Methylation profiling of normal individuals reveals mosaic: Promoter methylation of cancer-associated genes

Oncotarget

Volumn 3, Issue 4, 2012, Pages 450-461

  Kristensen, Lasse Sommer ^a,b   Raynor, Michael ^c   Candiloro, Ida ^a,d   Dobrovic, Alexander ^a,d  

^a PETER MACCALLUM CANCER CENTRE   (Australia)

^b AARHUS UNIVERSITY   (Denmark)

^c QUEEN ELIZABETH HOSPITAL   (Australia)

^d UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Biomarkers; constitutional methylation; DNA methylation; Epigenetics; High resolution melting (HRM); methylation specific PCR (MSP)

Indexed keywords

APC PROTEIN; BRCA1 PROTEIN; CYCLIN DEPENDENT KINASE INHIBITOR 2A; DNA; GLUTATHIONE TRANSFERASE P1; RAS ASSOCIATION DOMAIN FAMILY PROTEIN 1A; UVOMORULIN; CADHERIN; CDH1 PROTEIN, HUMAN; HIC1 PROTEIN, HUMAN; KRUPPEL LIKE FACTOR; NUCLEAR PROTEIN; TRANSCRIPTION FACTOR TWIST; TUMOR MARKER; TWIST1 PROTEIN, HUMAN;

ACCURACY; ADULT; AGED; ARTICLE; CDH1 GENE; CDKN2A GENE; CONTROLLED STUDY; DAPK1 GENE; DNA METHYLATION; FALSE POSITIVE RESULT; FEMALE; GENE; GENE IDENTIFICATION; GENE LOCATION; GENE LOCUS; GENETIC ASSOCIATION; GSTP1 GENE; HIC1 GENE; HIGH RESOLUTION MELTING ANALYSIS; HUMAN; HUMAN CELL; MALE; MOLECULAR DYNAMICS; ONCOGENE; PERIPHERAL BLOOD MONONUCLEAR CELL; PHENOTYPE; PROMOTER REGION; QUANTITATIVE ANALYSIS; RARB GENE; RASSF1A GENE; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; TUMOR SUPPRESSOR GENE; TWIST1 GENE; CYTOLOGY; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; METABOLISM; MONONUCLEAR CELL; NEOPLASM;

CADHERINS; DNA METHYLATION; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE SILENCING; HUMANS; KRUPPEL-LIKE TRANSCRIPTION FACTORS; LEUKOCYTES, MONONUCLEAR; NEOPLASMS; NUCLEAR PROTEINS; PROMOTER REGIONS, GENETIC; TUMOR MARKERS, BIOLOGICAL; TWIST TRANSCRIPTION FACTOR;

EID: 84867184362     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.480     Document Type: Article

References (40)

