A closed-tube methylation-sensitive high resolution melting assay (MS-HRMA) for the semi-quantitative determination of CST6 promoter methylation in clinical samples

BMC Cancer

Volumn 12, Issue , 2012, Pages

  Dimitrakopoulos, Lampros ^a   Vorkas, Panagiotis A ^a,c   Georgoulias, Vasilis ^b   Lianidou, Evi S ^a  

^a UNIVERSITY OF ATHENS   (Greece)

^b UNIVERSITY HOSPITAL OF HERAKLION   (Greece)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Breast cancer; CST6; Cystatin M; DNA methylation; Methylation specific PCR; Methylation sensitive high resolution melting analysis

Indexed keywords

ESTROGEN RECEPTOR; PROGESTERONE RECEPTOR;

ADULT; ARTICLE; BIOASSAY; BREAST CANCER; CANCER GRADING; CONTROLLED STUDY; CST6 GENE; DNA METHYLATION; DNA MODIFICATION; FEMALE; GENE AMPLIFICATION; GENE SEQUENCE; HUMAN; HUMAN TISSUE; METHYLATION SENSITIVE HIGH RESOLUTION MELTING ANALYSIS ASSAY; ONCOGENE; PILOT STUDY; POLYMERASE CHAIN REACTION; PROCESS OPTIMIZATION; PROMOTER REGION; SENSITIVITY AND SPECIFICITY;

BASE SEQUENCE; BREAST NEOPLASMS; CYSTATIN M; DNA METHYLATION; DNA, NEOPLASM; FEMALE; HUMANS; MIDDLE AGED; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; TRANSITION TEMPERATURE;

EID: 84867660686     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/1471-2407-12-486     Document Type: Article

References (47)

