Comparative analysis of dna methylation profiles in peripheral blood leukocytes versus lymphoblastoid cell lines

Epigenetics

Volumn 4, Issue 3, 2009, Pages 159-164

  Brennan, Eoin P ^a   Ehrich, Mathias ^b   Brazil, Derek P ^c   Crean, John K ^c   Murphy, Madeline ^c   Sadlier, Danise M ^c   Martin, Finian ^c   Godson, Catherine ^c   McKnight, Amy Jayne ^a   van den Boom, Dirk ^b   Maxwell, Alexander P ^a   Savage, David A ^a  

^a QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^b SEQUENOM INC   (United States)

^c UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

CpG island; Diabetic nephropathy; DNA methylation; Llymphoblastoid cell line; Peripheral blood leukocyte

Indexed keywords

CELL DNA;

ARTICLE; CONTROLLED STUDY; DIABETIC NEPHROPATHY; DNA METHYLATION; GENE IDENTIFICATION; HUMAN; HUMAN CELL; LEUKOCYTE; LYMPHOBLASTOID CELL; LYMPHOBLASTOID CELL LINE; NON INSULIN DEPENDENT DIABETES MELLITUS; NUCLEOTIDE SEQUENCE; PROMOTER REGION;

HUMAN HERPESVIRUS 4;

EID: 66449103823     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.4.3.8793     Document Type: Article

References (31)

