Hypermethylation of CpG islands is more prevalent than hypomethylation across the entire genome in breast carcinogenesis

Clinical and Experimental Medicine

Volumn 13, Issue 1, 2013, Pages 1-9

  Tan, Jianxin ^a   Gu, Yumei ^a   Zhang, Xiaomei ^a,b   You, Sihong ^a   Lu, Xiaowei ^c   Chen, Senqing ^b   Han, Xiao ^a   Sun, Yujie ^a  

^a NANJING MEDICAL UNIVERSITY   (China)

^b JIANGSU CANCER HOSPITAL   (China)

^c Maternal and Child Health Hospital   (China)

Author keywords

Breast cancer; Carcinogenesis; DHPLC; DNA methylation; MSRF

Indexed keywords

GENOMIC DNA; PRIMER DNA;

ARTICLE; BREAST CANCER; BREAST CARCINOGENESIS; CANCER TISSUE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; GENE MUTATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; HUMAN TISSUE; ONCOGENE; PRIORITY JOURNAL; RNA FINGERPRINTING;

EID: 84873739709     PISSN: 15918890     EISSN: 15919528     Source Type: Journal    
DOI: 10.1007/s10238-011-0173-2     Document Type: Article

References (37)

1. Herman JG, Baylin SB (2003) Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 349(21):2042-2054. doi: 10.1056/NEJMra023075
2. Feinberg AP, Tycko B (2004) The history of cancer epigenetics. Nat Rev Cancer 4(2):143-153. doi: 10.1038/nrc1279
3. Esteller M (2008) Epigenetics in cancer. N Engl J Med 358(11):1148-1159. doi: 10.1056/NEJMra072067
4. Baylin SB, Esteller M, Rountree MR, Bachman KE, Schuebel K, Herman JG (2001) Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum Mol Genet 10(7):687-692
5. Krassenstein R, Sauter E, Dulaimi E, Battagli C, Ehya H, Klein-Szanto A, Cairns P (2004) Detection of breast cancer in nipple aspirate fluid by CpG island hypermethylation. Clin Cancer Res 10(1 Pt 1):28-32
6. Breault JE, Shiina H, Igawa M, Ribeiro-Filho LA, Deguchi M, Enokida H, Urakami S, Terashima M, Nakagawa M, Kane CJ, Carroll PR, Dahiya R (2005) Methylation of the gamma-catenin gene is associated with poor prognosis of renal cell carcinoma. Clin Cancer Res 11(2 Pt 1):557-564
7. Brena RM, Huang TH, Plass C (2006) Quantitative assessment of DNA methylation: Potential applications for disease diagnosis, classification, and prognosis in clinical settings. J Mol Med 84(5):365-377. doi: 10.1007/s00109-005-0034-0
8. Issa JP (2007) DNA methylation as a therapeutic target in cancer. Clin Cancer Res 13(6):1634-1637. doi: 10.1158/1078-0432.CCR-06-2076
9. Zilberman D, Henikoff S (2007) Genome-wide analysis of DNA methylation patterns. Development 134(22):3959-3965. doi: 10.1242/dev.001131
10. Hurd PJ, Nelson CJ (2009) Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct Genomic Proteomic 8(3):174-183. doi: 10.1093/bfgp/elp013
11. Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA, Clark SJ (2006) Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat Genet 38(5):540-549. doi: 10.1038/ng1781
12. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41(2):178-186. doi: 10.1038/ng.298
13. Huang TH, Laux DE, Hamlin BC, Tran P, Tran H, Lubahn DB (1997) Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique. Cancer Res 57(6):1030-1034
14. Hayward AL, Oefner PJ, Sabatini S, Kainer DB, Hinojos CA, Doris PA (1998) Modeling and analysis of competitive RT-PCR. Nucleic Acids Res 26(11):2511-2518
15. Wu M, Ho SM (2004) PMP24, a gene identified by MSRF, undergoes DNA hypermethylation-associated gene silencing during cancer progression in an LNCaP model. Oncogene 23(1):250-259. doi: 10.1038/sj.onc.1207076
16. Lv Z, Zhang M, Bi J, Xu F, Hu S, Wen J (2006) Promoter hypermethylation of a novel gene, ZHX2, in hepatocellular carcinoma. Am J Clin Pathol 125(5):740-746. doi: 10.1309/09B4-52V7-R76K-7D6K
17. Ho SM, Tang WY (2007) Techniques used in studies of epigenome dysregulation due to aberrant DNA methylation: an emphasis on fetal-based adult diseases. Reprod Toxicol 23(3):267-282. doi: 10.1016/j.reprotox.2007.01.004
18. Li E, Beard C, Jaenisch R (1993) Role for DNA methylation in genomic imprinting. Nature 366(6453):362-365. doi: 10.1038/366362a0
