Discovery and Validation of DNA Hypomethylation Biomarkers for Liver Cancer Using HRM-Specific Probes

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Stefanska, Barbara ^a   Bouzelmat, Aurelie ^a   Huang, Jian ^b   Suderman, Matthew ^a   Hallett, Michael ^c   Han, Ze Guang ^b   Al Mahtab, Mamun ^d   Akbar, Sheikh Mohammad Fazle ^e   Khan, Wasif Ali ^f   Raqib, Rubhana ^f   Szyf, Moshe ^a  

^a MCGILL UNIVERSITY   (Canada)

^b CHINESE NATIONAL HUMAN GENOME CENTER AT SHANGHAI   (China)

^c MCGILL UNIVERSITY   (Canada)

^d BANGABANDHU SHEIKH MUJIB MEDICAL UNIVERSITY   (Bangladesh)

^e Shinagawa ku   (Japan)

^f INTERNATIONAL CENTRE FOR DIARRHOEAL DISEASE RESEARCH   (Bangladesh)

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR MARKER;

ADULT; AGED; AMPLICON; ARTICLE; CANCER STAGING; CLINICAL ARTICLE; CONTROLLED STUDY; DNA METHYLATION; FCRL1 GENE; FEMALE; GENE IDENTIFICATION; GENE PROBE; GENE STRUCTURE; GPM6B GENE; HEPATITIS B; HIGH RESOLUTION MELTING ANALYSIS; HUMAN; HUMAN TISSUE; LIVER CELL CARCINOMA; MAGEA12 GENE; MALE; MARKER GENE; PROMOTER REGION; TUMOR DIFFERENTIATION; TUMOR GENE; TUMOR INVASION; TUMOR PROMOTION;

ADULT; AGED; AGED, 80 AND OVER; ANTIGENS, NEOPLASM; CARCINOMA, HEPATOCELLULAR; DNA METHYLATION; DNA PROBES; FEMALE; HEPATITIS B, CHRONIC; HUMANS; LIVER NEOPLASMS; MALE; MEMBRANE GLYCOPROTEINS; MEMBRANE PROTEINS; MIDDLE AGED; NEOPLASM PROTEINS; NERVE TISSUE PROTEINS; NUCLEIC ACID DENATURATION; POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; SENSITIVITY AND SPECIFICITY; TRANSITION TEMPERATURE; TUMOR MARKERS, BIOLOGICAL; YOUNG ADULT;

EID: 84881345061     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068439     Document Type: Article

References (30)