1. Laird PW. The power and the promise of DNA methylation markers. Nat Rev Cancer 2003; 3:253-66.
2. Esteller M, Corn PG, Baylin SB, Herman JG. A gene hypermethylation profile of human cancer. Cancer Res 2001; 61:3225-9.
3. Dulaimi E, Ibanez de Caceres I, Uzzo RG, Al-Saleem T, Greenberg RE, Polascik TJ, et al. Promoter hypermethylation profile of kidney cancer. Clin Cancer Res 2004; 10:3972-9.
4. Smiraglia DJ, Rush LJ, Fruhwald MC, Dai Z, Held WA, Costello JF, et al. Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies. Hum Mol Genet 2001; 10:1413-9.
5. Paz MF, Fraga MF, Avila S, Guo M, Pollan M, Herman JG, et al. A systematic profile of DNA methylation in human cancer cell lines. Cancer Res 2003; 63:1114-21.
6. Toyooka S, Toyooka KO, Maruyama R, Virmani AK, Girard L, Miyajima K, et al. DNA methylation profiles of lung tumors. Mol Cancer Ther 2001; 1:61-7.
7. Stenvinkel P, Karimi M, Johansson S, Axelsson J, Suliman M, Lindholm B, et al. Impact of inflammation on epigenetic DNA methylation - a novel risk factor for cardiovascular disease? J Intern Med 2007; 261:488-99.
8. Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L, et al. Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 2008; 82:696-711.
9. Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G, et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci USA 2005; 102:15785-90.
10. Ehrich M, Turner J, Gibbs P, Lipton L, Giovanneti M, Cantor C, et al. Cytosine methylation profiling of cancer cell lines. Proc Natl Acad Sci USA 2008; 105:4844-9.
11. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 2006; 38:1378-85.
12. Tao Q and Robertson KD. Stealth technology: How Epstein-Barr virus utilizes DNA methylation to cloak itself from immune detection. Clin Immunol 2003; 109:53-63.
13. Robertson KD, Manns A, Swinnen LJ, Zong JC, Gulley ML, Ambinder RF. CpG methylation of the major Epstein-Barr virus latency promoter in Burkitt's lymphoma and Hodgkin's disease. Blood 1996; 88:3129-36.
14. Habib M, Fares F, Bourgeois CA, Bella C, Bernardino J, Hernandez-Blazquez F, et al. DNA global hypomethylation in EBV-transformed interphase nuclei. Exp Cell Res 1999; 249:46-53.
15. Chong JM, Sakuma K, Sudo M, Ushiku T, Uozaki H, Shibahara J, et al. Global and non-random CpG-island methylation in gastric carcinoma associated with Epstein-Barr virus. Cancer Sci 2003; 94:76-80.
16. Kang GH, Lee S, Kim WH, Lee HW, Kim JC, Rhyu MG, et al. Epstein-Barr virus-positive gastric carcinoma demonstrates frequent aberrant methylation of multiple genes and constitutes CpG island methylator phenotype-positive gastric carcinoma. Am J Pathol 2002; 160:787-94.
17. Vo QN, Geradts J, Gulley ML, Boudreau DA, Bravo JC, Schneider BG. Epstein-Barr virus in gastric adenocarcinomas: association with ethnicity and CDKN2A promoter methylation. J Clin Pathol 2002; 55:669-75.
18. INK4A in Epstein-Barr virus-associated gastric carcinoma. Int J Cancer 2004; 112:273-8.
19. Osawa T, Chong JM, Sudo M, Sakuma K, Uozaki H, Shibahara J, et al. Reduced expression and promoter methylation of p16 gene in Epstein-Barr virus-associated gastric carcinoma. Jpn J Cancer Res 2002; 93:1195-200.
20. Antequera F, Boyes J, Bird A. High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines. Cell 1990; 62:503-14.
21. Fuso A, Seminara L, Cavallaro RA, D'Anselmi F, Scarpa S. S-adenosylmethionine/homocysteine cycle alterations modify DNA methylation status with consequent deregulation of PS1 and BACE and beta-amyloid production. Mol Cell Neurosci 2005; 1:195-204.
22. Allegrucci C, Wu YZ, Thurston A, Denning CN, Priddle H, Mummery CL, et al. Restriction landmark genome scanning identifies culture-induced DNA methylation instability in the human embryonic stem cell epigenome. Hum Mol Genet 2007; 16:1253-68.
23. Murphy M, Godson C, Cannon S, Kato S, Mackenzie HS, Martin F, et al. Suppression subtractive hybridization identifies high glucose levels as a stimulus for expression of connective tissue growth factor and other genes in human mesangial cells. J Biol Chem 1999; 274:5830-4.
24. Clarkson MR, Murphy M, Gupta S, Lambe T, Mackenzie HS, Godson C, et al. High glucose-altered gene expression in mesangial cells. Actin-regulatory protein gene expression is triggered by oxidative stress and cytoskeletal disassembly. J Biol Chem 2002; 277:9707-12.
25. Walsh DW, Roxburgh SA, McGettigan P, Berthier CC, Higgins DG, Kretzler M, et al. Co-regulation of Gremlin and Notch signalling in diabetic nephropathy. Biochim Biophys Acta 2008; 1782:10-21.
26. Rodgers K, McMahon B, Mitchell D, Sadlier D, Godson C. Lipoxin A4 modifies platelet-derived growth factor-induced pro-fibrotic gene expression in human renal mesangial cells. Am J Pathol 2005; 167:683-94.
27. Zeng L, Kanwar YS, Amro N, Phillips C, Molitch M, Batlle D, et al. Epigenetic and genetic analysis of p16 in dermal fibroblasts from type 1 diabetic patients with nephropathy. Kidney Int 2003; 63:2094-102.
28. Geisel J, Schorr H, Heine GH, Bodis M, Hübner U, Knapp JP, et al. Decreased p66Shc promoter methylation in patients with end-stage renal disease. Clin Chem Lab Med 2007; 45:1764-70.
29. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res 2002; 12:996-1006.
30. Ehrich M, Zoll S, Sur S, van den Boom D. A new method for accurate assessment of DNA quality after bisulfite treatment. Nucleic Acids Res 2007; 35:29.
31. Coolen MW, Statham AL, Gardiner-Garden M, Clark SJ. Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements. Nucleic Acids Res 2007; 35:119.