan, Y. L., Bone, S. M., Fuery, C. J. & Todd, A. V. MNAzyme qPCR with superior multiplexing capacity. Clin Chem 59, 419-426, doi:10.1373/clinchem.2012.192930 (2013).
35. Zhang, Q. et al. A multiplex methylation-specific PCR assay for the detection of early-stage ovarian cancer using cell-free serum DNA. Gynecol Oncol 130, 132-139, doi:10.1016/j.ygyno.2013.04.048 (2013).
36. Kandimalla, R. et al. A 3-Plex Methylation Assay Combined with the FGFR3 Mutation Assay Sensitively Detects Recurrent Bladder Cancer in Voided Urine. Clin Cancer Res, doi:10.1158/1078-0432.CCR-12-3276 (2013).
37. Fackler, M. J. et al. Quantitative multiplex methylation-specific PCR assay for the detection of promoter hypermethylation in multiple genes in breast cancer. Cancer Res 64, 4442-4452, doi:10.1158/0008-5472.CAN-03-3341 (2004).
38. He, Q. et al. Development of a multiplex Methy Light assay for the detection of multigene methylation in human colorectal cancer. Cancer Genet Cytogenet 202, 1-10, doi:10.1016/j.cancergencyto.2010.05.018 (2010).
39. Snellenberg, S. et al. Development of a multiplex methylation-specific PCR as candidate triage test for women with an HPV-positive cervical scrape. BMC Cancer 12, 551; doi:10.1186/1471-2407-12-551 (2012).
40. Van Neste, L. et al. A tissue biopsy-based epigenetic multiplex PCR assay for prostate cancer detection. BMC Urol 12, 16; doi:10.1186/1471-2490-12-16 (2012).
41. Weisenberger, D. J. et al. DNA methylation analysis by digital bisulfite genomic sequencing and digital Methy Light. Nucleic Acids Res 36, 4689-4698, doi:10.1093/nar/gkn455 (2008).
42. Rawson, J. B. & Bapat, B. Epigenetic biomarkers in colorectal cancer diagnostics. Expert Rev Mol Diagn 12, 499-509, doi:10.1586/erm.12.39 (2012).
43. Lee, B. B. et al. Aberrant methylation of APC, MGMT, RASSF2A, and Wif-1 genes in plasma as a biomarker for early detection of colorectal cancer. Clin Cancer Res 15, 6185-6191, doi:10.1158/1078-0432.CCR-09-0111 (2009).
44. Olkhov-Mitsel, E. et al. Quantitative DNA methylation analysis of genes coding for kallikrein-related peptidases 6 and 10 as biomarkers for prostate cancer. Epigenetics 7, 1037-1045, doi:10.4161/epi.21524 (2012).