The role of pyrosequencing in head and neck cancer epigenetics: Correlation of quantitative methylation data with gene expression

Archives of Otolaryngology - Head and Neck Surgery

Volumn 134, Issue 3, 2008, Pages 251-256

  Shaw, Richard J ^a,b   Hall, Gillian L ^a   Lowe, Derek ^b   Liloglou, Triantafillos ^a   Field, John K ^a   Sloan, Phillip ^c   Risk, Janet M ^a  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b UNIVERSITY HOSPITAL AINTREE   (United Kingdom)

^c UNIVERSITY DENTAL HOSPITAL OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA; MESSENGER RNA; RNA;

ARTICLE; ATM GENE; CONTROLLED STUDY; CORRELATION COEFFICIENT; CYCLIN A1 GENE; DNA EXTRACTION; E CADHERIN GENE; EPIGENETICS; GENE; GENE EXPRESSION; HEAD AND NECK CANCER; HMLH1 GENE; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; METHYLATION; MGMT GENE; P16 GENE; PROMOTER REGION; PYROSEQUENCING; RARB GENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; STAINING; STAT1 GENE; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; TIMP3 GENE;

BASE SEQUENCE; CARCINOMA, SQUAMOUS CELL; CYCLIN-DEPENDENT KINASE INHIBITOR P16; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, NEOPLASTIC; HEAD AND NECK NEOPLASMS; HUMANS; IMMUNOENZYME TECHNIQUES; PROMOTER REGIONS (GENETICS); REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA;

EID: 41149110952     PISSN: 08864470     EISSN: 08864470     Source Type: Journal    
DOI: 10.1001/archoto.2007.50     Document Type: Article

References (28)

1. Shaw R. The epigenetics of oral cancer. Int J Oral Maxillofac Surg. 2006;35(2):101-108.
2. Ha PK, Califano JA. Promoter methylation and inactivation of tumour-suppressor genes in oral squamous-cell carcinoma. Lancet Oncol. 2006;7(1):77-82.
3. Singer-Sam J, LeBon JM, Tanguay RL, Riggs AD. A quantitative HpaII-PCR assay to measure methylation of DNA from a small number of cells. Nucleic Acids Res. 1990;18(3):687.
4. Hatada I, Hayashizaki Y, Hirotsune S, Komatsubara H, Mukai T. A genomic scanning method for higher organisms using restriction sites as landmarks. Proc Natl Acad Sci U S A. 1991;88(21):9523-9527.
5. Herman JG, Graff JR, Myöhänen S, Nelkin BD, Baylin SB. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A. 1996;93(18):9821-9826.
6. Adorján P, Distler J, Lipscher E, et al. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res. 2002;30(5):e21. http://nar.oxfordjournals.org/cgi/content/full/30/5/ e21. Accessed December 28, 2007.
7. Eads CA, Danenberg KD, Kawakami K, et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 2000;28(8):e32. http://nar.oxfordjournals.org/cgi/content/full/28/8/e32. Accessed December 28, 2007.
8. Gonzalgo ML, Jones PA. Rapid quantification of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (MS-SNuPE). Nucleic Acids Res. 1997;25(12):2529-2531.
9. 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 U S A. 1992;89(5):1827-1831.
10. Xiong Z, Laird PW. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res. 1997;25(12):2532-2534.
11. Colella S, Shen L, Baggerly KA, Issa JP, Krahe R. Sensitive and quantitative universal pyrosequencing methylation analysis of CpG sites. Biotechniques. 2003;35(1):146-150.
12. Tost J, Dunker J, Gut IG. Analysis and quantification of multiple methylation variable positions in CpG islands by pyrosequencing. Biotechniques. 2003;35(1):152-156.
13. Tokumaru Y, Yamashita K, Osada M, et al. Inverse correlation between cyclin A1 hypermethylation and p53 mutation in head and neck cancer identified by reversal of epigenetic silencing. Cancer Res. 2004;64(17):5982-5987.
14. Bolt J, Vo QN, Kim WJ, et al. The ATM/p53 pathway is commonly targeted for inactivation in squamous cell carcinoma of the head and neck (SCCHN) by multiple molecular mechanisms. Oral Oncol. 2005;41(10):1013-1020.
15. Deng G, Chen A, Hong J, Chae HS, Kim YS. Methylation of CpG in a small region of the hMLH1 promoter invariably correlates with the absence of gene expression. Cancer Res. 1999;59(9):2029-2033.
16. 6-methylguanine-DNA methyltransferase gene: epigenetic silencing and prognostic value in head and neck squamous cell carcinoma. Cancer Epidemiol Biomarkers Prev. 2004;13(6):967-975.
17. Youssef EM, Issa JP, Lotan R. Regulation of RAR1 expression in head and neck cancer cells by cell density-dependent chromatin remodeling. Cancer Biol Ther. 2004;3(10):1002-1006.
18. 2 gene in head and neck carcinogenesis. Clin Cancer Res. 2004;10(5):1733-1742.
19. Yeh KT, Shih MC, Lin TH, et al. The correlation between CpG methylation on promoter and protein expression of E-cadherin in oral squamous cell carcinoma. Anticancer Res. 2002;22(6C)(6C):3971-3975.
20. Xi S, Dyer KF, Kimak M, et al. Decreased STAT1 expression by promoter methylation in squamous cell carcinogenesis. J Natl Cancer Inst. 2006;98(3):181-189.
21. Clément G, Braunschweig R, Pasquier N, Bosman FT, Benhattar J. Methylation of APC, TIMP3, and TERT: a new predictive marker to distinguish Barrett's oesophagus patients at risk for malignant transformation. J Pathol. 2006;208(1):100-107.
22. Shaw RJ, Liloglou T, Rogers SN, et al. Promoter methylation of P16, RARβ, E-cadherin, cyclin A1 and cytoglobin in oral cancer: quantitative evaluation using pyrosequencing. Br J Cancer. 2006;94(4):561-568.
23. ΔΔC T method. Methods. 2001;25(4):402-408.
24. 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 Res. 2006;34(11):e78. doi:10.1093/nar/ gkl424.
25. Maruya S, Issa JP, Weber RS, et al. Differential methylation status of tumor-associated genes in head and neck squamous carcinoma: incidence and potential implications. Clin Cancer Res. 2004;10(11):3825-3830.
26. Ogi K, Toyota M, Ohe-Toyota M, et al. Aberrant methylation of multiple genes and clinicopathological features in oral squamous cell carcinoma. Clin Cancer Res. 2002;8(10):3164-3171.
27. Williams MD, Chakravarti N, Kies MS, et al. Implications of methylation patterns of cancer genes in salivary gland tumors. Clin Cancer Res. 2006;12(24):7353-7358.
28. Kelavkar UP, Harya NS, Hutzley J, et al. DNA methylation paradigm shift: 15-lipoxygenase-1 upregulation in prostatic intraepithelial neoplasia and prostate cancer by atypical promoter hypermethylation. Prostaglandins Other Lipid Mediat. 2007;82(1-4):185-197.