Total Knock-Down of the Cancer Epigenome by Methylation Subtraction (TKO)
Student: Pei-Chi Hou
Advisor: Yu-Wei Leu
Date: 05/07 2010
Abstract:
Aberrant DNA methylation was observed globally in different cancers and different from
patient to patient[1, 2]. Currently, there are genome wide methylation detection methods that
detect the global methylation differences but the identified methylation targets can not serve
as the targets of treatment directly. In order to develop an alternative for cancer treatment, we
established a method that combines the detection and modification of the global methylation
differences between cancer and normal cells. The new method was named total knock-down
of the cancer epigenome by methylation subtraction, abbreviated as TKO. In TKO, the
genomic DNAs from normal cells were used as baits and the DNAs from cancer cells were
considered as targets. The patenting TKO used subtraction method to identify the loci that are
hypermethylated in normal/the bait cells but hypomethylated in cancer/the target cells. Two
examples were evaluated in my studies, they are: (1) estrogen receptor expressing MCF7 cells
versus estrogen receptor nonexpressing MDA-MB-231; and (2) the normal mesenchymal
stem cell versus the transformed mesenchymal stem cell, me_H&R. High through-put
sequencing was used to detect the TKO subtraction and quantified the amplification
frequency at specific loci. The modified TKO subtraction was used to treat the target cells.
The methylation within the target loci were increased in target cells and their expression level
were decreased. The TKO treatment caused the cell death of MDA-MB-231 both in vitro and
in vivo; and reversed the drug resistance in the me_H&R. It is then concluded that the TKO
method is sufficient to identify and modify the methylation differences between two cells.
References:
1.
Baylin, S.B., DNA methylation and gene silencing in cancer. Nat Clin Pract
Oncol, 2005. 2 Suppl 1: p. S4-11.
2.
Bird, A., DNA methylation patterns and epigenetic memory. Genes Dev, 2002.
16(1): p. 6-21.
Comment for Pei-Chi Hou: