Genome-wide screening for methylation-silenced genes in colorectal cancer

International Journal of Oncology

Volumn 41, Issue 2, 2012, Pages 490-496

  Khamas, Ahmed ^a   Ishikawa, Toshiaki ^a   Mogushi, Kaoru ^b   Iida, Satoru ^a   Ishiguro, Megumi ^a   Tanaka, Hiroshi ^b   Uetake, Hiroyuki ^a   Sugihara, Kenichi ^a  

^a TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^b TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

Author keywords

5 aza 2 deoxycitidine; Colorectal cancer; CpG island; Methylation; Oligonucleotide microarray

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; GROWTH ARREST AND DNA DAMAGE INDUCIBLE BETA PROTEIN; MESSENGER RNA; OLIGONUCLEOTIDE; PROTEIN; THROMBOSPONDIN TYPE I DOMAIN CONTAINING 1 PROTEIN; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; CELL STRAIN HCT116; CELL STRAIN HT29; COLORECTAL CANCER; CONTROLLED STUDY; DEMETHYLATION; DNA METHYLATION; DOWN REGULATION; FEMALE; GENE; GENE EXPRESSION; GENE INACTIVATION; GENE SILENCING; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; MICROARRAY ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE ASSAY; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SCREENING;

ADULT; AGED; AGED, 80 AND OVER; ANTIGENS, DIFFERENTIATION; CELL LINE, TUMOR; COLORECTAL NEOPLASMS; DNA METHYLATION; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE SILENCING; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; THROMBOSPONDINS;

EID: 84863591414     PISSN: 10196439     EISSN: 17912423     Source Type: Journal    
DOI: 10.3892/ijo.2012.1500     Document Type: Article

References (39)

