A reinvestigation of somatic hypermethylation at the PTEN CpG island in cancer cell lines

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.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.Phosphatase and tensin homologue (PTEN) is a tumour suppressor gene with dual protein and lipid phosphatase activity. The main mechanism by which PTEN functions as a tumour suppressor is by negatively regulating the PI3K-AKT-mTOR pathway [1,2]. Inactivating germline mutations of PTEN result in a group of rare syndromes collectively known as the PTEN hamartoma tumour syndromes (PHTS), which includes Cowden syndrome and Bannayan-Zonana syndrome [3]. Germline mutations of PTEN account for approximately 80% of Cowden syndrome cases [4]. This syndrome is characterised by a range of clinical features including an increased risk of breast, thyroid and endometrial cancers [3]. Mutation of the PTEN tumour suppressor gene also occurs in various sporadic cancers, including 38% of endometrial, 14% of prostate, 7% of colorectal and 5% of lung carcinomas [5].Promoter CpG island hypermethylation, which can result in the transcriptional silencing of gene expression, is an alternative mechanism of gene inactivation. The importance of PTEN inactivation in PHTS and several types of sporadic cancers makes the gene an attractive candidate for epigenetic inactivation. The PTEN CpG island is shared with another gene, known as KLLN, which is tr