Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells.
E-cadherin (E-cad) is a transmembrane adhesion glycoprotein, the expression of which is often reduced in invasive or metastatic tumors. To assess E-cad's distribution among different types of cancer cells, we used bisulfite-sequencing for detailed, base-by-base measurement of CpG methylation in E-cad's promoter region in the NCI-60 cell lines. The mean methylation levels of the cell lines were distributed bimodally, with values pushed toward either the high or low end of the methylation scale. The 38 epithelial cell lines showed substantially lower (28%) mean methylation levels compared with the nonepithelial cell lines (58%). The CpG site at -143 with respect to the transcriptional start was commonly methylated at intermediate levels, even in cell lines with low overall DNA methylation. We also profiled the NCI-60 cell lines using Affymetrix U133 microarrays and found E-cad expression to be correlated with E-cad methylation at highly statistically significant levels. Above a threshold of approximately 20% to 30% mean methylation, the expression of E-cad was effectively silenced. Overall, this study provides a type of detailed analysis of methylation that can also be applied to other cancer-related genes. As has been shown in recent years, DNA methylation status can serve as a biomarker for use in choosing therapy.
Reinhold
William C
WC
Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Building 37, Room 5056, Bethesda, MD 20892-4255, USA. wcr@mail.nih.gov
Reimers
Mark A
MA
Maunakea
Alika K
AK
Kim
Sohyoung
S
Lababidi
Samir
S
Scherf
Uwe
U
Shankavaram
Uma T
UT
Ziegler
Micah S
MS
Stewart
Claudia
C
Kouros-Mehr
Hosein
H
Cui
Hengmi
H
Dolginow
Douglas
D
Scudiero
Dominic A
DA
Pommier
Yves G
YG
Munroe
David J
DJ
Feinberg
Andrew P
AP
Weinstein
John N
JN
D001483:Base Sequence; D015820:Cadherins / Q000235:genetics* / Q000378:metabolism; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D018899:CpG Islands; D019175:DNA Methylation; D015972:Gene Expression Regulation, Neoplastic; D020868:Gene Silencing; D006801:Humans; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
D015820:Cadherins