1. Laird PW. The power and promise of DNA methylation markers. Nat Rev Cancer 2003, 3:253-266. 10.1038/nrc1045, 12671664.
2. Ferguson AT, Evron E, Umbricht CB, Pandita TK, Chan TA, Hermeking H, Marks JR, Lambers AR, Futreal PA, Stampfer MR, Sukumar S. High frequency of hypermethylation at the 14.3.3 sigma locus leads to gene silencing in breast cancer. Proc Natl Acad Sci USA 2000, 97:6049-6054. 10.1073/pnas.100566997, 18556, 10811911.
3. Esteller M. Epigenetics in cancer (Review). N Engl J Med 2008, 358:1148-1159. 10.1056/NEJMra072067, 18337604.
4. Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet 2002, 3:415-428.
5. Esteller M. CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future. Oncogene 2002, 21:5427-5440. 10.1038/sj.onc.1205600, 12154405.
6. Wojdacz TK, Dobrovic A, Hansen LL. Methylation-sensitive high-resolution melting. Nat Protoc 2008, 3:1903-1908. 10.1038/nprot.2008.191, 19180074.
7. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-Resolution Genotyping by Amplicon Melting Analysis Using LCGreen. Clin Chem 2003, 49:853-860. 10.1373/49.6.853, 12765979.
8. Reed GH, Wittwer CT. Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 2004, 50:1748-1754. 10.1373/clinchem.2003.029751, 15308590.
9. Liew M, Pryor R, Palais R, Meadows C, Erali M, Lyon E, Wittwer C. Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin Chem 2004, 50:1156-1164. 10.1373/clinchem.2004.032136, 15229148.
10. Gundry CN, Dobrowolski SF, Martin YR, Robbins TC, Nay LM, Boyd N. Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons. Nucleic Acids Res 2008, 36:3401-3408. 10.1093/nar/gkn204, 2425497, 18448472.
11. Krypuy M, Newnham GM, Thomas DM, Conron M, Dobrovic A. High resolution melting analysis for the rapid and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutations in non-small cell lung cancer. BMC Cancer 2006, 6:295. 10.1186/1471-2407-6-295, 1769510, 17184525.
12. Zhou L, Wang Y, Wittwer CT. Rare allele enrichment and detection by allele-specific PCR, competitive probe blocking and melting analysis. Biotechniques 2011, 50:311-318.
13. Wojdacz TK, Dobrovic A. Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res 2007, 35:e41. 10.1093/nar/gkm013, 1874596, 17289753.
14. Turk V, Bode W. The cystatins: protein inhibitors of cystein proteininases. FEBS Lett 1991, 285:213-219. 10.1016/0014-5793(91)80804-C, 1855589.
15. Sotiropoulou G, Anisowicz A, Sager R. Identification, cloning, and characterization of cystatin M, a novel cysteine proteinase inhibitor, down-regulated in breast cancer. J Biol Chem 1997, 272:903-910. 10.1074/jbc.272.2.903, 8995380.
16. Ni J, Abrahamson M, Zhang M, Fernandez MA, Grubb A, Su J, Yu GL, Li Y, Parmelee D, Xing L, Coleman TA, Gentz S, Thotakura R, Nguyen N, Hesselberg M, Gentz R. Cystatin E is a novel human cysteine proteinase inhibitor with structural resemblance to family 2 cystatins. J Biol Chem 1997, 272:10853-10858. 10.1074/jbc.272.16.10853, 9099741.
17. Stenman G, Astrom AK, Roijer E, Sotiropoulou G, Zhang M, Sager R. Assignment of a novel cysteine proteinase inhibitor (CST6) to 11q13 by fluorescence in situ hybridization. Cytogenet Cell Gent 1997, 76:45-46.
18. Zeeuwen PL, Cheng T, Schalkwijk J. The biology of cystatin M/E and its cognate target proteases. J Invest Dermatol 2009, 129:1327-1338. 10.1038/jid.2009.40, 19262604.
19. Cheng T, Hitomi K, van Vlijmen-Willems IM, de Jongh GJ, Yamamoto K, Nishi K, Watts C, Reinheckel T, Schalkwijk J, Zeeuwen PL. Cystatin M/E is a high affinity inhibitor of cathepsin V and cathepsin L by a reactive site that is distinct from the legumain-binding site. A novel clue for the role of cystatin M/E in epidermal cornification. J Biol Chem 2006, 281:15893-15899. 10.1074/jbc.M600694200, 16565075.
20. Gawenda J, Traub F, Lück HJ, Kreipe H, von Wasielewski R. Legumain expression as a prognostic factor in breast cancer patients. Breast Cancer Res Treat 2007, 102:1-6. 10.1007/s10549-006-9311-z, 17028987.
21. Murthy RV, Arbman G, Gao J, Roodman GD, Sun XF. Legumain expression in relation to clinicopathologic and biological variables in colorectal cancer. Clin Cancer Res 2005, 11:2293-2299. 10.1158/1078-0432.CCR-04-1642, 15788679.
22. Mohamed MM, Sloane BF. Cysteine cathepsins: multifunctional enzymes in cancer. Nat Rev Cancer 2006, 6:764-775. 10.1038/nrc1949, 16990854.
23. Ai L, Kim W, Kim TY, Fields CR, Massoll NA, Robertson KD, Brown KD. Epigenetic silencing of the tumor suppressor cystatin M occurs during breast cancer progression. Cancer Res 2006, 66:7899-7909. 10.1158/0008-5472.CAN-06-0576, 16912163.
24. Rivenbark AG, Jones WD, Coleman WB. DNA methylation-dependent silencing of CST6 in human breast cancer cell lines. Lab Invest 2006, 86:1233-1242. 10.1038/labinvest.3700485, 17043665.
25. Schagdarsurengin U, Pfeifer GP, Dammann R. Frequent epigenetic inactivation of cystatin M in breast carcinoma. Oncogene 2007, 26:3089-3094. 10.1038/sj.onc.1210107, 17099723.
