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Biol Proced Online. 2012; 14: 5.
Published online Apr 10, 2012. doi:  10.1186/1480-9222-14-5
PMCID: PMC3342897
A reinvestigation of somatic hypermethylation at the PTEN CpG island in cancer cell lines
Luke B Hesson,1 Deborah Packham,1 Emily Pontzer,2,3 Pauline Funchain,2 Charis Eng,2,3 and Robyn L Wardcorresponding author1
1Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
2Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
3Department of Genetics and CASE Comprehensive Cancer Center, Cleveland, OH 44116, USA
corresponding authorCorresponding author.
Luke B Hesson: l.hesson/at/unsw.edu.au; Deborah Packham: d.packham/at/unsw.edu.au; Emily Pontzer: pontzee/at/ccf.org; Pauline Funchain: funchap/at/ccf.org; Charis Eng: engc/at/ccf.org; Robyn L Ward: robyn/at/unsw.edu.au
Received March 15, 2012; Accepted April 10, 2012.
Abstract
Background
PTEN is an important tumour suppressor gene that is mutated in Cowden syndrome as well as various sporadic cancers. CpG island hypermethylation is another route to tumour suppressor gene inactivation, however, the literature regarding PTEN hypermethylation in cancer is controversial. Furthermore, investigation of the methylation status of the PTEN CpG island is challenging due to sequence homology with the PTEN pseudogene, PTENP1. PTEN shares a CpG island promoter with another gene known as KLLN. Here we present a thorough reinvestigation of the methylation status of the PTEN CpG island in DNA from colorectal, breast, ovarian, glioma, lung and haematological cancer cell lines.
Results
Using a range of bisulphite-based PCR assays we investigated 6 regions across the PTEN CpG island. We found that regions 1-4 were not methylated in cancer cell lines (0/36). By allelic bisulphite sequencing and pyrosequencing methylation was detected in regions 5 and 6 in colorectal, breast and haematological cancer cell lines. However, methylation detected in this region was associated with the PTENP1 promoter and not the PTEN CpG island.
Conclusions
We show that methylation of the PTEN CpG island is a rare event in cancer cell lines and that apparent methylation most likely originates from homologous regions of the PTENP1 pseudogene promoter. Future studies should utilize assays that reliably discriminate between PTEN and PTENP1 to avoid data misinterpretation.
Keywords: DNA methylation, Epigenetic, PTEN, KILLIN, PTENP1, Pseudogene, Cowden syndrome
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