1. Hochedlinger K, Blelloch R, Brennan C, Yamada Y, Kim M, Chin L, Jaenisch R. Reprogramming of a melanoma genome by nuclear transplantation. Genes & Development. 2004; 18:1875-1885.
2. Schuebel KE, Chen W, Cope L, Glockner SC, Suzuki H, Yi JM, Chan TA, Van Neste L, Van Criekinge W, van den Bosch S, van Engeland M, Ting AH, Jair K, Yu W, Toyota M, Imai K, et al. Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genetics. 2007; 3:1709-1723.
3. Ushijima T, Asada K. Aberrant DNA methylation in contrast with mutations. Cancer Science. 2010; 101: 300-305.
4. Wade PA. Methyl CpG binding proteins: coupling chromatin architecture to gene regulation. Oncogene. 2001; 20:3166-3173.
5. Laird PW. The power and the promise of DNA methylation markers. Nature Reviews Cancer. 2003; 3:253-266.
6. Shi H, Wang MX, Caldwell CW. CpG islands: their potential as biomarkers for cancer. Expert Review of Molecular Diagnostics. 2007; 7:519-531.
7. Cottrell SE, Laird PW. Sensitive detection of DNA methylation. Annals of the New York Academy of Sciences. 2003; 983:120-130.
8. Mikeska T, Bock C., Do H, Dobrovic A. DNA methylation biomarkers in cancer: progress towards clinical implementation. Expert Review of Molecular Diagnostics (accepted for publication)
9. Dobrovic A. (2005). Methods for Analysis of DNA Methylation. In: Coleman WB and Tsongalis GJ, eds. Molecular diagnostics for the clinical laboratorian (Totowa, NJ: Humana Press), pp. 149-160.
10. Kristensen LS, Hansen LL. PCR-based methods for detecting single-locus DNA methylation biomarkers in cancer diagnostics, prognostics, and response to treatment. Clinical Chemistry. 2009; 55:1471-1483.
11. Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proceedings of the National Academy of Sciences of the United States of America. 1996; 93:9821-9826.
12. Kristensen LS, Mikeska T, Krypuy M, Dobrovic A. Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probefree quantitative DNA methylation detection. Nucleic Acids Research. 2008; 36:e42.
13. Rand K, Qu W, Ho T, Clark SJ, Molloy P. Conversionspecific detection of DNA methylation using real-time polymerase chain reaction (ConLight-MSP) to avoid false positives. Methods. 2002; 27:114-120.
14. Shaw RJ, Akufo-Tetteh EK, Risk JM, Field JK, Liloglou T. Methylation enrichment pyrosequencing: combining the specificity of MSP with validation by pyrosequencing. Nucleic Acids Research. 2006; 34:e78.
15. Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, Danenberg PV, Laird PW. MethyLight: a highthroughput assay to measure DNA methylation. Nucleic Acids Research. 2000; 28:E32.
16. Kristensen LS, Wojdacz TK, Thestrup BB, Wiuf C, Hager H, Hansen LL. Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMARTMSP and MS-HRM. BMC Cancer. 2009; 9:453.
17. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicon melting analysis using LC Green. Clinical Chemistry. 2003; 49:853-860.
18. Gudnason H, Dufva M, Bang DD, Wolff A. Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature. Nucleic Acids Research. 2007; 35:e127.
19. Belinsky SA, Nikula KJ, Palmisano WA, Michels R, Saccomanno G, Gabrielson E, Baylin SB, Herman JG. Aberrant methylation of p16(INK4a) is an early event in lung cancer and a potential biomarker for early diagnosis. Proceedings of the National Academy of Sciences of the United States of America. 1998; 95:11891-11896.
20. Palmisano WA, Divine KK, Saccomanno G, Gilliland FD, Baylin SB, Herman JG, Belinsky SA. Predicting lung cancer by detecting aberrant promoter methylation in sputum. Cancer Research. 2000; 60:5954-5958.
21. Hoque MO, Topaloglu O, Begum S, Henrique R, Rosenbaum E, Van Criekinge W, Westra WH, Sidransky D. Quantitative methylation-specific polymerase chain reaction gene patterns in urine sediment distinguish prostate cancer patients from control subjects. Journal of Clinical Oncology. 2005; 23:6569-6575.
22. Wang YC, Yu ZH, Liu C, Xu LZ, Yu W, Lu J, Zhu RM, Li GL, Xia XY, Wei XW, Ji HZ, Lu H, Gao Y, Gao WM, Chen LB. Detection of RASSF1A promoter hypermethylation in serum from gastric and colorectal adenocarcinoma patients. World Journal of Gastroenterol. 2008; 14:3074-3080.
23. Wong EM, Southey MC, Fox SB, Brown MA, Dowty JG, Jenkins MA, Giles GG, Hopper JL, Dobrovic A. Constitutional methylation of the BRCA1 promoter is specifically associated with BRCA1 mutation-associated pathology in early-onset breast cancer. Cancer Prev Res (Phila). 2011; 4:23-33.
24. Evron E, Dooley WC, Umbricht CB, Rosenthal D, Sacchi N, Gabrielson E, Soito AB, Hung DT, Ljung B, Davidson NE, Sukumar S. Detection of breast cancer cells in ductal lavage fluid by methylation-specific PCR. Lancet. 2001; 357:1335-1336.
25. Lombaerts M, Middeldorp JW, van der Weide E, Philippo K, van Wezel T, Smit VT, Cornelisse CJ, Cleton-Jansen AM. Infiltrating leukocytes confound the detection of E-cadherin promoter methylation in tumors. Biochemical and Biophysical Research Communications. 2004; 319:697-704.
26. Reddy AN, Jiang WW, Kim M, Benoit N, Taylor R, Clinger J, Sidransky D, Califano JA. Death-associated protein kinase promoter hypermethylation in normal human lymphocytes. Cancer Research. 2003; 63:7694-7698.
27. 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. Clinical Chemistry. 2004; 50:1156-1164.
28. Kristensen LS, Dobrovic A. Direct genotyping of single nucleotide polymorphisms in methyl metabolism genes using probe-free high-resolution melting analysis. Cancer Epidemiology, Biomarkers & Prevention. 2008; 17:1240-1247.
29. Candiloro IL, Mikeska T, Hokland P, Dobrovic A. Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene. Epigenetics Chromatin. 2008; 1:7.
30. Weisenberger DJ, Trinh BN, Campan M, Sharma S, Long TI, Ananthnarayan S, Liang G, Esteva FJ, Hortobagyi GN, McCormick F, Jones PA, Laird PW. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Research. 2008; 36:4689-4698.
31. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proceedings of the National Academy of Sciences of the United States of America. 1992; 89:1827-1833
32. Taylor KH, Kramer RS, Davis JW, Guo J, Duff DJ, Xu D, Caldwell CW, Shi H. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Research. 2007; 67:8511-8518.
33. Mikeska T, Candiloro IL, Dobrovic A. The implications of heterogeneous DNA methylation for the accurate quantification of methylation. Epigenomics. 2010; 2:561-573.
34. Dobrovic A, Kristensen LS. DNA methylation, epimutations and cancer predisposition. The International Journal of Biochemistry & Cell Biology. 2009; 41:34-39.
35. Pedersen KS, Bamlet WR, Oberg AL, de Andrade M, Matsumoto ME, Tang H, Thibodeau SN, Petersen GM, Wang L. Leukocyte DNA methylation signature differentiates pancreatic cancer patients from healthy controls. PLoS One. 2011; 6:e18223.
36. Wang L, Aakre JA, Jiang R, Marks RS, Wu Y, Chen J, Thibodeau SN, Pankratz VS, Yang P. Methylation markers for small cell lung cancer in peripheral blood leukocyte DNA. Journal of Thoracic Oncology. 2010; 5:778-785.
37. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Gayther SA, Apostolidou S, Jones A, Lechner M, Beck S, Jacobs IJ, Widschwendter M. An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One. 2009; 4:e8274.
38. Bhatia K, Siraj AK, Hussain A, Bu R, Gutierrez MI. The tumor suppressor gene 14-3-3 sigma is commonly methylated in normal and malignant lymphoid cells. Cancer Epidemiology, Biomarkers & Prevention. 2003; 12:165-169.
39. Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research. 1988; 16(3):1215.
40. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 2001; 25:402-408.