Limits...
Identification of novel methylation markers in hepatocellular carcinoma using a methylation array.

Shin SH, Kim BH, Jang JJ, Suh KS, Kang GH - J. Korean Med. Sci. (2010)

Bottom Line: Twenty-four new genes have been identified as hypermethylated at their promoter CpG island loci in a cancer-specific manner.Of these, TNFRSF10C, HOXA9, NPY, and IRF5 were frequently hypermethylated in hepatocellular carcinoma tissue samples and their methylation was found to be closely associated with inactivation of gene expression.Further study will be required to elucidate the clinicopathological implications of these newly found DNA methylation markers in hepatocellular carcinoma.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Epigenetics, Cancer Research Institute and Brain Korea 2nd Stage, Seoul National University, Seoul, Korea.

ABSTRACT
Promoter CpG island hypermethylation has become recognized as an important mechanism for inactivating tumor suppressor genes or tumor-related genes in human cancers of various tissues. Gene inactivation in association with promoter CpG island hypermethylation has been reported to be four times more frequent than genetic changes in human colorectal cancers. Hepatocellular carcinoma is also one of the human cancer types in which aberrant promoter CpG island hypermethylation is frequently found. However, the number of genes identified to date as hypermethylated for hepatocellular carcinoma (HCC) is fewer than that for colorectal cancer or gastric cancer, which can be attributed to fewer attempts to perform genome-wide methylation profiling for HCC. In the present study, we used bead-array technology and coupled methylation-specific PCR to identify new genes showing cancer-specific methylation in HCC. Twenty-four new genes have been identified as hypermethylated at their promoter CpG island loci in a cancer-specific manner. Of these, TNFRSF10C, HOXA9, NPY, and IRF5 were frequently hypermethylated in hepatocellular carcinoma tissue samples and their methylation was found to be closely associated with inactivation of gene expression. Further study will be required to elucidate the clinicopathological implications of these newly found DNA methylation markers in hepatocellular carcinoma.

Show MeSH

Related in: MedlinePlus

Representative examples of MSP analysis of DST, FLT3, PTCH2 and TIAM1 in 8 HCC cell lines. DNA extracted from 8 HCC cell lines were amplified with primers specific to the methylated (M) or unmethylated (UM) CpG islands of each gene after modification with sodium bisulfite. +, positive control; DW, distilled water. Positive controls for methylated MSP and unmethylated DNA are M.SssI-treated placental DNA and whole-genome amplified DNA, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2908783&req=5

Figure 2: Representative examples of MSP analysis of DST, FLT3, PTCH2 and TIAM1 in 8 HCC cell lines. DNA extracted from 8 HCC cell lines were amplified with primers specific to the methylated (M) or unmethylated (UM) CpG islands of each gene after modification with sodium bisulfite. +, positive control; DW, distilled water. Positive controls for methylated MSP and unmethylated DNA are M.SssI-treated placental DNA and whole-genome amplified DNA, respectively.

Mentions: For MSP analysis, we attempted to design primers for the 36 genes using both MSPPrimer (http://www.mspprimer.org) and MethPrimer (http://www.urogene.org/methprimer). However, for one gene (HOXB2), neither tool was able to design primers, because it has a short CpG island in the promoter. Therefore, we examined the methylation status of the remaining 35 genes in the 8 HCC cell lines. It was found that 26 of the genes (HOXA9, TNFRSF10C, NPY, TIAM1, PDGFRB, IRAK3, SH3BP2, IRF5, HIC2, TAL1, HS3ST2, MLF1, IGF2AS, ADCYAP1, FGF3, WNT2, ADAMTS12, FLT3, PTCH2, GP1BB, RBP1, FZD9, DST, NOTCH3, PLAGL1, and ZP3) were methylated in at least one HCC cell line (26 of 35; 74.3%). The remaining 9 genes (TESK2, IHH, MCM2, CTSL, F2R, PGF, NGFR, FLT4, and ICA1) were not found to be methylated in the HCC cell lines using the MSP assay (Figs. 2, 3).