19. Laird PW, Jaenisch R (1996) The role of DNA methylation in cancer genetic and epigenetics. Annu Rev Genet 30:441-464. doi: 10.1146/annurev.genet.30.1.441
20. Egger G, Liang G, Aparicio A, Jones PA (2004) Epigenetics in human disease and prospects for epigenetic therapy. Nature 429(6990):457-463. doi: 10.1038/nature02625
21. Hatada I, Hayashizaki Y, Hirotsune S, Komatsubara H, Mukai T (1991) A genomic scanning method for higher organisms using restriction sites as landmarks. Proc Natl Acad Sci USA 88(21):9523-9527
22. Toyota M, Ho C, Ahuja N, Jair KW, Li Q, Ohe-Toyota M, Baylin SB, Issa JP (1999) Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res 59(10):2307-2312
23. Huang TH, Perry MR, Laux DE (1999) Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 8(3):459-470
24. Widschwendter M, Jones PA (2002) DNA methylation and breast carcinogenesis. Oncogene 21(35):5462-5482. doi: 10.1038/sj.onc.1205606
25. Ehrlich M (2002) DNA methylation in cancer: too much, but also too little. Oncogene 21(35):5400-5413. doi: 10.1038/sj.onc.1205651
26. Ushijima T (2005) Detection and interpretation of altered methylation patterns in cancer cells. Nat Rev Cancer 5(3):223-231. doi: 10.1038/nrc1571
27. Bariol C, Suter C, Cheong K, Ku SL, Meagher A, Hawkins N, Ward R (2003) The relationship between hypomethylation and CpG island methylation in colorectal neoplasia. Am J Pathol 162(4):1361-1371. doi: 10.1016/S0002-9440(10) 63932-6
28. Narayan A, Ji W, Zhang XY, Marrogi A, Graff JR, Baylin SB, Ehrlich M (1998) Hypomethylation of pericentromeric DNA in breast adenocarcinomas. Int J Cancer 77(6):833-838. doi: 10.1002/(SICI)1097-0215(19980911)77:6<833:AID- IJC6>3.0.CO;2-V
29. Ehrlich M, Jiang G, Fiala E, Dome JS, Yu MC, Long TI, Youn B, Sohn OS, Widschwendter M, Tomlinson GE, Chintagumpala M, Champagne M, Parham D, Liang G, Malik K, Laird PW (2002) Hypomethylation and hypermethylation of DNA in Wilms tumors. Oncogene 21(43):6694-6702. doi: 10.1038/sj.onc.1205890
30. Paluszczak J, Baer-Dubowska W (2006) Epigenetic diagnostics of cancer-the application of DNA methylation markers. J Appl Genet 47(4):365-375
31. Maruyama R, Toyooka S, Toyooka KO, Virmani AK, Zochbauer-Muller S, Farinas AJ, Minna JD, McConnell J, Frenkel EP, Gazdar AF (2002) Aberrant promoter methylation profile of prostate cancers and its relationship to clinicopathological features. Clin Cancer Res 8(2):514-519
32. Ogi K, Toyota M, Ohe-Toyota M, Tanaka N, Noguchi M, Sonoda T, Kohama G, Tokino T (2002) Aberrant methylation of multiple genes and clinicopathological features in oral squamous cell carcinoma. Clin Cancer Res 8(10):3164-3171
33. Brait M, Begum S, Carvalho AL, Dasgupta S, Vettore AL, Czerniak B, Caballero OL, Westra WH, Sidransky D, Hoque MO (2008) Aberrant promoter methylation of multiple genes during pathogenesis of bladder cancer. Cancer Epidemiol Biomark Prev 17(10):2786-2794. doi: 10.1158/1055-9965.EPI-08-0192
34. Mirza S, Sharma G, Prasad CP, Parshad R, Srivastava A, Gupta SD, Ralhan R (2007) Promoter hypermethylation of TMS1, BRCA1, ERalpha and PRB in serum and tumor DNA of invasive ductal breast carcinoma patients. Life Sci 81(4):280-287. doi: 10.1016/j.lfs.2007.05.012
35. Anglim PP, Galler JS, Koss MN, Hagen JA, Turla S, Campan M, Weisenberger DJ, Laird PW, Siegmund KD, Laird-Offringa IA (2008) Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer. Mol Cancer 7:62. doi: 10.1186/1476-4598-7-62
36. Marsit CJ, Christensen BC, Houseman EA, Karagas MR, Wrensch MR, Yeh RF, Nelson HH, Wiemels JL, Zheng S, Posner MR, McClean MD, Wiencke JK, Kelsey KT (2009) Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma. Carcinogenesis 30(3):416-422. doi: 10.1093/carcin/bgp006
37. Killian JK, Bilke S, Davis S, Walker RL, Killian MS, Jaeger EB, Chen Y, Hipp J, Pittaluga S, Raffeld M, Cornelison R, Smith WI Jr, Bibikova M, Fan JB, Emmert-Buck MR, Jaffe ES, Meltzer PS (2009) Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome. Cancer Res 69(3):758-764. doi: 10.1158/0008-5472.CAN-08-2984