26. Kioulafa M, Balkouranidou I, Sotiropoulou G, Kaklamanis L, Mavroudis D, Georgoulias V, Lianidou ES. Methylation of cystatin M promoter is associated with unfavorable prognosis in operable breast cancer. Int J Cancer 2009, 125:2887-2892. 10.1002/ijc.24686, 19551853.
27. Chimonidou M, Strati A, Tzitzira A, Sotiropoulou G, Malamos N, Georgoulias V, Lianidou ES. DNA methylation of tumor suppressor and metastasis suppressor genes in circulating tumor cells. Clin Chem 2011, 57:1169-1177. 10.1373/clinchem.2011.165902, 21700955.
28. Kroupis C, Christopoulos K, Devetzoglou M, Tsiagas I, Lianidou ES. Asymmetric real-time PCR detection of BRCA1 5382insC mutation by melting curve analysis in the LightCycler. Clin Chim Acta 2008, 390:141-144. 10.1016/j.cca.2007.12.024, 18242166.
29. Warnecke PM, Stirzaker C, Melki JR, Millar DS, Paul CL, Clark SJ. Detection and measurement of PCR bias in quantitative methylation analysis of bisulphate-treated DNA. Nucleic Acids Res 1997, 25:4422-4426. 10.1093/nar/25.21.4422, 147052, 9336479.
30. Wojdacz TK, Borgbo T, Hansen LL. Primer design versus PCR bias in methylation independent PCR amplifications. Epigenetics 2009, 4(4):231-234.
31. Wojdacz TK, Dobrovic A. Melting curve assays for DNA methylation analysis. Methods Mol Biol 2009, 507:229-240. 10.1007/978-1-59745-522-0_17, 18987818.
32. Wojdacz TK, Hansen LL, Dobrovic A. A new approach to primer design for the control of PCR bias in methylation studies. BMC Res Notes. 2008, 1:54. 10.1186/1756-0500-1-54, 2525644, 18710507.
33. Wojdacz TK, Hansen LL. Reversal of PCR bias for improved sensitivity of the DNA methylation melting curve assay. Biotechniques 2006, 41:274, 276-278.
34. Rivenbark AG, Livasy CA, Boyd CE, Keppler D, Coleman WB. Methylation-dependent silencing of CST6 in primary human breast tumors and metastatic lesions. Exp Mol Pathol 2007, 83:188-197. 10.1016/j.yexmp.2007.03.008, 2693953, 17540367.
35. Kundel HL, Polansky M. Measurement of observer agreement. Radiology 2003, 228:303-308. 10.1148/radiol.2282011860, 12819342.
36. Qiu J, Ai L, Ramachandran C, Yao B, Gopalakrishnan S, Fields CR, Delmas AL, Dyer LM, Melnick SJ, Yachnis AT, Schwartz PH, Fine HA, Brown KD, Robertson KD. Invasion suppressor cystatin E/M (CST6): high-level cell type-specific expression in normal brain and epigenetic silencing in gliomas. Lab Invest 2008, 88:910-925. 10.1038/labinvest.2008.66, 2574902, 18607344.
37. Veena MS, Lee G, Keppler D, Mendonca MS, Redpath JL, Stanbridge EJ, Wilczynski SP, Srivatsan ES. Inactivation of the cystatin E/M tumor suppressor gene in cervical cancer. Genes Chromosomes Cancer 2008, 47:740-754. 10.1002/gcc.20576, 2974630, 18506750.
38. Pulukuri SM, Gorantla B, Knost JA, Rao JS. Frequent loss of cystatin E/M expression implicated in the progression of prostate cancer. Oncogene 2009, 28:2829-2838. 10.1038/onc.2009.134, 2722685, 19503093.
39. Lin HJ, et al. Breast cancer-associated fibroblasts confer AKT1-mediated epigenetic silencing of Cystatin M in epithelial cells. Cancer Res 2008, 68:10257-10266. 10.1158/0008-5472.CAN-08-0288, 2821873, 19074894.
40. Radpour R, Kohler C, Haghighi MM, Fan AX, Holzgreve W, Zhong XY. Methylation profiles of 22 candidate genes in breast cancer using high-throughput MALDI-TOF mass array. Oncogene 2009, 28:2969-2978. 10.1038/onc.2009.149, 19503099.
41. Rodenhiser DI, Andrews J, Kennette W, Sadikovic B, Mendlowitz A, Tuck AB, Chambers AF. Epigenetic mapping and functional analysis in a breast cancer metastasis model using whole-genome promoter tiling microarrays. Breast Cancer Res 2008, 10:R62. 10.1186/bcr2121, 2575535, 18638373.
42. Morris MR, Ricketts C, Gentle D, Abdulrahman M, Clarke N, Brown M, Kishida T, Yao M, Latif F, Maher ER. Identification of candidate tumour suppressor genes frequently methylated in renal cell carcinoma. Oncogene 2010, 29:2104-2117. 10.1038/onc.2009.493, 3021900, 20154727.
43. Ko E, Park SE, Cho EY, Kim Y, Hwang JA, Lee YS, Nam SJ, Bang S, Park J, Kim DH. Cystatin M loss is associated with the losses of estrogen receptor, progesterone receptor, and HER4 in invasive breast cancer. Breast Cancer Res 2010, 12:R100. 10.1186/bcr2783, 3046445, 21092257.
44. Dahl C, Guldberg P. High-Resolution Melting for Accurate Assessment of DNA Methylation. Clin Chem (editorial) 2007, 53:1877-1878.
45. Worm J, Aggerholm A, Guldberg P. In-tube DNA methylation profiling by fluorescence melting curve analysis. Clin Chem 2001, 47:1183-1189.
46. Guldberg P, Worm J, Grønbæk K. Profiling DNA methylation by melting analysis. Methods 2002, 27:121-127. 10.1016/S1046-2023(02)00063-4, 12095269.
47. Dahl C, Grønskov K, Larsen LA, Guldberg P, Brøndum-Nielsen K. A homogeneous assay for analysis of FMR1 promoter methylation in patients with fragile X syndrome. Clin Chem 2007, 53:790-793. 10.1373/clinchem.2006.080762, 17259243.