1. Jones PA and Laird PW: Cancer epigenetics comes of age. Nat Genet 21: 163-167, 1999. (Pubitemid 29070360)
2. Baylin SB, Herman JG, Graff JR, Vertino PM and Issa JP: Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res 72: 141-196, 1998. (Pubitemid 27435555)
3. Esteller M: Dormant hypermethylated tumour suppressor genes: questions and answers. J Pathol 205: 172-180, 2005.
4. Karpf AR and Jones DA: Reactivating the expression of methylation silenced genes in human cancer. Oncogene 21: 5496-5503, 2002. (Pubitemid 34983484)
5. Yamashita K, Upadhyay S, Osada M, et al: Pharmacologic un- masking of epigenetically silenced tumor suppressor genes in esophageal squamous cell carcinoma. Cancer Cell 2: 485-495, 2002. (Pubitemid 41043953)
6. Suzuki H, Gabrielson E, Chen W, et al: A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 31: 141-149, 2002.
7. Koul S, Houldsworth J, Mansukhani MM, et al: Characteristic promoter hypermethylation signatures in male germ cell tumors. Mol Cancer 1: 8, 2002.
8. Konduri SD, Srivenugopal KS, Yanamandra N, et al: Promoter methylation and silencing of the tissue factor pathway inhibitor-2 (TFPI-2), a gene encoding an inhibitor of matrix metalloproteinases in human glioma cells. Oncogene 22: 4509-4516, 2003. (Pubitemid 36920694)
9. Knobbe CB, Reifenberger J, Blaschke B and Reifenberger G: Hypermethylation and transcriptional downregulation of the carboxyl-terminal modulator protein gene in glioblastomas. J Natl Cancer Inst 96: 483-486, 2004. (Pubitemid 38443652)
10. Sawa H, Murakami H, Ohshima Y, et al: Histone deacetylase inhibitors such as sodium butyrate and trichostatin A inhibit vascular endothelial growth factor (VEGF) secretion from human glioblastoma cells. Brain Tumor Pathol 19: 77-81, 2002. (Pubitemid 36356314)
11. Schuebel KE, Chen W, Cope L, et al: Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet 3: 1709-1723, 2007. (Pubitemid 47510263)
12. Ishiguro M, Iida S, Uetake H, et al: Effect of combined therapy with low-dose 5-aza-2′-deoxycytidine and irinotecan on colon cancer cell line HCT-15. Ann Surg Oncol 14: 1752-1762, 2007. (Pubitemid 46790993)
13. Herman JG, Graff JR, Myöhänen S, Nelkin BD and Baylin SB: Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 93: 9821-9826, 1996. (Pubitemid 26296693)
14. Qiu W, Zhou B, Zou H, et al: Hypermethylation of growth arrest DNA damage-inducible gene 45 beta promoter in human hepatocellular carcinoma. Am J Pathol 165: 1689-1699, 2004. (Pubitemid 39435167)
15. Ko JM, Chan PL, Yau WL, et al: Monochromosome transfer and microarray analysis identify a critical tumor-suppressive region mapping to chromosome 13q14 and THSD1 in esophageal carcinoma. Mol Cancer Res 6: 592-603, 2008. (Pubitemid 351521841)
16. Mori Y, Yin J, Sato F, et al: Identification of genes uniquely involved in frequent microsatellite instability colon carcinogenesis by expression profiling combined with epigenetic scanning. Cancer Res 64: 2434-2438, 2004. (Pubitemid 38523897)
17. Khamas A, Ishikawa T, Shimokawa K, et al: Screening for epigenetically masked genes in colorectal cancer using 5-aza-2′-deoxycytidine, microarray and gene expression profile. Cancer Genomics Proteomics 9: 67-75, 2012.
18. Liang G, Gonzales FA, Jones PA, Orntoft TF and Thykjaer T: Analysis of gene induction in human fibroblasts and bladder cancer cells exposed to the methylation inhibitor 5-aza-2′-deoxycytidine. Cancer Res 62: 961-966, 2002. (Pubitemid 34160269)
19. Huang DW, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57, 2009.
20. Ali D: Identification of novel epigenetic biomarkers in colorectal cancer, GLDC and PPP1R14A. Department of Molecular Bio- sciences (IMBV), Faculty of Mathematics and Natural Sciences, University of Oslo, p97, 2010.
21. Easwaran HP, van Neste L, Cope L, et al: Aberrant silencing of cancer-related genes by CpG hypermethylation occurs independently of their spatial organization in the nucleus. Cancer Res 70: 8015-8024, 2010.
22. Kim MS, Lee J and Sidransky D: DNA methylation markers in colorectal cancer. Cancer Metastasis Rev 29: 181-206, 2010.
23. Xu L and Jain RK: Down-regulation of placenta growth factor by promoter hypermethylation in human lung and colon carcinoma. Mol Cancer Res 5: 873-880, 2007. (Pubitemid 47416664)
24. Gardiner-Garden M and Frommer M: CpG islands in vertebrate genomes. J Mol Biol 196: 261-282, 1987. (Pubitemid 17122132)
25. Takai D and Jones PA: The CpG island searcher: a new WWW resource. In Silico Biol 3: 235-240, 2003. (Pubitemid 37493047)
26. Karolchik D, Hinrichs AS, Furey TS, et al: The UCSC table browser data retrieval tool. Nucleic Acids Res 32: D493-D496, 2004. (Pubitemid 38081706)
27. Lind GE, Thorstensen L, Løvig T, et al: A CpG island hypermethylation profile of primary colorectal carcinomas and colon cancer cell lines. Mol Cancer 3: 28, 2004.
28. Zhang X and Lawler J: Thrombospondin-based antiangiogenic therapy. Microvasc Res 74: 90-99, 2007. (Pubitemid 350064284)
29. Rojas A, Meherem S, Kim YH, et al: The aberrant methylation of TSP1 suppresses TGF-beta1 activation in colorectal cancer. Int J Cancer 123: 14-21, 2008. (Pubitemid 351705187)
30. Moncada-Pazos A, Obaya AJ, Fraga MF, et al: The ADAMTS12 metalloprotease gene is epigenetically silenced in tumor cells and transcriptionally activated in the stroma during progression of colon cancer. J Cell Sci 122: 2906-2913, 2009.
31. Lai PS, Cheah PY, Kadam P, et al: Overexpression of RB1 transcript is significantly correlated with 13q14 allelic imbalance in colorectal carcinomas. Int J Cancer 119: 1061-1066, 2006. (Pubitemid 44116913)
32. Derks S, Postma C, Carvalho B, et al: Integrated analysis of chromosomal, microsatellite and epigenetic instability in colorectal cancer identifies specific associations between promoter methylation of pivotal tumour suppressor and DNA repair genes and specific chromosomal alterations. Carcinogenesis 29: 434-439, 2008. (Pubitemid 351359685)
33. Kis E, Szatmári T, Keszei M, et al: Microarray analysis of radiation response genes in primary human fibroblasts. Int J Radiat Oncol Biol Phys 66: 1506-1514, 2006.
34. Kazerounian S, Yee KO and Lawler J: Thrombospondins in cancer. Cell Mol Life Sci 65: 700-712, 2008.
35. Lagerstedt KK, Kristiansson E, Lönnroth C, et al: Genes with relevance for early to late progression of colon carcinoma based on combined genomic and transcriptomic information from the same patients. Cancer Inform 9: 79-91, 2010.
36. Cretu A, Sha X, Tront J, Hoffman B and Liebermann DA: Stress sensor Gadd45 genes as therapeutic targets in cancer. Cancer Ther 7: 268-276, 2009.
37. Ying J, Srivastava G, Hsieh WS, et al: The stress-responsive gene GADD45G is a functional tumor suppressor, with its response to environmental stresses frequently disrupted epigenetically in multiple tumors. Clin Cancer Res 11: 6442-6449, 2005. (Pubitemid 41338980)
38. Ju S, Zhu Y, Liu L, et al: Gadd45b and Gadd45g are important for anti-tumor immune responses. Eur J Immunol 39: 3010-3018, 2009.
39. Na YK, Lee SM, Hong HS, Kim JB, Park JY and Kim DS: Hypermethylation of growth arrest DNA-damage-inducible gene 45 in non-small cell lung cancer and its relationship with clinicopathologic features. Mol Cells 30: 89-92, 2010.