Methylation profiling of serum DNA from hepatocellular carcinoma patients using an Infinium Human Methylation 450 BeadChip

Hepatology International

Volumn 7, Issue 3, 2013, Pages 893-900

  Zhang, Pengjun ^a   Wen, Xinyu ^a   Gu, Feng ^a   Deng, Xinxin ^a   Li, Juan ^a   Dong, Jin ^a   Jiao, Jiao ^a   Tian, Yaping ^a,b  

^a CHINESE PLA GENERAL HOSPITAL   (China)

^b NANKAI UNIVERSITY   (China)

Author keywords

CpG sites; DNA methylation; Hepatocellular carcinoma; Hypermethylation; Serum

Indexed keywords

DNA; MEMBRANE PROTEIN; PROTEIN DBX2; PROTEIN THY1; UNCLASSIFIED DRUG;

ANALYTICAL EQUIPMENT; ARTICLE; BIOINFORMATICS; CANCER STAGING; CLINICAL ARTICLE; CONTROLLED STUDY; DIAGNOSTIC TEST ACCURACY STUDY; DIAGNOSTIC VALUE; DNA ISOLATION; DNA METHYLATION; FEMALE; GENE INTERACTION; GENETIC SCREENING; HEPATITIS B; HUMAN; LIVER CELL CARCINOMA; MALE; PRIORITY JOURNAL; PROMOTER REGION; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS;

EID: 84884356744     PISSN: 19360533     EISSN: 19360541     Source Type: Journal    
DOI: 10.1007/s12072-013-9437-0     Document Type: Article

References (26)

1. Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, Li JR, Clark D, et al. Genome-wide DNA methylation analysis in cohesin mutant human cell lines. Nucleic Acids Res 2010;38:5657-5671
2. Hernandez-Vargas H, Lambert MP, Le Calvez-Kelm F, Gouysse G, McKay-Chopin S, Tavtigian SV, Scoazec JY, et al. Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors. PLoS ONE 2010;5:e9749
3. Wang J, Qin Y, Li B, Sun Z, Yang B. Detection of aberrant promoter methylation of GSTP1 in the tumor and serum of Chinese human primary hepatocellular carcinoma patients. Clin Biochem 2006;39:344-348
4. Tangkijvanich P, Hourpai N, Rattanatanyong P, Wisedopas N, Mahachai V, Mutirangura A. Serum LINE-1 hypomethylation as a potential prognostic marker for hepatocellular carcinoma. Clin Chim Acta 2007;379:127-133
5. Hu L, Chen G, Yu H, Qiu X. Clinicopathological significance of RASSF1A reduced expression and hypermethylation in hepatocellular carcinoma. Hepatol Int 2010;4:423-432
6. Ren N, Ye QH, Qin LX, Zhang BH, Liu YK, Tang ZY. Circulating DNA level is negatively associated with the long-term survival of hepatocellular carcinoma patients. World J Gastroenterol 2006;12:3911-3914
7. Pathak AK, Bhutani M, Kumar S, Mohan A, Guleria R. Circulating cell-free DNA in plasma/serum of lung cancer patients as a potential screening and prognostic tool. Clin Chem 2006;52:1833-1842
8. Paci M, Maramotti S, Bellesia E, Formisano D, Albertazzi L, Ricchetti T, Ferrari G, et al. Circulating plasma DNA as diagnostic biomarker in non-small cell lung cancer. Lung Cancer 2009;64:92-97
9. Widschwendter A, Muller HM, Fiegl H, Ivarsson L, Wiedemair A, Muller-Holzner E, Goebel G, et al. DNA methylation in serum and tumors of cervical cancer patients. Clin Cancer Res 2004;10:565-571
10. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 1995;57:289-300
11. Zheng Q, Wang XJ. GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 2008;36:W358-W363
12. Huttenhower C, Mehmood SO, Troyanskaya OG. Graphle: interactive exploration of large, dense graphs. BMC Bioinform 2009;10:417
13. Shen L, Toyota M, Kondo Y, Lin E, Zhang L, Guo Y, Hernandez NS, et al. Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proc Natl Acad Sci USA 2007;104:18654-18659
14. Lee HS, Kim BH, Cho NY, Yoo EJ, Choi M, Shin SH, Jang JJ, et al. Prognostic implications of and relationship between CpG island hypermethylation and repetitive DNA hypomethylation in hepatocellular carcinoma. Clin Cancer Res 2009;15:812-820
15. Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet 2006;7:21-33
16. Ehrlich M. DNA methylation in cancer: too much, but also too little. Oncogene 2002;21:5400-5413
17. Barrio S, Gallardo M, Albizua E, Jimenez A, Rapado I, Ayala R, Gilsanz F, et al. Epigenomic profiling in polycythaemia vera and essential thrombocythaemia shows low levels of aberrant DNA methylation. J Clin Pathol 2011;64:1010-1013
18. Deneberg S, Guardiola P, Lennartsson A, Qu Y, Gaidzik V, Blanchet O, Karimi M, et al. Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks. Blood 2011;118:5573-5582
19. Tao R, Li J, Xin J, Wu J, Guo J, Zhang L, Jiang L, et al. Methylation profile of single hepatocytes derived from hepatitis B virus-related hepatocellular carcinoma. PLoS ONE 2011;6:e19862
20. Etcheverry A, Aubry M, de Tayrac M, Vauleon E, Boniface R, Guenot F, Saikali S, et al. DNA methylation in glioblastoma: impact on gene expression and clinical outcome. BMC Genomics 2010;11:701
21. Sandoval J, Heyn HA, Moran S, Serra-Musach J, Pujana MA, Bibikova M, Esteller M. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 2011;6:692-702
22. Navarro A, Yin P, Monsivais D, Lin SM, Du P, Wei JJ, Bulun SE. Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyoma. PLoS ONE 2012;7:e33284
23. Fan M, Yan PS, Hartman-Frey C, Chen L, Paik H, Oyer SL, Salisbury JD, et al. Diverse gene expression and DNA methylation profiles correlate with differential adaptation of breast cancer cells to the antiestrogens tamoxifen and fulvestrant. Cancer Res 2006;66:11954-11966
24. Watts GS, Futscher BW, Holtan N, Degeest K, Domann FE, Rose SL. DNA methylation changes in ovarian cancer are cumulative with disease progression and identify tumor stage. BMC Med Genomics 2008;1:47
25. Abeysinghe HR, Cao Q, Xu J, Pollock S, Veyberman Y, Guckert NL, Keng P, et al. THY1 expression is associated with tumor suppression of human ovarian cancer. Cancer Genet Cytogenet 2003;143:125-132
26. Abeysinghe HR, Pollock SJ, Guckert NL, Veyberman Y, Keng P, Halterman M, Federoff HJ, et al. The role of the THY1 gene in human ovarian cancer suppression based on transfection studies. Cancer Genet Cytogenet 2004;149:1-10