1. Jones PA, Baylin SB, (2007) The epigenomics of cancer. Cell 128: 683-692.
2. Szyf M, (2005) DNA methylation and demethylation as targets for anticancer therapy. Biochemistry (Mosc) 70: 533-549.
3. Baylin SB, Esteller M, Rountree MR, Bachman KE, Schuebel K, et al. (2001) Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum Mol Genet 10: 687-692.
4. Stefanska B, Huang J, Bhattacharyya B, Suderman M, Hallett M, et al. (2011) Definition of the landscape of promoter DNA hypomethylation in liver cancer. Cancer Res 71: 5891-5903.
5. Mayol G, Martin-Subero JI, Rios J, Queiros A, Kulis M, et al. (2012) DNA hypomethylation affects cancer-related biological functions and genes relevant in neuroblastoma pathogenesis. PLoS One 7: e48401.
6. Martens JW, Margossian AL, Schmitt M, Foekens J, Harbeck N, (2009) DNA methylation as a biomarker in breast cancer. Future Oncol 5: 1245-1256.
7. deVos T, Tetzner R, Model F, Weiss G, Schuster M, et al. (2009) Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer. Clin Chem 55: 1337-1346.
8. Campan M, Moffitt M, Houshdaran S, Shen H, Widschwendter M, et al. (2011) Genome-scale screen for DNA methylation-based detection markers for ovarian cancer. PLoS One 6: e28141.
9. Takayama T, (2011) Surgical treatment for hepatocellular carcinoma. Jpn J Clin Oncol 41: 447-454.
10. Kristensen LS, Mikeska T, Krypuy M, Dobrovic A, (2008) Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection. Nucleic Acids Res 36: e42.
11. Drabek K, van de Peppel J, Eijken M, van Leeuwen JP, (2011) GPM6B regulates osteoblast function and induction of mineralization by controlling cytoskeleton and matrix vesicle release. J Bone Miner Res 26: 2045-2051.
12. Werner HB, Kramer-Albers EM, Strenzke N, Saher G, Tenzer S, et al. (2013) A critical role for the cholesterol-associated proteolipids PLP and M6B in myelination of the central nervous system. Glia 61: 567-586.
13. Castells X, Garcia-Gomez JM, Navarro A, Acebes JJ, Godino O, et al. (2009) Automated brain tumor biopsy prediction using single-labeling cDNA microarrays-based gene expression profiling. Diagn Mol Pathol 18: 206-218.
14. Castells X, Acebes JJ, Boluda S, Moreno-Torres A, Pujol J, et al. (2010) Development of a predictor for human brain tumors based on gene expression values obtained from two types of microarray technologies. OMICS 14: 157-164.
15. Charfi C, Voisin V, Levros LC Jr, Edouard E, Rassart E, (2011) Gene profiling of Graffi murine leukemia virus-induced lymphoid leukemias: identification of leukemia markers and Fmn2 as a potential oncogene. Blood 117: 1899-1910.
16. Heidecker L, Brasseur F, Probst-Kepper M, Gueguen M, Boon T, et al. (2000) Cytolytic T lymphocytes raised against a human bladder carcinoma recognize an antigen encoded by gene MAGE-A12. J Immunol 164: 6041-6045.
17. Gibbs P, Hutchins AM, Dorian KT, Vaughan HA, Davis ID, et al. (2000) MAGE-12 and MAGE-6 are frequently expressed in malignant melanoma. Melanoma Res 10: 259-264.
18. Otte M, Zafrakas M, Riethdorf L, Pichlmeier U, Loning T, et al. (2001) MAGE-A gene expression pattern in primary breast cancer. Cancer Res 61: 6682-6687.
19. Mollaoglu N, Vairaktaris E, Nkenke E, Neukam FW, Ries J, (2008) Expression of MAGE-A12 in oral squamous cell carcinoma. Dis Markers 24: 27-32.
20. Du X, Nagata S, Ise T, Stetler-Stevenson M, Pastan I, (2008) FCRL1 on chronic lymphocytic leukemia, hairy cell leukemia, and B-cell non-Hodgkin lymphoma as a target of immunotoxins. Blood 111: 338-343.
21. Koh SS, Wei JP, Li X, Huang RR, Doan NB, et al. (2012) Differential gene expression profiling of primary cutaneous melanoma and sentinel lymph node metastases. Mod Pathol 25: 828-837.
22. Wischnewski F, Friese O, Pantel K, Schwarzenbach H, (2007) Methyl-CpG binding domain proteins and their involvement in the regulation of the MAGE-A1, MAGE-A2, MAGE-A3, and MAGE-A12 gene promoters. Mol Cancer Res 5: 749-759.
23. Wischnewski F, Pantel K, Schwarzenbach H, (2006) Promoter demethylation and histone acetylation mediate gene expression of MAGE-A1,-A2,-A3, and-A12 in human cancer cells. Mol Cancer Res 4: 339-349.
24. Colella S, Shen L, Baggerly KA, Issa JP, Krahe R, (2003) Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. Biotechniques 35: 146-150.
25. Tost J, Gut IG, (2007) DNA methylation analysis by pyrosequencing. Nat Protoc 2: 2265-2275.
26. Kuo TC, Chang PY, Huang SF, Chou CK, Chao CC, (2012) Knockdown of HURP inhibits the proliferation of hepacellular carcinoma cells via downregulation of gankyrin and accumulation of p53. Biochem Pharmacol 83: 758-768.
27. Liao M, Tong P, Zhao J, Zhang Y, Li Z, et al. (2012) Prognostic value of matrix metalloproteinase-1/proteinase-activated receptor-1 signaling axis in hepatocellular carcinoma. Pathol Oncol Res 18: 397-403.
28. Song MA, Tiirikainen M, Kwee S, Okimoto G, Yu H, et al. (2013) Elucidating the landscape of aberrant DNA methylation in hepatocellular carcinoma. PLoS One 8: e55761.
29. Miyashiro I, Kuo C, Huynh K, Iida A, Morton D, et al. (2001) Molecular strategy for detecting metastatic cancers with use of multiple tumor-specific MAGE-A genes. Clin Chem 47: 505-512.
30. Brennan K, Garcia-Closas M, Orr N, Fletcher O, Jones M, et al. (2012) Intragenic ATM methylation in peripheral blood DNA as a biomarker of breast cancer risk. Cancer Res 72: 2304-2313.