TY - JOUR
T1 - DNA methylation profiles of primary colorectal carcinoma and matched liver metastasis
AU - Konishi, Kazuo
AU - Watanabe, Yoshiyuki
AU - Shen, Lanlan
AU - Guo, Yi
AU - Castoro, Ryan J.
AU - Kondo, Kimie
AU - Chung, Woonbok
AU - Ahmed, Saira
AU - Jelinek, Jaroslav
AU - Boumber, Yanis A.
AU - Estecio, Marcos R.
AU - Maegawa, Shinji
AU - Kondo, Yutaka
AU - Itoh, Fumio
AU - Imawari, Michio
AU - Hamilton, Stanley R.
AU - Issa, Jean Pierre J.
PY - 2011/11/21
Y1 - 2011/11/21
N2 - Background: The contribution of DNA methylation to the metastatic process in colorectal cancers (CRCs) is unclear. Methods: We evaluated the methylation status of 13 genes (MINT1, MINT2, MINT31, MLH1, p16, p14, TIMP3, CDH1, CDH13, THBS1, MGMT, HPP1 and ERα) by bisulfite-pyrosequencing in 79 CRCs comprising 36 CRCs without liver metastasis and 43 CRCs with liver metastasis, including 16 paired primary CRCs and liver metastasis. We also performed methylated CpG island amplification microarrays (MCAM) in three paired primary and metastatic cancers. Results: Methylation of p14, TIMP3 and HPP1 in primary CRCs progressively decreased from absence to presence of liver metastasis (13.1% vs. 4.3%; 14.8% vs. 3.7%; 43.9% vs. 35.8%, respectively) (P<.05). When paired primary and metastatic tumors were compared, only MGMT methylation was significantly higher in metastatic cancers (27.4% vs. 13.4%, P =. 013), and this difference was due to an increase in methylation density rather than frequency in the majority of cases. MCAM showed an average 7.4% increase in DNA methylated genes in the metastatic samples. The numbers of differentially hypermethylated genes in the liver metastases increased with increasing time between resection of the primary and resection of the liver metastasis. Bisulfite-pyrosequencing validation in 12 paired samples showed that most of these increases were not conserved, and could be explained by differences in methylation density rather than frequency. Conclusions: Most DNA methylation differences between primary CRCs and matched liver metastasis are due to random variation and an increase in DNA methylation density rather than de-novo inactivation and silencing. Thus, DNA methylation changes occur for the most part before progression to liver metastasis.
AB - Background: The contribution of DNA methylation to the metastatic process in colorectal cancers (CRCs) is unclear. Methods: We evaluated the methylation status of 13 genes (MINT1, MINT2, MINT31, MLH1, p16, p14, TIMP3, CDH1, CDH13, THBS1, MGMT, HPP1 and ERα) by bisulfite-pyrosequencing in 79 CRCs comprising 36 CRCs without liver metastasis and 43 CRCs with liver metastasis, including 16 paired primary CRCs and liver metastasis. We also performed methylated CpG island amplification microarrays (MCAM) in three paired primary and metastatic cancers. Results: Methylation of p14, TIMP3 and HPP1 in primary CRCs progressively decreased from absence to presence of liver metastasis (13.1% vs. 4.3%; 14.8% vs. 3.7%; 43.9% vs. 35.8%, respectively) (P<.05). When paired primary and metastatic tumors were compared, only MGMT methylation was significantly higher in metastatic cancers (27.4% vs. 13.4%, P =. 013), and this difference was due to an increase in methylation density rather than frequency in the majority of cases. MCAM showed an average 7.4% increase in DNA methylated genes in the metastatic samples. The numbers of differentially hypermethylated genes in the liver metastases increased with increasing time between resection of the primary and resection of the liver metastasis. Bisulfite-pyrosequencing validation in 12 paired samples showed that most of these increases were not conserved, and could be explained by differences in methylation density rather than frequency. Conclusions: Most DNA methylation differences between primary CRCs and matched liver metastasis are due to random variation and an increase in DNA methylation density rather than de-novo inactivation and silencing. Thus, DNA methylation changes occur for the most part before progression to liver metastasis.
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U2 - 10.1371/journal.pone.0027889
DO - 10.1371/journal.pone.0027889
M3 - Article
C2 - 22132162
AN - SCOPUS:81455125557
SN - 1932-6203
VL - 6
JO - PloS one
JF - PloS one
IS - 11
M1 - e27889
ER -