Identification of novel methylation markers in hepatocellular carcinoma using a methylation array.

Shin SH, Kim BH, Jang JJ, Suh KS, Kang GH - J. Korean Med. Sci. (2010)

Representative examples of MSP analysis of DST, FLT3, PTCH2 and TIAM1 in 8 HCC cell lines. DNA extracted from 8 HCC cell lines were amplified with primers specific to the methylated (M) or unmethylated (UM) CpG islands of each gene after modification with sodium bisulfite. +, positive control; DW, distilled water. Positive controls for methylated MSP and unmethylated DNA are M.SssI-treated placental DNA and whole-genome amplified DNA, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2908783&req=5

Figure 2: Representative examples of MSP analysis of DST, FLT3, PTCH2 and TIAM1 in 8 HCC cell lines. DNA extracted from 8 HCC cell lines were amplified with primers specific to the methylated (M) or unmethylated (UM) CpG islands of each gene after modification with sodium bisulfite. +, positive control; DW, distilled water. Positive controls for methylated MSP and unmethylated DNA are M.SssI-treated placental DNA and whole-genome amplified DNA, respectively.
Mentions: For MSP analysis, we attempted to design primers for the 36 genes using both MSPPrimer (http://www.mspprimer.org) and MethPrimer (http://www.urogene.org/methprimer). However, for one gene (HOXB2), neither tool was able to design primers, because it has a short CpG island in the promoter. Therefore, we examined the methylation status of the remaining 35 genes in the 8 HCC cell lines. It was found that 26 of the genes (HOXA9, TNFRSF10C, NPY, TIAM1, PDGFRB, IRAK3, SH3BP2, IRF5, HIC2, TAL1, HS3ST2, MLF1, IGF2AS, ADCYAP1, FGF3, WNT2, ADAMTS12, FLT3, PTCH2, GP1BB, RBP1, FZD9, DST, NOTCH3, PLAGL1, and ZP3) were methylated in at least one HCC cell line (26 of 35; 74.3%). The remaining 9 genes (TESK2, IHH, MCM2, CTSL, F2R, PGF, NGFR, FLT4, and ICA1) were not found to be methylated in the HCC cell lines using the MSP assay (Figs. 2, 3).

Bottom Line: Twenty-four new genes have been identified as hypermethylated at their promoter CpG island loci in a cancer-specific manner.Of these, TNFRSF10C, HOXA9, NPY, and IRF5 were frequently hypermethylated in hepatocellular carcinoma tissue samples and their methylation was found to be closely associated with inactivation of gene expression.Further study will be required to elucidate the clinicopathological implications of these newly found DNA methylation markers in hepatocellular carcinoma.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Epigenetics, Cancer Research Institute and Brain Korea 2nd Stage, Seoul National University, Seoul, Korea.

ABSTRACT
Promoter CpG island hypermethylation has become recognized as an important mechanism for inactivating tumor suppressor genes or tumor-related genes in human cancers of various tissues. Gene inactivation in association with promoter CpG island hypermethylation has been reported to be four times more frequent than genetic changes in human colorectal cancers. Hepatocellular carcinoma is also one of the human cancer types in which aberrant promoter CpG island hypermethylation is frequently found. However, the number of genes identified to date as hypermethylated for hepatocellular carcinoma (HCC) is fewer than that for colorectal cancer or gastric cancer, which can be attributed to fewer attempts to perform genome-wide methylation profiling for HCC. In the present study, we used bead-array technology and coupled methylation-specific PCR to identify new genes showing cancer-specific methylation in HCC. Twenty-four new genes have been identified as hypermethylated at their promoter CpG island loci in a cancer-specific manner. Of these, TNFRSF10C, HOXA9, NPY, and IRF5 were frequently hypermethylated in hepatocellular carcinoma tissue samples and their methylation was found to be closely associated with inactivation of gene expression. Further study will be required to elucidate the clinicopathological implications of these newly found DNA methylation markers in hepatocellular carcinoma.

Show MeSH
Related in: MedlinePlus